From d2c7f76294cd7a1158402cdc67e0382bead17619 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 28 Apr 2020 11:48:45 -0500
Subject: Added some metadata to the trait export
---
wqflask/wqflask/show_trait/export_trait_data.py | 30 ++++++++++++++++++++++++-
wqflask/wqflask/user_manager.py | 24 ++++++++++----------
2 files changed, 41 insertions(+), 13 deletions(-)
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 7ca4a4c0..107f87c6 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -4,11 +4,17 @@ import simplejson as json
from pprint import pformat as pf
+from base.trait import GeneralTrait
+from base import data_set
+
def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
trait_name = targs['trait_display_name']
- final_sample_data = []
+
+ meta_data = get_export_metadata(targs['trait_id'], targs['dataset'])
+
+ final_sample_data = meta_data
for sample_group in ['primary_samples', 'other_samples']:
for row in sample_data[sample_group]:
@@ -18,6 +24,28 @@ def export_sample_table(targs):
return trait_name, final_sample_data
+def get_export_metadata(trait_id, dataset_name):
+ dataset = data_set.create_dataset(dataset_name)
+ this_trait = GeneralTrait(dataset=dataset,
+ name=trait_id,
+ cellid=None,
+ get_qtl_info=False)
+
+ metadata = []
+ if dataset.type == "Publish":
+ metadata.append(["Phenotype ID: " + trait_id])
+ metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name])
+ metadata.append(["Group: " + dataset.group.name])
+ metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
+ metadata.append(["Authors: " + this_trait.authors])
+ metadata.append(["Title: " + this_trait.title])
+ metadata.append(["Journal: " + this_trait.journal])
+ metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
+ metadata.append([])
+
+ return metadata
+
+
def dict_to_sorted_list(dictionary):
sorted_list = [item for item in dictionary.iteritems()]
sorted_list = sorted(sorted_list, cmp=cmp_samples)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 1b27d7cb..4dc3e18c 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -350,12 +350,12 @@ class UserSession(object):
Redis.delete(self.cookie_name)
logger.debug("At end of delete_session")
-@app.before_request
+#@app.before_request
def before_request():
g.user_session = UserSession()
g.cookie_session = AnonUser()
-@app.after_request
+#@app.after_request
def set_cookie(response):
if not request.cookies.get(g.cookie_session.cookie_name):
response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
@@ -537,7 +537,7 @@ def basic_info():
ip_address = request.remote_addr,
user_agent = request.headers.get('User-Agent'))
-@app.route("/manage/verify_email")
+#@app.route("/manage/verify_email")
def verify_email():
user = DecodeUser(VerificationEmail.key_prefix).user
user.confirmed = json.dumps(basic_info(), sort_keys=True)
@@ -551,7 +551,7 @@ def verify_email():
response.set_cookie(UserSession.cookie_name, session_id_signed)
return response
-@app.route("/n/password_reset", methods=['GET'])
+#@app.route("/n/password_reset", methods=['GET'])
def password_reset():
"""Entry point after user clicks link in E-mail"""
logger.debug("in password_reset request.url is:", request.url)
@@ -575,7 +575,7 @@ def password_reset():
else:
return redirect(url_for("login"))
-@app.route("/n/password_reset_step2", methods=('POST',))
+#@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
logger.debug("in password_reset request.url is:", request.url)
@@ -619,7 +619,7 @@ class DecodeUser(object):
logger.debug("data is:", data)
return model.User.query.get(data['id'])
-@app.route("/n/login", methods=('GET', 'POST'))
+#@app.route("/n/login", methods=('GET', 'POST'))
def login():
lu = LoginUser()
login_type = request.args.get("type")
@@ -629,7 +629,7 @@ def login():
else:
return lu.standard_login()
-@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+#@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET
code = request.args.get("code")
@@ -660,7 +660,7 @@ def github_oauth2():
url = "/n/login?type=github&uid="+user_details["user_id"]
return redirect(url)
-@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+#@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
def orcid_oauth2():
from uuid import uuid4
from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
@@ -840,7 +840,7 @@ class LoginUser(object):
db_session.add(login_rec)
db_session.commit()
-@app.route("/n/logout")
+#@app.route("/n/logout")
def logout():
logger.debug("Logging out...")
UserSession().delete_session()
@@ -851,7 +851,7 @@ def logout():
return response
-@app.route("/n/forgot_password", methods=['GET'])
+#@app.route("/n/forgot_password", methods=['GET'])
def forgot_password():
"""Entry point for forgotten password"""
print("ARGS: ", request.args)
@@ -859,7 +859,7 @@ def forgot_password():
print("ERRORS: ", errors)
return render_template("new_security/forgot_password.html", errors=errors)
-@app.route("/n/forgot_password_submit", methods=('POST',))
+#@app.route("/n/forgot_password_submit", methods=('POST',))
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
params = request.form
@@ -944,7 +944,7 @@ def is_redis_available():
# return LoginUser().actual_login(user, assumed_by=assumed_by)
-@app.route("/n/register", methods=('GET', 'POST'))
+#@app.route("/n/register", methods=('GET', 'POST'))
def register():
params = None
errors = None
--
cgit v1.2.3
From 10b8dc7af35f0d221daf121d0e3c0a52d9223368 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 29 Apr 2020 04:38:42 -0500
Subject: Fixing loading of the ITP data as a 4way cross, worked on
http://gn2-test3.genenetwork.org/
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index e1aa290b..9909b6d4 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -128,7 +128,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(type == '4-way'){
genocodes <- c('1','2','3','4')
} else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
@@ -139,7 +139,11 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
- cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ if(type == '4-way'){
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else{
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ }
if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
return(cross)
}
--
cgit v1.2.3
From 98d54f1861f2bbc82cffa049fef408b43351688a Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 29 Apr 2020 04:50:31 -0500
Subject: Adding some debug, so we have some info in the output
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 9909b6d4..c1a56787 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -140,11 +140,16 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
if(type == '4-way'){
+ cat('Loading in as 4-WAY\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
}else{
+ cat('Loading in as normal\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
}
- if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ if(type == 'riset'){
+ cat('Converting to RISELF\n')
+ cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ }
return(cross)
}
""" % (dataset.group.genofile))
--
cgit v1.2.3
From 5b57353c5325a2677fef07630d2576a01641787a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 29 Apr 2020 11:19:21 -0500
Subject: Fixed issue with global search when description field is empty
---
wqflask/wqflask/gsearch.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 3d9b508a..04e3d578 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -75,7 +75,10 @@ class GSearch(object):
this_trait['group'] = line[1]
this_trait['tissue'] = line[2]
this_trait['symbol'] = line[6]
- this_trait['description'] = line[7].decode('utf-8', 'replace')
+ if line[7]:
+ this_trait['description'] = line[7].decode('utf-8', 'replace')
+ else:
+ this_trait['description'] = "N/A"
this_trait['location_repr'] = 'N/A'
if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9]))
--
cgit v1.2.3
From 77e3974eebfc48e49af07e07c08cd312edd34b99 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 29 Apr 2020 16:34:58 -0500
Subject: Changed a lot about how mapping scale is read and gave the option to
change mapping scale when both scales are available
---
.../marker_regression/display_mapping_results.py | 25 +++---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 48 +++++-------
wqflask/wqflask/marker_regression/run_mapping.py | 18 +++--
wqflask/wqflask/show_trait/show_trait.py | 89 +++++++++++++++++++++-
.../new/javascript/show_trait_mapping_tools.js | 19 +++++
wqflask/wqflask/templates/mapping_results.html | 4 +
.../templates/show_trait_mapping_tools.html | 22 +++++-
7 files changed, 177 insertions(+), 48 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 2a53b60e..f70bc555 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -265,14 +265,12 @@ class DisplayMappingResults(object):
else:
self.colorCollection = [self.LRS_COLOR]
+ self.dataset.group.genofile = self.genofile_string.split(":")[0]
if self.mapping_method == "reaper" and self.manhattan_plot != True:
self.genotype = self.dataset.group.read_genotype_file(use_reaper=True)
else:
self.genotype = self.dataset.group.read_genotype_file()
- #if self.mapping_method == "rqtl_geno" and self.genotype.filler == True:
- # self.genotype = self.genotype.read_rdata_output(self.qtlresults)
-
#Darwing Options
try:
if self.selectedChr > -1:
@@ -1761,9 +1759,9 @@ class DisplayMappingResults(object):
break
if all_int:
- max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 30
+ max_lrs_width = canvas.stringWidth("%d" % LRS_LOD_Max, font=LRSScaleFont) + 40
else:
- max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 20
+ max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30
#draw the "LRS" or "LOD" string to the left of the axis
canvas.drawString(self.LRS_LOD, xLeftOffset - max_lrs_width - 15*(zoom-1), \
@@ -1899,13 +1897,16 @@ class DisplayMappingResults(object):
this_chr = str(self.ChrList[self.selectedChr][1]+1)
if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
- if self.plotScale != "physic" and self.genotype.filler == True:
- if self.selectedChr != -1:
- start_cm = self.genotype[self.selectedChr - 1][0].cM
- Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
- else:
- start_cm = self.genotype[previous_chr_as_int][0].cM
- Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
+ if self.plotScale != "physic" and self.mapping_method == "reaper" and not self.manhattan_plot:
+ Xc = startPosX + (qtlresult['cM']-startMb)*plotXScale
+ if hasattr(self.genotype, "filler"):
+ if self.genotype.filler:
+ if self.selectedChr != -1:
+ start_cm = self.genotype[self.selectedChr - 1][0].cM
+ Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
+ else:
+ start_cm = self.genotype[previous_chr_as_int][0].cM
+ Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
else:
Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c1a56787..8c294460 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -11,7 +11,7 @@ from utility.tools import locate, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
-def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -33,7 +33,13 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
# genofilelocation = locate(crossname + ".RData", "genotype/rdata")
# cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
#except:
- generate_cross_from_geno(dataset)
+
+ if mapping_scale == "morgan":
+ scale_units = "cM"
+ else:
+ scale_units = "Mb"
+
+ generate_cross_from_geno(dataset, scale_units)
GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
crossfilelocation = TMPDIR + crossname + ".cross"
if dataset.group.genofile:
@@ -47,6 +53,8 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
else:
cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
+ logger.debug("VAL LEN:", len(vals))
+
pheno_string = sanitize_rqtl_phenotype(vals)
cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
@@ -94,11 +102,9 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
- the_scale = check_mapping_scale(genofilelocation)
- return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
else:
- the_scale = check_mapping_scale(genofilelocation)
- return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ return process_rqtl_results(result_data_frame, dataset.group.species)
def generate_cross_from_rdata(dataset):
rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
@@ -110,7 +116,7 @@ def generate_cross_from_rdata(dataset):
}
""" % (rdata_location))
-def generate_cross_from_geno(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
ro.r("""
trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
@@ -127,21 +133,23 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
type <- getGenoCode(header, 'type')
if(type == '4-way'){
genocodes <- c('1','2','3','4')
+ genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#', crosstype="4way")
} else {
genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
}
- genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
c('sex', '', '', sex), # Sex phenotype for the mice
- cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
+ cbind(genodata[,c('Locus','Chr', '%s')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
if(type == '4-way'){
cat('Loading in as 4-WAY\n')
- cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes)
+ #cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
}else{
cat('Loading in as normal\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
@@ -152,7 +160,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
}
return(cross)
}
- """ % (dataset.group.genofile))
+ """ % (dataset.group.genofile, scale_units))
def add_perm_strata(cross, perm_strata):
col_string = 'c("the_strata")'
@@ -300,20 +308,4 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
marker['lod_score'] = output[i][2]
qtl_results.append(marker)
- return qtl_results
-
-def check_mapping_scale(genofile_location):
- scale = "physic"
- with open(genofile_location, "r") as geno_fh:
- for line in geno_fh:
- if line[0] == "@" or line[0] == "#":
-
- if "@scale" in line:
- scale = line.split(":")[1].strip()
- break
- else:
- continue
- else:
- break
-
- return scale
\ No newline at end of file
+ return qtl_results
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 589be702..7449d8ce 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -156,6 +156,8 @@ class RunMapping(object):
self.transform = ""
self.score_type = "LRS" #ZS: LRS or LOD
self.mapping_scale = "physic"
+ if "mapping_scale" in start_vars:
+ self.mapping_scale = start_vars['mapping_scale']
self.num_perm = 0
self.perm_output = []
self.bootstrap_results = []
@@ -255,9 +257,9 @@ class RunMapping(object):
#if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
- results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
@@ -429,7 +431,7 @@ class RunMapping(object):
with Bench("Trimming Markers for Table"):
self.trimmed_markers = trim_markers_for_table(results)
- chr_lengths = get_chr_lengths(self.mapping_scale, self.dataset, self.qtl_results)
+ chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
#ZS: For zooming into genome browser, need to pass chromosome name instead of number
if self.dataset.group.species == "mouse":
@@ -643,7 +645,7 @@ def geno_db_exists(this_dataset):
except:
return "False"
-def get_chr_lengths(mapping_scale, dataset, qtl_results):
+def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
chr_lengths = []
if mapping_scale == "physic":
for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes):
@@ -666,8 +668,12 @@ def get_chr_lengths(mapping_scale, dataset, qtl_results):
this_chr = chr_as_num
highest_pos = 0
else:
- if float(result['Mb']) > highest_pos:
- highest_pos = float(result['Mb'])
+ if mapping_method == "reaper":
+ if float(result['cM']) > highest_pos:
+ highest_pos = float(result['cM'])
+ else:
+ if float(result['Mb']) > highest_pos:
+ highest_pos = float(result['Mb'])
return chr_lengths
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 8883e627..40e344b8 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -22,6 +22,7 @@ from base import webqtlConfig
from base import webqtlCaseData
from wqflask.show_trait.SampleList import SampleList
from utility import webqtlUtil, Plot, Bunch, helper_functions
+from utility.tools import locate_ignore_error
from base.trait import GeneralTrait
from base import data_set
from db import webqtlDatabaseFunction
@@ -170,6 +171,17 @@ class ShowTrait(object):
self.genofiles = self.dataset.group.get_genofiles()
+ if "QTLReaper" or "R/qtl" in dataset.group.mapping_names: #ZS: No need to grab scales from .geno file unless it's using a mapping method that reads .geno files
+ if self.genofiles:
+ self.scales_in_geno = get_genotype_scales(self.genofiles)
+ else:
+ self.scales_in_geno = get_genotype_scales(self.dataset.group + ".geno")
+
+ if len(self.scales_in_geno) < 2:
+ hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
+ else:
+ self.scales_in_geno = {}
+
self.has_num_cases = has_num_cases(self.this_trait)
self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
@@ -239,6 +251,7 @@ class ShowTrait(object):
#hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
hddn['do_control'] = False
hddn['maf'] = 0.05
+ hddn['mapping_scale'] = "physic"
hddn['compare_traits'] = []
hddn['export_data'] = ""
hddn['export_format'] = "excel"
@@ -251,6 +264,7 @@ class ShowTrait(object):
short_description = short_description,
unit_type = trait_units,
dataset_type = self.dataset.type,
+ scales_in_geno = self.scales_in_geno,
data_scale = self.dataset.data_scale,
sample_group_types = self.sample_group_types,
sample_lists = sample_lists,
@@ -597,4 +611,77 @@ def get_categorical_variables(this_trait, sample_list):
if num_distinct < 10:
categorical_var_list.append(sample_list.attributes[attribute].name)
- return categorical_var_list
\ No newline at end of file
+ return categorical_var_list
+
+def get_genotype_scales(genofiles):
+ geno_scales = {}
+ if type(genofiles) is list:
+ for the_file in genofiles:
+ file_location = the_file['location']
+ geno_scales[file_location] = get_scales_from_genofile(file_location)
+ else:
+ geno_scales[genofiles] = get_scales_from_genofile(genofiles)
+
+ return geno_scales
+
+def get_scales_from_genofile(file_location):
+ geno_path = locate_ignore_error(file_location, 'genotype')
+
+ if not geno_path: #ZS: This is just to allow the code to run when
+ return [["physic", "Mb"]]
+ cm_and_mb_cols_exist = True
+ cm_column = None
+ mb_column = None
+ with open(geno_path, "r") as geno_fh:
+ for i, line in enumerate(geno_fh):
+ if line[0] == "#" or line[0] == "@":
+ if "@scale" in line: #ZS: If the scale is made explicit in the metadata, use that
+ scale = line.split(":")[1].strip()
+ if scale == "morgan":
+ return [["morgan", "cM"]]
+ else:
+ return [["physic", "Mb"]]
+ else:
+ continue
+ if line[:3] == "Chr":
+ first_marker_line = i + 1
+ if line.split("\t")[2].strip() == "cM":
+ cm_column = 2
+ elif line.split("\t")[3].strip() == "cM":
+ cm_column = 3
+ if line.split("\t")[2].strip() == "Mb":
+ mb_column = 2
+ elif line.split("\t")[3].strip() == "Mb":
+ mb_column = 3
+ break
+
+ #ZS: This attempts to check whether the cM and Mb columns are 'real', since some .geno files have one column be a copy of the other column, or have one column that is all 0s
+ cm_all_zero = True
+ mb_all_zero = True
+ cm_mb_all_equal = True
+ for i, line in enumerate(geno_fh):
+ if first_marker_line <= i < first_marker_line + 10: #ZS: I'm assuming there won't be more than 10 markers where the position is listed as 0
+ if cm_column:
+ cm_val = line.split("\t")[cm_column].strip()
+ if cm_val != "0":
+ cm_all_zero = False
+ if mb_column:
+ mb_val = line.split("\t")[mb_column].strip()
+ if mb_val != "0":
+ mb_all_zero = False
+ if cm_column and mb_column:
+ if cm_val != mb_val:
+ cm_mb_all_equal = False
+ else:
+ if i > first_marker_line + 10:
+ break
+
+ #ZS: This assumes that both won't be all zero, since if that's the case mapping shouldn't be an option to begin with
+ if mb_all_zero:
+ return [["morgan", "cM"]]
+ elif cm_mb_all_equal:
+ return [["physic", "Mb"]]
+ elif cm_and_mb_cols_exist:
+ return [["physic", "Mb"], ["morgan", "cM"]]
+ else:
+ return [["physic", "Mb"]]
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 478ed87e..7176a0da 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -165,6 +165,7 @@
url = "/loading";
$('input[name=method]').val("rqtl_geno");
$('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
+ $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val());
$('input[name=genofile]').val($('#genofile_rqtl_geno').val());
$('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
$('input[name=categorical_vars]').val(js_data.categorical_vars)
@@ -210,6 +211,7 @@
url = "/loading";
$('input[name=method]').val("reaper");
$('input[name=selected_chr]').val($('#chr_reaper').val());
+ $('input[name=mapping_scale]').val($('#scale_reaper').val());
$('input[name=genofile]').val($('#genofile_reaper').val());
$('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
$('input[name=control_marker]').val($('input[name=control_reaper]').val());
@@ -289,4 +291,21 @@
return toggle_enable_disable("#suggestive_lrs");
});
+ $('#genofile_rqtl_geno').change(function() {
+ geno_location = $(this).children("option:selected").val().split(":")[0]
+ $('#scale_rqtl_geno').empty()
+ the_scales = js_data.scales_in_geno[geno_location]
+ for (var i = 0; i < the_scales.length; i++){
+ $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+ }
+ });
+ $('#genofile_reaper').change(function() {
+ geno_location = $(this).children("option:selected").val().split(":")[0]
+ $('#scale_reaper').empty()
+ the_scales = js_data.scales_in_geno[geno_location]
+ for (var i = 0; i < the_scales.length; i++){
+ $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1]));
+ }
+ });
+
}).call(this);
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7e05be18..94ac0350 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -274,7 +274,11 @@
{% endif %}
<td align="right">{{marker.chr}}</td>
{% if plotScale != "physic" %}
+ {% if 'cM' in marker %}
+ <td align="right">{{ '%0.3f' | format(marker.cM|float) }}</td>
+ {% else %}
<td align="right">{{ '%0.3f' | format(marker.Mb|float) }}</td>
+ {% endif %}
{% else %}
<td align="right">{{ '%0.6f' | format(marker.Mb|float) }}</td>
{% endif %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 777d4a2d..7c897409 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -120,6 +120,16 @@
</div>
</div>
{% if genofiles and genofiles|length>0 %}
+ <div class="mapping_method_fields form-group">
+ <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="scale_reaper" class="form-control" style="width: 80px;">
+ {% for item in scales_in_geno[genofiles[0]['location']] %}
+ <option value="{{ item[0] }}">{{ item[1] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
<div class="mapping_method_fields form-group">
<label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
@@ -225,7 +235,17 @@
</select>
</div>
</div>
- {% if genofiles and genofiles|length>0 %}
+ {% if genofiles and genofiles|length > 0 %}
+ <div class="mapping_method_fields form-group">
+ <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="scale_rqtl_geno" class="form-control" style="width: 80px;">
+ {% for item in scales_in_geno[genofiles[0]['location']] %}
+ <option value="{{ item[0] }}">{{ item[1] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
<div class="mapping_method_fields form-group">
<label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
<div style="margin-left:20px;" class="col-xs-4 controls">
--
cgit v1.2.3
From 1bcc4959fe3572f619ddfd8948d2260de27b84d4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 30 Apr 2020 12:08:29 -0500
Subject: Fixed the way it gets the N displayed on the loading page
---
wqflask/wqflask/marker_regression/run_mapping.py | 2 +-
wqflask/wqflask/views.py | 23 ++++++++++++++++-------
2 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7449d8ce..5f7710ab 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -124,7 +124,7 @@ class RunMapping(object):
self.samples.append(sample)
self.vals.append(value)
- self.num_vals = start_vars['num_vals']
+ self.num_vals = len(self.vals)
#ZS: Check if genotypes exist in the DB in order to create links for markers
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 44752246..938570f3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -40,7 +40,7 @@ from wqflask import update_search_results
from wqflask import docs
from wqflask import news
from wqflask.submit_bnw import get_bnw_input
-from base.data_set import DataSet # Used by YAML in marker_regression
+from base.data_set import create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
from wqflask.show_trait import export_trait_data
from wqflask.heatmap import heatmap
@@ -593,12 +593,21 @@ def loading_page():
if 'num_vals' in start_vars:
num_vals = int(start_vars['num_vals'])
else:
- if 'primary_samples' in start_vars:
- samples = start_vars['primary_samples'].split(",")
- for sample in samples:
- value = start_vars.get('value:' + sample)
- if value != "x":
- num_vals += 1
+ dataset = create_dataset(start_vars['dataset'])
+ genofile_samplelist = []
+ samples = start_vars['primary_samples'].split(",")
+ if 'genofile' in start_vars:
+ if start_vars['genofile'] != "":
+ genofile_string = start_vars['genofile']
+ dataset.group.genofile = genofile_string.split(":")[0]
+ genofile_samples = run_mapping.get_genofile_samplelist(dataset)
+ if len(genofile_samples) > 1:
+ samples = genofile_samples
+
+ for sample in samples:
+ value = start_vars.get('value:' + sample)
+ if value != "x":
+ num_vals += 1
start_vars['num_vals'] = num_vals
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
--
cgit v1.2.3
From 5e23e579b731fd150d01511c622ffb6fd9dafdbc Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 1 May 2020 12:10:58 -0500
Subject: Aesthetic table changes to view collection and correlation result
pages
---
wqflask/wqflask/templates/collections/view.html | 8 ++++----
wqflask/wqflask/templates/correlation_page.html | 8 +++++++-
2 files changed, 11 insertions(+), 5 deletions(-)
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 6639f46a..1a622bb4 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -8,7 +8,7 @@
{% block content %}
<!-- Start of body -->
- <div class="container" style="min-width: 1250px;">
+ <div class="container" style="min-width: 2050px;">
<h1>
<span id="collection_name">{{ uc.name }}</span>
<input type="text" name="new_collection_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ uc.name }}">
@@ -122,9 +122,9 @@
</a>
</TD>
{% if this_trait.symbol %}
- <TD data-export="{{ this_trait.symbol }}">{{ this_trait.symbol }}</TD>
+ <TD title="{{ this_trait.symbol }}" data-export="{{ this_trait.symbol }}">{% if this_trait.symbol|length > 20 %}{{ this_trait.symbol[:20] }}...{% else %}{{ this_trait.symbol }}{% endif %}</TD>
{% elif this_trait.abbreviation %}
- <TD data-export="{{ this_trait.abbreviation }}">{{ this_trait.abbreviation }}</TD>
+ <TD title="{{ this_trait.abbreviation }}" data-export="{{ this_trait.abbreviation }}">{% if this_trait.abbreviation|length > 20 %}{{ this_trait.abbreviation[:20] }}...{% else %}{{ this_trait.abbreviation }}{% endif %}</TD>
{% else %}
<TD data-export="N/A">N/A</TD>
{% endif %}
@@ -190,7 +190,7 @@
{ "type": "natural", "width": 50 },
{ "type": "natural" },
{ "type": "natural", "width": 120 },
- { "type": "natural", "width": 120 },
+ { "type": "natural" },
{ "type": "natural" },
{ "type": "natural", "width": 130 },
{ "type": "natural", "width": 35 },
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 03b03aa7..b73a6981 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -126,7 +126,7 @@
{% for trait in correlation_results %}
<tr>
<td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="padding-right: 0px;" VALUE="{{ data_hmac('{}:{}'.format(trait.name, trait.dataset.name)) }}"></td>
- <td data-export="{{ loop.index }}" style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: center;">{{ loop.index }}</td>
+ <td data-export="{{ loop.index }}" style="padding-left: 8px; padding-right: 0px; padding-top: 4px; align: right;">{{ loop.index }}</td>
<td data-export="{{ trait.name }}">
<a href="{{ url_for('show_trait_page',
trait_id = trait.name,
@@ -159,6 +159,11 @@
<td data-export="{{ trait.LRS_location_repr }}" align="right">{{ trait.LRS_location_repr }}</td>
<td data-export={% if trait.additive != "" %}"{{ '%0.3f' % trait.additive|float }}"{% else %}"N/A"{% endif %} align="right">{% if trait.additive != "" %}{{ '%0.3f' % trait.additive|float }}{% else %}N/A{% endif %}</td>
{% elif target_dataset.type == "Publish" %}
+ {% if trait.abbreviation %}
+ <TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
+ {% else %}
+ <TD data-export="{{ trait.abbreviation }}">N/A</TD>
+ {% endif %}
<td data-export="{{ trait.description_display }}">{{ trait.description_display }}</td>
<td data-export="{{ trait.authors }}">{{ trait.authors }}</td>
<td data-export="{{ trait.pubmed_text }}">
@@ -398,6 +403,7 @@
{ "type": "natural" },
{ "type": "natural" },
{ "type": "natural" },
+ { "type": "natural" },
{ "type": "natural", "width": "20%" },
{ "type": "natural", "width": "12%" },
{ "orderDataType": "dom-innertext" },
--
cgit v1.2.3
From 3b1bcd0ff7dc199e6ea83a766cb1d9e6081776a7 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Mon, 4 May 2020 05:05:25 -0500
Subject: Working on covariate mapping, making sure the addcovars are numeric
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index c1a56787..46b54f36 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -45,7 +45,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
if manhattan_plot:
cross_object = calc_genoprob(cross_object)
else:
- cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
+ cross_object = calc_genoprob(cross_object, step=5, stepwidth="max")
pheno_string = sanitize_rqtl_phenotype(vals)
@@ -59,9 +59,15 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
+
+ # Force all covaraites to be numeric (which is wrong for ITP year, season, etc... But required for R/qtl)
+ ro.r('covarnames <- colnames(all_covars)')
+ ro.r('all_covars <- apply(all_covars, 2, as.numeric)')
+ ro.r('colnames(all_covars) <- covarnames')
covars = ro.r['all_covars']
-
+ #DEBUG to save the session object to file
+ #ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
if pair_scan:
if do_control == "true":
logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
@@ -187,7 +193,8 @@ def sanitize_rqtl_phenotype(vals):
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
- ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
return ro.r["the_cross"]
def pull_var(var_name, cross, var_string):
--
cgit v1.2.3
From a1db50c2a09e9666b18aeada21785c86e715b865 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 May 2020 13:42:48 -0500
Subject: Committing some changes for testing covariates
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 624 +++++++++++-----------
wqflask/wqflask/marker_regression/run_mapping.py | 8 +-
wqflask/wqflask/show_trait/show_trait.py | 7 +-
3 files changed, 322 insertions(+), 317 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 8c294460..ed63ad92 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,311 +1,313 @@
-import rpy2.robjects as ro
-import rpy2.robjects.numpy2ri as np2r
-import numpy as np
-
-from base.webqtlConfig import TMPDIR
-from base.trait import GeneralTrait
-from base.data_set import create_dataset
-from utility import webqtlUtil
-from utility.tools import locate, TEMPDIR
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
-
-def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
- ## Get pointers to some common R functions
- r_library = ro.r["library"] # Map the library function
- r_c = ro.r["c"] # Map the c function
- plot = ro.r["plot"] # Map the plot function
- png = ro.r["png"] # Map the png function
- dev_off = ro.r["dev.off"] # Map the device off function
-
- print(r_library("qtl")) # Load R/qtl
-
- ## Get pointers to some R/qtl functions
- scanone = ro.r["scanone"] # Map the scanone function
- scantwo = ro.r["scantwo"] # Map the scantwo function
- calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
-
- crossname = dataset.group.name
- #try:
- # generate_cross_from_rdata(dataset)
- # read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function
- # genofilelocation = locate(crossname + ".RData", "genotype/rdata")
- # cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
- #except:
-
- if mapping_scale == "morgan":
- scale_units = "cM"
- else:
- scale_units = "Mb"
-
- generate_cross_from_geno(dataset, scale_units)
- GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
- crossfilelocation = TMPDIR + crossname + ".cross"
- if dataset.group.genofile:
- genofilelocation = locate(dataset.group.genofile, "genotype")
- else:
- genofilelocation = locate(dataset.group.name + ".geno", "genotype")
- cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
-
- if manhattan_plot:
- cross_object = calc_genoprob(cross_object)
- else:
- cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
-
- logger.debug("VAL LEN:", len(vals))
-
- pheno_string = sanitize_rqtl_phenotype(vals)
-
- cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
-
- # Scan for QTLs
- marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
-
- if cofactors != "":
- cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
- ro.r('all_covars <- cbind(marker_covars, trait_covars)')
- else:
- ro.r('all_covars <- marker_covars')
-
- covars = ro.r['all_covars']
-
- if pair_scan:
- if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
- else:
- logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
-
- pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
- png(file=TEMPDIR+pair_scan_filename)
- plot(result_data_frame)
- dev_off()
-
- return process_pair_scan_results(result_data_frame)
- else:
- if do_control == "true" or cofactors != "":
- logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
- else:
- logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
-
- if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
- if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping
- cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
- if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
- else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method)
- else:
- if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method)
- else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
-
- perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
- return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
- else:
- return process_rqtl_results(result_data_frame, dataset.group.species)
-
-def generate_cross_from_rdata(dataset):
- rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
- ro.r("""
- generate_cross_from_rdata <- function(filename = '%s') {
- load(file=filename)
- cross = cunique
- return(cross)
- }
- """ % (rdata_location))
-
-def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
-
- ro.r("""
- trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
-
- getGenoCode <- function(header, name = 'unk'){
- mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
- return(trim(strsplit(header[mat],':')[[1]][2]))
- }
-
- GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
- header = readLines(genotypes, 40) # Assume a geno header is not longer than 40 lines
- toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
-
- type <- getGenoCode(header, 'type')
- if(type == '4-way'){
- genocodes <- c('1','2','3','4')
- genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#', crosstype="4way")
- } else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
- genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
- }
- cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
- if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
- if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
- outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
- c('sex', '', '', sex), # Sex phenotype for the mice
- cbind(genodata[,c('Locus','Chr', '%s')], genodata[, 5:ncol(genodata)])) # Genotypes
- write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
- require(qtl)
- if(type == '4-way'){
- cat('Loading in as 4-WAY\n')
- cross = read.cross(file=out, 'csvr', genotypes=genocodes)
- #cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
- }else{
- cat('Loading in as normal\n')
- cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
- }
- if(type == 'riset'){
- cat('Converting to RISELF\n')
- cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
- }
- return(cross)
- }
- """ % (dataset.group.genofile, scale_units))
-
-def add_perm_strata(cross, perm_strata):
- col_string = 'c("the_strata")'
- perm_strata_string = "c("
- for item in perm_strata:
- perm_strata_string += str(item) + ","
-
- perm_strata_string = perm_strata_string[:-1] + ")"
-
- cross = add_phenotype(cross, perm_strata_string, "the_strata")
-
- strata_ob = pull_var("perm_strata", cross, col_string)
-
- return cross, strata_ob
-
-def sanitize_rqtl_phenotype(vals):
- pheno_as_string = "c("
- for i, val in enumerate(vals):
- if val == "x":
- if i < (len(vals) - 1):
- pheno_as_string += "NA,"
- else:
- pheno_as_string += "NA"
- else:
- if i < (len(vals) - 1):
- pheno_as_string += str(val) + ","
- else:
- pheno_as_string += str(val)
- pheno_as_string += ")"
-
- return pheno_as_string
-
-def add_phenotype(cross, pheno_as_string, col_name):
- ro.globalenv["the_cross"] = cross
- ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
- return ro.r["the_cross"]
-
-def pull_var(var_name, cross, var_string):
- ro.globalenv["the_cross"] = cross
- ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
-
- return ro.r[var_name]
-
-def add_cofactors(cross, this_dataset, covariates, samples):
- ro.numpy2ri.activate()
-
- covariate_list = covariates.split(",")
- covar_name_string = "c("
- for i, covariate in enumerate(covariate_list):
- this_covar_data = []
- covar_as_string = "c("
- trait_name = covariate.split(":")[0]
- dataset_ob = create_dataset(covariate.split(":")[1])
- trait_ob = GeneralTrait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
-
- this_dataset.group.get_samplelist()
- trait_samples = this_dataset.group.samplelist
- trait_sample_data = trait_ob.data
- for index, sample in enumerate(trait_samples):
- if sample in samples:
- if sample in trait_sample_data:
- sample_value = trait_sample_data[sample].value
- this_covar_data.append(sample_value)
- else:
- this_covar_data.append("NA")
-
- for j, item in enumerate(this_covar_data):
- if j < (len(this_covar_data) - 1):
- covar_as_string += str(item) + ","
- else:
- covar_as_string += str(item)
-
- covar_as_string += ")"
-
- col_name = "covar_" + str(i)
- cross = add_phenotype(cross, covar_as_string, col_name)
-
- if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
- else:
- covar_name_string += '"' + col_name + '"'
-
- covar_name_string += ")"
-
- covars_ob = pull_var("trait_covars", cross, covar_name_string)
-
- return cross, covars_ob
-
-def create_marker_covariates(control_marker, cross):
- ro.globalenv["the_cross"] = cross
- ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
- userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
- covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
- ro.r('covnames <- c(' + covariate_names + ')')
- ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
- ro.r('covnames <- covnames[covInGeno]')
- ro.r("cat('covnames (purged): ', covnames,'\n')")
- ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
-
- return ro.r["marker_covars"]
-
-def process_pair_scan_results(result):
- pair_scan_results = []
-
- result = result[1]
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-
- for i, line in enumerate(result.iter_row()):
- marker = {}
- marker['name'] = result.rownames[i]
- marker['chr1'] = output[i][0]
- marker['Mb'] = output[i][1]
- marker['chr2'] = int(output[i][2])
- pair_scan_results.append(marker)
-
- return pair_scan_results
-
-def process_rqtl_perm_results(num_perm, results):
- perm_vals = []
- for line in str(results).split("\n")[1:(num_perm+1)]:
- #print("R/qtl permutation line:", line.split())
- perm_vals.append(float(line.split()[1]))
-
- perm_output = perm_vals
- suggestive = np.percentile(np.array(perm_vals), 67)
- significant = np.percentile(np.array(perm_vals), 95)
-
- return perm_output, suggestive, significant
-
-def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
- qtl_results = []
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-
- for i, line in enumerate(result.iter_row()):
- marker = {}
- marker['name'] = result.rownames[i]
- if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
- marker['chr'] = "X"
- else:
- marker['chr'] = output[i][0]
- marker['cM'] = output[i][1]
- marker['Mb'] = output[i][1]
- marker['lod_score'] = output[i][2]
- qtl_results.append(marker)
-
- return qtl_results
\ No newline at end of file
+import rpy2.robjects as ro
+import rpy2.robjects.numpy2ri as np2r
+import numpy as np
+
+from base.webqtlConfig import TMPDIR
+from base.trait import GeneralTrait
+from base.data_set import create_dataset
+from utility import webqtlUtil
+from utility.tools import locate, TEMPDIR
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+ ## Get pointers to some common R functions
+ r_library = ro.r["library"] # Map the library function
+ r_c = ro.r["c"] # Map the c function
+ plot = ro.r["plot"] # Map the plot function
+ png = ro.r["png"] # Map the png function
+ dev_off = ro.r["dev.off"] # Map the device off function
+
+ print(r_library("qtl")) # Load R/qtl
+
+ ## Get pointers to some R/qtl functions
+ scanone = ro.r["scanone"] # Map the scanone function
+ scantwo = ro.r["scantwo"] # Map the scantwo function
+ calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
+
+ crossname = dataset.group.name
+ #try:
+ # generate_cross_from_rdata(dataset)
+ # read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function
+ # genofilelocation = locate(crossname + ".RData", "genotype/rdata")
+ # cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
+ #except:
+ generate_cross_from_geno(dataset)
+ GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
+ crossfilelocation = TMPDIR + crossname + ".cross"
+ if dataset.group.genofile:
+ genofilelocation = locate(dataset.group.genofile, "genotype")
+ else:
+ genofilelocation = locate(dataset.group.name + ".geno", "genotype")
+ cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
+
+ the_version = ro.r["packageVersion('qtl')"]
+ logger.debug("THE R VERSION:", the_version)
+
+ ro.r('save.image(file = "/home/zas1024/gn2-zach/tmp/HET3_cofactor_test2.RData")')
+
+ if manhattan_plot:
+ cross_object = calc_genoprob(cross_object)
+ else:
+ cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
+
+ pheno_string = sanitize_rqtl_phenotype(vals)
+
+ cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
+
+ # Scan for QTLs
+ marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
+
+ if cofactors != "":
+ cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
+ ro.r('all_covars <- cbind(marker_covars, trait_covars)')
+ else:
+ ro.r('all_covars <- marker_covars')
+
+ covars = ro.r['all_covars']
+
+ if pair_scan:
+ if do_control == "true":
+ logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
+ else:
+ logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
+
+ pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
+ png(file=TEMPDIR+pair_scan_filename)
+ plot(result_data_frame)
+ dev_off()
+
+ return process_pair_scan_results(result_data_frame)
+ else:
+ if do_control == "true" or cofactors != "":
+ logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
+ else:
+ logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+
+ if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
+ if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping
+ cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
+ if do_control == "true" or cofactors != "":
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
+ else:
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method)
+ else:
+ if do_control == "true" or cofactors != "":
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method)
+ else:
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
+
+ perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
+ the_scale = check_mapping_scale(genofilelocation)
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ else:
+ the_scale = check_mapping_scale(genofilelocation)
+ return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+
+def generate_cross_from_rdata(dataset):
+ rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
+ ro.r("""
+ generate_cross_from_rdata <- function(filename = '%s') {
+ load(file=filename)
+ cross = cunique
+ return(cross)
+ }
+ """ % (rdata_location))
+
+def generate_cross_from_geno(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+
+ ro.r("""
+ trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
+ getGenoCode <- function(header, name = 'unk'){
+ mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
+ return(trim(strsplit(header[mat],':')[[1]][2]))
+ }
+ GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
+ header = readLines(genotypes, 40) # Assume a geno header is not longer than 40 lines
+ toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
+ type <- getGenoCode(header, 'type')
+ if(type == '4-way'){
+ genocodes <- c('1','2','3','4')
+ } else {
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ }
+ genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
+ cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
+ if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
+ if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
+ outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
+ c('sex', '', '', sex), # Sex phenotype for the mice
+ cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
+ write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
+ require(qtl)
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ #cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ return(cross)
+ }
+ """ % (dataset.group.genofile))
+
+def add_perm_strata(cross, perm_strata):
+ col_string = 'c("the_strata")'
+ perm_strata_string = "c("
+ for item in perm_strata:
+ perm_strata_string += str(item) + ","
+
+ perm_strata_string = perm_strata_string[:-1] + ")"
+
+ cross = add_phenotype(cross, perm_strata_string, "the_strata")
+
+ strata_ob = pull_var("perm_strata", cross, col_string)
+
+ return cross, strata_ob
+
+def sanitize_rqtl_phenotype(vals):
+ pheno_as_string = "c("
+ for i, val in enumerate(vals):
+ if val == "x":
+ if i < (len(vals) - 1):
+ pheno_as_string += "NA,"
+ else:
+ pheno_as_string += "NA"
+ else:
+ if i < (len(vals) - 1):
+ pheno_as_string += str(val) + ","
+ else:
+ pheno_as_string += str(val)
+ pheno_as_string += ")"
+
+ return pheno_as_string
+
+def add_phenotype(cross, pheno_as_string, col_name):
+ ro.globalenv["the_cross"] = cross
+ ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
+ return ro.r["the_cross"]
+
+def pull_var(var_name, cross, var_string):
+ ro.globalenv["the_cross"] = cross
+ ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
+
+ return ro.r[var_name]
+
+def add_cofactors(cross, this_dataset, covariates, samples):
+ ro.numpy2ri.activate()
+
+ covariate_list = covariates.split(",")
+ covar_name_string = "c("
+ for i, covariate in enumerate(covariate_list):
+ this_covar_data = []
+ covar_as_string = "c("
+ trait_name = covariate.split(":")[0]
+ dataset_ob = create_dataset(covariate.split(":")[1])
+ trait_ob = GeneralTrait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+
+ this_dataset.group.get_samplelist()
+ trait_samples = this_dataset.group.samplelist
+ trait_sample_data = trait_ob.data
+ for index, sample in enumerate(trait_samples):
+ if sample in samples:
+ if sample in trait_sample_data:
+ sample_value = trait_sample_data[sample].value
+ this_covar_data.append(sample_value)
+ else:
+ this_covar_data.append("NA")
+
+ for j, item in enumerate(this_covar_data):
+ if j < (len(this_covar_data) - 1):
+ covar_as_string += str(item) + ","
+ else:
+ covar_as_string += str(item)
+
+ covar_as_string += ")"
+
+ col_name = "covar_" + str(i)
+ cross = add_phenotype(cross, covar_as_string, col_name)
+
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
+
+ covar_name_string += ")"
+
+ covars_ob = pull_var("trait_covars", cross, covar_name_string)
+
+ return cross, covars_ob
+
+def create_marker_covariates(control_marker, cross):
+ ro.globalenv["the_cross"] = cross
+ ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
+ userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
+ covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
+ ro.r('covnames <- c(' + covariate_names + ')')
+ ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
+ ro.r('covnames <- covnames[covInGeno]')
+ ro.r("cat('covnames (purged): ', covnames,'\n')")
+ ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
+
+ return ro.r["marker_covars"]
+
+def process_pair_scan_results(result):
+ pair_scan_results = []
+
+ result = result[1]
+ output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+
+ for i, line in enumerate(result.iter_row()):
+ marker = {}
+ marker['name'] = result.rownames[i]
+ marker['chr1'] = output[i][0]
+ marker['Mb'] = output[i][1]
+ marker['chr2'] = int(output[i][2])
+ pair_scan_results.append(marker)
+
+ return pair_scan_results
+
+def process_rqtl_perm_results(num_perm, results):
+ perm_vals = []
+ for line in str(results).split("\n")[1:(num_perm+1)]:
+ #print("R/qtl permutation line:", line.split())
+ perm_vals.append(float(line.split()[1]))
+
+ perm_output = perm_vals
+ suggestive = np.percentile(np.array(perm_vals), 67)
+ significant = np.percentile(np.array(perm_vals), 95)
+
+ return perm_output, suggestive, significant
+
+def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
+ qtl_results = []
+ output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+
+ for i, line in enumerate(result.iter_row()):
+ marker = {}
+ marker['name'] = result.rownames[i]
+ if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
+ marker['chr'] = "X"
+ else:
+ marker['chr'] = output[i][0]
+ marker['cM'] = output[i][1]
+ marker['Mb'] = output[i][1]
+ marker['lod_score'] = output[i][2]
+ qtl_results.append(marker)
+
+ return qtl_results
+
+def check_mapping_scale(genofile_location):
+ scale = "physic"
+ with open(genofile_location, "r") as geno_fh:
+ for line in geno_fh:
+ if line[0] == "@" or line[0] == "#":
+
+ if "@scale" in line:
+ scale = line.split(":")[1].strip()
+ break
+ else:
+ continue
+ else:
+ break
+
+ return scale
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 5f7710ab..8fea295f 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -257,9 +257,13 @@ class RunMapping(object):
#if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
- results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ # if self.permCheck and self.num_perm > 0:
+ # self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ # else:
+ # results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 40e344b8..f73079f8 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -175,10 +175,7 @@ class ShowTrait(object):
if self.genofiles:
self.scales_in_geno = get_genotype_scales(self.genofiles)
else:
- self.scales_in_geno = get_genotype_scales(self.dataset.group + ".geno")
-
- if len(self.scales_in_geno) < 2:
- hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
+ self.scales_in_geno = get_genotype_scales(self.dataset.group.name + ".geno")
else:
self.scales_in_geno = {}
@@ -255,6 +252,8 @@ class ShowTrait(object):
hddn['compare_traits'] = []
hddn['export_data'] = ""
hddn['export_format'] = "excel"
+ if len(self.scales_in_geno) < 2:
+ hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
# We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
self.hddn = hddn
--
cgit v1.2.3
From a5647d41c8814d67a6c2f0e5d4c237b330899c97 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 May 2020 15:00:53 +0300
Subject: Add missing columns to db downloaded from AWS
---
scripts/add_missing_columns.sh | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
create mode 100644 scripts/add_missing_columns.sh
diff --git a/scripts/add_missing_columns.sh b/scripts/add_missing_columns.sh
new file mode 100644
index 00000000..70d5fdeb
--- /dev/null
+++ b/scripts/add_missing_columns.sh
@@ -0,0 +1,24 @@
+ #! /bin/bash
+ #
+ # Add missing columns to test db downloaded from:
+ # https://s3.amazonaws.com/genenetwork2/db_webqtl_s.zip
+
+ QUERY="
+ ALTER TABLE InbredSet
+ ADD Family varchar(20) AFTER FullName,
+ ADD FamilyOrder varchar(20) AFTER Family,
+ ADD MenuOrderId smallint(6) AFTER FamilyOrder,
+ ADD InbredSetCode varchar(5) AFTER MenuOrderId;
+
+ ALTER TABLE PublishXRef
+ ADD mean double AFTER DataId;
+
+ -- This takes some time
+ ALTER TABLE ProbeSet
+ ADD UniProtID varchar(20) AFTER ProteinName;
+ "
+
+ USER=gn2
+ DBNAME=db_webqtl_s
+ PASS=mysql_password
+ mysql -u"$USER" -p"$PASS" -h localhost -D "$DBNAME" -e "$QUERY"
--
cgit v1.2.3
From bb1f1608edb23d5e5be16b5c4573d7696d985aff Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 5 May 2020 15:17:52 +0300
Subject: Use GUIX javascript Datatables package
---
wqflask/wqflask/templates/admin/group_manager.html | 2 +-
wqflask/wqflask/templates/collections/list.html | 2 +-
wqflask/wqflask/templates/collections/view.html | 2 +-
wqflask/wqflask/templates/correlation_matrix.html | 2 +-
wqflask/wqflask/templates/correlation_page.html | 2 +-
wqflask/wqflask/templates/gsearch_gene.html | 2 +-
wqflask/wqflask/templates/gsearch_pheno.html | 2 +-
wqflask/wqflask/templates/mapping_results.html | 2 +-
wqflask/wqflask/templates/pair_scan_results.html | 2 +-
wqflask/wqflask/templates/search_result_page.html | 2 +-
10 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index ea9026a6..1c536cb2 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -46,7 +46,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 3829b950..34224d68 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -66,7 +66,7 @@
{% block js %}
<script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 6639f46a..f7065cdb 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -166,7 +166,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9af52021..2a207c80 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -135,7 +135,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/chroma.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/loadings_plot.js"></script>
<script type="text/javascript" src="/static/new/javascript/create_corr_matrix.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 03b03aa7..c4782bb9 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -193,7 +193,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/buttons.colVis.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 556d46d3..555f9aa1 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index f6ffff47..ed892ec0 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -48,7 +48,7 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 7e05be18..a1ea6d89 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -333,7 +333,7 @@
<script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script type="text/javascript" src="/static/new/js_external/plotly-latest.min.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.12/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 1ccb2b27..38c0489c 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -65,7 +65,7 @@
<script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.scientific.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 0f5c39b0..3cd51e2e 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -152,7 +152,7 @@
<script language="javascript" type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
- <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/1.10.13/js/jquery.dataTables.min.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.buttons.min.js"></script>
--
cgit v1.2.3
From 8df6a19e487e31dfa4a184444e8eace11cda9b15 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 6 May 2020 01:24:36 +0300
Subject: Replace CSS dependencies for datatables
---
wqflask/utility/tools.py | 2 +-
wqflask/wqflask/templates/collections/list.html | 2 +-
wqflask/wqflask/templates/collections/view.html | 2 +-
wqflask/wqflask/templates/corr_scatterplot.html | 2 +-
wqflask/wqflask/templates/correlation_matrix.html | 2 +-
wqflask/wqflask/templates/correlation_page.html | 2 +-
wqflask/wqflask/templates/gsearch_gene.html | 2 +-
wqflask/wqflask/templates/gsearch_pheno.html | 2 +-
wqflask/wqflask/templates/mapping_results.html | 2 +-
wqflask/wqflask/templates/pair_scan_results.html | 2 +-
wqflask/wqflask/templates/search_error.html | 2 +-
wqflask/wqflask/templates/search_result_page.html | 2 +-
wqflask/wqflask/templates/show_trait.html | 2 +-
wqflask/wqflask/templates/snp_browser.html | 2 +-
14 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 2914d354..89d88516 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -292,7 +292,7 @@ JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
assert_dir(JS_GUIX_PATH)
assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
-CSS_PATH = "UNKNOWN"
+CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
# assert_dir(JS_PATH)
JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 34224d68..c8705c7d 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Your Collections{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index f7065cdb..34734a01 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}View Collection{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
diff --git a/wqflask/wqflask/templates/corr_scatterplot.html b/wqflask/wqflask/templates/corr_scatterplot.html
index ffc8244d..5877e367 100644
--- a/wqflask/wqflask/templates/corr_scatterplot.html
+++ b/wqflask/wqflask/templates/corr_scatterplot.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
<link rel="stylesheet" type="text/css" href="//cdnjs.cloudflare.com/ajax/libs/nvd3/1.8.5/nv.d3.min.css">
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 2a207c80..cb9fb815 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/corr_matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index c4782bb9..b696a3fa 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
{% endblock %}
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 555f9aa1..8c261eec 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index ed892ec0..05b2f988 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index a1ea6d89..8699343f 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Mapping Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous">
<link rel="stylesheet" type="text/css" href="/static/packages/purescript_genome_browser/css/purescript-genetics-browser.css" />
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 38c0489c..b13b393f 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Pair Scan{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
diff --git a/wqflask/wqflask/templates/search_error.html b/wqflask/wqflask/templates/search_error.html
index 7399b377..df8d9dff 100644
--- a/wqflask/wqflask/templates/search_error.html
+++ b/wqflask/wqflask/templates/search_error.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
{% endblock %}
{% block content %}
<!-- Start of body -->
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 3cd51e2e..767e3487 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -1,7 +1,7 @@
{% extends "base.html" %}
{% block title %}Search Results{% endblock %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 27c3e398..d29be30b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -6,7 +6,7 @@
<link rel="stylesheet" type="text/css" href="/static/new/css/prob_plot.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/scatter-matrix.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/d3-tip.min.css" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 4422ba73..88cb4d31 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -1,6 +1,6 @@
{% extends "base.html" %}
{% block css %}
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/typeahead-bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/css/snp_browser.css" />
--
cgit v1.2.3
From 8c05b01213019735fcf72ffbacf4d02e4f803b07 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 6 May 2020 05:21:59 -0500
Subject: Fix the covariate, added debug, more output to track what it is doing
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 53 +++++++++++++++++------
1 file changed, 40 insertions(+), 13 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 46b54f36..a64a9f9a 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -12,6 +12,7 @@ import utility.logger
logger = utility.logger.getLogger(__name__ )
def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+ logger.info("Start run_rqtl_geno");
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
r_c = ro.r["c"] # Map the c function
@@ -21,6 +22,8 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
print(r_library("qtl")) # Load R/qtl
+ logger.info("QTL library loaded");
+
## Get pointers to some R/qtl functions
scanone = ro.r["scanone"] # Map the scanone function
scantwo = ro.r["scantwo"] # Map the scantwo function
@@ -40,31 +43,32 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
genofilelocation = locate(dataset.group.genofile, "genotype")
else:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
+ logger.info("Going to create a cross from geno");
cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
-
+ logger.info("before calc_genoprob");
if manhattan_plot:
cross_object = calc_genoprob(cross_object)
else:
cross_object = calc_genoprob(cross_object, step=5, stepwidth="max")
-
+ logger.info("after calc_genoprob");
pheno_string = sanitize_rqtl_phenotype(vals)
-
+ logger.info("phenostring done");
+ names_string = sanitize_rqtl_names(samples)
+ logger.info("sanitized pheno and names");
cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
-
+ cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype
+ logger.info("Added pheno and names");
# Scan for QTLs
marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
-
+ logger.info("Marker covars done");
if cofactors != "":
cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
-
- # Force all covaraites to be numeric (which is wrong for ITP year, season, etc... But required for R/qtl)
- ro.r('covarnames <- colnames(all_covars)')
- ro.r('all_covars <- apply(all_covars, 2, as.numeric)')
- ro.r('colnames(all_covars) <- covarnames')
-
+ logger.info("Saving");
+ ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
+ logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
#ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
@@ -191,12 +195,35 @@ def sanitize_rqtl_phenotype(vals):
return pheno_as_string
+def sanitize_rqtl_names(vals):
+ pheno_as_string = "c("
+ for i, val in enumerate(vals):
+ if val == "x":
+ if i < (len(vals) - 1):
+ pheno_as_string += "NA,"
+ else:
+ pheno_as_string += "NA"
+ else:
+ if i < (len(vals) - 1):
+ pheno_as_string += "'" + str(val) + "',"
+ else:
+ pheno_as_string += "'" + str(val) + "'"
+ pheno_as_string += ")"
+
+ return pheno_as_string
+
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
return ro.r["the_cross"]
+def add_names(cross, names_as_string, col_name):
+ ro.globalenv["the_cross"] = cross
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = '+ names_as_string +')')
+ return ro.r["the_cross"]
+
def pull_var(var_name, cross, var_string):
ro.globalenv["the_cross"] = cross
ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
@@ -220,8 +247,8 @@ def add_cofactors(cross, this_dataset, covariates, samples):
this_dataset.group.get_samplelist()
trait_samples = this_dataset.group.samplelist
trait_sample_data = trait_ob.data
- for index, sample in enumerate(trait_samples):
- if sample in samples:
+ for index, sample in enumerate(samples):
+ if sample in trait_samples:
if sample in trait_sample_data:
sample_value = trait_sample_data[sample].value
this_covar_data.append(sample_value)
--
cgit v1.2.3
From ab098bd0f298a0461a1c13c075029a2b7278d140 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 6 May 2020 10:11:53 -0500
Subject: Disable saving of RData
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index a64a9f9a..152bb5be 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -66,9 +66,9 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
- logger.info("Saving");
- ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
- logger.info("Saving Done");
+ #logger.info("Saving");
+ #ro.r('save.image(file = "/home/dannya/gn2-danny/cross.RData")')
+ #logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
#ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
--
cgit v1.2.3
From 18a6ada32ea8453a6ac939f20ef78b722d1b1b6c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 6 May 2020 10:22:09 -0500
Subject: Commiting a few minor changes plus returning rqtl_mapping.py to the
same as on testing branch before merging Danny's changes and testing them
---
wqflask/utility/redis_tools.py | 18 +
wqflask/wqflask/marker_regression/rqtl_mapping.py | 618 ++++++++++-----------
wqflask/wqflask/marker_regression/run_mapping.py | 8 +-
.../templates/show_trait_mapping_tools.html | 2 +-
4 files changed, 327 insertions(+), 319 deletions(-)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 0754e16f..573f9945 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -78,3 +78,21 @@ def check_verification_code(code):
else:
return None
flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
+def get_user_groups(user_id):
+ #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
+ admin_group_ids = [] #ZS: Group IDs where user is an admin
+ user_group_ids = [] #ZS: Group IDs where user is a regular user
+ groups_list = Redis.hgetall("groups")
+ for key in groups_list:
+ group_ob = json.loads(groups_list[key])
+ group_admins = set(group_ob['admins'])
+ group_users = set(group_ob['users'])
+ if user_id in group_admins:
+ admin_group_ids.append(group_ob['id'])
+ elif user_id in group_users:
+ user_group_ids.append(group_ob['id'])
+ else:
+ continue
+
+ return admin_group_ids, user_group_ids
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index ed63ad92..f111b6d3 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,313 +1,307 @@
-import rpy2.robjects as ro
-import rpy2.robjects.numpy2ri as np2r
-import numpy as np
-
-from base.webqtlConfig import TMPDIR
-from base.trait import GeneralTrait
-from base.data_set import create_dataset
-from utility import webqtlUtil
-from utility.tools import locate, TEMPDIR
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
-
-def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
- ## Get pointers to some common R functions
- r_library = ro.r["library"] # Map the library function
- r_c = ro.r["c"] # Map the c function
- plot = ro.r["plot"] # Map the plot function
- png = ro.r["png"] # Map the png function
- dev_off = ro.r["dev.off"] # Map the device off function
-
- print(r_library("qtl")) # Load R/qtl
-
- ## Get pointers to some R/qtl functions
- scanone = ro.r["scanone"] # Map the scanone function
- scantwo = ro.r["scantwo"] # Map the scantwo function
- calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
-
- crossname = dataset.group.name
- #try:
- # generate_cross_from_rdata(dataset)
- # read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function
- # genofilelocation = locate(crossname + ".RData", "genotype/rdata")
- # cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
- #except:
- generate_cross_from_geno(dataset)
- GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
- crossfilelocation = TMPDIR + crossname + ".cross"
- if dataset.group.genofile:
- genofilelocation = locate(dataset.group.genofile, "genotype")
- else:
- genofilelocation = locate(dataset.group.name + ".geno", "genotype")
- cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
-
- the_version = ro.r["packageVersion('qtl')"]
- logger.debug("THE R VERSION:", the_version)
-
- ro.r('save.image(file = "/home/zas1024/gn2-zach/tmp/HET3_cofactor_test2.RData")')
-
- if manhattan_plot:
- cross_object = calc_genoprob(cross_object)
- else:
- cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
-
- pheno_string = sanitize_rqtl_phenotype(vals)
-
- cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
-
- # Scan for QTLs
- marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
-
- if cofactors != "":
- cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
- ro.r('all_covars <- cbind(marker_covars, trait_covars)')
- else:
- ro.r('all_covars <- marker_covars')
-
- covars = ro.r['all_covars']
-
- if pair_scan:
- if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
- else:
- logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
-
- pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
- png(file=TEMPDIR+pair_scan_filename)
- plot(result_data_frame)
- dev_off()
-
- return process_pair_scan_results(result_data_frame)
- else:
- if do_control == "true" or cofactors != "":
- logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
- else:
- logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
-
- if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
- if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping
- cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
- if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
- else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method)
- else:
- if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method)
- else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
-
- perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
- the_scale = check_mapping_scale(genofilelocation)
- return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
- else:
- the_scale = check_mapping_scale(genofilelocation)
- return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
-
-def generate_cross_from_rdata(dataset):
- rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
- ro.r("""
- generate_cross_from_rdata <- function(filename = '%s') {
- load(file=filename)
- cross = cunique
- return(cross)
- }
- """ % (rdata_location))
-
-def generate_cross_from_geno(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
-
- ro.r("""
- trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
- getGenoCode <- function(header, name = 'unk'){
- mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
- return(trim(strsplit(header[mat],':')[[1]][2]))
- }
- GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
- header = readLines(genotypes, 40) # Assume a geno header is not longer than 40 lines
- toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
- type <- getGenoCode(header, 'type')
- if(type == '4-way'){
- genocodes <- c('1','2','3','4')
- } else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
- }
- genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
- cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
- if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
- if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
- outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
- c('sex', '', '', sex), # Sex phenotype for the mice
- cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
- write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
- require(qtl)
- cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
- #cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
- if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
- return(cross)
- }
- """ % (dataset.group.genofile))
-
-def add_perm_strata(cross, perm_strata):
- col_string = 'c("the_strata")'
- perm_strata_string = "c("
- for item in perm_strata:
- perm_strata_string += str(item) + ","
-
- perm_strata_string = perm_strata_string[:-1] + ")"
-
- cross = add_phenotype(cross, perm_strata_string, "the_strata")
-
- strata_ob = pull_var("perm_strata", cross, col_string)
-
- return cross, strata_ob
-
-def sanitize_rqtl_phenotype(vals):
- pheno_as_string = "c("
- for i, val in enumerate(vals):
- if val == "x":
- if i < (len(vals) - 1):
- pheno_as_string += "NA,"
- else:
- pheno_as_string += "NA"
- else:
- if i < (len(vals) - 1):
- pheno_as_string += str(val) + ","
- else:
- pheno_as_string += str(val)
- pheno_as_string += ")"
-
- return pheno_as_string
-
-def add_phenotype(cross, pheno_as_string, col_name):
- ro.globalenv["the_cross"] = cross
- ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
- return ro.r["the_cross"]
-
-def pull_var(var_name, cross, var_string):
- ro.globalenv["the_cross"] = cross
- ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
-
- return ro.r[var_name]
-
-def add_cofactors(cross, this_dataset, covariates, samples):
- ro.numpy2ri.activate()
-
- covariate_list = covariates.split(",")
- covar_name_string = "c("
- for i, covariate in enumerate(covariate_list):
- this_covar_data = []
- covar_as_string = "c("
- trait_name = covariate.split(":")[0]
- dataset_ob = create_dataset(covariate.split(":")[1])
- trait_ob = GeneralTrait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
-
- this_dataset.group.get_samplelist()
- trait_samples = this_dataset.group.samplelist
- trait_sample_data = trait_ob.data
- for index, sample in enumerate(trait_samples):
- if sample in samples:
- if sample in trait_sample_data:
- sample_value = trait_sample_data[sample].value
- this_covar_data.append(sample_value)
- else:
- this_covar_data.append("NA")
-
- for j, item in enumerate(this_covar_data):
- if j < (len(this_covar_data) - 1):
- covar_as_string += str(item) + ","
- else:
- covar_as_string += str(item)
-
- covar_as_string += ")"
-
- col_name = "covar_" + str(i)
- cross = add_phenotype(cross, covar_as_string, col_name)
-
- if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
- else:
- covar_name_string += '"' + col_name + '"'
-
- covar_name_string += ")"
-
- covars_ob = pull_var("trait_covars", cross, covar_name_string)
-
- return cross, covars_ob
-
-def create_marker_covariates(control_marker, cross):
- ro.globalenv["the_cross"] = cross
- ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
- userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
- covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
- ro.r('covnames <- c(' + covariate_names + ')')
- ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
- ro.r('covnames <- covnames[covInGeno]')
- ro.r("cat('covnames (purged): ', covnames,'\n')")
- ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
-
- return ro.r["marker_covars"]
-
-def process_pair_scan_results(result):
- pair_scan_results = []
-
- result = result[1]
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-
- for i, line in enumerate(result.iter_row()):
- marker = {}
- marker['name'] = result.rownames[i]
- marker['chr1'] = output[i][0]
- marker['Mb'] = output[i][1]
- marker['chr2'] = int(output[i][2])
- pair_scan_results.append(marker)
-
- return pair_scan_results
-
-def process_rqtl_perm_results(num_perm, results):
- perm_vals = []
- for line in str(results).split("\n")[1:(num_perm+1)]:
- #print("R/qtl permutation line:", line.split())
- perm_vals.append(float(line.split()[1]))
-
- perm_output = perm_vals
- suggestive = np.percentile(np.array(perm_vals), 67)
- significant = np.percentile(np.array(perm_vals), 95)
-
- return perm_output, suggestive, significant
-
-def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
- qtl_results = []
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
-
- for i, line in enumerate(result.iter_row()):
- marker = {}
- marker['name'] = result.rownames[i]
- if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
- marker['chr'] = "X"
- else:
- marker['chr'] = output[i][0]
- marker['cM'] = output[i][1]
- marker['Mb'] = output[i][1]
- marker['lod_score'] = output[i][2]
- qtl_results.append(marker)
-
- return qtl_results
-
-def check_mapping_scale(genofile_location):
- scale = "physic"
- with open(genofile_location, "r") as geno_fh:
- for line in geno_fh:
- if line[0] == "@" or line[0] == "#":
-
- if "@scale" in line:
- scale = line.split(":")[1].strip()
- break
- else:
- continue
- else:
- break
-
+import rpy2.robjects as ro
+import rpy2.robjects.numpy2ri as np2r
+import numpy as np
+
+from base.webqtlConfig import TMPDIR
+from base.trait import GeneralTrait
+from base.data_set import create_dataset
+from utility import webqtlUtil
+from utility.tools import locate, TEMPDIR
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+ ## Get pointers to some common R functions
+ r_library = ro.r["library"] # Map the library function
+ r_c = ro.r["c"] # Map the c function
+ plot = ro.r["plot"] # Map the plot function
+ png = ro.r["png"] # Map the png function
+ dev_off = ro.r["dev.off"] # Map the device off function
+
+ print(r_library("qtl")) # Load R/qtl
+
+ ## Get pointers to some R/qtl functions
+ scanone = ro.r["scanone"] # Map the scanone function
+ scantwo = ro.r["scantwo"] # Map the scantwo function
+ calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
+
+ crossname = dataset.group.name
+ #try:
+ # generate_cross_from_rdata(dataset)
+ # read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function
+ # genofilelocation = locate(crossname + ".RData", "genotype/rdata")
+ # cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
+ #except:
+ generate_cross_from_geno(dataset)
+ GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
+ crossfilelocation = TMPDIR + crossname + ".cross"
+ if dataset.group.genofile:
+ genofilelocation = locate(dataset.group.genofile, "genotype")
+ else:
+ genofilelocation = locate(dataset.group.name + ".geno", "genotype")
+ cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
+
+ if manhattan_plot:
+ cross_object = calc_genoprob(cross_object)
+ else:
+ cross_object = calc_genoprob(cross_object, step=1, stepwidth="max")
+
+ pheno_string = sanitize_rqtl_phenotype(vals)
+
+ cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
+
+ # Scan for QTLs
+ marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
+
+ if cofactors != "":
+ cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
+ ro.r('all_covars <- cbind(marker_covars, trait_covars)')
+ else:
+ ro.r('all_covars <- marker_covars')
+
+ covars = ro.r['all_covars']
+
+ if pair_scan:
+ if do_control == "true":
+ logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
+ else:
+ logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
+
+ pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
+ png(file=TEMPDIR+pair_scan_filename)
+ plot(result_data_frame)
+ dev_off()
+
+ return process_pair_scan_results(result_data_frame)
+ else:
+ if do_control == "true" or cofactors != "":
+ logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
+ else:
+ logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+
+ if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
+ if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping
+ cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
+ if do_control == "true" or cofactors != "":
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
+ else:
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method)
+ else:
+ if do_control == "true" or cofactors != "":
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method)
+ else:
+ perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
+
+ perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
+ the_scale = check_mapping_scale(genofilelocation)
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ else:
+ the_scale = check_mapping_scale(genofilelocation)
+ return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+
+def generate_cross_from_rdata(dataset):
+ rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
+ ro.r("""
+ generate_cross_from_rdata <- function(filename = '%s') {
+ load(file=filename)
+ cross = cunique
+ return(cross)
+ }
+ """ % (rdata_location))
+
+def generate_cross_from_geno(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+
+ ro.r("""
+ trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
+ getGenoCode <- function(header, name = 'unk'){
+ mat = which(unlist(lapply(header,function(x){ length(grep(paste('@',name,sep=''), x)) })) == 1)
+ return(trim(strsplit(header[mat],':')[[1]][2]))
+ }
+ GENOtoCSVR <- function(genotypes = '%s', out = 'cross.csvr', phenotype = NULL, sex = NULL, verbose = FALSE){
+ header = readLines(genotypes, 40) # Assume a geno header is not longer than 40 lines
+ toskip = which(unlist(lapply(header, function(x){ length(grep("Chr\t", x)) })) == 1)-1 # Major hack to skip the geno headers
+ type <- getGenoCode(header, 'type')
+ if(type == '4-way'){
+ genocodes <- c('1','2','3','4')
+ } else {
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ }
+ genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
+ cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
+ if(is.null(phenotype)) phenotype <- runif((ncol(genodata)-4)) # If there isn't a phenotype, generate a random one
+ if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
+ outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
+ c('sex', '', '', sex), # Sex phenotype for the mice
+ cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
+ write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
+ require(qtl)
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ return(cross)
+ }
+ """ % (dataset.group.genofile))
+
+def add_perm_strata(cross, perm_strata):
+ col_string = 'c("the_strata")'
+ perm_strata_string = "c("
+ for item in perm_strata:
+ perm_strata_string += str(item) + ","
+
+ perm_strata_string = perm_strata_string[:-1] + ")"
+
+ cross = add_phenotype(cross, perm_strata_string, "the_strata")
+
+ strata_ob = pull_var("perm_strata", cross, col_string)
+
+ return cross, strata_ob
+
+def sanitize_rqtl_phenotype(vals):
+ pheno_as_string = "c("
+ for i, val in enumerate(vals):
+ if val == "x":
+ if i < (len(vals) - 1):
+ pheno_as_string += "NA,"
+ else:
+ pheno_as_string += "NA"
+ else:
+ if i < (len(vals) - 1):
+ pheno_as_string += str(val) + ","
+ else:
+ pheno_as_string += str(val)
+ pheno_as_string += ")"
+
+ return pheno_as_string
+
+def add_phenotype(cross, pheno_as_string, col_name):
+ ro.globalenv["the_cross"] = cross
+ ro.r('the_cross$pheno <- cbind(pull.pheno(the_cross), ' + col_name + ' = '+ pheno_as_string +')')
+ return ro.r["the_cross"]
+
+def pull_var(var_name, cross, var_string):
+ ro.globalenv["the_cross"] = cross
+ ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
+
+ return ro.r[var_name]
+
+def add_cofactors(cross, this_dataset, covariates, samples):
+ ro.numpy2ri.activate()
+
+ covariate_list = covariates.split(",")
+ covar_name_string = "c("
+ for i, covariate in enumerate(covariate_list):
+ this_covar_data = []
+ covar_as_string = "c("
+ trait_name = covariate.split(":")[0]
+ dataset_ob = create_dataset(covariate.split(":")[1])
+ trait_ob = GeneralTrait(dataset=dataset_ob,
+ name=trait_name,
+ cellid=None)
+
+ this_dataset.group.get_samplelist()
+ trait_samples = this_dataset.group.samplelist
+ trait_sample_data = trait_ob.data
+ for index, sample in enumerate(trait_samples):
+ if sample in samples:
+ if sample in trait_sample_data:
+ sample_value = trait_sample_data[sample].value
+ this_covar_data.append(sample_value)
+ else:
+ this_covar_data.append("NA")
+
+ for j, item in enumerate(this_covar_data):
+ if j < (len(this_covar_data) - 1):
+ covar_as_string += str(item) + ","
+ else:
+ covar_as_string += str(item)
+
+ covar_as_string += ")"
+
+ col_name = "covar_" + str(i)
+ cross = add_phenotype(cross, covar_as_string, col_name)
+
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
+
+ covar_name_string += ")"
+
+ covars_ob = pull_var("trait_covars", cross, covar_name_string)
+
+ return cross, covars_ob
+
+def create_marker_covariates(control_marker, cross):
+ ro.globalenv["the_cross"] = cross
+ ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
+ userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
+ covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
+ ro.r('covnames <- c(' + covariate_names + ')')
+ ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
+ ro.r('covnames <- covnames[covInGeno]')
+ ro.r("cat('covnames (purged): ', covnames,'\n')")
+ ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
+
+ return ro.r["marker_covars"]
+
+def process_pair_scan_results(result):
+ pair_scan_results = []
+
+ result = result[1]
+ output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+
+ for i, line in enumerate(result.iter_row()):
+ marker = {}
+ marker['name'] = result.rownames[i]
+ marker['chr1'] = output[i][0]
+ marker['Mb'] = output[i][1]
+ marker['chr2'] = int(output[i][2])
+ pair_scan_results.append(marker)
+
+ return pair_scan_results
+
+def process_rqtl_perm_results(num_perm, results):
+ perm_vals = []
+ for line in str(results).split("\n")[1:(num_perm+1)]:
+ #print("R/qtl permutation line:", line.split())
+ perm_vals.append(float(line.split()[1]))
+
+ perm_output = perm_vals
+ suggestive = np.percentile(np.array(perm_vals), 67)
+ significant = np.percentile(np.array(perm_vals), 95)
+
+ return perm_output, suggestive, significant
+
+def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
+ qtl_results = []
+ output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+
+ for i, line in enumerate(result.iter_row()):
+ marker = {}
+ marker['name'] = result.rownames[i]
+ if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
+ marker['chr'] = "X"
+ else:
+ marker['chr'] = output[i][0]
+ marker['cM'] = output[i][1]
+ marker['Mb'] = output[i][1]
+ marker['lod_score'] = output[i][2]
+ qtl_results.append(marker)
+
+ return qtl_results
+
+def check_mapping_scale(genofile_location):
+ scale = "physic"
+ with open(genofile_location, "r") as geno_fh:
+ for line in geno_fh:
+ if line[0] == "@" or line[0] == "#":
+
+ if "@scale" in line:
+ scale = line.split(":")[1].strip()
+ break
+ else:
+ continue
+ else:
+ break
+
return scale
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 8fea295f..5f7710ab 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -257,13 +257,9 @@ class RunMapping(object):
#if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
- results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
- # if self.permCheck and self.num_perm > 0:
- # self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
- # else:
- # results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 7c897409..a2416ced 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -399,7 +399,7 @@
<dt style="padding-top: 20px;">GEMMA</dt>
<dd>Maps traits with correction for kinship among samples using a linear mixed model method, and also allows users to fit multiple covariates such as sex, age, treatment, and genetic markers (<a href="https://www.ncbi.nlm.nih.gov/pubmed/24531419">PMID: 2453419</a>, and <a href="https://github.com/genetics-statistics/GEMMA"> GitHub code</a>). GEMMA incorporates the Leave One Chromosome Out (LOCO) method to ensure that the correction for kinship does not remove useful genetic variance near each marker. Markers can be filtered to include only those with minor allele frequencies (MAF) above a threshold. The default MAF is 0.05.</dd>
{% elif mapping_method == "R/qtl" %}
- <dt style="margin-top: 20px;">R/qtl</dt>
+ <dt style="margin-top: 20px;">R/qtl (version 1.44.9</dt>
<dd>The original R/qtl mapping package that supports classic experimental crosses including 4-parent F2 intercrosses (e.g., NIA ITP UM-HET3). R/qtl is ideal for populations that do not have complex kinship or admixture (<a href="https://www.ncbi.nlm.nih.gov/pubmed/12724300">PMID: 12724300</a>). Both R/qtl as implemented here, and R/qtl2 (<a href="https://www.ncbi.nlm.nih.gov/pubmed/30591514">PMID: 30591514</a>) are available as <a href="https://kbroman.org/pages/software.html">R suites</a>.</dd>
{% elif mapping_method == "QTLReaper" %}
<dt style="margin-top: 20px;">Haley-Knott Regression</dt>
--
cgit v1.2.3
From bcd0110bbf8d3e290023891852c21de3d5b7ebc6 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Wed, 6 May 2020 12:06:40 -0500
Subject: Put in TODOs for MariaDB query and Design Matrix
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 152bb5be..4070e9f5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -62,6 +62,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
logger.info("Marker covars done");
if cofactors != "":
+ logger.info("Cofactors: " + cofactors);
cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
@@ -71,7 +72,6 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
#logger.info("Saving Done");
covars = ro.r['all_covars']
#DEBUG to save the session object to file
- #ro.r('save.image(file = "/home/dannya/gn2-danny/all.RData")')
if pair_scan:
if do_control == "true":
logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
@@ -274,7 +274,8 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_name_string += ")"
covars_ob = pull_var("trait_covars", cross, covar_name_string)
-
+ # TODO: Pull in the types of the covars from MariaDB
+ # TODO: Iterate through the covar types and create a design matrix based on it
return cross, covars_ob
def create_marker_covariates(control_marker, cross):
@@ -287,7 +288,7 @@ def create_marker_covariates(control_marker, cross):
ro.r('covnames <- covnames[covInGeno]')
ro.r("cat('covnames (purged): ', covnames,'\n')")
ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
-
+ # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
def process_pair_scan_results(result):
--
cgit v1.2.3
From 8a2f61a999e6dc653a9ca2de802137a1a4107e35 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 6 May 2020 13:22:41 -0500
Subject: Added function for getting trait data type, plus added mapping scale
changes to Danny's partially fixed R/qtl code
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 62 ++++++++++++++---------
1 file changed, 37 insertions(+), 25 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index ad3a4cb7..dd35d89a 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,6 +1,9 @@
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri as np2r
import numpy as np
+import json
+
+from flask import g
from base.webqtlConfig import TMPDIR
from base.trait import GeneralTrait
@@ -11,7 +14,7 @@ from utility.tools import locate, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
-def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
+def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
logger.info("Start run_rqtl_geno");
## Get pointers to some common R functions
r_library = ro.r["library"] # Map the library function
@@ -36,7 +39,13 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
# genofilelocation = locate(crossname + ".RData", "genotype/rdata")
# cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
#except:
- generate_cross_from_geno(dataset)
+
+ if mapping_scale == "morgan":
+ scale_units = "cM"
+ else:
+ scale_units = "Mb"
+
+ generate_cross_from_geno(dataset, scale_units)
GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
crossfilelocation = TMPDIR + crossname + ".cross"
if dataset.group.genofile:
@@ -104,11 +113,9 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
- the_scale = check_mapping_scale(genofilelocation)
- return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
else:
- the_scale = check_mapping_scale(genofilelocation)
- return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
+ return process_rqtl_results(result_data_frame, dataset.group.species)
def generate_cross_from_rdata(dataset):
rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
@@ -120,7 +127,7 @@ def generate_cross_from_rdata(dataset):
}
""" % (rdata_location))
-def generate_cross_from_geno(dataset): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
ro.r("""
trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
@@ -135,7 +142,7 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(type == '4-way'){
genocodes <- c('1','2','3','4')
} else {
- genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
+ genocodes <- c(getGenoCode(header, 'mat'), getGenoCode(header, 'het'), getGenoCode(header, 'pat')) # Get the genotype codes
}
genodata <- read.csv(genotypes, sep='\t', skip=toskip, header=TRUE, na.strings=getGenoCode(header,'unk'), colClasses='character', comment.char = '#')
cat('Genodata:', toskip, " ", dim(genodata), genocodes, '\n')
@@ -143,14 +150,23 @@ def generate_cross_from_geno(dataset): # TODO: Need to figure out why som
if(is.null(sex)) sex <- rep('m', (ncol(genodata)-4)) # If there isn't a sex phenotype, treat all as males
outCSVR <- rbind(c('Pheno', '', '', phenotype), # Phenotype
c('sex', '', '', sex), # Sex phenotype for the mice
- cbind(genodata[,c('Locus','Chr', 'cM')], genodata[, 5:ncol(genodata)])) # Genotypes
+ cbind(genodata[,c('Locus','Chr', '%s')], genodata[, 5:ncol(genodata)])) # Genotypes
write.table(outCSVR, file = out, row.names=FALSE, col.names=FALSE,quote=FALSE, sep=',') # Save it to a file
require(qtl)
- cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
- if(type == 'riset') cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ if(type == '4-way'){
+ cat('Loading in as 4-WAY\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else{
+ cat('Loading in as normal\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
+ }
+ if(type == 'riset'){
+ cat('Converting to RISELF\n')
+ cross <- convert2riself(cross) # If its a RIL, convert to a RIL in R/qtl
+ }
return(cross)
}
- """ % (dataset.group.genofile))
+ """ % (dataset.group.genofile, scale_units))
def add_perm_strata(cross, perm_strata):
col_string = 'c("the_strata")'
@@ -324,18 +340,14 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
return qtl_results
-def check_mapping_scale(genofile_location):
- scale = "physic"
- with open(genofile_location, "r") as geno_fh:
- for line in geno_fh:
- if line[0] == "@" or line[0] == "#":
+def get_trait_data_type(trait_db_string):
+ # Get a trait's type (numeric, categorical, etc) from the DB
+ the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
+ results_json = g.db.execute(the_query).fetchone()
- if "@scale" in line:
- scale = line.split(":")[1].strip()
- break
- else:
- continue
- else:
- break
+ results_ob = json.loads(results_json[0])
- return scale
\ No newline at end of file
+ if trait_db_string in results_ob:
+ return results_ob[trait_db_string]
+ else:
+ return "numeric"
--
cgit v1.2.3
From 67ecc774ac70c5ba528f0ac1536d8d35f7301dac Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 May 2020 14:36:50 -0500
Subject: Committing current progress on group manager + a minor fix in
dataset.py
---
wqflask/base/data_set.py | 2 +-
wqflask/utility/redis_tools.py | 72 +++++++++++
wqflask/wqflask/templates/admin/group_manager.html | 134 +++++++++++++--------
3 files changed, 159 insertions(+), 49 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cab708ef..5f08c34c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -131,7 +131,7 @@ Publish or ProbeSet. E.g.
ProbeSetFreeze.Name = "{0}"
""".format(name)
- results = g.db.execute(geno_query).fetchall()
+ results = g.db.execute(mrna_expr_query).fetchall()
if len(results):
self.datasets[name] = "ProbeSet"
Redis.set("dataset_structure", json.dumps(self.datasets))
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 573f9945..16bf911a 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -96,3 +96,75 @@ def get_user_groups(user_id):
continue
return admin_group_ids, user_group_ids
+
+def get_group_info(group_id):
+ group_json = Redis.hget("groups", group_id)
+ group_info = None
+ if group_json:
+ group_info = json.loads(group_json)
+
+ return group_info
+
+def create_group(admin_member_ids, user_member_ids = [], group_name = ""):
+ group_id = str(uuid.uuid4())
+ new_group = {
+ "id" : group_id
+ "admins": admin_member_ids,
+ "users" : user_member_ids,
+ "name" : group_name,
+ "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+ "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ }
+
+ Redis.hset("groups", group_id, new_group)
+
+ return new_group
+
+def delete_group(user_id, group_id):
+ #ZS: If user is an admin of a group, remove it from the groups hash
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]:
+ Redis.hdel("groups", group_id)
+ return get_user_groups(user_id)
+ else:
+ None
+
+def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are
+ if admins:
+ group_users = set(group_info["admins"])
+ else:
+ group_users = set(group_info["users"])
+
+ for email in user_emails:
+ user_id = get_user_id("email_address", email)
+ group_users.add(user_id)
+
+ if admins:
+ group_info["admins"] = list(group_users)
+ else:
+ group_info["users"] = list(group_users)
+
+ group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ Redis.hset("groups", group_id, json.dumps(group_info))
+ return group_info
+ else:
+ return None
+
+def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "users"): #ZS: User type is because I assume admins can remove other admins
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]:
+ group_users = set(group_info[user_type])
+ group_users -= set(users_to_remove_ids)
+ group_info[user_type] = list(group_users)
+ group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ Redis.hset("groups", group_id, json.dumps(group_info))
+
+def change_group_name(user_id, group_id, new_name):
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]:
+ group_info["name"] = new_name
+ return group_info
+ else:
+ return None
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index ea9026a6..50c2a42c 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -6,40 +6,71 @@
<div class="container">
<div class="page-header">
-
+ <h1>Manage Groups</h1>
</div>
- <form>
- <div class="control-group">
- <b>Group Name: </b>
- <div class="input-append">
- <input type="text" name="group_name">
- <button type="submit" class="btn btn-primary">Save</button>
- </div>
+ <form action="/manage/groups" method="POST">
+ <div class="container" style="margin-bottom: 30px;">
+ <div><h3>Admin Groups</h3></div>
+ <hr>
+ <table id="admin_groups" class="table table-hover">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Index</th>
+ <th>Name</th>
+ <th># Members</th>
+ <th>Created</th>
+ <th>Last Changed</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for group in admin_groups %}
+ <tr>
+ <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
+ <td>{{ loop.index }}</td>
+ <td>{{ group.name }}</td>
+ <td>{{ group.admins|length + group.users|length }}</td>
+ <td>{{ group.created_timestamp }}</td>
+ <td>{{ group.changed_timestamp }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ </div>
+ <hr>
+ <div class="container">
+ <div><h3>User Groups</h3></div>
+ <hr>
+ <table id="user_groups" class="table table-hover">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Index</th>
+ <th>Name</th>
+ <th># Members</th>
+ <th>Created</th>
+ <th>Last Changed</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for group in user_groups %}
+ <tr>
+ <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
+ <td>{{ loop.index }}</td>
+ <td>{{ group.name }}</td>
+ <td>{{ group.admins|length + group.users|length }}</td>
+ <td>{{ group.created_timestamp }}</td>
+ <td>{{ group.changed_timestamp }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
</div>
-
- <table id="dataset_list" class="table table-hover">
- <thead>
- <tr>
- <th>Read</th>
- <th>Type</th>
- <th>ID</th>
- <th>Name</th>
- <th>Full Name</th>
- </tr>
- </thead>
- {% for dataset in datasets %}
- <tr>
- <td><input type="checkbox" name="read" value="{{ dataset.type }}:{{ dataset.name }}"></td>
- <td>{{ dataset.type }}</td>
- <td>{{ dataset.id }}</td>
- <td>{{ dataset.name }}</td>
- <td>{{ dataset.fullname }}</td>
- </tr>
- {% endfor %}
- </table>
</form>
</div>
+
+
<!-- End of body -->
{% endblock %}
@@ -47,33 +78,40 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
- console.time("Creating table");
- $('#dataset_list').dataTable( {
- "sDom": "Tftipr",
- "oTableTools": {
- "aButtons": [
- "copy",
- "print",
- {
- "sExtends": "collection",
- "sButtonText": 'Save <span class="caret" />',
- "aButtons": [ "csv", "xls", "pdf" ]
- }
- ],
- "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+ $('#admin_groups, #user_groups').dataTable( {
+ "drawCallback": function( settings ) {
+ $('#admin_groups tr').click(function(event) {
+ if (event.target.type !== 'checkbox') {
+ $(':checkbox', this).trigger('click');
+ }
+ });
},
- "iDisplayLength": 50,
- "bLengthChange": true,
+ "columns": [
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" }
+ ],
+ "columnDefs": [ {
+ "targets": 0,
+ "orderable": false
+ } ],
+ "order": [[1, "asc" ]],
+ "sDom": "Ztr",
+ "iDisplayLength": -1,
+ "autoWidth": true,
"bDeferRender": true,
- "bSortClasses": false
+ "bSortClasses": false,
+ "paging": false,
+ "orderClasses": true
} );
- console.timeEnd("Creating table");
});
</script>
{% endblock %}
--
cgit v1.2.3
From ecb0a828de3ba744da82a45e1dc7a55906fd5fb1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 7 May 2020 19:38:27 -0500
Subject: Fixed blatseq issue and geno correlation issue
---
wqflask/base/data_set.py | 3 +--
wqflask/wqflask/show_trait/show_trait.py | 26 +++++++++++-----------
.../wqflask/static/new/javascript/show_trait.js | 2 +-
wqflask/wqflask/templates/show_trait_details.html | 2 +-
4 files changed, 16 insertions(+), 17 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5f08c34c..1457ba8d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -165,12 +165,11 @@ Publish or ProbeSet. E.g.
geno_query = """
SELECT
- GenoFreezeId
+ GenoFreeze.Id
FROM
GenoFreeze
WHERE
GenoFreeze.Name = "{0}"
- {1}
""".format(name)
results = g.db.execute(geno_query).fetchall()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f73079f8..072d7f8c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -73,16 +73,16 @@ class ShowTrait(object):
#ZS: Get verify/rna-seq link URLs
try:
- blatsequence = self.this_trait.blatseq
+ blatsequence = self.this_trait.sequence
if not blatsequence:
#XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
query1 = """SELECT Probe.Sequence, Probe.Name
- FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s' AND
- Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+ FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s' AND
+ Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
seqs = g.db.execute(query1).fetchall()
if not seqs:
raise ValueError
@@ -98,10 +98,10 @@ class ShowTrait(object):
query2 = """SELECT Probe.Sequence, Probe.Name
FROM Probe, ProbeSet, ProbeSetFreeze, ProbeSetXRef
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s' AND
- Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s' AND
+ Probe.ProbeSetId = ProbeSet.Id order by Probe.SerialOrder""" % (self.this_trait.dataset.name, self.this_trait.name)
seqs = g.db.execute(query2).fetchall()
for seqt in seqs:
@@ -121,8 +121,8 @@ class ShowTrait(object):
self.UCSC_BLAT_URL = ""
self.UTHSC_BLAT_URL = ""
except:
- self.UCSC_BLAT_URL = ""
- self.UTHSC_BLAT_URL = ""
+ self.UCSC_BLAT_URL = ""
+ self.UTHSC_BLAT_URL = ""
if self.dataset.type == "ProbeSet":
self.show_probes = "True"
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index d94a2347..785e5332 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -518,7 +518,7 @@ submit_special = function(url) {
return $("#trait_data_form").submit();
};
-var corr_input_list = ['corr_type', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 20dee54e..62268a54 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -212,7 +212,7 @@
<a href="#redirect">
<button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
</a>
- {% if this_trait.dataset.type == 'ProbeSet' %}
+ {% if this_trait.dataset.type == 'ProbeSet' or this_trait.dataset.type == 'Geno' %}
{% if this_trait.symbol != None %}
<a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&gene={{ this_trait.symbol }}&alias=1&species={{ dataset.group.species }}">
<button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
--
cgit v1.2.3
From 74ddd3556a838fd48c425a73d76d504996fb3644 Mon Sep 17 00:00:00 2001
From: Danny Arends
Date: Tue, 12 May 2020 06:57:58 -0500
Subject: Mapping Rqtl using the correct way to use categorical covars
---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 79 ++++++++++++++++++++---
1 file changed, 71 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 4070e9f5..f3d9a70e 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,16 +1,36 @@
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri as np2r
import numpy as np
+import json
from base.webqtlConfig import TMPDIR
from base.trait import GeneralTrait
from base.data_set import create_dataset
from utility import webqtlUtil
from utility.tools import locate, TEMPDIR
+from flask import g
import utility.logger
logger = utility.logger.getLogger(__name__ )
+# Get a trait's type (numeric, categorical, etc) from the DB
+def get_trait_data_type(trait_db_string):
+ logger.info("get_trait_data_type");
+ the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
+ logger.info("the_query done");
+ results_json = g.db.execute(the_query).fetchone()
+ logger.info("the_query executed");
+ results_ob = json.loads(results_json[0])
+ logger.info("json results loaded");
+ if trait_db_string in results_ob:
+ logger.info("found");
+ return results_ob[trait_db_string]
+ else:
+ logger.info("not found");
+ return "numeric"
+
+
+# Run qtl mapping using R/qtl
def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
logger.info("Start run_rqtl_geno");
## Get pointers to some common R functions
@@ -63,7 +83,7 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
logger.info("Marker covars done");
if cofactors != "":
logger.info("Cofactors: " + cofactors);
- cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
+ cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
@@ -218,6 +238,34 @@ def add_phenotype(cross, pheno_as_string, col_name):
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
return ro.r["the_cross"]
+def add_categorical_covar(cross, covar_as_string, i):
+ ro.globalenv["the_cross"] = cross
+ logger.info("cross set");
+ ro.r('covar <- as.factor(' + covar_as_string + ')')
+ logger.info("covar set");
+ ro.r('newcovar <- model.matrix(~covar-1)')
+ logger.info("model.matrix finished");
+ ro.r('cat("new covar columns", ncol(newcovar), "\n")')
+ nCol = ro.r('ncol(newcovar)')
+ logger.info("ncol covar done: " + str(nCol[0]));
+ ro.r('pheno <- data.frame(pull.pheno(the_cross))')
+ logger.info("pheno pulled from cross");
+ nCol = int(nCol[0])
+ logger.info("nCol python int:" + str(nCol));
+ col_names = []
+ #logger.info("loop")
+ for x in range(1, (nCol+1)):
+ #logger.info("loop" + str(x));
+ col_name = "covar_" + str(i) + "_" + str(x)
+ #logger.info("col_name" + col_name);
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])')
+ col_names.append(col_name)
+ #logger.info("loop" + str(x) + "done");
+
+ logger.info("returning from add_categorical_covar");
+ return ro.r["the_cross"], col_names
+
+
def add_names(cross, names_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
@@ -236,6 +284,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covariate_list = covariates.split(",")
covar_name_string = "c("
for i, covariate in enumerate(covariate_list):
+ logger.info("Covariate: " + covariate);
this_covar_data = []
covar_as_string = "c("
trait_name = covariate.split(":")[0]
@@ -263,19 +312,33 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_as_string += ")"
- col_name = "covar_" + str(i)
- cross = add_phenotype(cross, covar_as_string, col_name)
+ datatype = get_trait_data_type(covariate)
+ logger.info("Covariate: " + covariate + " is of type: " + datatype);
+ if(datatype == "categorical"): # Cat variable
+ logger.info("call of add_categorical_covar");
+ cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
+ logger.info("add_categorical_covar returned");
+ for z, col_name in enumerate(col_names): # Go through the additional covar names
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ if(z < (len(col_names) -1)):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
- if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
+ logger.info("covar_name_string:" + covar_name_string);
else:
+ col_name = "covar_" + str(i)
+ cross = add_phenotype(cross, covar_as_string, col_name)
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
covar_name_string += '"' + col_name + '"'
covar_name_string += ")"
-
+ logger.info("covar_name_string:" + covar_name_string);
covars_ob = pull_var("trait_covars", cross, covar_name_string)
- # TODO: Pull in the types of the covars from MariaDB
- # TODO: Iterate through the covar types and create a design matrix based on it
return cross, covars_ob
def create_marker_covariates(control_marker, cross):
--
cgit v1.2.3
From 313b6e7d936f3982c9c6c83c909a8e68f7232ceb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 May 2020 09:57:13 -0500
Subject: Added change for F2s in r/qtl and fixed minor issue in save_user in
redis_tools
---
wqflask/utility/redis_tools.py | 2 +-
wqflask/wqflask/marker_regression/rqtl_mapping.py | 3 +++
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 16bf911a..ca42f7b7 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -108,7 +108,7 @@ def get_group_info(group_id):
def create_group(admin_member_ids, user_member_ids = [], group_name = ""):
group_id = str(uuid.uuid4())
new_group = {
- "id" : group_id
+ "id" : group_id,
"admins": admin_member_ids,
"users" : user_member_ids,
"name" : group_name,
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index dd35d89a..ecce9a07 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -156,6 +156,9 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur
if(type == '4-way'){
cat('Loading in as 4-WAY\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="4way", convertXdata=FALSE) # Load the created cross file using R/qtl read.cross
+ }else if(type == 'f2'){
+ cat('Loading in as F2\n')
+ cross = read.cross(file=out, 'csvr', genotypes=genocodes, crosstype="f2") # Load the created cross file using R/qtl read.cross
}else{
cat('Loading in as normal\n')
cross = read.cross(file=out, 'csvr', genotypes=genocodes) # Load the created cross file using R/qtl read.cross
--
cgit v1.2.3
From 2a2a14899beade4b2dff0c977162ddfe361841a4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 12 May 2020 09:57:46 -0500
Subject: Replaced redis_user_id with user_id since there's no real need for
the first if things are working correctly
---
wqflask/wqflask/user_session.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 4c2305ba..50419146 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -119,10 +119,10 @@ class UserSession(object):
@property
def user_id(self):
"""Shortcut to the user_id"""
- if 'user_id' in self.record:
- return self.record['user_id']
- else:
- return ''
+ if 'user_id' not in self.record:
+ self.record['user_id'] = str(uuid.uuid4())
+
+ return self.record['user_id']
@property
def redis_user_id(self):
@@ -161,7 +161,7 @@ class UserSession(object):
"""List of user's collections"""
#ZS: Get user's collections if they exist
- collections = get_user_collections(self.redis_user_id)
+ collections = get_user_collections(self.user_id)
collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] #ZS: Ensure Default Collection is last in list
return collections
@@ -277,7 +277,7 @@ class UserSession(object):
def update_collections(self, updated_collections):
collection_body = json.dumps(updated_collections)
- save_collections(self.redis_user_id, collection_body)
+ save_collections(self.user_id, collection_body)
def import_traits_to_user(self, anon_id):
collections = get_user_collections(anon_id)
--
cgit v1.2.3
From 481dc87ee2a04671c98066e4c1f30d9b4c4809fc Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 12 May 2020 22:53:30 +0200
Subject: Remove eventlet
---
bin/genenetwork2 | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 759c71dc..3ae08e0a 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -209,7 +209,7 @@ if [ "$1" = '-gunicorn-prod' ] ; then
echo PYTHONPATH=$PYTHONPATH
if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
PID=$TMPDIR/gunicorn.$USER.pid
- cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID -k eventlet --workers 20 --keep-alive 6000 --max-requests 1000 --timeout 1200 wsgi"
+ cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 1000 --timeout 1200 wsgi"
echo RUNNING gunicorn $cmd
gunicorn $cmd
exit $?
--
cgit v1.2.3
From 81205be9a657c3fb350fe797ecefe615c0b9a4b7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 18 May 2020 11:48:14 -0500
Subject: Fixed issue with phenotype correlation table and added Plotly Chart
Studio link to correlation scatterplots
---
wqflask/wqflask/correlation/show_corr_results.py | 2 ++
.../static/new/javascript/draw_corr_scatterplot.js | 2 ++
wqflask/wqflask/templates/correlation_page.html | 34 +++++++++++++++-------
3 files changed, 27 insertions(+), 11 deletions(-)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index cc74c8e4..b099b83d 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -609,6 +609,7 @@ def get_header_fields(data_type, corr_method):
if corr_method == "spearman":
header_fields = ['Index',
'Record',
+ 'Abbreviation',
'Description',
'Authors',
'Year',
@@ -621,6 +622,7 @@ def get_header_fields(data_type, corr_method):
else:
header_fields = ['Index',
'Record',
+ 'Abbreviation',
'Description',
'Authors',
'Year',
diff --git a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
index a0a88773..956e0467 100644
--- a/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_corr_scatterplot.js
@@ -132,6 +132,8 @@ var modebar_options = {
Plotly.downloadImage(gd, {format: 'jpeg'})
}
}],
+ showEditInChartStudio: true,
+ plotlyServerURL: "https://chart-studio.plotly.com",
modeBarButtonsToRemove:['toImage', 'sendDataToCloud', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines'],
displaylogo: false
}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 23136257..1c84239c 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -82,6 +82,7 @@
<button id="redraw" class="btn btn-default" type="button">Reset Columns</button>
</form>
<br />
+ {% if target_dataset.type != "Publish" %}
<br />
<button id="more_options" class="btn btn-primary">More Options...</button>
<br />
@@ -107,6 +108,7 @@
<br />
<br />
</div>
+ {% endif %}
</div>
<div style="margin-bottom: 5px;">
<b>Show/Hide Columns:</b>
@@ -162,9 +164,9 @@
{% if trait.abbreviation %}
<TD title="{{ trait.abbreviation }}" data-export="{{ trait.abbreviation }}">{% if trait.abbreviation|length > 20 %}{{ trait.abbreviation[:20] }}...{% else %}{{ trait.abbreviation }}{% endif %}</TD>
{% else %}
- <TD data-export="{{ trait.abbreviation }}">N/A</TD>
+ <TD data-export="N/A">N/A</TD>
{% endif %}
- <td data-export="{{ trait.description_display }}">{{ trait.description_display }}</td>
+ <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 50 %}{{ trait.description_display[:50] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
<td data-export="{{ trait.authors }}">{{ trait.authors }}</td>
<td data-export="{{ trait.pubmed_text }}">
<a href="{{ trait.pubmed_link }}">
@@ -192,7 +194,7 @@
{% endblock %}
{% block js %}
- <script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>
+ <!--<script type="text/javascript" src="/static/new/js_external/md5.min.js"></script>-->
<script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
@@ -239,8 +241,7 @@
return ((x < y) ? 1 : ((x > y) ? -1 : 0));
};
- //$.fn.dataTableExt.afnFiltering.push(
-
+ {% if target_dataset.type != "Publish" %}
$.fn.dataTable.ext.search.push( function( settings, data, dataIndex ) {
var r_column = {{ filter_cols[0] }};
var r_greater = parseFloat($('input[name=r_greater_select]').val())
@@ -280,6 +281,7 @@
}
return true
});
+ {% endif %}
$(document).ready( function () {
@@ -303,7 +305,6 @@
$(button).prop("disabled", false);
}
}
- //});
if ($(this).is(":checked")) {
if (!$(this).closest('tr').hasClass('selected')) {
$(this).closest('tr').addClass('selected')
@@ -382,8 +383,15 @@
{% elif target_dataset.type == "Publish" %}
table_conf = {
- "paging": false,
- buttons: [
+ "drawCallback": function( settings ) {
+ $('#trait_table tr').click(function(event) {
+ if (event.target.type !== 'checkbox') {
+ $(':checkbox', this).trigger('click');
+ }
+ });
+ $('.trait_checkbox:checkbox').on("change", change_buttons);
+ },
+ "buttons": [
{
extend: 'columnsToggle',
columns: function( idx, data, node ) {
@@ -426,10 +434,14 @@
$('td', row).eq(4).text($('td', row).eq(4).text() + '...')
}
},
- "order": [[8, "asc" ]],
+ "order": [[9, "asc" ]],
"sDom": "Btir",
+ "iDisplayLength": -1,
"autoWidth": false,
- "bDeferRender": true
+ "deferRender": true,
+ "bSortClasses": false,
+ "paging": false,
+ "orderClasses": true,
}
{% elif target_dataset.type == "Geno" %}
table_conf = {
@@ -468,7 +480,7 @@
}
{% endif %}
- var the_table = $('#trait_table').DataTable(table_conf);
+ the_table = $('#trait_table').DataTable(table_conf);
console.timeEnd("Creating table");
--
cgit v1.2.3
From 9d0c8a43cdcfb5ee7c30897495b4617d58f98386 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 18 May 2020 11:48:50 -0500
Subject: Fixed Bar Chart left margin issue and fixed issue where 0 values
didn't have +1 added when doing log transforms
---
wqflask/wqflask/static/new/javascript/show_trait.js | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 785e5332..2f276021 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -758,7 +758,7 @@ check_for_zero_to_one_vals = function() {
return;
} else {
current_value = parseFloat(current_value)
- if (0 < current_value && current_value < 1){
+ if (0 <= current_value && current_value < 1){
zero_to_one_vals_exist = true
return false;
}
@@ -1033,12 +1033,16 @@ val_range = root.chart_range[1] - root.chart_range[0]
if (val_range < 0.05){
tick_digits = '.3f'
+ left_margin = 80
} else if (val_range < 0.5) {
tick_digits = '.2f'
+ left_margin = 70
} else if (val_range < 5){
tick_digits = '.1f'
+ left_margin = 60
} else {
tick_digits = 'f'
+ left_margin = 55
}
if (js_data.num_values < 256) {
@@ -1077,7 +1081,7 @@ if (js_data.num_values < 256) {
width: bar_chart_width,
height: 600,
margin: {
- l: 55,
+ l: left_margin,
r: 30,
t: 30,
b: bottom_margin
--
cgit v1.2.3
From 442ec66a603bdc312f760027d4c000ba7af14fe6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 18 May 2020 11:49:32 -0500
Subject: Partial fix to issue of the top margin being too small when using
R/qtl and cofactors
---
wqflask/wqflask/marker_regression/display_mapping_results.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f70bc555..a648667b 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -508,7 +508,10 @@ class DisplayMappingResults(object):
yTopOffset = max(90, yTopOffset)
else:
if self.legendChecked:
- yTopOffset = max(90, yTopOffset)
+ if self.covariates != "" and self.controlLocus and self.doControl != "false":
+ yTopOffset = max(120, yTopOffset)
+ else:
+ yTopOffset = max(100, yTopOffset)
else:
pass
--
cgit v1.2.3
From 80709f6573a85f2d1195f938006f46044651320b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 18 May 2020 15:35:29 -0500
Subject: Added warning that 1 is being added when doing log transform on
traits with sample values between 0 and 1
---
.../wqflask/static/new/javascript/show_trait.js | 28 ++++++++++++++++++----
.../new/javascript/show_trait_mapping_tools.js | 5 +---
wqflask/wqflask/templates/show_trait.html | 3 ++-
.../templates/show_trait_transform_and_filter.html | 2 +-
4 files changed, 28 insertions(+), 10 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 2f276021..c0b2e6db 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -755,12 +755,12 @@ check_for_zero_to_one_vals = function() {
$('.trait_value_input').each(function() {
current_value = $(this).data("value")
if(isNaN(current_value)) {
- return;
+ return true;
} else {
current_value = parseFloat(current_value)
if (0 <= current_value && current_value < 1){
zero_to_one_vals_exist = true
- return false;
+ return false
}
}
});
@@ -769,7 +769,6 @@ check_for_zero_to_one_vals = function() {
normalize_data = function() {
if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){
- zero_to_one_vals_exist = check_for_zero_to_one_vals();
if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
log2_normalize_data(zero_to_one_vals_exist)
$('input[name="transform"]').val("log2")
@@ -810,7 +809,28 @@ normalize_data = function() {
}
}
-$('#normalize').click(normalize_data);
+zero_to_one_vals_exist = false
+
+show_transform_warning = function() {
+ transform_type = $('#norm_method option:selected').val()
+ zero_to_one_vals_exist = check_for_zero_to_one_vals();
+ if (transform_type == "log2" || transform_type == "log10"){
+ if (zero_to_one_vals_exist){
+ $('#transform_alert').css("display", "block")
+ }
+ } else {
+ $('#transform_alert').css("display", "none")
+ }
+}
+
+$('#norm_method').change(function(){
+ show_transform_warning()
+});
+$('#normalize').hover(function(){
+ show_transform_warning()
+});
+
+$('#normalize').click(normalize_data)
switch_qnorm_data = function() {
return $('.trait_value_input').each((function(_this) {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 7176a0da..01da3f74 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -131,11 +131,8 @@
};
outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results.";
-
- runtime_warning_text = "This function could take as long as 10-20 minutes to run, so please do not close your browser window until it finishes."
-
showalert = function(message, alerttype) {
- return $('#alert_placeholder').append('<div id="alertdiv" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
+ return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>');
};
$('#suggestive').hide();
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index d29be30b..7380d198 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -74,6 +74,7 @@
<div class="panel-body">
{% include 'show_trait_transform_and_filter.html' %}
</div>
+ <div id="transform_alert_placeholder"><div id="transform_alert" style="display: none;"class="alert alert-success outlier-alert"><a class="close" data-dismiss="alert">�</a><span>Because there are some values between 0 and 1, log2 and log10 transforms will add 1 to each value.</span></div></div>
</div>
</div>
<div class="panel panel-default">
@@ -98,7 +99,7 @@
<div class="panel-body">
{% include 'show_trait_mapping_tools.html' %}
</div>
- <div id="alert_placeholder"></div>
+ <div id="outlier_alert_placeholder"></div>
</div>
</div>
<div class="panel panel-default">
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
index 4be6d249..b4118b04 100644
--- a/wqflask/wqflask/templates/show_trait_transform_and_filter.html
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -70,7 +70,7 @@
<div>
<p>Outliers highlighted in
- <strong style="background-color:yellow;">yellow</strong>
+ <strong style="background-color:orange;">orange</strong>
can be hidden using
the <strong>Hide Outliers</strong> button.
</p>
--
cgit v1.2.3
From dc002daace320135b4d32ac08de2ee568e68ba51 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 20 May 2020 14:17:17 -0500
Subject: Fixed issue when some case attribute values don't exist + added
phenogen link to trait page
---
wqflask/wqflask/show_trait/show_trait.py | 9 ++++++---
wqflask/wqflask/templates/show_trait_details.html | 6 ++++++
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 072d7f8c..29b2f77e 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -294,7 +294,7 @@ class ShowTrait(object):
if check_if_attr_exists(self.this_trait, 'uniprotid'):
self.uniprot_link = webqtlConfig.UNIPROT_URL % self.this_trait.uniprotid
- self.genotation_link = self.rgd_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None
+ self.genotation_link = self.rgd_link = self.phenogen_link = self.gtex_link = self.genebridge_link = self.ucsc_blat_link = self.biogps_link = self.protein_atlas_link = None
self.string_link = self.panther_link = self.aba_link = self.ebi_gwas_link = self.wiki_pi_link = self.genemania_link = self.ensembl_link = None
if self.this_trait.symbol:
self.genotation_link = webqtlConfig.GENOTATION_URL % self.this_trait.symbol
@@ -332,6 +332,7 @@ class ShowTrait(object):
if self.dataset.group.species == "rat":
self.rgd_link = webqtlConfig.RGD_URL % (self.this_trait.symbol, self.dataset.group.species.capitalize())
+ self.phenogen_link = webqtlConfig.PHENOGEN_URL % (self.this_trait.symbol)
self.genemania_link = webqtlConfig.GENEMANIA_URL % ("rattus-norvegicus", self.this_trait.symbol)
query = """SELECT kgID, chromosome, txStart, txEnd
@@ -603,8 +604,10 @@ def get_categorical_variables(this_trait, sample_list):
for attribute in sample_list.attributes:
attribute_vals = []
for sample_name in this_trait.data.keys():
- attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
-
+ if sample_list.attributes[attribute].name in this_trait.data[sample_name].extra_attributes:
+ attribute_vals.append(this_trait.data[sample_name].extra_attributes[sample_list.attributes[attribute].name])
+ else:
+ attribute_vals.append("N/A")
num_distinct = len(set(attribute_vals))
if num_distinct < 10:
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 62268a54..878b6ced 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -141,6 +141,12 @@
GTEx Portal
</a>
+ {% if phenogen_link %}
+ <a href="{{ phenogen_link }}" target="_blank">
+ PhenoGen
+ </a>
+
+ {% endif %}
{% if genebridge_link %}
<a href="{{ genebridge_link }}" target="_blank">
GeneBridge
--
cgit v1.2.3
From 81ba67bb1f8f18983ae983e70d985eebe16acde1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 May 2020 12:45:31 -0500
Subject: Fixed search page table widths by setting max-width, at least for the
time being
---
wqflask/wqflask/templates/search_result_page.html | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 767e3487..89ca6681 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -8,7 +8,7 @@
{% endblock %}
{% block content %}
<!-- Start of body -->
- <div style="padding-left: 10px; {% if dataset.type == 'Publish' %}min-width: 1000px;{% else %}min-width: 1200px;{% endif %}">
+ <div style="padding-left: 10px;">
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
<div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
@@ -133,7 +133,7 @@
<b>Show/Hide Columns:</b>
</div>
<div id="table_container">
- <table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
+ <table class="table-hover table-striped cell-border" id='trait_table' style="max-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px; float: left;">
<tbody>
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
@@ -265,7 +265,7 @@
'columns': [
{
'data': null,
- 'width': "30px",
+ 'width': "25px",
'orderDataType': "dom-checkbox",
'orderSequence': [ "desc", "asc"],
'render': function(data, type, row, meta) {
@@ -322,18 +322,20 @@
'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
'type': "natural",
'data': "lrs_score",
+ 'width': "80px",
'orderSequence': [ "desc", "asc"]
},
{
'title': "Max LRS Location",
'type': "natural",
- 'width': "120px",
+ 'width': "150px",
'data': "lrs_location"
},
{
'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
'type': "natural",
'data': "additive",
+ 'width': "120px",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Publish' %},
{
@@ -380,6 +382,7 @@
'type': "natural",
'orderDataType': "dom-inner-text",
'data': null,
+ 'width': "80px",
'render': function(data, type, row, meta) {
if (data.pubmed_id != "N/A"){
return '<a href="' + data.pubmed_link + '">' + data.pubmed_text + '</a>'
@@ -393,25 +396,26 @@
'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
'type': "natural",
'data': "lrs_score",
+ 'width': "80px",
'orderSequence': [ "desc", "asc"]
},
{
'title': "Max LRS Location",
'type': "natural",
- 'width': "200px",
+ 'width': "150px",
'data': "lrs_location"
},
{
- 'title': "Additive<br>Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+ 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
'type': "natural",
- 'width': "100px",
+ 'width': "120px",
'data': "additive",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Geno' %},
{
'title': "Location",
'type': "natural",
- 'width': "160px",
+ 'width': "140px",
'data': "location"
}{% endif %}
],
--
cgit v1.2.3
From 24baaf4dc03844d34f4c4101179223cc4e0d9184 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 May 2020 15:57:49 -0500
Subject: Made search result table width variable again and fixed row
highlighting, though later I need to go through and redo a bunch of CSS stuff
---
wqflask/base/webqtlConfig.py | 1 +
wqflask/wqflask/static/new/css/show_trait.css | 4 ++
wqflask/wqflask/templates/search_result_page.html | 46 +++++++++++++----------
3 files changed, 32 insertions(+), 19 deletions(-)
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 018d5d54..55407123 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -58,6 +58,7 @@ PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
+PHENOGEN_URL = "https://phenogen.org/gene.jsp?speciesCB=Rn&auto=Y&geneTxt=%s&genomeVer=rn6§ion=geneEQTL"
# Temporary storage (note that this TMPDIR can be set as an
# environment variable - use utility.tools.TEMPDIR when you
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 09d5e1e3..a0e84474 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -2,6 +2,10 @@ tr .outlier {
background-color: #ffff99;
}
+table.dataTable tbody tr.selected {
+ background-color: #ffff00
+}
+
#bar_chart_container {
overflow-x:scroll;
}
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 89ca6681..b238a28a 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -8,7 +8,7 @@
{% endblock %}
{% block content %}
<!-- Start of body -->
- <div style="padding-left: 10px;">
+ <div style="padding-left: 10px;>
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
<div style="padding-top: 10px; padding-bottom: 10px; font-size: 16px;">
@@ -59,7 +59,7 @@
</div>
- <div>
+ <div style="min-width: 950px;">
<form id="trait_submission_form" target="_blank" action="/corr_matrix" method="post">
<input type="hidden" name="tool_used" value="" />
<input type="hidden" name="form_url" value="" />
@@ -111,29 +111,34 @@
<div>
<br />
<form id="export_form" method="POST" action="/export_traits_csv" style="display: inline;">
- <input type="hidden" name="headers" id="headers" value="{% for field in header_fields %}{{ field }},{% endfor %}">
- <input type="hidden" name="search_string" id="search_string" value="{{ original_search_string }}">
- <input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}">
- <input type="hidden" name="file_name" id="file_name" value="search_results">
- <input type="hidden" name="filter_term" id="filter_term" value="None">
- {% if dataset.accession_id is defined %}
- <input type="hidden" name="accession_id" id="accession_id" value="{{ dataset.accession_id }}">
- {% endif %}
- <input type="hidden" name="export_data" id="export_data" value="">
- <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
- <button class="btn btn-default" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
- <button class="btn btn-default" id="export_traits">Download CSV</button>
- <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
- <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
- <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
+ <div style="min-width: 950px;">
+ <input type="hidden" name="headers" id="headers" value="{% for field in header_fields %}{{ field }},{% endfor %}">
+ <input type="hidden" name="search_string" id="search_string" value="{{ original_search_string }}">
+ <input type="hidden" name="database_name" id="database_name" value="{{ dataset.fullname }}">
+ <input type="hidden" name="file_name" id="file_name" value="search_results">
+ <input type="hidden" name="filter_term" id="filter_term" value="None">
+ {% if dataset.accession_id is defined %}
+ <input type="hidden" name="accession_id" id="accession_id" value="{{ dataset.accession_id }}">
+ {% endif %}
+ <input type="hidden" name="export_data" id="export_data" value="">
+ <button class="btn btn-default" id="select_all" type="button"><span class="glyphicon glyphicon-ok"></span> Select</button>
+ <button class="btn btn-default" id="add" type="button" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
+ <button class="btn btn-default" id="export_traits">Download CSV</button>
+ <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
+ <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
+ <button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
+ </div>
</form>
<br />
+ {% if dataset.type != 'Geno' %}
<br />
<div style="margin-bottom: 5px;">
<b>Show/Hide Columns:</b>
</div>
+ {% endif %}
+ <!--<div id="table_container" style="min-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px;">-->
<div id="table_container">
- <table class="table-hover table-striped cell-border" id='trait_table' style="max-width: {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}2000{% else %}380{% endif %}px; float: left;">
+ <table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
<tbody>
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
@@ -341,7 +346,6 @@
{
'title': "Description",
'type': "natural",
- 'width': "800px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -420,6 +424,7 @@
}{% endif %}
],
"order": [[1, "asc" ]],
+ {% if dataset.type != 'Geno' %}
buttons: [
{
extend: 'columnsToggle',
@@ -434,6 +439,9 @@
}
],
'sDom': "Bitir",
+ {% else %}
+ 'sDom': "itir",
+ {% endif %}
'deferRender': true,
'paging': false,
'orderClasses': true,
--
cgit v1.2.3
From 2c3301d25c505c217518e7133e0f4cf53797c5b9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 21 May 2020 16:34:09 -0500
Subject: More adjusting to table widths
---
wqflask/wqflask/templates/search_result_page.html | 3 +++
1 file changed, 3 insertions(+)
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index b238a28a..3dfae3dd 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -296,11 +296,13 @@
{
'title': "Symbol",
'type': "natural",
+ 'width': "120px",
'data': "symbol"
},
{
'title': "Description",
'type': "natural",
+ 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -346,6 +348,7 @@
{
'title': "Description",
'type': "natural",
+ 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
--
cgit v1.2.3
From 55b654a9f40bb247272c45671c58c772874f43f6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 23 May 2020 13:12:22 -0500
Subject: Changed row highlight color to the more pale yellow it was before
---
wqflask/wqflask/static/new/css/show_trait.css | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index a0e84474..d3e6672a 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -3,7 +3,7 @@ tr .outlier {
}
table.dataTable tbody tr.selected {
- background-color: #ffff00
+ background-color: #ffee99;
}
#bar_chart_container {
--
cgit v1.2.3
From ff94904574c51eeb7aecb327d6f2679fa4a60fb4 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 28 May 2020 20:24:01 -0500
Subject: Added lines calling proxy for publish datasets + added some resource
redis queries and a missing import for the hmac functions
---
wqflask/base/trait.py | 12 ++++++----
wqflask/utility/hmac.py | 2 ++
wqflask/utility/redis_tools.py | 54 ++++++++++++++++++++++++++++++++++++++----
3 files changed, 59 insertions(+), 9 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index e454c593..1b7cb23c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -5,9 +5,6 @@ import resource
import codecs
import requests
-import redis
-Redis = redis.StrictRedis()
-
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
@@ -15,6 +12,8 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility import hmac
from utility.tools import GN2_BASE_URL
+from utility.redis_tools import get_redis_conn
+Redis = get_redis_conn()
from wqflask import app
@@ -349,8 +348,13 @@ def jsonable_table_row(trait, dataset_name, index):
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
-
+
if dataset.type == 'Publish':
+ resource_id = hmac.data_hmac("{}:{}".format(dataset.id, trait.name))
+
+ the_url = "http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+ trait_data = json.loads(requests.get("http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)))
+
query = """
SELECT
PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index d8a0eace..b08be97e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -3,6 +3,8 @@ from __future__ import print_function, division, absolute_import
import hmac
import hashlib
+from flask import url_for
+
from wqflask import app
def hmac_creation(stringy):
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index ca42f7b7..15841032 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -1,17 +1,25 @@
from __future__ import print_function, division, absolute_import
+import uuid
import simplejson as json
import redis # used for collections
-Redis = redis.StrictRedis()
import logging
from flask import (render_template, flash)
+from utility import hmac
+
from utility.logger import getLogger
logger = getLogger(__name__)
+def get_redis_conn():
+ Redis = redis.StrictRedis(port=6380)
+ return Redis
+
+Redis = get_redis_conn()
+
def is_redis_available():
try:
Redis.ping()
@@ -70,14 +78,15 @@ def check_verification_code(code):
email_address = None
user_details = None
email_address = Redis.hget("verification_codes", code)
- return email_address
if email_address:
user_details = get_user_by_unique_column('email_address', email_address)
- return user_details
+ if user_details:
+ return user_details
+ else:
+ return None
else:
return None
- flash("Invalid code: Password reset code does not exist or might have expired!", "error")
def get_user_groups(user_id):
#ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
@@ -167,4 +176,39 @@ def change_group_name(user_id, group_id, new_name):
group_info["name"] = new_name
return group_info
else:
- return None
\ No newline at end of file
+ return None
+
+def get_resources():
+ resource_list = Redis.hgetall("resources")
+ return resource_list
+
+def get_resource_id(dataset_type, dataset_id, trait_id = None, all_resources = None):
+ if not all_resources:
+ all_resources = get_resources()
+
+ resource_list = [[key, json.loads(value)] for key, value in all_resources.items()]
+
+ if not trait_id:
+ matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id]
+ else:
+ matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id and resource[1]['data']['trait'] == trait_id]
+
+ if len(matched_resources):
+ return matched_resources[0]
+ else:
+ return False
+
+def get_resource_info(resource_id):
+ resource_info = Redis.hget("resources", resource_id)
+ return json.loads(resource_info)
+
+def add_resource(resource_info):
+
+ if 'trait' in resource_info['data']:
+ resource_id = hmac.data_hmac('{}:{}'.format(str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+ else:
+ resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset'])))
+
+ Redis.hset("resources", resource_id, json.dumps(resource_info))
+
+ return resource_info
--
cgit v1.2.3
From 1a663f987bf3a640d21c2c89402318d5433efd9e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 4 Jun 2020 14:23:30 -0500
Subject: Really should have split this into many more commits:
- Now use proxy to pull trait data and hide traits/results that the user
doesn't have view permission for
- Created a factory method for creating trait ob so it can return None
when user doesn't have view permissions (this is why such a large number
of files are changed)
- Added metadata to permutation export
- Added current group management code
- Added fixed password verification e-mail code
---
wqflask/base/trait.py | 177 ++++----
wqflask/utility/helper_functions.py | 11 +-
wqflask/utility/redis_tools.py | 58 +--
wqflask/wqflask/api/correlation.py | 472 ++++++++++-----------
wqflask/wqflask/api/gen_menu.py | 11 +-
wqflask/wqflask/api/mapping.py | 4 +-
wqflask/wqflask/collect.py | 15 +-
.../comparison_bar_chart/comparison_bar_chart.py | 4 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 8 +-
wqflask/wqflask/correlation/show_corr_results.py | 8 +-
.../wqflask/correlation_matrix/show_corr_matrix.py | 22 +-
wqflask/wqflask/ctl/ctl_analysis.py | 10 +-
wqflask/wqflask/do_search.py | 11 +-
wqflask/wqflask/gsearch.py | 13 +-
.../marker_regression/display_mapping_results.py | 6 +
wqflask/wqflask/marker_regression/gemma_mapping.py | 4 +-
wqflask/wqflask/marker_regression/rqtl_mapping.py | 64 ++-
wqflask/wqflask/marker_regression/run_mapping.py | 3 +-
wqflask/wqflask/network_graph/network_graph.py | 4 +-
wqflask/wqflask/search_results.py | 106 ++---
wqflask/wqflask/show_trait/export_trait_data.py | 4 +-
wqflask/wqflask/show_trait/show_trait.py | 21 +-
wqflask/wqflask/templates/admin/group_manager.html | 45 +-
wqflask/wqflask/templates/correlation_page.html | 1 +
wqflask/wqflask/templates/email/verification.txt | 7 -
wqflask/wqflask/templates/gsearch_pheno.html | 2 +-
wqflask/wqflask/templates/mapping_results.html | 31 +-
wqflask/wqflask/user_login.py | 43 +-
wqflask/wqflask/user_session.py | 18 +-
wqflask/wqflask/views.py | 71 +++-
30 files changed, 637 insertions(+), 617 deletions(-)
delete mode 100644 wqflask/wqflask/templates/email/verification.txt
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 1b7cb23c..b133bf21 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -11,6 +11,7 @@ from base.data_set import create_dataset
from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility import hmac
+from utility.authentication_tools import check_resource_availability
from utility.tools import GN2_BASE_URL
from utility.redis_tools import get_redis_conn
Redis = get_redis_conn()
@@ -21,11 +22,33 @@ import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g, request, url_for
+from flask import Flask, g, request, url_for, redirect
from utility.logger import getLogger
logger = getLogger(__name__ )
+def create_trait(**kw):
+ assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+
+ permitted = True
+ if kw.get('name'):
+ if kw.get('dataset_name'):
+ if kw.get('dataset_name') != "Temp":
+ dataset = create_dataset(kw.get('dataset_name'))
+ else:
+ dataset = kw.get('dataset')
+
+ if kw.get('dataset_name') != "Temp":
+ if dataset.type == 'Publish':
+ permitted = check_resource_availability(dataset, kw.get('name'))
+ else:
+ permitted = check_resource_availability(dataset)
+
+ if permitted:
+ return GeneralTrait(**kw)
+ else:
+ return None
+
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -50,6 +73,7 @@ class GeneralTrait(object):
self.haveinfo = kw.get('haveinfo', False)
self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet
self.data = kw.get('data', {})
+ self.view = True
# Sets defaults
self.locus = None
@@ -77,6 +101,7 @@ class GeneralTrait(object):
# So we could add a simple if statement to short-circuit this if necessary
if self.dataset.type != "Temp":
self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+
if get_sample_info != False:
self = retrieve_sample_data(self, self.dataset)
@@ -212,26 +237,28 @@ def get_sample_data():
trait = params['trait']
dataset = params['dataset']
- trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
-
- trait_dict = {}
- trait_dict['name'] = trait
- trait_dict['db'] = dataset
- trait_dict['type'] = trait_ob.dataset.type
- trait_dict['group'] = trait_ob.dataset.group.name
- trait_dict['tissue'] = trait_ob.dataset.tissue
- trait_dict['species'] = trait_ob.dataset.group.species
- trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
- trait_dict['description'] = trait_ob.description_display
- if trait_ob.dataset.type == "ProbeSet":
- trait_dict['symbol'] = trait_ob.symbol
- trait_dict['location'] = trait_ob.location_repr
- elif trait_ob.dataset.type == "Publish":
- if trait_ob.pubmed_id:
- trait_dict['pubmed_link'] = trait_ob.pubmed_link
- trait_dict['pubmed_text'] = trait_ob.pubmed_text
-
- return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
+ trait_ob = create_trait(name=trait, dataset_name=dataset)
+ if trait_ob:
+ trait_dict = {}
+ trait_dict['name'] = trait
+ trait_dict['db'] = dataset
+ trait_dict['type'] = trait_ob.dataset.type
+ trait_dict['group'] = trait_ob.dataset.group.name
+ trait_dict['tissue'] = trait_ob.dataset.tissue
+ trait_dict['species'] = trait_ob.dataset.group.species
+ trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+ trait_dict['description'] = trait_ob.description_display
+ if trait_ob.dataset.type == "ProbeSet":
+ trait_dict['symbol'] = trait_ob.symbol
+ trait_dict['location'] = trait_ob.location_repr
+ elif trait_ob.dataset.type == "Publish":
+ if trait_ob.pubmed_id:
+ trait_dict['pubmed_link'] = trait_ob.pubmed_link
+ trait_dict['pubmed_text'] = trait_ob.pubmed_text
+
+ return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
+ else:
+ return None
def jsonable(trait):
"""Return a dict suitable for using as json
@@ -350,91 +377,36 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
if dataset.type == 'Publish':
- resource_id = hmac.data_hmac("{}:{}".format(dataset.id, trait.name))
-
- the_url = "http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
- trait_data = json.loads(requests.get("http://localhost:8080/run_action/?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)))
-
- query = """
- SELECT
- PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
- Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
- Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
- Publication.Authors, Publication.Title, Publication.Abstract,
- Publication.Journal, Publication.Volume, Publication.Pages,
- Publication.Month, Publication.Year, PublishXRef.Sequence,
- Phenotype.Units, PublishXRef.comments
- FROM
- PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
- WHERE
- PublishXRef.Id = %s AND
- Phenotype.Id = PublishXRef.PhenotypeId AND
- Publication.Id = PublishXRef.PublicationId AND
- PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
- PublishXRef.InbredSetId = InbredSet.Id AND
- PublishFreeze.Id = %s
- """ % (trait.name, dataset.id)
-
- logger.sql(query)
- trait_info = g.db.execute(query).fetchone()
-
-
- #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
- #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+ resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait.name))
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
elif dataset.type == 'ProbeSet':
- display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
- display_fields_string = 'ProbeSet.' + display_fields_string
- query = """
- SELECT %s
- FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
- ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
- ProbeSetFreeze.Name = '%s' AND
- ProbeSet.Name = '%s'
- """ % (escape(display_fields_string),
- escape(dataset.name),
- escape(str(trait.name)))
- logger.sql(query)
- trait_info = g.db.execute(query).fetchone()
- #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
- # to avoid the problem of same marker name from different species.
- elif dataset.type == 'Geno':
- display_fields_string = string.join(dataset.display_fields,',Geno.')
- display_fields_string = 'Geno.' + display_fields_string
- query = """
- SELECT %s
- FROM Geno, GenoFreeze, GenoXRef
- WHERE
- GenoXRef.GenoFreezeId = GenoFreeze.Id AND
- GenoXRef.GenoId = Geno.Id AND
- GenoFreeze.Name = '%s' AND
- Geno.Name = '%s'
- """ % (escape(display_fields_string),
- escape(dataset.name),
- escape(trait.name))
- logger.sql(query)
- trait_info = g.db.execute(query).fetchone()
- else: #Temp type
- query = """SELECT %s FROM %s WHERE Name = %s"""
- logger.sql(query)
- trait_info = g.db.execute(query,
- (string.join(dataset.display_fields,','),
- dataset.type, trait.name)).fetchone()
+ resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+ else:
+ resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+
+ try:
+ response = requests.get(the_url).content
+ if response.strip() == "no-access":
+ trait.view = False
+ return trait
+ except:
+ resource_info = get_resource_info(resource_id)
+ default_permissions = resource_info['default_mask']['data']
+ if 'view' not in default_persmissions:
+ trait.view = False
+ return trait
+
+ trait_info = json.loads(response)
if trait_info:
trait.haveinfo = True
- #XZ: assign SQL query result to trait attributes.
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
- # if isinstance(trait_info[i], basestring):
- # logger.debug("HOLDER:", holder)
- # logger.debug("HOLDER2:", holder.decode(encoding='latin1'))
- # holder = unicode(trait_info[i], "utf-8", "ignore")
- if isinstance(trait_info[i], basestring):
- holder = holder.encode('latin1')
+ #if isinstance(trait_info[i], basestring):
+ # holder = holder.encode('latin1')
setattr(trait, field, holder)
if dataset.type == 'Publish':
@@ -453,13 +425,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait.confidential:
trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
-
- #if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
- # privilege=self.dataset.privilege,
- # userName=self.dataset.userName,
- # authorized_users=self.authorized_users):
- #
- # description = self.pre_publication_description
else:
trait.abbreviation = trait.post_publication_abbreviation
if description:
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index e7c04fef..9ce809b6 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -1,7 +1,7 @@
from __future__ import absolute_import, print_function, division
-from base.trait import GeneralTrait
from base import data_set
+from base.trait import create_trait
from base.species import TheSpecies
from utility import hmac
@@ -11,7 +11,6 @@ from flask import Flask, g
import logging
logger = logging.getLogger(__name__ )
-
def get_species_dataset_trait(self, start_vars):
#assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
if "temp_trait" in start_vars.keys():
@@ -24,7 +23,7 @@ def get_species_dataset_trait(self, start_vars):
logger.debug("After creating dataset")
self.species = TheSpecies(dataset=self.dataset)
logger.debug("After creating species")
- self.this_trait = GeneralTrait(dataset=self.dataset,
+ self.this_trait = create_trait(dataset=self.dataset,
name=start_vars['trait_id'],
cellid=None,
get_qtl_info=True)
@@ -34,7 +33,6 @@ def get_species_dataset_trait(self, start_vars):
#self.dataset.group.read_genotype_file()
#self.genotype = self.dataset.group.genotype
-
def get_trait_db_obs(self, trait_db_list):
if isinstance(trait_db_list, basestring):
trait_db_list = trait_db_list.split(",")
@@ -49,10 +47,11 @@ def get_trait_db_obs(self, trait_db_list):
dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2])
else:
dataset_ob = data_set.create_dataset(dataset_name)
- trait_ob = GeneralTrait(dataset=dataset_ob,
+ trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
- self.trait_list.append((trait_ob, dataset_ob))
+ if trait_ob:
+ self.trait_list.append((trait_ob, dataset_ob))
def get_species_groups():
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 15841032..0ad96879 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -2,6 +2,7 @@ from __future__ import print_function, division, absolute_import
import uuid
import simplejson as json
+import datetime
import redis # used for collections
@@ -96,15 +97,22 @@ def get_user_groups(user_id):
for key in groups_list:
group_ob = json.loads(groups_list[key])
group_admins = set(group_ob['admins'])
- group_users = set(group_ob['users'])
+ group_members = set(group_ob['members'])
if user_id in group_admins:
admin_group_ids.append(group_ob['id'])
- elif user_id in group_users:
+ elif user_id in group_members:
user_group_ids.append(group_ob['id'])
else:
continue
- return admin_group_ids, user_group_ids
+ admin_groups = []
+ user_groups = []
+ for the_id in admin_group_ids:
+ admin_groups.append(get_group_info(the_id))
+ for the_id in user_group_ids:
+ user_groups.append(get_group_info(the_id))
+
+ return admin_groups, user_groups
def get_group_info(group_id):
group_json = Redis.hget("groups", group_id)
@@ -114,18 +122,18 @@ def get_group_info(group_id):
return group_info
-def create_group(admin_member_ids, user_member_ids = [], group_name = ""):
+def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
group_id = str(uuid.uuid4())
new_group = {
"id" : group_id,
- "admins": admin_member_ids,
- "users" : user_member_ids,
+ "admins": admin_user_ids,
+ "members" : member_user_ids,
"name" : group_name,
"created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
"changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
}
- Redis.hset("groups", group_id, new_group)
+ Redis.hset("groups", group_id, json.dumps(new_group))
return new_group
@@ -144,7 +152,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
if admins:
group_users = set(group_info["admins"])
else:
- group_users = set(group_info["users"])
+ group_users = set(group_info["members"])
for email in user_emails:
user_id = get_user_id("email_address", email)
@@ -153,7 +161,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
if admins:
group_info["admins"] = list(group_users)
else:
- group_info["users"] = list(group_users)
+ group_info["members"] = list(group_users)
group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
Redis.hset("groups", group_id, json.dumps(group_info))
@@ -161,7 +169,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
else:
return None
-def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "users"): #ZS: User type is because I assume admins can remove other admins
+def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
group_info = get_group_info(group_id)
if user_id in group_info["admins"]:
group_users = set(group_info[user_type])
@@ -174,6 +182,7 @@ def change_group_name(user_id, group_id, new_name):
group_info = get_group_info(group_id)
if user_id in group_info["admins"]:
group_info["name"] = new_name
+ Redis.hset("groups", group_id, json.dumps(group_info))
return group_info
else:
return None
@@ -182,22 +191,21 @@ def get_resources():
resource_list = Redis.hgetall("resources")
return resource_list
-def get_resource_id(dataset_type, dataset_id, trait_id = None, all_resources = None):
- if not all_resources:
- all_resources = get_resources()
-
- resource_list = [[key, json.loads(value)] for key, value in all_resources.items()]
-
- if not trait_id:
- matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id]
- else:
- matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id and resource[1]['data']['trait'] == trait_id]
-
- if len(matched_resources):
- return matched_resources[0]
+def get_resource_id(dataset, trait_id=None):
+ if dataset.type == "Publish":
+ if trait_id:
+ resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+ else:
+ return False
+ elif dataset.type == "ProbeSet":
+ resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+ elif dataset.type == "Geno":
+ resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
else:
return False
+ return resource_id
+
def get_resource_info(resource_id):
resource_info = Redis.hget("resources", resource_id)
return json.loads(resource_info)
@@ -205,9 +213,9 @@ def get_resource_info(resource_id):
def add_resource(resource_info):
if 'trait' in resource_info['data']:
- resource_id = hmac.data_hmac('{}:{}'.format(str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+ resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
else:
- resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset'])))
+ resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
Redis.hset("resources", resource_id, json.dumps(resource_info))
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index 66eb94ac..7f5312c1 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -1,237 +1,237 @@
-from __future__ import absolute_import, division, print_function
-
-import collections
-
-import scipy
-
-from MySQLdb import escape_string as escape
-
-from flask import g
-
-from base import data_set
-from base.trait import GeneralTrait, retrieve_sample_data
-
-from wqflask.correlation.show_corr_results import generate_corr_json
-from wqflask.correlation import correlation_functions
-
-from utility import webqtlUtil, helper_functions, corr_result_helpers
-from utility.benchmark import Bench
-
-import utility.logger
-logger = utility.logger.getLogger(__name__ )
-
-def do_correlation(start_vars):
- assert('db' in start_vars)
- assert('target_db' in start_vars)
- assert('trait_id' in start_vars)
-
- this_dataset = data_set.create_dataset(dataset_name = start_vars['db'])
- target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db'])
- this_trait = GeneralTrait(dataset = this_dataset, name = start_vars['trait_id'])
- this_trait = retrieve_sample_data(this_trait, this_dataset)
-
- corr_params = init_corr_params(start_vars)
-
- corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params)
- #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
-
- final_results = []
- for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]):
- if corr_params['type'] == "tissue":
- [sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
- result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "#_strains" : num_overlap,
- "p_value" : sample_p,
- "symbol" : symbol
- }
- elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
- [gene_id, sample_r] = corr_results[trait]
- result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "gene_id" : gene_id
- }
- else:
- [sample_r, sample_p, num_overlap] = corr_results[trait]
- result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "#_strains" : num_overlap,
- "p_value" : sample_p
- }
-
- final_results.append(result_dict)
-
- # json_corr_results = generate_corr_json(final_corr_results, this_trait, this_dataset, target_dataset, for_api = True)
-
- return final_results
-
-def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
- corr_results = {}
-
- target_dataset.get_trait_data()
-
- if corr_params['type'] == "tissue":
- trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
- corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
- sorted_results = collections.OrderedDict(sorted(corr_results.items(),
- key=lambda t: -abs(t[1][1])))
- elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature"
- trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
- corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
- sorted_results = collections.OrderedDict(sorted(corr_results.items(),
- key=lambda t: -abs(t[1][1])))
- else:
- for target_trait, target_vals in target_dataset.trait_data.iteritems():
- result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
- if result is not None:
- corr_results[target_trait] = result
-
- sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
-
- return sorted_results
-
-def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
- #Gets tissue expression values for the primary trait
- primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol])
-
- if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
- primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
-
- corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values())
-
- tissue_corr_data = {}
- for trait, symbol in trait_symbol_dict.iteritems():
- if symbol and symbol.lower() in corr_result_tissue_vals_dict:
- this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
-
- result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
- this_trait_tissue_values,
- corr_params['method'])
-
- tissue_corr_data[trait] = [result[0], result[1], result[2], symbol]
-
- return tissue_corr_data
-
-def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
- input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
-
- lit_corr_data = {}
- for trait, gene_id in trait_geneid_dict.iteritems():
- mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id)
-
- if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
- result = g.db.execute(
- """SELECT value
- FROM LCorrRamin3
- WHERE GeneId1='%s' and
- GeneId2='%s'
- """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
- ).fetchone()
- if not result:
- result = g.db.execute("""SELECT value
- FROM LCorrRamin3
- WHERE GeneId2='%s' and
- GeneId1='%s'
- """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
- ).fetchone()
- if result:
- lit_corr = result.value
- lit_corr_data[trait] = [gene_id, lit_corr]
- else:
- lit_corr_data[trait] = [gene_id, 0]
- else:
- lit_corr_data[trait] = [gene_id, 0]
-
- return lit_corr_data
-
-def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
- """
- Calculates the sample r (or rho) and p-value
-
- Given a primary trait and a target trait's sample values,
- calculates either the pearson r or spearman rho and the p-value
- using the corresponding scipy functions.
- """
-
- this_trait_vals = []
- shared_target_vals = []
- for i, sample in enumerate(target_dataset.group.samplelist):
- if sample in this_trait.data:
- this_sample_value = this_trait.data[sample].value
- target_sample_value = target_vals[i]
- this_trait_vals.append(this_sample_value)
- shared_target_vals.append(target_sample_value)
-
- this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals)
-
- if type == 'pearson':
- sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals)
- else:
- sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals)
-
- if num_overlap > 5:
- if scipy.isnan(sample_r):
- return None
- else:
- return [sample_r, sample_p, num_overlap]
-
-def convert_to_mouse_gene_id(species=None, gene_id=None):
- """If the species is rat or human, translate the gene_id to the mouse geneid
-
- If there is no input gene_id or there's no corresponding mouse gene_id, return None
-
- """
- if not gene_id:
- return None
-
- mouse_gene_id = None
-
- if species == 'mouse':
- mouse_gene_id = gene_id
-
- elif species == 'rat':
-
- query = """SELECT mouse
- FROM GeneIDXRef
- WHERE rat='%s'""" % escape(gene_id)
-
- result = g.db.execute(query).fetchone()
- if result != None:
- mouse_gene_id = result.mouse
-
- elif species == 'human':
-
- query = """SELECT mouse
- FROM GeneIDXRef
- WHERE human='%s'""" % escape(gene_id)
-
- result = g.db.execute(query).fetchone()
- if result != None:
- mouse_gene_id = result.mouse
-
- return mouse_gene_id
-
-def init_corr_params(start_vars):
- method = "pearson"
- if 'method' in start_vars:
- method = start_vars['method']
-
- type = "sample"
- if 'type' in start_vars:
- type = start_vars['type']
-
- return_count = 500
- if 'return_count' in start_vars:
- assert(start_vars['return_count'].isdigit())
- return_count = int(start_vars['return_count'])
-
- corr_params = {
- 'method' : method,
- 'type' : type,
- 'return_count' : return_count
- }
-
+from __future__ import absolute_import, division, print_function
+
+import collections
+
+import scipy
+
+from MySQLdb import escape_string as escape
+
+from flask import g
+
+from base import data_set
+from base.trait import create_trait, retrieve_sample_data
+
+from wqflask.correlation.show_corr_results import generate_corr_json
+from wqflask.correlation import correlation_functions
+
+from utility import webqtlUtil, helper_functions, corr_result_helpers
+from utility.benchmark import Bench
+
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def do_correlation(start_vars):
+ assert('db' in start_vars)
+ assert('target_db' in start_vars)
+ assert('trait_id' in start_vars)
+
+ this_dataset = data_set.create_dataset(dataset_name = start_vars['db'])
+ target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db'])
+ this_trait = create_trait(dataset = this_dataset, name = start_vars['trait_id'])
+ this_trait = retrieve_sample_data(this_trait, this_dataset)
+
+ corr_params = init_corr_params(start_vars)
+
+ corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params)
+ #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
+
+ final_results = []
+ for _trait_counter, trait in enumerate(corr_results.keys()[:corr_params['return_count']]):
+ if corr_params['type'] == "tissue":
+ [sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
+ result_dict = {
+ "trait" : trait,
+ "sample_r" : sample_r,
+ "#_strains" : num_overlap,
+ "p_value" : sample_p,
+ "symbol" : symbol
+ }
+ elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
+ [gene_id, sample_r] = corr_results[trait]
+ result_dict = {
+ "trait" : trait,
+ "sample_r" : sample_r,
+ "gene_id" : gene_id
+ }
+ else:
+ [sample_r, sample_p, num_overlap] = corr_results[trait]
+ result_dict = {
+ "trait" : trait,
+ "sample_r" : sample_r,
+ "#_strains" : num_overlap,
+ "p_value" : sample_p
+ }
+
+ final_results.append(result_dict)
+
+ # json_corr_results = generate_corr_json(final_corr_results, this_trait, this_dataset, target_dataset, for_api = True)
+
+ return final_results
+
+def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
+ corr_results = {}
+
+ target_dataset.get_trait_data()
+
+ if corr_params['type'] == "tissue":
+ trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
+ corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
+ sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+ key=lambda t: -abs(t[1][1])))
+ elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature"
+ trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
+ corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
+ sorted_results = collections.OrderedDict(sorted(corr_results.items(),
+ key=lambda t: -abs(t[1][1])))
+ else:
+ for target_trait, target_vals in target_dataset.trait_data.iteritems():
+ result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
+ if result is not None:
+ corr_results[target_trait] = result
+
+ sorted_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
+
+ return sorted_results
+
+def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
+ #Gets tissue expression values for the primary trait
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol])
+
+ if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
+
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=trait_symbol_dict.values())
+
+ tissue_corr_data = {}
+ for trait, symbol in trait_symbol_dict.iteritems():
+ if symbol and symbol.lower() in corr_result_tissue_vals_dict:
+ this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
+
+ result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
+ this_trait_tissue_values,
+ corr_params['method'])
+
+ tissue_corr_data[trait] = [result[0], result[1], result[2], symbol]
+
+ return tissue_corr_data
+
+def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
+ input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
+
+ lit_corr_data = {}
+ for trait, gene_id in trait_geneid_dict.iteritems():
+ mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id)
+
+ if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
+ result = g.db.execute(
+ """SELECT value
+ FROM LCorrRamin3
+ WHERE GeneId1='%s' and
+ GeneId2='%s'
+ """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
+ ).fetchone()
+ if not result:
+ result = g.db.execute("""SELECT value
+ FROM LCorrRamin3
+ WHERE GeneId2='%s' and
+ GeneId1='%s'
+ """ % (escape(mouse_gene_id), escape(input_trait_mouse_gene_id))
+ ).fetchone()
+ if result:
+ lit_corr = result.value
+ lit_corr_data[trait] = [gene_id, lit_corr]
+ else:
+ lit_corr_data[trait] = [gene_id, 0]
+ else:
+ lit_corr_data[trait] = [gene_id, 0]
+
+ return lit_corr_data
+
+def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
+ """
+ Calculates the sample r (or rho) and p-value
+
+ Given a primary trait and a target trait's sample values,
+ calculates either the pearson r or spearman rho and the p-value
+ using the corresponding scipy functions.
+ """
+
+ this_trait_vals = []
+ shared_target_vals = []
+ for i, sample in enumerate(target_dataset.group.samplelist):
+ if sample in this_trait.data:
+ this_sample_value = this_trait.data[sample].value
+ target_sample_value = target_vals[i]
+ this_trait_vals.append(this_sample_value)
+ shared_target_vals.append(target_sample_value)
+
+ this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals)
+
+ if type == 'pearson':
+ sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals)
+ else:
+ sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals)
+
+ if num_overlap > 5:
+ if scipy.isnan(sample_r):
+ return None
+ else:
+ return [sample_r, sample_p, num_overlap]
+
+def convert_to_mouse_gene_id(species=None, gene_id=None):
+ """If the species is rat or human, translate the gene_id to the mouse geneid
+
+ If there is no input gene_id or there's no corresponding mouse gene_id, return None
+
+ """
+ if not gene_id:
+ return None
+
+ mouse_gene_id = None
+
+ if species == 'mouse':
+ mouse_gene_id = gene_id
+
+ elif species == 'rat':
+
+ query = """SELECT mouse
+ FROM GeneIDXRef
+ WHERE rat='%s'""" % escape(gene_id)
+
+ result = g.db.execute(query).fetchone()
+ if result != None:
+ mouse_gene_id = result.mouse
+
+ elif species == 'human':
+
+ query = """SELECT mouse
+ FROM GeneIDXRef
+ WHERE human='%s'""" % escape(gene_id)
+
+ result = g.db.execute(query).fetchone()
+ if result != None:
+ mouse_gene_id = result.mouse
+
+ return mouse_gene_id
+
+def init_corr_params(start_vars):
+ method = "pearson"
+ if 'method' in start_vars:
+ method = start_vars['method']
+
+ type = "sample"
+ if 'type' in start_vars:
+ type = start_vars['type']
+
+ return_count = 500
+ if 'return_count' in start_vars:
+ assert(start_vars['return_count'].isdigit())
+ return_count = int(start_vars['return_count'])
+
+ corr_params = {
+ 'method' : method,
+ 'type' : type,
+ 'return_count' : return_count
+ }
+
return corr_params
\ No newline at end of file
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index c7bcb65d..bdcc3bf7 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -126,9 +126,7 @@ def build_types(species, group):
InbredSet.Name = '{1}' AND
ProbeFreeze.TissueId = Tissue.Id AND
ProbeFreeze.InbredSetId = InbredSet.Id AND
- ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
- ProbeSetFreeze.public > 0 AND
- ProbeSetFreeze.confidentiality < 1
+ ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
ORDER BY Tissue.Name""".format(species, group)
results = []
@@ -194,9 +192,7 @@ def build_datasets(species, group, type_name):
FROM InfoFiles, GenoFreeze, InbredSet
WHERE InbredSet.Name = '{}' AND
GenoFreeze.InbredSetId = InbredSet.Id AND
- InfoFiles.InfoPageName = GenoFreeze.ShortName AND
- GenoFreeze.public > 0 AND
- GenoFreeze.confidentiality < 1
+ InfoFiles.InfoPageName = GenoFreeze.ShortName
ORDER BY GenoFreeze.CreateTime DESC""".format(group)).fetchone()
if results != None:
@@ -214,8 +210,7 @@ def build_datasets(species, group, type_name):
Species.Id = InbredSet.SpeciesId AND
InbredSet.Name = '{1}' AND
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and Tissue.Name = '{2}' AND
- ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id AND
- ProbeSetFreeze.confidentiality < 1 and ProbeSetFreeze.public > 0
+ ProbeFreeze.TissueId = Tissue.Id and ProbeFreeze.InbredSetId = InbredSet.Id
ORDER BY ProbeSetFreeze.CreateTime DESC""".format(species, group, type_name)).fetchall()
datasets = []
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index d830cefc..92c27c9b 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -4,7 +4,7 @@ import string
from base import data_set
from base import webqtlConfig
-from base.trait import GeneralTrait, retrieve_sample_data
+from base.trait import create_trait, retrieve_sample_data
from utility import helper_functions
from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
@@ -18,7 +18,7 @@ def do_mapping_for_api(start_vars):
dataset = data_set.create_dataset(dataset_name = start_vars['db'])
dataset.group.get_markers()
- this_trait = GeneralTrait(dataset = dataset, name = start_vars['trait_id'])
+ this_trait = create_trait(dataset = dataset, name = start_vars['trait_id'])
this_trait = retrieve_sample_data(this_trait, dataset)
samples = []
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index b22e0004..4fb8e69b 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -14,9 +14,6 @@ import urlparse
import simplejson as json
-import redis
-Redis = redis.StrictRedis()
-
from flask import (Flask, g, render_template, url_for, request, make_response,
redirect, flash, jsonify)
@@ -30,8 +27,10 @@ from wqflask import model
from utility import Bunch, Struct, hmac
from utility.formatting import numify
+from utility.redis_tools import get_redis_conn
+Redis = get_redis_conn()
-from base import trait
+from base.trait import create_trait, retrieve_trait_info, jsonable
from base.data_set import create_dataset
import logging
@@ -208,14 +207,14 @@ def view_collection():
if dataset_name == "Temp":
group = name.split("_")[2]
dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group)
- trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
+ trait_ob = create_trait(name=name, dataset=dataset)
else:
dataset = create_dataset(dataset_name)
- trait_ob = trait.GeneralTrait(name=name, dataset=dataset)
- trait_ob = trait.retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
+ trait_ob = create_trait(name=name, dataset=dataset)
+ trait_ob = retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
trait_obs.append(trait_ob)
- json_version.append(trait.jsonable(trait_ob))
+ json_version.append(jsonable(trait_ob))
collection_info = dict(trait_obs=trait_obs,
uc = uc)
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 21eb1493..5d74dc9d 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -37,7 +37,7 @@ from pprint import pformat as pf
import reaper
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
from db import webqtlDatabaseFunction
@@ -108,7 +108,7 @@ class ComparisonBarChart(object):
trait_name, dataset_name = trait_db.split(":")
#print("dataset_name:", dataset_name)
dataset_ob = data_set.create_dataset(dataset_name)
- trait_ob = GeneralTrait(dataset=dataset_ob,
+ trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
self.trait_list.append((trait_ob, dataset_ob))
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index dfb81c54..04ec427d 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -4,7 +4,7 @@ import math
from flask import g
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
from utility import corr_result_helpers
from scipy import stats
@@ -20,9 +20,9 @@ class CorrScatterPlot(object):
self.data_set_1 = data_set.create_dataset(params['dataset_1'])
self.data_set_2 = data_set.create_dataset(params['dataset_2'])
#self.data_set_3 = data_set.create_dataset(params['dataset_3'])
- self.trait_1 = GeneralTrait(name=params['trait_1'], dataset=self.data_set_1)
- self.trait_2 = GeneralTrait(name=params['trait_2'], dataset=self.data_set_2)
- #self.trait_3 = GeneralTrait(name=params['trait_3'], dataset=self.data_set_3)
+ self.trait_1 = create_trait(name=params['trait_1'], dataset=self.data_set_1)
+ self.trait_2 = create_trait(name=params['trait_2'], dataset=self.data_set_2)
+ #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.data_set_3)
samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index b099b83d..7eab7184 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -47,7 +47,7 @@ import reaper
from base import webqtlConfig
from utility.THCell import THCell
from utility.TDCell import TDCell
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers, hmac
from db import webqtlDatabaseFunction
@@ -97,7 +97,7 @@ class CorrelationResults(object):
if start_vars['dataset'] == "Temp":
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
self.trait_id = start_vars['trait_id']
- self.this_trait = GeneralTrait(dataset=self.dataset,
+ self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
else:
@@ -199,7 +199,9 @@ class CorrelationResults(object):
range_chr_as_int = order_id
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
- trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
+ trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
+ if not trait_object:
+ continue
if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
#ZS: Convert trait chromosome to an int for the location range option
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b5c45d05..2b9467d1 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -43,14 +43,16 @@ from pprint import pformat as pf
import reaper
-import redis
-Redis = redis.StrictRedis()
+from utility.redis_tools import get_redis_conn
+Redis = get_redis_conn()
+THIRTY_DAYS = 60 * 60 * 24 * 30
from utility.THCell import THCell
from utility.TDCell import TDCell
from base.trait import GeneralTrait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
+
from db import webqtlDatabaseFunction
import utility.webqtlUtil #this is for parallel computing only.
from wqflask.correlation import correlation_functions
@@ -204,20 +206,6 @@ class CorrelationMatrix(object):
samples = self.all_sample_list,
sample_data = self.sample_data,)
# corr_results = [result[1] for result in result_row for result_row in self.corr_results])
-
- def get_trait_db_obs(self, trait_db_list):
-
- self.trait_list = []
- for i, trait_db in enumerate(trait_db_list):
- if i == (len(trait_db_list) - 1):
- break
- trait_name, dataset_name = trait_db.split(":")
- #print("dataset_name:", dataset_name)
- dataset_ob = data_set.create_dataset(dataset_name)
- trait_ob = GeneralTrait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
- self.trait_list.append((trait_ob, dataset_ob))
def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
base = importr('base')
@@ -257,7 +245,7 @@ class CorrelationMatrix(object):
this_vals_string += "x "
this_vals_string = this_vals_string[:-1]
- Redis.set(trait_id, this_vals_string)
+ Redis.set(trait_id, this_vals_string, ex=THIRTY_DAYS)
self.pca_trait_ids.append(trait_id)
return pca
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 4415b86a..35067036 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -17,7 +17,7 @@ import csv
import itertools
from base import data_set
-from base import trait as TRAIT
+from base.trait import create_trait, retrieve_sample_data
from utility import helper_functions
from utility.tools import locate, GN2_BRANCH_URL
@@ -122,8 +122,8 @@ class CTL(object):
logger.debug("retrieving data for", trait)
if trait != "":
ts = trait.split(':')
- gt = TRAIT.GeneralTrait(name = ts[0], dataset_name = ts[1])
- gt = TRAIT.retrieve_sample_data(gt, dataset, individuals)
+ gt = create_trait(name = ts[0], dataset_name = ts[1])
+ gt = retrieve_sample_data(gt, dataset, individuals)
for ind in individuals:
if ind in gt.data.keys():
traits.append(gt.data[ind].value)
@@ -180,8 +180,8 @@ class CTL(object):
logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console
tsS = significant[0][x].split(':') # Source
tsT = significant[2][x].split(':') # Target
- gtS = TRAIT.GeneralTrait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB
- gtT = TRAIT.GeneralTrait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB
+ gtS = create_trait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB
+ gtT = create_trait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB
self.addNode(gtS)
self.addNode(gtT)
self.addEdge(gtS, gtT, significant, x)
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index b0ca5ced..1e15d28f 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -34,10 +34,7 @@ class DoSearch(object):
self.search_type = search_type
if self.dataset:
- logger.debug("self.dataset is boo: ", type(self.dataset), pf(self.dataset))
- logger.debug("self.dataset.group is: ", pf(self.dataset.group))
#Get group information for dataset and the species id
-
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def execute(self, query):
@@ -54,10 +51,6 @@ class DoSearch(object):
return keyword
- #def escape(self, stringy):
- # """Shorter name than self.db_conn.escape_string"""
- # return escape(str(stringy))
-
def mescape(self, *items):
"""Multiple escape"""
escaped = [escape(str(item)) for item in items]
@@ -71,8 +64,6 @@ class DoSearch(object):
@classmethod
def get_search(cls, search_type):
- logger.debug("search_types are:", pf(cls.search_types))
-
search_type_string = search_type['dataset_type']
if 'key' in search_type and search_type['key'] != None:
search_type_string += '_' + search_type['key']
@@ -648,7 +639,7 @@ class CisTransLrsSearch(DoSearch):
escape(self.dataset.type),
chromosome)
else:
- location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type))
+ location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type))
where_clause = sub_clause + """
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 04e3d578..c65a1415 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -4,7 +4,7 @@ import json
from flask import Flask, g
from base.data_set import create_dataset
-from base.trait import GeneralTrait
+from base.trait import create_trait
from db import webqtlDatabaseFunction
from base import webqtlConfig
@@ -96,7 +96,9 @@ class GSearch(object):
#dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
#trait_id = line[4]
#with Bench("Building trait object"):
- trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
+ trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
+ if not trait_ob:
+ continue
max_lrs_text = "N/A"
if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
max_lrs_text = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
@@ -210,13 +212,12 @@ class GSearch(object):
if line[11] != "" and line[11] != None:
this_trait['additive'] = '%.3f' % line[11]
- #dataset = create_dataset(line[2], "Publish")
- #trait_id = line[3]
- #this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
this_trait['max_lrs_text'] = "N/A"
+ trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
+ if not trait_ob:
+ continue
if this_trait['dataset'] == this_trait['group'] + "Publish":
try:
- trait_ob = GeneralTrait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
this_trait['max_lrs_text'] = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
except:
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index a648667b..74fa4329 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -246,6 +246,12 @@ class DisplayMappingResults(object):
if 'output_files' in start_vars:
self.output_files = ",".join(start_vars['output_files'])
+ self.categorical_vars = ""
+ self.perm_strata = ""
+ if 'perm_strata' in start_vars.keys() and 'categorical_vars' in start_vars.keys():
+ self.categorical_vars = start_vars['categorical_vars']
+ self.perm_strata = start_vars['perm_strata']
+
self.selectedChr = int(start_vars['selected_chr'])
self.strainlist = start_vars['samples']
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index e2b15c26..88d27517 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,7 +1,7 @@
import os, math, string, random, json
from base import webqtlConfig
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base.data_set import create_dataset
from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, WEBSERVER_MODE
@@ -129,7 +129,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
this_covariate_data = []
trait_name = covariate.split(":")[0]
dataset_ob = create_dataset(covariate.split(":")[1])
- trait_ob = GeneralTrait(dataset=dataset_ob,
+ trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index e4a4d127..c5590a85 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -6,7 +6,7 @@ import json
from flask import g
from base.webqtlConfig import TMPDIR
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base.data_set import create_dataset
from utility import webqtlUtil
from utility.tools import locate, TEMPDIR
@@ -86,7 +86,6 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype
logger.info("Added pheno and names");
- # Scan for QTLs
marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
logger.info("Marker covars done");
if cofactors != "":
@@ -115,6 +114,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
else:
if do_control == "true" or cofactors != "":
logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
+ ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")')
else:
logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
@@ -295,7 +295,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covar_as_string = "c("
trait_name = covariate.split(":")[0]
dataset_ob = create_dataset(covariate.split(":")[1])
- trait_ob = GeneralTrait(dataset=dataset_ob,
+ trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
@@ -321,27 +321,27 @@ def add_cofactors(cross, this_dataset, covariates, samples):
datatype = get_trait_data_type(covariate)
logger.info("Covariate: " + covariate + " is of type: " + datatype);
if(datatype == "categorical"): # Cat variable
- logger.info("call of add_categorical_covar");
- cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
- logger.info("add_categorical_covar returned");
- for z, col_name in enumerate(col_names): # Go through the additional covar names
+ logger.info("call of add_categorical_covar");
+ cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
+ logger.info("add_categorical_covar returned");
+ for z, col_name in enumerate(col_names): # Go through the additional covar names
+ if i < (len(covariate_list) - 1):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ if(z < (len(col_names) -1)):
+ covar_name_string += '"' + col_name + '", '
+ else:
+ covar_name_string += '"' + col_name + '"'
+
+ logger.info("covar_name_string:" + covar_name_string)
+ else:
+ col_name = "covar_" + str(i)
+ cross = add_phenotype(cross, covar_as_string, col_name)
if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
- else:
- if(z < (len(col_names) -1)):
covar_name_string += '"' + col_name + '", '
- else:
+ else:
covar_name_string += '"' + col_name + '"'
- logger.info("covar_name_string:" + covar_name_string);
- else:
- col_name = "covar_" + str(i)
- cross = add_phenotype(cross, covar_as_string, col_name)
- if i < (len(covariate_list) - 1):
- covar_name_string += '"' + col_name + '", '
- else:
- covar_name_string += '"' + col_name + '"'
-
covar_name_string += ")"
logger.info("covar_name_string:" + covar_name_string);
covars_ob = pull_var("trait_covars", cross, covar_name_string)
@@ -350,9 +350,13 @@ def add_cofactors(cross, this_dataset, covariates, samples):
def create_marker_covariates(control_marker, cross):
ro.globalenv["the_cross"] = cross
ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
- userinputS = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
- covariate_names = ', '.join('"{0}"'.format(w) for w in userinputS)
- ro.r('covnames <- c(' + covariate_names + ')')
+ userinput_sanitized = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
+ logger.debug(userinput_sanitized)
+ if len(userinput_sanitized) > 0:
+ covariate_names = ', '.join('"{0}"'.format(w) for w in userinput_sanitized)
+ ro.r('covnames <- c(' + covariate_names + ')')
+ else:
+ ro.r('covnames <- c()')
ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
ro.r('covnames <- covnames[covInGeno]')
ro.r("cat('covnames (purged): ', covnames,'\n')")
@@ -404,16 +408,4 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
marker['lod_score'] = output[i][2]
qtl_results.append(marker)
- return qtl_results
-
-def get_trait_data_type(trait_db_string):
- # Get a trait's type (numeric, categorical, etc) from the DB
- the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
- results_json = g.db.execute(the_query).fetchone()
-
- results_ob = json.loads(results_json[0])
-
- if trait_db_string in results_ob:
- return results_ob[trait_db_string]
- else:
- return "numeric"
+ return qtl_results
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 5f7710ab..0711b852 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -161,7 +161,7 @@ class RunMapping(object):
self.num_perm = 0
self.perm_output = []
self.bootstrap_results = []
- self.covariates = start_vars['covariates'] if "covariates" in start_vars else None
+ self.covariates = start_vars['covariates'] if "covariates" in start_vars else ""
#ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
@@ -467,6 +467,7 @@ class RunMapping(object):
#mapping_scale = self.mapping_scale,
#chromosomes = chromosome_mb_lengths,
#qtl_results = self.qtl_results,
+ categorical_vars = self.categorical_vars,
chr_lengths = chr_lengths,
num_perm = self.num_perm,
perm_results = self.perm_output,
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 152e4168..f41f3017 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -44,7 +44,7 @@ import reaper
from utility.THCell import THCell
from utility.TDCell import TDCell
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
from utility.tools import GN2_BRANCH_URL
@@ -217,7 +217,7 @@ class NetworkGraph(object):
break
trait_name, dataset_name = trait_db.split(":")
dataset_ob = data_set.create_dataset(dataset_name)
- trait_ob = GeneralTrait(dataset=dataset_ob,
+ trait_ob = create_trait(dataset=dataset_ob,
name=trait_name,
cellid=None)
self.trait_list.append((trait_ob, dataset_ob))
\ No newline at end of file
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 8f702d58..de4b01eb 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -1,15 +1,9 @@
-# from __future__ import absolute_import, print_function, division
+from __future__ import absolute_import, print_function, division
-
-import os
-import cPickle
import re
import uuid
from math import *
import time
-import math
-import datetime
-import collections
import re
import requests
@@ -18,18 +12,16 @@ from pprint import pformat as pf
import json
from base.data_set import create_dataset
-from base import trait
+from base.trait import create_trait
from wqflask import parser
from wqflask import do_search
-from utility import webqtlUtil,tools
from db import webqtlDatabaseFunction
-from flask import render_template, Flask, g
+from flask import Flask, g
-from utility import formatting
-from utility import hmac
+from utility import hmac, helper_functions
from utility.tools import GN2_BASE_URL
-from utility.type_checking import is_float, is_int, is_str, get_float, get_int, get_string
+from utility.type_checking import is_str
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -86,7 +78,7 @@ views.py).
try:
self.search()
except:
- self.search_term_exists = False
+ self.search_term_exists = False
if self.search_term_exists:
self.gen_search_result()
@@ -113,50 +105,49 @@ views.py).
trait_dict = {}
trait_id = result[0]
- trait_dict['index'] = index + 1
- this_trait = trait.GeneralTrait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
- trait_dict['name'] = this_trait.name
- if this_trait.dataset.type == "Publish":
- trait_dict['display_name'] = this_trait.display_name
- else:
- trait_dict['display_name'] = this_trait.name
- trait_dict['dataset'] = this_trait.dataset.name
- trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
- if this_trait.dataset.type == "ProbeSet":
- trait_dict['symbol'] = this_trait.symbol
- trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace')
- trait_dict['location'] = this_trait.location_repr
- trait_dict['mean'] = "N/A"
- trait_dict['additive'] = "N/A"
- if this_trait.mean != "" and this_trait.mean != None:
- trait_dict['mean'] = '%.3f' % this_trait.mean
- trait_dict['lrs_score'] = this_trait.LRS_score_repr
- trait_dict['lrs_location'] = this_trait.LRS_location_repr
- if this_trait.additive != "":
- trait_dict['additive'] = '%.3f' % this_trait.additive
- elif this_trait.dataset.type == "Geno":
- trait_dict['location'] = this_trait.location_repr
- elif this_trait.dataset.type == "Publish":
- trait_dict['description'] = this_trait.description_display
- trait_dict['authors'] = this_trait.authors
- trait_dict['pubmed_id'] = "N/A"
- if this_trait.pubmed_id:
- trait_dict['pubmed_id'] = this_trait.pubmed_id
- trait_dict['pubmed_link'] = this_trait.pubmed_link
- trait_dict['pubmed_text'] = this_trait.pubmed_text
- trait_dict['mean'] = "N/A"
- if this_trait.mean != "" and this_trait.mean != None:
- trait_dict['mean'] = '%.3f' % this_trait.mean
- trait_dict['lrs_score'] = this_trait.LRS_score_repr
- trait_dict['lrs_location'] = this_trait.LRS_location_repr
- trait_dict['additive'] = "N/A"
- if this_trait.additive != "":
- trait_dict['additive'] = '%.3f' % this_trait.additive
- trait_list.append(trait_dict)
- #json_trait_list.append(trait.jsonable_table_row(this_trait, self.dataset.name, index + 1))
+ this_trait = create_trait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ if this_trait:
+ trait_dict['index'] = index + 1
+ trait_dict['name'] = this_trait.name
+ if this_trait.dataset.type == "Publish":
+ trait_dict['display_name'] = this_trait.display_name
+ else:
+ trait_dict['display_name'] = this_trait.name
+ trait_dict['dataset'] = this_trait.dataset.name
+ trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
+ if this_trait.dataset.type == "ProbeSet":
+ trait_dict['symbol'] = this_trait.symbol
+ trait_dict['description'] = this_trait.description_display.decode('utf-8', 'replace')
+ trait_dict['location'] = this_trait.location_repr
+ trait_dict['mean'] = "N/A"
+ trait_dict['additive'] = "N/A"
+ if this_trait.mean != "" and this_trait.mean != None:
+ trait_dict['mean'] = '%.3f' % this_trait.mean
+ trait_dict['lrs_score'] = this_trait.LRS_score_repr
+ trait_dict['lrs_location'] = this_trait.LRS_location_repr
+ if this_trait.additive != "":
+ trait_dict['additive'] = '%.3f' % this_trait.additive
+ elif this_trait.dataset.type == "Geno":
+ trait_dict['location'] = this_trait.location_repr
+ elif this_trait.dataset.type == "Publish":
+ trait_dict['description'] = this_trait.description_display
+ trait_dict['authors'] = this_trait.authors
+ trait_dict['pubmed_id'] = "N/A"
+ if this_trait.pubmed_id:
+ trait_dict['pubmed_id'] = this_trait.pubmed_id
+ trait_dict['pubmed_link'] = this_trait.pubmed_link
+ trait_dict['pubmed_text'] = this_trait.pubmed_text
+ trait_dict['mean'] = "N/A"
+ if this_trait.mean != "" and this_trait.mean != None:
+ trait_dict['mean'] = '%.3f' % this_trait.mean
+ trait_dict['lrs_score'] = this_trait.LRS_score_repr
+ trait_dict['lrs_location'] = this_trait.LRS_location_repr
+ trait_dict['additive'] = "N/A"
+ if this_trait.additive != "":
+ trait_dict['additive'] = '%.3f' % this_trait.additive
+ trait_list.append(trait_dict)
self.trait_list = json.dumps(trait_list)
- #self.json_trait_list = json.dumps(json_trait_list)
def search(self):
"""
@@ -234,7 +225,6 @@ views.py).
self.header_fields = the_search.header_fields
def get_search_ob(self, a_search):
- logger.debug("[kodak] item is:", pf(a_search))
search_term = a_search['search_term']
search_operator = a_search['separator']
search_type = {}
@@ -243,12 +233,10 @@ views.py).
search_type['key'] = a_search['key'].upper()
else:
search_type['key'] = None
- logger.debug("search_type is:", pf(search_type))
search_ob = do_search.DoSearch.get_search(search_type)
if search_ob:
search_class = getattr(do_search, search_ob)
- logger.debug("search_class is: ", pf(search_class))
the_search = search_class(search_term,
search_operator,
self.dataset,
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 107f87c6..253c887b 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -4,7 +4,7 @@ import simplejson as json
from pprint import pformat as pf
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
def export_sample_table(targs):
@@ -26,7 +26,7 @@ def export_sample_table(targs):
def get_export_metadata(trait_id, dataset_name):
dataset = data_set.create_dataset(dataset_name)
- this_trait = GeneralTrait(dataset=dataset,
+ this_trait = create_trait(dataset=dataset,
name=trait_id,
cellid=None,
get_qtl_info=False)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 29b2f77e..c77e247f 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -10,9 +10,6 @@ import json as json
from collections import OrderedDict
-import redis
-Redis = redis.StrictRedis()
-
import numpy as np
import scipy.stats as ss
@@ -21,11 +18,15 @@ from flask import Flask, g
from base import webqtlConfig
from base import webqtlCaseData
from wqflask.show_trait.SampleList import SampleList
-from utility import webqtlUtil, Plot, Bunch, helper_functions
-from utility.tools import locate_ignore_error
-from base.trait import GeneralTrait
+from base.trait import create_trait
from base import data_set
from db import webqtlDatabaseFunction
+from utility import webqtlUtil, Plot, Bunch, helper_functions
+from utility.authentication_tools import check_owner
+from utility.tools import locate_ignore_error
+from utility.redis_tools import get_redis_conn, get_resource_id
+Redis = get_redis_conn()
+ONE_YEAR = 60 * 60 * 24 * 365
from pprint import pformat as pf
@@ -55,9 +56,9 @@ class ShowTrait(object):
self.temp_group = kw['group']
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
# Put values in Redis so they can be looked up later if added to a collection
- Redis.set(self.trait_id, kw['trait_paste'])
+ Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR)
self.trait_vals = kw['trait_paste'].split()
- self.this_trait = GeneralTrait(dataset=self.dataset,
+ self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
else:
@@ -66,11 +67,13 @@ class ShowTrait(object):
self.temp_species = self.trait_id.split("_")[1]
self.temp_group = self.trait_id.split("_")[2]
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
- self.this_trait = GeneralTrait(dataset=self.dataset,
+ self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
self.trait_vals = Redis.get(self.trait_id).split()
+ self.resource_id = check_owner(self.dataset, self.trait_id)
+
#ZS: Get verify/rna-seq link URLs
try:
blatsequence = self.this_trait.sequence
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index ac5c1350..b7df1aad 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -2,17 +2,25 @@
{% block title %}Group Manager{% endblock %}
{% block content %}
<!-- Start of body -->
- {{ header("List of groups", "" )}}
-
<div class="container">
<div class="page-header">
<h1>Manage Groups</h1>
+ <button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
</div>
- <form action="/manage/groups" method="POST">
+ <form id="groups_form" action="/groups/manage" method="POST">
+ <input type="hidden" name="selected_group_ids" value="">
<div class="container" style="margin-bottom: 30px;">
+ {% if admin_groups|length == 0 and user_groups|length == 0 %}
+ <h4>You currently aren't a member or admin of any groups.</h4>
+ <br>
+ <button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
+ {% else %}
<div><h3>Admin Groups</h3></div>
<hr>
- <table id="admin_groups" class="table table-hover">
+ {% if admin_groups|length == 0 %}
+ <h4>You currently aren't the administrator of any groups.</h4>
+ {% else %}
+ <table id="admin_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
<thead>
<tr>
<th></th>
@@ -26,7 +34,7 @@
<tbody>
{% for group in admin_groups %}
<tr>
- <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
+ <td><input type="checkbox" name="group_id" value="{{ group.id }}"></td>
<td>{{ loop.index }}</td>
<td>{{ group.name }}</td>
<td>{{ group.admins|length + group.users|length }}</td>
@@ -36,12 +44,16 @@
{% endfor %}
</tbody>
</table>
+ {% endif %}
</div>
<hr>
<div class="container">
<div><h3>User Groups</h3></div>
<hr>
- <table id="user_groups" class="table table-hover">
+ {% if user_groups|length == 0 %}
+ <h4>You currently aren't a member of any groups.</h4>
+ {% else %}
+ <table id="user_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
<thead>
<tr>
<th></th>
@@ -65,12 +77,12 @@
{% endfor %}
</tbody>
</table>
+ {% endif %}
+ {% endif %}
</div>
</form>
</div>
-
-
<!-- End of body -->
{% endblock %}
@@ -79,7 +91,6 @@
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
<script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
<script type="text/javascript" charset="utf-8">
@@ -113,6 +124,22 @@
"paging": false,
"orderClasses": true
} );
+
+ submit_special = function(url) {
+ $("#groups_form").attr("action", url);
+ return $("#groups_form").submit();
+ };
+
+ $("#remove_groups").on("click", function() {
+ url = $(this).data("url")
+ groups = []
+ $("input[name=group_id]:checked").each(function() {
+ groups.push($(this).val());
+ });
+ groups_string = groups.join(":")
+ $("input[name=selected_group_ids]").val(groups_string)
+ return submit_special(url)
+ });
});
</script>
{% endblock %}
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 1c84239c..71705390 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -1,4 +1,5 @@
{% extends "base.html" %}
+{% block title %}Correlation Results{% endblock %}
{% block css %}
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
diff --git a/wqflask/wqflask/templates/email/verification.txt b/wqflask/wqflask/templates/email/verification.txt
deleted file mode 100644
index 76149a3a..00000000
--- a/wqflask/wqflask/templates/email/verification.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-Thank you for signing up for GeneNetwork.
-
-We need to verify your email address.
-
-To do that please click the following link, or cut and paste it into your browser window:
-
-{{ url_for_hmac("verify_email", code = verification_code, _external=True )}}
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 05b2f988..04b45659 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -31,7 +31,7 @@
</form>
<br />
<br />
- <div style="width: 100%;">
+ <div style="min-width: 2000px; width: 100%;">
<table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
<tbody>
<td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index b4429b46..c5d49168 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -41,7 +41,8 @@
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
<input type="hidden" name="num_perm" value="{{ nperm }}">
- <input type="hidden" name="perm_results" value="">
+ <input type="hidden" name="perm_info" value="">
+ <input type="hidden" name="perm_strata" value="{{ perm_strata }}">
<input type="hidden" name="num_bootstrap" value="{{ nboot }}">
<input type="hidden" name="do_control" value="{{ doControl }}">
<input type="hidden" name="control_marker" value="{{ controlLocus }}">
@@ -464,13 +465,27 @@
{% if mapping_method != "gemma" and mapping_method != "plink" %}
$('#download_perm').click(function(){
- var num_perm, perm_data;
- num_perm = js_data.num_perm
- perm_data = js_data.perm_results
- json_perm_data = JSON.stringify(perm_data);
- $('input[name=perm_results]').val(json_perm_data);
- $('#marker_regression_form').attr('action', '/export_perm_data');
- return $('#marker_regression_form').submit();
+ perm_info_dict = {
+ perm_data: js_data.perm_results,
+ num_perm: "{{ nperm }}",
+ trait_name: "{{ this_trait.display_name }}",
+ trait_description: "{{ this_trait.description_display }}",
+ cofactors: "{{ covariates }}",
+ n_samples: {{ n_samples }},
+ n_genotypes: {{ qtl_results|length }},
+ {% if genofile_string is defined %}
+ genofile: "{{ genofile_string }}",
+ {% else %}
+ genofile: "",
+ {% endif %}
+ units_linkage: "{{ LRS_LOD }}",
+ strat_cofactors: js_data.categorical_vars
+ }
+ json_perm_data = JSON.stringify(perm_info_dict);
+
+ $('input[name=perm_info]').val(json_perm_data);
+ $('#marker_regression_form').attr('action', '/export_perm_data');
+ return $('#marker_regression_form').submit();
});
modebar_options = {
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index edd272c2..cfee0079 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -12,9 +12,6 @@ import requests
import simplejson as json
-import redis # used for collections
-Redis = redis.StrictRedis()
-
from flask import (Flask, g, render_template, url_for, request, make_response,
redirect, flash, abort)
@@ -23,7 +20,8 @@ from wqflask import pbkdf2
from wqflask.user_session import UserSession
from utility import hmac
-from utility.redis_tools import is_redis_available, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
+from utility.redis_tools import is_redis_available, get_redis_conn, get_user_id, get_user_by_unique_column, set_user_attribute, save_user, save_verification_code, check_verification_code, get_user_collections, save_collections
+Redis = get_redis_conn()
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -127,7 +125,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to "+toaddr)
-def send_verification_email(user_details, template_name = "email/verification.txt", key_prefix = "verification_code", subject = "GeneNetwork email verification"):
+def send_verification_email(user_details, template_name = "email/user_verification.txt", key_prefix = "verification_code", subject = "GeneNetwork e-mail verification"):
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
@@ -141,6 +139,21 @@ def send_verification_email(user_details, template_name = "email/verification.tx
send_email(recipient, subject, body)
return {"recipient": recipient, "subject": subject, "body": body}
+@app.route("/manage/verify_email")
+def verify_email():
+ if 'code' in request.args:
+ user_details = check_verification_code(request.args['code'])
+ if user_details:
+ # As long as they have access to the email account
+ # We might as well log them in
+ session_id_signed = get_signed_session_id(user_details)
+ flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success")
+ response = make_response(redirect(url_for('index_page', import_collections = import_col, anon_id = anon_id)))
+ response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None)
+ return response
+ else:
+ flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
@app.route("/n/login", methods=('GET', 'POST'))
def login():
params = request.form if request.form else request.args
@@ -204,7 +217,7 @@ def login():
response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None)
return response
else:
- email_ob = send_verification_email(user_details)
+ email_ob = send_verification_email(user_details, template_name = "email/user_verification.txt")
return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject'])
else: # Incorrect password
#ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis
@@ -374,16 +387,13 @@ def password_reset():
hmac = request.args.get('hm')
if verification_code:
- user_email = check_verification_code(verification_code)
- if user_email:
- user_details = get_user_by_unique_column('email_address', user_email)
- if user_details:
- return render_template(
- "new_security/password_reset.html", user_encode=user_details["email_address"])
- else:
- flash("Invalid code: User no longer exists!", "error")
+ user_details = check_verification_code(verification_code)
+ if user_details:
+ return render_template(
+ "new_security/password_reset.html", user_encode=user_details["email_address"])
else:
flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+ return redirect(url_for("login"))
else:
return redirect(url_for("login"))
@@ -394,6 +404,7 @@ def password_reset_step2():
errors = []
user_email = request.form['user_encode']
+ user_id = get_user_id("email_address", user_email)
password = request.form['password']
encoded_password = set_password(password)
@@ -401,9 +412,7 @@ def password_reset_step2():
set_user_attribute(user_id, "password", encoded_password)
flash("Password changed successfully. You can now sign in.", "alert-info")
- response = make_response(redirect(url_for('login')))
-
- return response
+ return redirect(url_for('login'))
def register_user(params):
thank_you_mode = False
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 50419146..ec6d4ae3 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -6,10 +6,6 @@ import uuid
import simplejson as json
-import redis # used for collections
-Redis = redis.StrictRedis()
-
-
from flask import (Flask, g, render_template, url_for, request, make_response,
redirect, flash, abort)
@@ -17,7 +13,8 @@ from wqflask import app
from utility import hmac
#from utility.elasticsearch_tools import get_elasticsearch_connection
-from utility.redis_tools import get_user_id, get_user_by_unique_column, get_user_collections, save_collections
+from utility.redis_tools import get_redis_conn, get_user_id, get_user_collections, save_collections
+Redis = get_redis_conn()
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -29,6 +26,11 @@ THIRTY_DAYS = 60 * 60 * 24 * 30
def get_user_session():
logger.info("@app.before_request get_session")
g.user_session = UserSession()
+ #ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired
+ if not g.user_session:
+ response = make_response(redirect(url_for('login')))
+ response.set_cookie('session_id_v2', '', expires=0)
+ return response
@app.after_request
def set_user_session(response):
@@ -37,7 +39,6 @@ def set_user_session(response):
response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
return response
-
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -88,14 +89,11 @@ class UserSession(object):
user_id = str(uuid.uuid4()))
Redis.hmset(self.redis_key, self.record)
Redis.expire(self.redis_key, THIRTY_DAYS)
- response = make_response(redirect(url_for('login')))
- response.set_cookie(self.user_cookie_name, '', expires=0)
########### Grrr...this won't work because of the way flask handles cookies
# Delete the cookie
flash("Due to inactivity your session has expired. If you'd like please login again.")
- return response
- #return
+ return None
else:
self.record = dict(login_time = time.time(),
user_type = "anon",
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 938570f3..24a4dcee 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -23,16 +23,13 @@ import uuid
import simplejson as json
import yaml
-#Switching from Redis to StrictRedis; might cause some issues
-import redis
-Redis = redis.StrictRedis()
-
import flask
import base64
import array
import sqlalchemy
from wqflask import app
-from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect
+from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for
+from wqflask import group_manager
from wqflask import search_results
from wqflask import export_traits
from wqflask import gsearch
@@ -55,11 +52,13 @@ from wqflask.correlation import corr_scatter_plot
from wqflask.wgcna import wgcna_analysis
from wqflask.ctl import ctl_analysis
from wqflask.snp_browser import snp_browser
-#from wqflask.trait_submission import submit_trait
from utility import temp_data
from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
from utility.helper_functions import get_species_groups
+from utility.authentication_tools import check_resource_availability
+from utility.redis_tools import get_redis_conn
+Redis = get_redis_conn()
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility.benchmark import Bench
@@ -87,6 +86,24 @@ def connect_db():
g.db = g._database = sqlalchemy.create_engine(SQL_URI, encoding="latin1")
logger.debug(g.db)
+@app.before_request
+def check_access_permissions():
+ logger.debug("@app.before_request check_access_permissions")
+ if "temp_trait" in request.args:
+ if request.args['temp_trait'] == "True":
+ pass
+ else:
+ if 'dataset' in request.args:
+ dataset = create_dataset(request.args['dataset'])
+ logger.debug("USER:", Redis.hget("users"))
+ if 'trait_id' in request.args:
+ available = check_resource_availability(dataset, request.args['trait_id'])
+ else:
+ available = check_resource_availability(dataset)
+
+ if not available:
+ return redirect(url_for("no_access_page"))
+
@app.teardown_appcontext
def shutdown_session(exception=None):
db = getattr(g, '_database', None)
@@ -120,6 +137,10 @@ def handle_bad_request(e):
resp.set_cookie(err_msg[:32],animation)
return resp
+@app.route("/authentication_needed")
+def no_access_page():
+ return render_template("new_security/not_authenticated.html")
+
@app.route("/")
def index_page():
logger.info("Sending index_page")
@@ -401,25 +422,43 @@ def export_traits_csv():
def export_perm_data():
"""CSV file consisting of the permutation data for the mapping results"""
logger.info(request.url)
- num_perm = float(request.form['num_perm'])
- perm_data = json.loads(request.form['perm_results'])
+ perm_info = json.loads(request.form['perm_info'])
+
+ now = datetime.datetime.now()
+ time_str = now.strftime('%H:%M_%d%B%Y')
+
+ file_name = "Permutation_" + perm_info['num_perm'] + "_" + perm_info['trait_name'] + "_" + time_str
+
+ the_rows = [
+ ["#Permutation Test"],
+ ["#File_name: " + file_name],
+ ["#Metadata: From GeneNetwork.org"],
+ ["#Trait_ID: " + perm_info['trait_name']],
+ ["#Trait_description: " + perm_info['trait_description']],
+ ["#N_permutations: " + str(perm_info['num_perm'])],
+ ["#Cofactors: " + perm_info['cofactors']],
+ ["#N_cases: " + str(perm_info['n_samples'])],
+ ["#N_genotypes: " + str(perm_info['n_genotypes'])],
+ ["#Genotype_file: " + perm_info['genofile']],
+ ["#Units_linkage: " + perm_info['units_linkage']],
+ ["#Permutation_stratified_by: " + ", ".join([ str(cofactor) for cofactor in perm_info['strat_cofactors']])],
+ ["#RESULTS_1: Suggestive LRS(p=0.63) = " + str(np.percentile(np.array(perm_info['perm_data']), 67))],
+ ["#RESULTS_2: Significant LRS(p=0.05) = " + str(np.percentile(np.array(perm_info['perm_data']), 95))],
+ ["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(np.percentile(np.array(perm_info['perm_data']), 99))],
+ ["#Comment: Results sorted from low to high peak linkage"]
+ ]
buff = StringIO.StringIO()
writer = csv.writer(buff)
- writer.writerow(["Suggestive LRS (p=0.63) = " + str(np.percentile(np.array(perm_data), 67))])
- writer.writerow(["Significant LRS (p=0.05) = " + str(np.percentile(np.array(perm_data), 95))])
- writer.writerow(["Highly Significant LRS (p=0.01) = " + str(np.percentile(np.array(perm_data), 99))])
- writer.writerow("")
- writer.writerow([str(num_perm) + " Permutations"])
- writer.writerow("")
- for item in perm_data:
+ writer.writerows(the_rows)
+ for item in perm_info['perm_data']:
writer.writerow([item])
csv_data = buff.getvalue()
buff.close()
return Response(csv_data,
mimetype='text/csv',
- headers={"Content-Disposition":"attachment;filename=perm_data.csv"})
+ headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
--
cgit v1.2.3
From 218576a04f90cc0bc9e53685323e1caa8cffe986 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 4 Jun 2020 15:50:56 -0500
Subject: Added back in trait info queries for situations where the proxy isn't
running
---
wqflask/base/trait.py | 94 +++++++++++++++++++++++++++++++++++++++++++--------
1 file changed, 80 insertions(+), 14 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index b133bf21..405c4ebf 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,9 +1,11 @@
from __future__ import absolute_import, division, print_function
+import os
import string
import resource
import codecs
import requests
+import random
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
@@ -12,8 +14,8 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility import hmac
from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
-from utility.redis_tools import get_redis_conn
+from utility.tools import GN2_BASE_URL, GN_VERSION
+from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
Redis = get_redis_conn()
from wqflask import app
@@ -22,7 +24,7 @@ import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g, request, url_for, redirect
+from flask import Flask, g, request, url_for, redirect, make_response, render_template
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -45,7 +47,10 @@ def create_trait(**kw):
permitted = check_resource_availability(dataset)
if permitted:
- return GeneralTrait(**kw)
+ the_trait = GeneralTrait(**kw)
+ if the_trait.dataset.type != "Temp":
+ the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
+ return the_trait
else:
return None
@@ -99,9 +104,6 @@ class GeneralTrait(object):
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
- if self.dataset.type != "Temp":
- self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
-
if get_sample_info != False:
self = retrieve_sample_data(self, self.dataset)
@@ -373,17 +375,15 @@ def jsonable_table_row(trait, dataset_name, index):
else:
return dict()
+
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
+ resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
- resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait.name))
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
- elif dataset.type == 'ProbeSet':
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
else:
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
try:
@@ -394,11 +394,77 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
except:
resource_info = get_resource_info(resource_id)
default_permissions = resource_info['default_mask']['data']
- if 'view' not in default_persmissions:
+ if 'view' not in default_permissions:
trait.view = False
return trait
- trait_info = json.loads(response)
+ if dataset.type == 'Publish':
+ query = """
+ SELECT
+ PublishXRef.Id, Publication.PubMed_ID,
+ Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
+ Publication.Authors, Publication.Title, Publication.Abstract,
+ Publication.Journal, Publication.Volume, Publication.Pages,
+ Publication.Month, Publication.Year, PublishXRef.Sequence,
+ Phenotype.Units, PublishXRef.comments
+ FROM
+ PublishXRef, Publication, Phenotype, PublishFreeze
+ WHERE
+ PublishXRef.Id = %s AND
+ Phenotype.Id = PublishXRef.PhenotypeId AND
+ Publication.Id = PublishXRef.PublicationId AND
+ PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishFreeze.Id = %s
+ """ % (trait.name, dataset.id)
+
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+
+
+ #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+ #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+ elif dataset.type == 'ProbeSet':
+ display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
+ display_fields_string = 'ProbeSet.' + display_fields_string
+ query = """
+ SELECT %s
+ FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s'
+ """ % (escape(display_fields_string),
+ escape(dataset.name),
+ escape(str(trait.name)))
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+ #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+ # to avoid the problem of same marker name from different species.
+ elif dataset.type == 'Geno':
+ display_fields_string = string.join(dataset.display_fields,',Geno.')
+ display_fields_string = 'Geno.' + display_fields_string
+ query = """
+ SELECT %s
+ FROM Geno, GenoFreeze, GenoXRef
+ WHERE
+ GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+ GenoXRef.GenoId = Geno.Id AND
+ GenoFreeze.Name = '%s' AND
+ Geno.Name = '%s'
+ """ % (escape(display_fields_string),
+ escape(dataset.name),
+ escape(trait.name))
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+ else: #Temp type
+ query = """SELECT %s FROM %s WHERE Name = %s"""
+ logger.sql(query)
+ trait_info = g.db.execute(query,
+ (string.join(dataset.display_fields,','),
+ dataset.type, trait.name)).fetchone()
if trait_info:
trait.haveinfo = True
--
cgit v1.2.3
From a302a2b0ac0e7c0f26a0d063c3f2b057f61d47f1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 5 Jun 2020 16:52:56 -0500
Subject: Commiting other current group/resource management code, plus the new
files
---
wqflask/base/trait.py | 2 +
wqflask/maintenance/set_resource_defaults.py | 155 +++++++++++++++++++++
wqflask/utility/authentication_tools.py | 46 ++++++
wqflask/utility/redis_tools.py | 37 +++--
wqflask/wqflask/group_manager.py | 77 ++++++++++
wqflask/wqflask/resource_manager.py | 72 ++++++++++
.../wqflask/static/new/javascript/group_manager.js | 38 +++++
wqflask/wqflask/templates/admin/create_group.html | 89 ++++++++++++
wqflask/wqflask/templates/admin/group_manager.html | 68 ++++-----
.../wqflask/templates/admin/manage_resource.html | 92 ++++++++++++
.../wqflask/templates/admin/search_for_groups.html | 64 +++++++++
.../templates/admin/select_group_to_add.html | 54 +++++++
.../templates/new_security/not_authenticated.html | 11 ++
wqflask/wqflask/templates/show_trait_details.html | 5 +
wqflask/wqflask/views.py | 3 +-
15 files changed, 764 insertions(+), 49 deletions(-)
create mode 100644 wqflask/maintenance/set_resource_defaults.py
create mode 100644 wqflask/utility/authentication_tools.py
create mode 100644 wqflask/wqflask/group_manager.py
create mode 100644 wqflask/wqflask/resource_manager.py
create mode 100644 wqflask/wqflask/static/new/javascript/group_manager.js
create mode 100644 wqflask/wqflask/templates/admin/create_group.html
create mode 100644 wqflask/wqflask/templates/admin/manage_resource.html
create mode 100644 wqflask/wqflask/templates/admin/search_for_groups.html
create mode 100644 wqflask/wqflask/templates/admin/select_group_to_add.html
create mode 100644 wqflask/wqflask/templates/new_security/not_authenticated.html
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 405c4ebf..2a945588 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -391,6 +391,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if response.strip() == "no-access":
trait.view = False
return trait
+ else:
+ trait_info = json.loads(response)
except:
resource_info = get_resource_info(resource_id)
default_permissions = resource_info['default_mask']['data']
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
new file mode 100644
index 00000000..ba102d9c
--- /dev/null
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -0,0 +1,155 @@
+"""
+
+Script that sets default resource access masks for use with the DB proxy
+
+Defaults will be:
+Owner - omni_gn
+Mask - Public/non-confidential: { data: "view",
+ metadata: "view",
+ admin: "not-admin" }
+ Private/confidentia: { data: "no-access",
+ metadata: "no-access",
+ admin: "not-admin" }
+
+To run:
+./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
+
+"""
+
+from __future__ import print_function, division
+
+import sys
+import json
+
+# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
+sys.path.insert(0,'./')
+
+# NEW: import app to avoid a circular dependency on utility.tools
+from wqflask import app
+
+from utility.tools import SQL_URI
+from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources
+Redis = get_redis_conn()
+
+import MySQLdb
+
+import urlparse
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+def parse_db_uri():
+ """Converts a database URI to the db name, host name, user name, and password"""
+
+ parsed_uri = urlparse.urlparse(SQL_URI)
+
+ db_conn_info = dict(
+ db = parsed_uri.path[1:],
+ host = parsed_uri.hostname,
+ user = parsed_uri.username,
+ passwd = parsed_uri.password)
+
+ print(db_conn_info)
+ return db_conn_info
+
+def insert_probeset_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public
+ FROM
+ ProbeSetFreeze""")
+
+ resource_results = Cursor.fetchall()
+ for i, resource in enumerate(resource_results):
+ if i % 20 == 0:
+ print(i)
+ resource_ob = {}
+ resource_ob['name'] = resource[1]
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[0])}
+ resource_ob['type'] = "dataset-probeset"
+ if resource[2] < 1 and resource[3] > 0:
+ resource_ob['default_mask'] = { "data": ["no-access", "view"] }
+ else:
+ resource_ob['default_mask'] = { "data": ["no-access"] }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+def insert_publish_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode
+ FROM
+ PublishXRef, PublishFreeze, InbredSet, Publication
+ WHERE
+ PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND
+ InbredSet.Id = PublishXRef.InbredSetId AND
+ Publication.Id = PublishXRef.PublicationId""")
+
+ resource_results = Cursor.fetchall()
+ for resource in resource_results:
+ if resource[2]:
+ resource_ob = {}
+ if resource[2]:
+ resource_ob['name'] = resource[2] + "_" + str(resource[0])
+ else:
+ resource_ob['name'] = str(resource[0])
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[1]) ,
+ "trait" : str(resource[0])}
+ resource_ob['type'] = "dataset-publish"
+ resource_ob['default_mask'] = { "data": "view" }
+
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+ else:
+ continue
+
+def insert_geno_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality
+ FROM
+ GenoFreeze""")
+
+ resource_results = Cursor.fetchall()
+ for i, resource in enumerate(resource_results):
+ if i % 20 == 0:
+ print(i)
+ resource_ob = {}
+ resource_ob['name'] = resource[1]
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[0]) }
+ resource_ob['type'] = "dataset-geno"
+ if resource[2] < 1:
+ resource_ob['default_mask'] = { "data": "view" }
+ else:
+ resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+def insert_resources(default_owner_id):
+ current_resources = get_resources()
+ print("START")
+ insert_publish_resources(default_owner_id)
+ print("AFTER PUBLISH")
+ insert_geno_resources(default_owner_id)
+ print("AFTER GENO")
+ insert_probeset_resources(default_owner_id)
+ print("AFTER PROBESET")
+
+def main():
+ """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+
+ Redis.delete("resources")
+
+ owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com")
+ insert_resources(owner_id)
+
+if __name__ == '__main__':
+ Conn = MySQLdb.Connect(**parse_db_uri())
+ Cursor = Conn.cursor()
+ main()
\ No newline at end of file
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
new file mode 100644
index 00000000..537881a5
--- /dev/null
+++ b/wqflask/utility/authentication_tools.py
@@ -0,0 +1,46 @@
+from __future__ import absolute_import, print_function, division
+
+import json
+import requests
+
+from base import data_set
+
+from utility import hmac
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+
+from flask import Flask, g, redirect, url_for
+
+import logging
+logger = logging.getLogger(__name__ )
+
+def check_resource_availability(dataset, trait_id=None):
+ resource_id = get_resource_id(dataset, trait_id)
+
+ if resource_id:
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ try:
+ response = json.loads(requests.get(the_url).content)['data']
+ except:
+ resource_info = get_resource_info(resource_id)
+ response = resource_info['default_mask']['data']
+
+ if 'view' in response:
+ return True
+ else:
+ return redirect(url_for("no_access_page"))
+
+ return True
+
+def check_owner(dataset=None, trait_id=None, resource_id=None):
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return resource_id
+ else:
+ resource_id = get_resource_id(dataset, trait_id)
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return resource_id
+
+ return False
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 0ad96879..bc30a0af 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -95,14 +95,17 @@ def get_user_groups(user_id):
user_group_ids = [] #ZS: Group IDs where user is a regular user
groups_list = Redis.hgetall("groups")
for key in groups_list:
- group_ob = json.loads(groups_list[key])
- group_admins = set(group_ob['admins'])
- group_members = set(group_ob['members'])
- if user_id in group_admins:
- admin_group_ids.append(group_ob['id'])
- elif user_id in group_members:
- user_group_ids.append(group_ob['id'])
- else:
+ try:
+ group_ob = json.loads(groups_list[key])
+ group_admins = set(group_ob['admins'])
+ group_members = set(group_ob['members'])
+ if user_id in group_admins:
+ admin_group_ids.append(group_ob['id'])
+ elif user_id in group_members:
+ user_group_ids.append(group_ob['id'])
+ else:
+ continue
+ except:
continue
admin_groups = []
@@ -122,6 +125,24 @@ def get_group_info(group_id):
return group_info
+def get_group_by_unique_column(column_name, column_value):
+ """ Get group by column; not sure if there's a faster way to do this """
+
+ matched_groups = []
+
+ all_group_list = Redis.hgetall("groups")
+ for key in all_group_list:
+ group_info = json.loads(all_group_list[key])
+ if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+ if column_value in group_info[column_name]:
+ matched_groups.append(group_info)
+ else:
+ if group_info[column_name] == column_value:
+ matched_groups.append(group_info)
+
+ return matched_groups
+
+
def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
group_id = str(uuid.uuid4())
new_group = {
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
new file mode 100644
index 00000000..f41ae56d
--- /dev/null
+++ b/wqflask/wqflask/group_manager.py
@@ -0,0 +1,77 @@
+
+from __future__ import print_function, division, absolute_import
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+ redirect, flash)
+
+from wqflask import app
+from wqflask.user_login import send_verification_email
+
+from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \
+ change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/groups/manage", methods=('GET', 'POST'))
+def manage_groups():
+ params = request.form if request.form else request.args
+ if "add_new_group" in params:
+ return redirect(url_for('add_group'))
+ else:
+ admin_groups, user_groups = get_user_groups(g.user_session.user_id)
+ return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
+
+@app.route("/groups/remove", methods=('POST',))
+def remove_groups():
+ group_ids_to_remove = request.form['selected_group_ids']
+ for group_id in group_ids_to_remove.split(":"):
+ delete_group(g.user_session.user_id, group_id)
+
+ return redirect(url_for('manage_groups'))
+
+@app.route("/groups/create", methods=('GET', 'POST'))
+def add_group():
+ params = request.form if request.form else request.args
+ if "group_name" in params:
+ member_user_ids = set()
+ admin_user_ids = set()
+ admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
+ if "admin_emails" in params:
+ admin_emails = params['admin_emails_to_add'].split(",")
+ for email in admin_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ admin_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
+ if "user_emails" in params:
+ member_emails = params['member_emails_to_add'].split(",")
+ for email in member_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ member_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
+
+ create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
+ return redirect(url_for('manage_groups'))
+ else:
+ return render_template("admin/create_group.html")
+
+#ZS: Will integrate this later, for now just letting users be added directly
+def send_group_invites(group_id, user_email_list = [], user_type="members"):
+ for user_email in user_email_list:
+ user_details = get_user_by_unique_column("email_address", user_email)
+ if user_details:
+ group_info = get_group_info(group_id)
+ #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
+ # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
+ if group_info:
+ #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
+ # but do add them if they're a regular user and are added as an admin
+ if (user_details['user_id'] in group_info['admins']) or \
+ ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
+ continue
+ else:
+ send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
+
+#@app.route()
\ No newline at end of file
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
new file mode 100644
index 00000000..7d88b8ed
--- /dev/null
+++ b/wqflask/wqflask/resource_manager.py
@@ -0,0 +1,72 @@
+from __future__ import print_function, division, absolute_import
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+ redirect, flash)
+
+from wqflask import app
+
+from utility.authentication_tools import check_owner
+from utility.redis_tools import get_resource_info, get_group_info, get_group_by_unique_column, get_user_id
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/resources/manage", methods=('GET', 'POST'))
+def view_resource():
+ params = request.form if request.form else request.args
+ if 'resource_id' in request.args:
+ resource_id = request.args['resource_id']
+ if check_owner(resource_id=resource_id):
+ resource_info = get_resource_info(resource_id)
+ group_masks = resource_info['group_masks']
+ group_masks_with_names = get_group_names(group_masks)
+ default_mask = resource_info['default_mask']['data']
+ return render_template("admin/manage_resource.html", resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names)
+ else:
+ return redirect(url_for("no_access_page"))
+
+@app.route("/resources/add_group", methods=('POST',))
+def add_group_to_resource():
+ resource_id = request.form['resource_id']
+ if check_owner(resource_id=resource_id):
+ if all(key in request.form for key in ('group_id', 'group_name', 'user_name', 'user_email')):
+ group_list = []
+ if request.form['group_id'] != "":
+ the_group = get_group_info(request.form['group_id'])
+ if the_group:
+ group_list.append(the_group)
+ if request.form['group_name'] != "":
+ matched_groups = get_group_by_unique_column("name", request.form['group_name'])
+ for group in matched_groups:
+ group_list.append(group)
+ if request.form['user_name'] != "":
+ user_id = get_user_id("user_name", request.form['user_name'])
+ if user_id:
+ matched_groups = get_group_by_unique_column("admins", user_id)
+ matched_groups += get_group_by_unique_column("members", user_id)
+ for group in matched_groups:
+ group_list.append(group)
+ if request.form['user_email'] != "":
+ user_id = get_user_id("email_address", request.form['user_email'])
+ if user_id:
+ matched_groups = get_group_by_unique_column("admins", user_id)
+ matched_groups += get_group_by_unique_column("members", user_id)
+ for group in matched_groups:
+ group_list.append(group)
+ return render_template("admin/select_group_to_add.html", group_list=group_list, resource_id = resource_id)
+ elif 'selected_group' in request.form:
+ group_id = request.form['selected_group']
+ return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id)
+ else:
+ return render_template("admin/search_for_groups.html", resource_id = resource_id)
+ else:
+ return redirect(url_for("no_access_page"))
+
+def get_group_names(group_masks):
+ group_masks_with_names = {}
+ for group_id, group_mask in group_masks.iteritems():
+ this_mask = group_mask
+ group_name = get_group_info(group_id)['name']
+ this_mask['name'] = group_name
+
+ return group_masks_with_names
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js
new file mode 100644
index 00000000..5e82d104
--- /dev/null
+++ b/wqflask/wqflask/static/new/javascript/group_manager.js
@@ -0,0 +1,38 @@
+$('#add_to_admins').click(function() {
+ add_emails('admin')
+})
+
+$('#add_to_members').click(function() {
+ add_emails('member')
+})
+
+$('#clear_admins').click(function(){
+ clear_emails('admin')
+})
+
+$('#clear_members').click(function(){
+ clear_emails('member')
+})
+
+
+function add_emails(user_type){
+ var email_address = $('input[name=user_email]').val();
+ var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val()
+ console.log(email_list_string)
+ if (email_list_string == ""){
+ var email_set = new Set();
+ } else {
+ var email_set = new Set(email_list_string.split(","))
+ }
+ email_set.add(email_address)
+
+ $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(','))
+
+ var emails_display_string = Array.from(email_set).join('\n')
+ $('.added_' + user_type + 's').val(emails_display_string)
+}
+
+function clear_emails(user_type){
+ $('input[name=' + user_type + '_emails_to_add]').val("")
+ $('.added_' + user_type + 's').val("")
+}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
new file mode 100644
index 00000000..55c3fa0b
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -0,0 +1,89 @@
+{% extends "base.html" %}
+{% block title %}Group Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Create Group</h1>
+ </div>
+ <form action="/groups/create" method="POST">
+ <input type="hidden" name="admin_emails_to_add" value="">
+ <input type="hidden" name="member_emails_to_add" value="">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-12">
+ <input name="group_name" type="text" style="width:100%;"></input>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Add User Email:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-12">
+ <input name="user_email" type="text" style="width:100%;"></input>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="button" id="add_to_admins" class="btn btn-default">Add to Admins</button>
+ </div>
+ <div class="col-xs-6">
+ <button type="button" id="add_to_members" class="btn btn-default">Add to Members</button>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="font-size: 18px;">Members to be added:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_admins"></textarea>
+ </div>
+ <div class="col-xs-6">
+ <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_members"></textarea>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="button" id="clear_admins" class="btn btn-default">Clear</button>
+ </div>
+ <div class="col-xs-6">
+ <button type="button" id="clear_members" class="btn btn-default">Clear</button>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="create_group" class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="button" id="create_group" class="btn btn-primary">Create Group</button>
+ </div>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ </form>
+ </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index b7df1aad..23d8205a 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -1,15 +1,23 @@
{% extends "base.html" %}
{% block title %}Group Manager{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
{% block content %}
<!-- Start of body -->
<div class="container">
<div class="page-header">
<h1>Manage Groups</h1>
- <button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
+ <div style="display: inline;">
+ <button type="button" id="create_group" class="btn btn-primary" data-url="/groups/create">Create Group</button>
+ <button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
+ </div>
</div>
<form id="groups_form" action="/groups/manage" method="POST">
<input type="hidden" name="selected_group_ids" value="">
- <div class="container" style="margin-bottom: 30px;">
+ <div style="min-width: 800px; max-width: 1000px;">
{% if admin_groups|length == 0 and user_groups|length == 0 %}
<h4>You currently aren't a member or admin of any groups.</h4>
<br>
@@ -20,7 +28,7 @@
{% if admin_groups|length == 0 %}
<h4>You currently aren't the administrator of any groups.</h4>
{% else %}
- <table id="admin_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
+ <table id="admin_groups" class="table-hover table-striped cell-border" style="float: left;">
<thead>
<tr>
<th></th>
@@ -29,17 +37,19 @@
<th># Members</th>
<th>Created</th>
<th>Last Changed</th>
+ <th>Group ID</th>
</tr>
</thead>
<tbody>
{% for group in admin_groups %}
<tr>
<td><input type="checkbox" name="group_id" value="{{ group.id }}"></td>
- <td>{{ loop.index }}</td>
+ <td align="right">{{ loop.index }}</td>
<td>{{ group.name }}</td>
- <td>{{ group.admins|length + group.users|length }}</td>
+ <td align="right">{{ group.admins|length + group.users|length }}</td>
<td>{{ group.created_timestamp }}</td>
<td>{{ group.changed_timestamp }}</td>
+ <td>{{ group.id }}</td>
</tr>
{% endfor %}
</tbody>
@@ -47,13 +57,13 @@
{% endif %}
</div>
<hr>
- <div class="container">
+ <div style="min-width: 800px; max-width: 1000px;">
<div><h3>User Groups</h3></div>
<hr>
{% if user_groups|length == 0 %}
<h4>You currently aren't a member of any groups.</h4>
{% else %}
- <table id="user_groups" class="table table-hover" style="min-width: 800px; max-width: 1000px;">
+ <table id="user_groups" class="table-hover table-striped cell-border" style="float: left;">
<thead>
<tr>
<th></th>
@@ -88,48 +98,26 @@
{% endblock %}
{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
- $('#admin_groups, #user_groups').dataTable( {
- "drawCallback": function( settings ) {
- $('#admin_groups tr').click(function(event) {
- if (event.target.type !== 'checkbox') {
- $(':checkbox', this).trigger('click');
- }
- });
- },
- "columns": [
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" }
- ],
- "columnDefs": [ {
- "targets": 0,
- "orderable": false
- } ],
- "order": [[1, "asc" ]],
- "sDom": "Ztr",
- "iDisplayLength": -1,
- "autoWidth": true,
- "bDeferRender": true,
- "bSortClasses": false,
- "paging": false,
- "orderClasses": true
- } );
-
+ {% if admin_groups|length != 0 %}
+ $('#admin_groups').dataTable();
+ {% endif %}
+ {% if user_groups|length != 0 %}
+ $('#user_groups').dataTable();
+ {% endif %}
submit_special = function(url) {
$("#groups_form").attr("action", url);
return $("#groups_form").submit();
};
+ $("#create_group").on("click", function() {
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+
$("#remove_groups").on("click", function() {
url = $(this).data("url")
groups = []
diff --git a/wqflask/wqflask/templates/admin/manage_resource.html b/wqflask/wqflask/templates/admin/manage_resource.html
new file mode 100644
index 00000000..a47f47ad
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/manage_resource.html
@@ -0,0 +1,92 @@
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Resource Manager</h1>
+ </div>
+ <form id="manage_resource" action="/resources/manage" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Resource Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ {{ resource_info.name }}
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Open to Public:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <label class="radio-inline">
+ <input type="radio" name="default_mask" value="True" checked="">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="default_mask" value="False">
+ No
+ </label>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <button id="save_changes" class="btn btn-primary">Save Changes</button>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ </div>
+ <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
+ <button id="add_group_to_resource" class="btn btn-primary" style="margin-bottom: 30px;" data-url="/resources/add_group">Add Group</button>
+ <br>
+ {% if group_masks|length > 0 %}
+ <h3>Current Group Permissions</h3>
+ <table>
+ <thead>
+ <tr>
+ <th>Name</th>
+ <th>Data</th>
+ <th>Metadata</th>
+ <th>Admin</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for key, value in group_masks.iteritems() %}
+ <tr>
+ <td>{{ value.name }}</td>
+ <td>{{ value.data }}</td>
+ <td>{{ value.metadata }}</td>
+ <td>{{ value.admin }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% else %}
+ <h3>No groups are currently added to this resource.</h3>
+ {% endif %}
+ </div>
+ </form>
+ </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ $('#add_group_to_resource').click(function(){
+ url = $(this).data("url");
+ $('#manage_resource').attr("action", url)
+ $('#manage_resource').submit()
+ })
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
new file mode 100644
index 00000000..89eb11dd
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -0,0 +1,64 @@
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Find Groups</h1>
+ </div>
+ <form id="find_groups" action="/resources/add_group" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px;">
+ <div style="margin-bottom: 30px;">
+ <h2>Search by:</h2>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group ID:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="group_id" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="group_name" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_name" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User E-mail:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_email" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <button type="submit" id="find_groups" class="btn btn-primary">Search</button>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/select_group_to_add.html b/wqflask/wqflask/templates/admin/select_group_to_add.html
new file mode 100644
index 00000000..df70fb2f
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/select_group_to_add.html
@@ -0,0 +1,54 @@
+{% extends "base.html" %}
+{% block title %}Matched Groups{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <h1>The following groups were found:</h1>
+ <br>
+ <form id="add_groups">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div id="groups_list" style="min-width: 600px; max-width: 800px;">
+ {% if group_list|length > 0 %}
+ <button type="submit" class="btn btn-primary" style="margin-bottom: 40px;">Add Selected Group</button>
+ <table id="groups_table" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Name</th>
+ <th>Created</th>
+ <th>Last Changed</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for group in group_list %}
+ <tr>
+ <td align="center" style="padding: 0px;"><input type="radio" name="selected_group" VALUE="{{ group.id }}"></td>
+ <td>{% if 'name' in group %}{{ group.name }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'created_timestamp' in group %}{{ group.created_timestamp }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'changed_timestamp' in group %}{{ group.changed_timestamp }}{% else %}N/A{% endif %}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% else %}
+ <h2>No matching groups were found.</h2>
+ {% endif %}
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script>
+ $('#groups_table').dataTable();
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/new_security/not_authenticated.html b/wqflask/wqflask/templates/new_security/not_authenticated.html
new file mode 100644
index 00000000..7d0d3060
--- /dev/null
+++ b/wqflask/wqflask/templates/new_security/not_authenticated.html
@@ -0,0 +1,11 @@
+{% extends "base.html" %}
+{% block title %}Authentication Needed{% endblock %}
+{% block content %}
+ <div class="container">
+ <div class="page-header">
+ <h3>You lack the permissions to view this data.</h3>
+ </div>
+ <p>Please contact the data's owner or GN administrators if you believe you should have access to this data.</p>
+ </div>
+
+{% endblock %}
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 878b6ced..5c315878 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -248,6 +248,11 @@
<a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
<button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
</a>
+ {% if resource_id %}
+ <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
+ <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
+ </a>
+ {% endif %}
</div>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 24a4dcee..ee827ba3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -30,6 +30,7 @@ import sqlalchemy
from wqflask import app
from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for
from wqflask import group_manager
+from wqflask import resource_manager
from wqflask import search_results
from wqflask import export_traits
from wqflask import gsearch
@@ -89,13 +90,13 @@ def connect_db():
@app.before_request
def check_access_permissions():
logger.debug("@app.before_request check_access_permissions")
+ available = True
if "temp_trait" in request.args:
if request.args['temp_trait'] == "True":
pass
else:
if 'dataset' in request.args:
dataset = create_dataset(request.args['dataset'])
- logger.debug("USER:", Redis.hget("users"))
if 'trait_id' in request.args:
available = check_resource_availability(dataset, request.args['trait_id'])
else:
--
cgit v1.2.3
From ccae8abe246af7b8f27fbcb9a37a3d242e594126 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 13:10:11 -0500
Subject: Fixed issue where removing traits and then running a tool from
collection page still included the removed traits
---
wqflask/wqflask/collect.py | 5 +----
wqflask/wqflask/templates/collections/view.html | 7 ++++++-
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 4fb8e69b..e8459821 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -159,13 +159,10 @@ def remove_traits():
uc_id = params['uc_id']
traits_to_remove = params.getlist('traits[]')
traits_to_remove = process_traits(traits_to_remove)
- logger.debug("\n\n after processing, traits_to_remove:", traits_to_remove)
members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove)
- # We need to return something so we'll return this...maybe in the future
- # we can use it to check the results
- return str(len(members_now))
+ return redirect(url_for("view_collection", uc_id=uc_id))
@app.route("/collections/delete", methods=('POST',))
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 60a1a081..ec0e0220 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -80,7 +80,7 @@
<input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Search Table For ...">
<input type="text" id="select_top" class="form-control" style="width: 200px; display: inline; padding-bottom: 9px;" placeholder="Select Top ...">
<button class="btn btn-default" id="deselect_all" type="button"><span class="glyphicon glyphicon-remove"></span> Deselect</button>
- <button class="btn btn-danger" id="remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button>
+ <button id="remove" class="btn btn-danger" data-url="/collections/remove" disabled="disabled" type="button"><i class="icon-minus-sign"></i> Delete Rows</button>
<button id="delete" class="btn btn-danger submit_special" data-url="/collections/delete" title="Delete this collection" > Delete Collection</button>
</form>
<div style="margin-top: 10px; margin-bottom: 5px;">
@@ -230,6 +230,11 @@
return submit_special(url)
});
+ $("#remove").on("click", function() {
+ url = $(this).data("url")
+ return submit_special(url)
+ });
+
$("#change_collection_name").on("click", function() {
if ($('input[name=new_collection_name]').css('display') == 'none') {
$('input[name=new_collection_name]').css('display', 'inline');
--
cgit v1.2.3
From 7438f3c45122f02c25155b42ede703ad2845649c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 13:40:10 -0500
Subject: Fixed issue caused by mapping scale sometimes being wrong + fixed
Verify link
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 2 --
wqflask/wqflask/marker_regression/run_mapping.py | 1 +
wqflask/wqflask/show_trait/show_trait.py | 8 ++++----
.../wqflask/static/new/javascript/show_trait_mapping_tools.js | 4 ++--
wqflask/wqflask/templates/show_trait_mapping_tools.html | 11 +++++++++++
5 files changed, 18 insertions(+), 8 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 88d27517..b858b573 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -136,9 +136,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
#trait_samples = this_dataset.group.all_samples_ordered()
this_dataset.group.get_samplelist()
trait_samples = this_dataset.group.samplelist
- logger.debug("SAMPLES:", trait_samples)
trait_sample_data = trait_ob.data
- logger.debug("SAMPLE DATA:", trait_sample_data)
for index, sample in enumerate(trait_samples):
if sample in samples:
if sample in trait_sample_data:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 0711b852..c859fdaa 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -162,6 +162,7 @@ class RunMapping(object):
self.perm_output = []
self.bootstrap_results = []
self.covariates = start_vars['covariates'] if "covariates" in start_vars else ""
+ self.categorical_vars = []
#ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c77e247f..ed4ff0ad 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -22,7 +22,7 @@ from base.trait import create_trait
from base import data_set
from db import webqtlDatabaseFunction
from utility import webqtlUtil, Plot, Bunch, helper_functions
-from utility.authentication_tools import check_owner
+from utility.authentication_tools import check_owner_or_admin
from utility.tools import locate_ignore_error
from utility.redis_tools import get_redis_conn, get_resource_id
Redis = get_redis_conn()
@@ -72,11 +72,11 @@ class ShowTrait(object):
cellid=None)
self.trait_vals = Redis.get(self.trait_id).split()
- self.resource_id = check_owner(self.dataset, self.trait_id)
+ self.admin_status = check_owner_or_admin(self.dataset, self.trait_id)
#ZS: Get verify/rna-seq link URLs
try:
- blatsequence = self.this_trait.sequence
+ blatsequence = self.this_trait.blatseq
if not blatsequence:
#XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead.
query1 = """SELECT Probe.Sequence, Probe.Name
@@ -256,7 +256,7 @@ class ShowTrait(object):
hddn['export_data'] = ""
hddn['export_format'] = "excel"
if len(self.scales_in_geno) < 2:
- hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0]
+ hddn['mapping_scale'] = self.scales_in_geno[self.scales_in_geno.keys()[0]][0][0]
# We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
self.hddn = hddn
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 01da3f74..db17af40 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -3,9 +3,9 @@
var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining;
submit_special = function(url) {
- console.log("In submit_special");
$("#trait_data_form").attr("action", url);
- return $("#trait_data_form").submit();
+ $("#trait_data_form").submit();
+ return false;
};
update_time_remaining = function(percent_complete) {
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index a2416ced..e851a81e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -140,6 +140,17 @@
</select>
</div>
</div>
+ {% else %}
+ <div class="mapping_method_fields form-group">
+ <label for="scale_select" style="text-align: right;" class="col-xs-3 control-label">Map Scale</label>
+ <div style="margin-left:20px;" class="col-xs-2 controls">
+ <select id="scale_reaper" class="form-control" style="width: 80px;">
+ {% for item in scales_in_geno[dataset.group.name + ".geno"] %}
+ <option value="{{ item[0] }}">{{ item[1] }}</option>
+ {% endfor %}
+ </select>
+ </div>
+ </div>
{% endif %}
<div class="mapping_method_fields form-group">
<label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
--
cgit v1.2.3
From ea47eb228b1224ea83e3f50a056bf715b3bf5ec6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 14:49:40 -0500
Subject: Adding all the authentication stuff
---
wqflask/base/data_set.py | 36 +--
wqflask/base/trait.py | 5 +-
wqflask/maintenance/set_resource_defaults.py | 307 ++++++++++-----------
wqflask/utility/authentication_tools.py | 132 ++++++---
wqflask/utility/redis_tools.py | 67 ++++-
wqflask/wqflask/docs.py | 4 +-
wqflask/wqflask/group_manager.py | 220 ++++++++++-----
wqflask/wqflask/resource_manager.py | 204 +++++++++-----
.../wqflask/static/new/javascript/group_manager.js | 74 ++---
.../static/new/javascript/search_results.js | 1 -
.../templates/admin/change_resource_owner.html | 116 ++++++++
wqflask/wqflask/templates/admin/create_group.html | 178 ++++++------
wqflask/wqflask/templates/admin/group_manager.html | 18 +-
.../wqflask/templates/admin/manage_resource.html | 200 ++++++++------
.../wqflask/templates/admin/search_for_groups.html | 198 ++++++++-----
.../templates/admin/select_group_to_add.html | 54 ----
.../templates/admin/set_group_privileges.html | 102 +++++++
wqflask/wqflask/templates/admin/view_group.html | 238 ++++++++++++++++
wqflask/wqflask/templates/base.html | 5 +
.../wqflask/templates/set_group_privileges.html | 77 ++++++
wqflask/wqflask/templates/show_trait_details.html | 4 +-
wqflask/wqflask/views.py | 2 +-
22 files changed, 1516 insertions(+), 726 deletions(-)
create mode 100644 wqflask/wqflask/templates/admin/change_resource_owner.html
delete mode 100644 wqflask/wqflask/templates/admin/select_group_to_add.html
create mode 100644 wqflask/wqflask/templates/admin/set_group_privileges.html
create mode 100644 wqflask/wqflask/templates/admin/view_group.html
create mode 100644 wqflask/wqflask/templates/set_group_privileges.html
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1457ba8d..92dc8615 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -486,25 +486,18 @@ class DatasetGroup(object):
def datasets(group_name, this_group = None):
key = "group_dataset_menu:v2:" + group_name
- logger.debug("key is2:", key)
dataset_menu = []
- logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
- logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
the_results = fetchall('''
(SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
- and PublishFreeze.public > %s
- and PublishFreeze.confidentiality < 1
ORDER BY PublishFreeze.Id ASC)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
- and InbredSet.Name = '%s'
- and GenoFreeze.public > %s
- and GenoFreeze.confidentiality < 1)
+ and InbredSet.Name = '%s')
UNION
(SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -512,12 +505,10 @@ def datasets(group_name, this_group = None):
and ProbeFreeze.TissueId = Tissue.Id
and ProbeFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name like %s
- and ProbeSetFreeze.public > %s
- and ProbeSetFreeze.confidentiality < 1
ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
- ''' % (group_name, webqtlConfig.PUBLICTHRESH,
- group_name, webqtlConfig.PUBLICTHRESH,
- "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
+ ''' % (group_name,
+ group_name,
+ "'" + group_name + "'"))
sorted_results = sorted(the_results, key=lambda kv: kv[0])
@@ -637,29 +628,25 @@ class DataSet(object):
"""
-
try:
if self.type == "ProbeSet":
query_args = tuple(escape(x) for x in (
- str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
-SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-FROM ProbeSetFreeze, ProbeFreeze, Tissue
-WHERE ProbeSetFreeze.public > %s
-AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-AND ProbeFreeze.TissueId = Tissue.Id
-AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
+ SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
+ FROM ProbeSetFreeze, ProbeFreeze, Tissue
+ WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+ AND ProbeFreeze.TissueId = Tissue.Id
+ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
""" % (query_args),"/dataset/"+self.name+".json",
lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
)
else:
query_args = tuple(escape(x) for x in (
(self.type + "Freeze"),
- str(webqtlConfig.PUBLICTHRESH),
self.name,
self.name,
self.name))
@@ -668,9 +655,8 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
self.id, self.name, self.fullname, self.shortname = fetchone("""
SELECT Id, Name, FullName, ShortName
FROM %s
- WHERE public > %s AND
- (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
- """ % (query_args))
+ WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args))
except TypeError:
logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2a945588..7700ecd5 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -46,9 +46,10 @@ def create_trait(**kw):
else:
permitted = check_resource_availability(dataset)
- if permitted:
+ if permitted != "no-access":
the_trait = GeneralTrait(**kw)
if the_trait.dataset.type != "Temp":
+
the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
return the_trait
else:
@@ -383,7 +384,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if dataset.type == 'Publish':
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
else:
-
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
try:
@@ -424,7 +424,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
-
#XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
#XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
elif dataset.type == 'ProbeSet':
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index ba102d9c..344e6a23 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -1,155 +1,154 @@
-"""
-
-Script that sets default resource access masks for use with the DB proxy
-
-Defaults will be:
-Owner - omni_gn
-Mask - Public/non-confidential: { data: "view",
- metadata: "view",
- admin: "not-admin" }
- Private/confidentia: { data: "no-access",
- metadata: "no-access",
- admin: "not-admin" }
-
-To run:
-./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
-
-"""
-
-from __future__ import print_function, division
-
-import sys
-import json
-
-# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
-
-# NEW: import app to avoid a circular dependency on utility.tools
-from wqflask import app
-
-from utility.tools import SQL_URI
-from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources
-Redis = get_redis_conn()
-
-import MySQLdb
-
-import urlparse
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-def parse_db_uri():
- """Converts a database URI to the db name, host name, user name, and password"""
-
- parsed_uri = urlparse.urlparse(SQL_URI)
-
- db_conn_info = dict(
- db = parsed_uri.path[1:],
- host = parsed_uri.hostname,
- user = parsed_uri.username,
- passwd = parsed_uri.password)
-
- print(db_conn_info)
- return db_conn_info
-
-def insert_probeset_resources(default_owner_id):
- current_resources = Redis.hgetall("resources")
- Cursor.execute(""" SELECT
- ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public
- FROM
- ProbeSetFreeze""")
-
- resource_results = Cursor.fetchall()
- for i, resource in enumerate(resource_results):
- if i % 20 == 0:
- print(i)
- resource_ob = {}
- resource_ob['name'] = resource[1]
- resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[0])}
- resource_ob['type'] = "dataset-probeset"
- if resource[2] < 1 and resource[3] > 0:
- resource_ob['default_mask'] = { "data": ["no-access", "view"] }
- else:
- resource_ob['default_mask'] = { "data": ["no-access"] }
- resource_ob['group_masks'] = {}
-
- add_resource(resource_ob)
-
-def insert_publish_resources(default_owner_id):
- current_resources = Redis.hgetall("resources")
- Cursor.execute(""" SELECT
- PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode
- FROM
- PublishXRef, PublishFreeze, InbredSet, Publication
- WHERE
- PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND
- InbredSet.Id = PublishXRef.InbredSetId AND
- Publication.Id = PublishXRef.PublicationId""")
-
- resource_results = Cursor.fetchall()
- for resource in resource_results:
- if resource[2]:
- resource_ob = {}
- if resource[2]:
- resource_ob['name'] = resource[2] + "_" + str(resource[0])
- else:
- resource_ob['name'] = str(resource[0])
- resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[1]) ,
- "trait" : str(resource[0])}
- resource_ob['type'] = "dataset-publish"
- resource_ob['default_mask'] = { "data": "view" }
-
- resource_ob['group_masks'] = {}
-
- add_resource(resource_ob)
- else:
- continue
-
-def insert_geno_resources(default_owner_id):
- current_resources = Redis.hgetall("resources")
- Cursor.execute(""" SELECT
- GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality
- FROM
- GenoFreeze""")
-
- resource_results = Cursor.fetchall()
- for i, resource in enumerate(resource_results):
- if i % 20 == 0:
- print(i)
- resource_ob = {}
- resource_ob['name'] = resource[1]
- resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[0]) }
- resource_ob['type'] = "dataset-geno"
- if resource[2] < 1:
- resource_ob['default_mask'] = { "data": "view" }
- else:
- resource_ob['default_mask'] = { "data": "no-access" }
- resource_ob['group_masks'] = {}
-
- add_resource(resource_ob)
-
-def insert_resources(default_owner_id):
- current_resources = get_resources()
- print("START")
- insert_publish_resources(default_owner_id)
- print("AFTER PUBLISH")
- insert_geno_resources(default_owner_id)
- print("AFTER GENO")
- insert_probeset_resources(default_owner_id)
- print("AFTER PROBESET")
-
-def main():
- """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
-
- Redis.delete("resources")
-
- owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com")
- insert_resources(owner_id)
-
-if __name__ == '__main__':
- Conn = MySQLdb.Connect(**parse_db_uri())
- Cursor = Conn.cursor()
+"""
+
+Script that sets default resource access masks for use with the DB proxy
+
+Defaults will be:
+Owner - omni_gn
+Mask - Public/non-confidential: { data: "view",
+ metadata: "view",
+ admin: "not-admin" }
+ Private/confidentia: { data: "no-access",
+ metadata: "no-access",
+ admin: "not-admin" }
+
+To run:
+./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
+
+"""
+
+from __future__ import print_function, division
+
+import sys
+import json
+
+# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
+sys.path.insert(0,'./')
+
+# NEW: import app to avoid a circular dependency on utility.tools
+from wqflask import app
+
+from utility.tools import SQL_URI
+from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources
+Redis = get_redis_conn()
+
+import MySQLdb
+
+import urlparse
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+def parse_db_uri():
+ """Converts a database URI to the db name, host name, user name, and password"""
+
+ parsed_uri = urlparse.urlparse(SQL_URI)
+
+ db_conn_info = dict(
+ db = parsed_uri.path[1:],
+ host = parsed_uri.hostname,
+ user = parsed_uri.username,
+ passwd = parsed_uri.password)
+
+ print(db_conn_info)
+ return db_conn_info
+
+def insert_probeset_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public
+ FROM
+ ProbeSetFreeze""")
+
+ resource_results = Cursor.fetchall()
+ for i, resource in enumerate(resource_results):
+ resource_ob = {}
+ resource_ob['name'] = resource[1]
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[0])}
+ resource_ob['type'] = "dataset-probeset"
+ if resource[2] < 1 and resource[3] > 0:
+ resource_ob['default_mask'] = { "data": "view" }
+ else:
+ resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+def insert_publish_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode
+ FROM
+ PublishXRef, PublishFreeze, InbredSet, Publication
+ WHERE
+ PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND
+ InbredSet.Id = PublishXRef.InbredSetId AND
+ Publication.Id = PublishXRef.PublicationId""")
+
+ resource_results = Cursor.fetchall()
+ for resource in resource_results:
+ if resource[2]:
+ resource_ob = {}
+ if resource[2]:
+ resource_ob['name'] = resource[2] + "_" + str(resource[0])
+ else:
+ resource_ob['name'] = str(resource[0])
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[1]) ,
+ "trait" : str(resource[0])}
+ resource_ob['type'] = "dataset-publish"
+ resource_ob['default_mask'] = { "data": "view" }
+
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+ else:
+ continue
+
+def insert_geno_resources(default_owner_id):
+ current_resources = Redis.hgetall("resources")
+ Cursor.execute(""" SELECT
+ GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality
+ FROM
+ GenoFreeze""")
+
+ resource_results = Cursor.fetchall()
+ for i, resource in enumerate(resource_results):
+ resource_ob = {}
+ resource_ob['name'] = resource[1]
+ if resource[1] == "HET3-ITPGeno":
+ resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e"
+ else:
+ resource_ob['owner_id'] = default_owner_id
+ resource_ob['data'] = { "dataset" : str(resource[0]) }
+ resource_ob['type'] = "dataset-geno"
+ if resource[2] < 1:
+ resource_ob['default_mask'] = { "data": "view" }
+ else:
+ resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+def insert_resources(default_owner_id):
+ current_resources = get_resources()
+ print("START")
+ insert_publish_resources(default_owner_id)
+ print("AFTER PUBLISH")
+ insert_geno_resources(default_owner_id)
+ print("AFTER GENO")
+ insert_probeset_resources(default_owner_id)
+ print("AFTER PROBESET")
+
+def main():
+ """Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
+
+ Redis.delete("resources")
+
+ owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com")
+ insert_resources(owner_id)
+
+if __name__ == '__main__':
+ Conn = MySQLdb.Connect(**parse_db_uri())
+ Cursor = Conn.cursor()
main()
\ No newline at end of file
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 537881a5..07ceacc0 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,46 +1,86 @@
-from __future__ import absolute_import, print_function, division
-
-import json
-import requests
-
-from base import data_set
-
-from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
-
-from flask import Flask, g, redirect, url_for
-
-import logging
-logger = logging.getLogger(__name__ )
-
-def check_resource_availability(dataset, trait_id=None):
- resource_id = get_resource_id(dataset, trait_id)
-
- if resource_id:
- the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
- try:
- response = json.loads(requests.get(the_url).content)['data']
- except:
- resource_info = get_resource_info(resource_id)
- response = resource_info['default_mask']['data']
-
- if 'view' in response:
- return True
- else:
- return redirect(url_for("no_access_page"))
-
- return True
-
-def check_owner(dataset=None, trait_id=None, resource_id=None):
- if resource_id:
- resource_info = get_resource_info(resource_id)
- if g.user_session.user_id == resource_info['owner_id']:
- return resource_id
- else:
- resource_id = get_resource_id(dataset, trait_id)
- if resource_id:
- resource_info = get_resource_info(resource_id)
- if g.user_session.user_id == resource_info['owner_id']:
- return resource_id
-
- return False
\ No newline at end of file
+from __future__ import absolute_import, print_function, division
+
+import json
+import requests
+
+from base import data_set
+
+from utility import hmac
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+
+from flask import Flask, g, redirect, url_for
+
+import logging
+logger = logging.getLogger(__name__ )
+
+def check_resource_availability(dataset, trait_id=None):
+ resource_id = get_resource_id(dataset, trait_id)
+
+ response = None
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ try:
+ response = json.loads(requests.get(the_url).content)['data']
+ except:
+ response = resource_info['default_mask']['data']
+
+ if 'edit' in response:
+ return "edit"
+ elif 'view' in response:
+ return "view"
+ else:
+ return "no-access"
+
+ return False
+
+def check_admin(resource_id=None):
+
+ return "not-admin"
+
+ # ZS: commented out until proxy can return this
+ # the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ # try:
+ # response = json.loads(requests.get(the_url).content)
+ # except:
+ # response = resource_info['default_mask']['admin']
+
+ # if 'edit-admins' in response:
+ # return "edit-admins"
+ # elif 'edit-access' in response:
+ # return "edit-access"
+ # else:
+ # return "not-admin"
+
+def check_owner(dataset=None, trait_id=None, resource_id=None):
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return resource_id
+ else:
+ resource_id = get_resource_id(dataset, trait_id)
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return resource_id
+
+ return False
+
+def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return [resource_id, "owner"]
+ else:
+ return [resource_id, check_admin(resource_id)]
+ else:
+ resource_id = get_resource_id(dataset, trait_id)
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return [resource_id, "owner"]
+ else:
+ return [resource_id, check_admin(resource_id)]
+
+ return [resource_id, "not-admin"]
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index bc30a0af..c6d221ff 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -16,7 +16,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
def get_redis_conn():
- Redis = redis.StrictRedis(port=6380)
+ Redis = redis.StrictRedis(port=6379)
return Redis
Redis = get_redis_conn()
@@ -51,6 +51,27 @@ def get_user_by_unique_column(column_name, column_value):
return item_details
+def get_users_like_unique_column(column_name, column_value):
+ """
+ Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+ """
+ matched_users = []
+
+ if column_value != "":
+ user_list = Redis.hgetall("users")
+ if column_name != "user_id":
+ for key in user_list:
+ user_ob = json.loads(user_list[key])
+ if column_name in user_ob:
+ if column_value in user_ob[column_name]:
+ matched_users.append(user_ob)
+ else:
+ matched_users.append(json.loads(user_list[column_value]))
+
+ return matched_users
+
+# def search_users_by_unique_column(column_name, column_value):
+
def set_user_attribute(user_id, column_name, column_value):
user_info = json.loads(Redis.hget("users", user_id))
user_info[column_name] = column_value
@@ -142,6 +163,28 @@ def get_group_by_unique_column(column_name, column_value):
return matched_groups
+def get_groups_like_unique_column(column_name, column_value):
+ """
+ Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+ """
+ matched_groups = []
+
+ if column_value != "":
+ group_list = Redis.hgetall("groups")
+ if column_name != "group_id":
+ for key in group_list:
+ group_info = json.loads(group_list[key])
+ if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+ if column_value in group_info[column_name]:
+ matched_groups.append(group_info)
+ else:
+ if column_name in group_info:
+ if column_value in group_info[column_name]:
+ matched_groups.append(group_info)
+ else:
+ matched_groups.append(json.loads(group_list[column_value]))
+
+ return matched_groups
def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
group_id = str(uuid.uuid4())
@@ -192,9 +235,13 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
group_info = get_group_info(group_id)
+
if user_id in group_info["admins"]:
+ users_to_remove_set = set(users_to_remove_ids)
+ if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less
+ users_to_remove_set.remove(user_id)
group_users = set(group_info[user_type])
- group_users -= set(users_to_remove_ids)
+ group_users -= users_to_remove_set
group_info[user_type] = list(group_users)
group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
Redis.hset("groups", group_id, json.dumps(group_info))
@@ -232,7 +279,6 @@ def get_resource_info(resource_id):
return json.loads(resource_info)
def add_resource(resource_info):
-
if 'trait' in resource_info['data']:
resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
else:
@@ -241,3 +287,18 @@ def add_resource(resource_info):
Redis.hset("resources", resource_id, json.dumps(resource_info))
return resource_info
+
+def add_access_mask(resource_id, group_id, access_mask):
+ the_resource = get_resource_info(resource_id)
+ the_resource['group_masks'][group_id] = access_mask
+
+ Redis.hset("resources", resource_id, json.dumps(the_resource))
+
+ return the_resource
+
+def change_resource_owner(resource_id, new_owner_id):
+ the_resource= get_resource_info(resource_id)
+ the_resource['owner_id'] = new_owner_id
+
+ Redis.delete("resource")
+ Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 0187f32e..78407e22 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -1,5 +1,7 @@
from __future__ import absolute_import, print_function, division
+import codecs
+
from flask import g
from utility.logger import getLogger
@@ -20,7 +22,7 @@ class Docs(object):
self.content = ""
else:
self.title = result[0]
- self.content = result[1]
+ self.content = result[1].encode("latin1")
self.editable = "false"
# ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index f41ae56d..9afc016b 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -1,77 +1,145 @@
-
-from __future__ import print_function, division, absolute_import
-
-from flask import (Flask, g, render_template, url_for, request, make_response,
- redirect, flash)
-
-from wqflask import app
-from wqflask.user_login import send_verification_email
-
-from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \
- change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-@app.route("/groups/manage", methods=('GET', 'POST'))
-def manage_groups():
- params = request.form if request.form else request.args
- if "add_new_group" in params:
- return redirect(url_for('add_group'))
- else:
- admin_groups, user_groups = get_user_groups(g.user_session.user_id)
- return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
-
-@app.route("/groups/remove", methods=('POST',))
-def remove_groups():
- group_ids_to_remove = request.form['selected_group_ids']
- for group_id in group_ids_to_remove.split(":"):
- delete_group(g.user_session.user_id, group_id)
-
- return redirect(url_for('manage_groups'))
-
-@app.route("/groups/create", methods=('GET', 'POST'))
-def add_group():
- params = request.form if request.form else request.args
- if "group_name" in params:
- member_user_ids = set()
- admin_user_ids = set()
- admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
- if "admin_emails" in params:
- admin_emails = params['admin_emails_to_add'].split(",")
- for email in admin_emails:
- user_details = get_user_by_unique_column("email_address", email)
- if user_details:
- admin_user_ids.add(user_details['user_id'])
- #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
- if "user_emails" in params:
- member_emails = params['member_emails_to_add'].split(",")
- for email in member_emails:
- user_details = get_user_by_unique_column("email_address", email)
- if user_details:
- member_user_ids.add(user_details['user_id'])
- #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
-
- create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
- return redirect(url_for('manage_groups'))
- else:
- return render_template("admin/create_group.html")
-
-#ZS: Will integrate this later, for now just letting users be added directly
-def send_group_invites(group_id, user_email_list = [], user_type="members"):
- for user_email in user_email_list:
- user_details = get_user_by_unique_column("email_address", user_email)
- if user_details:
- group_info = get_group_info(group_id)
- #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
- # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
- if group_info:
- #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
- # but do add them if they're a regular user and are added as an admin
- if (user_details['user_id'] in group_info['admins']) or \
- ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
- continue
- else:
- send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
-
+
+from __future__ import print_function, division, absolute_import
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+ redirect, flash)
+
+from wqflask import app
+from wqflask.user_login import send_verification_email
+
+from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \
+ change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/groups/manage", methods=('GET', 'POST'))
+def manage_groups():
+ params = request.form if request.form else request.args
+ if "add_new_group" in params:
+ return redirect(url_for('add_group'))
+ else:
+ admin_groups, user_groups = get_user_groups(g.user_session.user_id)
+ return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
+
+@app.route("/groups/view", methods=('GET', 'POST'))
+def view_group():
+ params = request.form if request.form else request.args
+ group_id = params['id']
+ group_info = get_group_info(group_id)
+ admins_info = []
+ user_is_admin = False
+ if g.user_session.user_id in group_info['admins']:
+ user_is_admin = True
+ for user_id in group_info['admins']:
+ if user_id:
+ user_info = get_user_by_unique_column("user_id", user_id)
+ admins_info.append(user_info)
+ members_info = []
+ for user_id in group_info['members']:
+ if user_id:
+ user_info = get_user_by_unique_column("user_id", user_id)
+ members_info.append(user_info)
+
+ #ZS: This whole part might not scale well with many resources
+ resources_info = []
+ all_resources = get_resources()
+ for resource_id in all_resources:
+ resource_info = get_resource_info(resource_id)
+ group_masks = resource_info['group_masks']
+ if group_id in group_masks:
+ this_resource = {}
+ privileges = group_masks[group_id]
+ this_resource['id'] = resource_id
+ this_resource['name'] = resource_info['name']
+ this_resource['data'] = privileges['data']
+ this_resource['metadata'] = privileges['metadata']
+ this_resource['admin'] = privileges['admin']
+ resources_info.append(this_resource)
+
+ return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
+
+@app.route("/groups/remove", methods=('POST',))
+def remove_groups():
+ group_ids_to_remove = request.form['selected_group_ids']
+ for group_id in group_ids_to_remove.split(":"):
+ delete_group(g.user_session.user_id, group_id)
+
+ return redirect(url_for('manage_groups'))
+
+@app.route("/groups/remove_users", methods=('POST',))
+def remove_users():
+ group_id = request.form['group_id']
+ admin_ids_to_remove = request.form['selected_admin_ids']
+ member_ids_to_remove = request.form['selected_member_ids']
+
+ remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins")
+ remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members")
+
+ return redirect(url_for('view_group', id=group_id))
+
+@app.route("/groups/add_<path:user_type>", methods=('POST',))
+def add_users(user_type='members'):
+ group_id = request.form['group_id']
+ if user_type == "admins":
+ user_emails = request.form['admin_emails_to_add'].split(",")
+ add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = True)
+ elif user_type == "members":
+ user_emails = request.form['member_emails_to_add'].split(",")
+ add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = False)
+
+ return redirect(url_for('view_group', id=group_id))
+
+@app.route("/groups/change_name", methods=('POST',))
+def change_name():
+ group_id = request.form['group_id']
+ new_name = request.form['new_name']
+ group_info = change_group_name(g.user_session.user_id, group_id, new_name)
+
+ return new_name
+
+@app.route("/groups/create", methods=('GET', 'POST'))
+def add_or_edit_group():
+ params = request.form if request.form else request.args
+ if "group_name" in params:
+ member_user_ids = set()
+ admin_user_ids = set()
+ admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
+ if "admin_emails_to_add" in params:
+ admin_emails = params['admin_emails_to_add'].split(",")
+ for email in admin_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ admin_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
+ if "member_emails_to_add" in params:
+ member_emails = params['member_emails_to_add'].split(",")
+ for email in member_emails:
+ user_details = get_user_by_unique_column("email_address", email)
+ if user_details:
+ member_user_ids.add(user_details['user_id'])
+ #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
+
+ create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
+ return redirect(url_for('manage_groups'))
+ else:
+ return render_template("admin/create_group.html")
+
+#ZS: Will integrate this later, for now just letting users be added directly
+def send_group_invites(group_id, user_email_list = [], user_type="members"):
+ for user_email in user_email_list:
+ user_details = get_user_by_unique_column("email_address", user_email)
+ if user_details:
+ group_info = get_group_info(group_id)
+ #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
+ # but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
+ if group_info:
+ #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
+ # but do add them if they're a regular user and are added as an admin
+ if (user_details['user_id'] in group_info['admins']) or \
+ ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
+ continue
+ else:
+ send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
+
#@app.route()
\ No newline at end of file
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 7d88b8ed..0f9f5c9d 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -1,72 +1,134 @@
-from __future__ import print_function, division, absolute_import
-
-from flask import (Flask, g, render_template, url_for, request, make_response,
- redirect, flash)
-
-from wqflask import app
-
-from utility.authentication_tools import check_owner
-from utility.redis_tools import get_resource_info, get_group_info, get_group_by_unique_column, get_user_id
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-@app.route("/resources/manage", methods=('GET', 'POST'))
-def view_resource():
- params = request.form if request.form else request.args
- if 'resource_id' in request.args:
- resource_id = request.args['resource_id']
- if check_owner(resource_id=resource_id):
- resource_info = get_resource_info(resource_id)
- group_masks = resource_info['group_masks']
- group_masks_with_names = get_group_names(group_masks)
- default_mask = resource_info['default_mask']['data']
- return render_template("admin/manage_resource.html", resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names)
- else:
- return redirect(url_for("no_access_page"))
-
-@app.route("/resources/add_group", methods=('POST',))
-def add_group_to_resource():
- resource_id = request.form['resource_id']
- if check_owner(resource_id=resource_id):
- if all(key in request.form for key in ('group_id', 'group_name', 'user_name', 'user_email')):
- group_list = []
- if request.form['group_id'] != "":
- the_group = get_group_info(request.form['group_id'])
- if the_group:
- group_list.append(the_group)
- if request.form['group_name'] != "":
- matched_groups = get_group_by_unique_column("name", request.form['group_name'])
- for group in matched_groups:
- group_list.append(group)
- if request.form['user_name'] != "":
- user_id = get_user_id("user_name", request.form['user_name'])
- if user_id:
- matched_groups = get_group_by_unique_column("admins", user_id)
- matched_groups += get_group_by_unique_column("members", user_id)
- for group in matched_groups:
- group_list.append(group)
- if request.form['user_email'] != "":
- user_id = get_user_id("email_address", request.form['user_email'])
- if user_id:
- matched_groups = get_group_by_unique_column("admins", user_id)
- matched_groups += get_group_by_unique_column("members", user_id)
- for group in matched_groups:
- group_list.append(group)
- return render_template("admin/select_group_to_add.html", group_list=group_list, resource_id = resource_id)
- elif 'selected_group' in request.form:
- group_id = request.form['selected_group']
- return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id)
- else:
- return render_template("admin/search_for_groups.html", resource_id = resource_id)
- else:
- return redirect(url_for("no_access_page"))
-
-def get_group_names(group_masks):
- group_masks_with_names = {}
- for group_id, group_mask in group_masks.iteritems():
- this_mask = group_mask
- group_name = get_group_info(group_id)['name']
- this_mask['name'] = group_name
-
+from __future__ import print_function, division, absolute_import
+
+import json
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+ redirect, flash)
+
+from wqflask import app
+
+from utility.authentication_tools import check_owner_or_admin
+from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/resources/manage", methods=('GET', 'POST'))
+def manage_resource():
+ params = request.form if request.form else request.args
+ if 'resource_id' in request.args:
+ resource_id = request.args['resource_id']
+ admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+
+ resource_info = get_resource_info(resource_id)
+ group_masks = resource_info['group_masks']
+ group_masks_with_names = get_group_names(group_masks)
+ default_mask = resource_info['default_mask']['data']
+ owner_id = resource_info['owner_id']
+ owner_info = get_user_by_unique_column("user_id", owner_id)
+
+ if 'name' in owner_info:
+ owner_display_name = owner_info['full_name']
+ elif 'user_name' in owner_info:
+ owner_display_name = owner_info['user_name']
+ elif 'email_address' in owner_info:
+ owner_display_name = owner_info['email_address']
+ else:
+ owner_display_name = None
+
+ return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
+
+@app.route("/search_for_users", methods=('POST',))
+def search_for_user():
+ params = request.form
+ user_list = []
+ user_list += get_users_like_unique_column("full_name", params['user_name'])
+ user_list += get_users_like_unique_column("email_address", params['user_email'])
+
+ return json.dumps(user_list)
+
+@app.route("/search_for_groups", methods=('POST',))
+def search_for_groups():
+ params = request.form
+ group_list = []
+ group_list += get_groups_like_unique_column("id", params['group_id'])
+ group_list += get_groups_like_unique_column("name", params['group_name'])
+
+ user_list = []
+ user_list += get_users_like_unique_column("full_name", params['user_name'])
+ user_list += get_users_like_unique_column("email_address", params['user_email'])
+ for user in user_list:
+ group_list += get_groups_like_unique_column("admins", user['user_id'])
+ group_list += get_groups_like_unique_column("members", user['user_id'])
+
+ return json.dumps(group_list)
+
+@app.route("/resources/change_owner", methods=('POST',))
+def change_owner():
+ resource_id = request.form['resource_id']
+ if 'new_owner' in request.form:
+ admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+ if admin_status == "owner":
+ new_owner_id = request.form['new_owner']
+ change_resource_owner(resource_id, new_owner_id)
+ flash("The resource's owner has beeen changed.", "alert-info")
+ return redirect(url_for("manage_resource", resource_id=resource_id))
+ else:
+ flash("You lack the permissions to make this change.", "error")
+ return redirect(url_for("manage_resource", resource_id=resource_id))
+ else:
+ return render_template("admin/change_resource_owner.html", resource_id = resource_id)
+
+@app.route("/resources/change_default_privileges", methods=('POST',))
+def change_default_privileges():
+ resource_id = request.form['resource_id']
+ admin_status = check_owner_or_admin(resource_id=resource_id)
+ if admin_status == "owner" or admin_status == "edit-admins":
+ resource_info = get_resource_info(resource_id)
+ default_mask = resource_info['default_mask']
+ if request.form['open_to_public'] == "True":
+ default_mask['data'] = 'view'
+ else:
+ default_mask['data'] = 'no-access'
+ resource_info['default_mask'] = default_mask
+ add_resource(resource_info)
+ flash("Your changes have been saved.", "alert-info")
+ return redirect(url_for("manage_resource", resource_id=resource_id))
+ else:
+ return redirect(url_for("no_access_page"))
+
+@app.route("/resources/add_group", methods=('POST',))
+def add_group_to_resource():
+ resource_id = request.form['resource_id']
+ admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+ if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access":
+ if 'selected_group' in request.form:
+ group_id = request.form['selected_group']
+ resource_info = get_resource_info(resource_id)
+ default_privileges = resource_info['default_mask']
+ return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id, default_privileges = default_privileges)
+ elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')):
+ group_id = request.form['group_id']
+ group_name = get_group_info(group_id)['name']
+ access_mask = {
+ 'data': request.form['data_privilege'],
+ 'metadata': request.form['metadata_privilege'],
+ 'admin': request.form['admin_privilege']
+ }
+ add_access_mask(resource_id, group_id, access_mask)
+ flash("Privileges have been added for group {}.".format(group_name), "alert-info")
+ return redirect(url_for("manage_resource", resource_id=resource_id))
+ else:
+ return render_template("admin/search_for_groups.html", resource_id = resource_id)
+ else:
+ return redirect(url_for("no_access_page"))
+
+def get_group_names(group_masks):
+ group_masks_with_names = {}
+ for group_id, group_mask in group_masks.iteritems():
+ this_mask = group_mask
+ group_name = get_group_info(group_id)['name']
+ this_mask['name'] = group_name
+ group_masks_with_names[group_id] = this_mask
+
return group_masks_with_names
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js
index 5e82d104..4c172cbf 100644
--- a/wqflask/wqflask/static/new/javascript/group_manager.js
+++ b/wqflask/wqflask/static/new/javascript/group_manager.js
@@ -1,38 +1,38 @@
-$('#add_to_admins').click(function() {
- add_emails('admin')
-})
-
-$('#add_to_members').click(function() {
- add_emails('member')
-})
-
-$('#clear_admins').click(function(){
- clear_emails('admin')
-})
-
-$('#clear_members').click(function(){
- clear_emails('member')
-})
-
-
-function add_emails(user_type){
- var email_address = $('input[name=user_email]').val();
- var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val()
- console.log(email_list_string)
- if (email_list_string == ""){
- var email_set = new Set();
- } else {
- var email_set = new Set(email_list_string.split(","))
- }
- email_set.add(email_address)
-
- $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(','))
-
- var emails_display_string = Array.from(email_set).join('\n')
- $('.added_' + user_type + 's').val(emails_display_string)
-}
-
-function clear_emails(user_type){
- $('input[name=' + user_type + '_emails_to_add]').val("")
- $('.added_' + user_type + 's').val("")
+$('#add_to_admins').click(function() {
+ add_emails('admin')
+})
+
+$('#add_to_members').click(function() {
+ add_emails('member')
+})
+
+$('#clear_admins').click(function(){
+ clear_emails('admin')
+})
+
+$('#clear_members').click(function(){
+ clear_emails('member')
+})
+
+
+function add_emails(user_type){
+ var email_address = $('input[name=user_email]').val();
+ var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim()
+ console.log(email_list_string)
+ if (email_list_string == ""){
+ var email_set = new Set();
+ } else {
+ var email_set = new Set(email_list_string.split(","))
+ }
+ email_set.add(email_address)
+
+ $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(','))
+
+ var emails_display_string = Array.from(email_set).join('\n')
+ $('.added_' + user_type + 's').val(emails_display_string)
+}
+
+function clear_emails(user_type){
+ $('input[name=' + user_type + '_emails_to_add]').val("")
+ $('.added_' + user_type + 's').val("")
}
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 8fa698b4..115dac13 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -296,7 +296,6 @@ $(function() {
$("#deselect_all").click(deselect_all);
$("#invert").click(invert);
$("#add").click(add);
- $("#remove").click(remove);
$("#submit_bnw").click(submit_bnw);
$("#export_traits").click(export_traits);
$('.trait_checkbox, .btn').click(change_buttons);
diff --git a/wqflask/wqflask/templates/admin/change_resource_owner.html b/wqflask/wqflask/templates/admin/change_resource_owner.html
new file mode 100644
index 00000000..ae9409b0
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/change_resource_owner.html
@@ -0,0 +1,116 @@
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Search for user to assign ownership to:</h1>
+ </div>
+ <form id="change_owner_form" action="/resources/change_owner" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px;">
+ <div style="margin-bottom: 30px;">
+ <h2>Search for user by either name or e-mail:</h2>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User's Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_name" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User's E-mail:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_email" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <button type="button" id="find_users" class="btn btn-primary">Search</button>
+ <button style="margin-left: 20px; display: none;" type="submit" id="submit_new_owner" class="btn btn-success">Assign Ownership to Selected User</button>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ <hr>
+ <div id="user_results">
+ </div>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+ <script language="javascript">
+ $('#find_users').click(function() {
+ $.ajax({
+ method: "POST",
+ url: "/search_for_users",
+ data: {
+ user_name: $('input[name=user_name]').val(),
+ user_email: $('input[name=user_email]').val()
+ },
+ success: populate_users
+ });
+ })
+
+ populate_users = function(json_user_list){
+ var user_list = JSON.parse(json_user_list)
+
+ var the_html = ""
+ if (user_list.length > 0){
+ the_html += "<table id='users_table' style='padding-top: 10px; width: 100%;' class='table-hover table-striped cell-border'>";
+ the_html += "<thead><tr><th></th><th>Index</th><th>Name</th><th>E-mail Address</th><th>Organization</th></tr></thead>";
+ the_html += "<tbody>";
+ for (_i = 0, _len = user_list.length; _i < _len; _i++) {
+ this_user = user_list[_i]
+ the_html += "<tr>";
+ the_html += "<td align='center' class='select_user'><input type='radio' name='new_owner' value='" + this_user.user_id + "'></td>";
+ the_html += "<td>" + (_i + 1).toString() + "</td>"
+ if ("full_name" in this_user) {
+ the_html += "<td>" + this_user.full_name + "</td>";
+ } else {
+ the_html += "<td>N/A</td>"
+ }
+ if ("email_address" in this_user) {
+ the_html += "<td>" + this_user.email_address + "</td>";
+ } else {
+ the_html += "<td>N/A</td>"
+ }
+ if ("organization" in this_user) {
+ the_html += "<td>" + this_user.organization + "</td>";
+ } else {
+ the_html += "<td>N/A</td>"
+ }
+ the_html += "</tr>"
+ }
+ the_html += "</tbody>";
+ the_html += "</table>";
+ } else {
+ the_html = "<span>No users were found matching the entered criteria.</span>"
+ }
+
+ $('#user_results').html(the_html)
+ if (user_list.length > 0){
+ $('#users_table').dataTable({
+ 'order': [[1, "asc" ]],
+ 'sDom': 'tr'
+ });
+ $('input[name=select_user]:eq(0)').prop("checked", true)
+ $('#submit_new_owner').css("display", "inline-block")
+ }
+ }
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 55c3fa0b..5a6929fb 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -1,89 +1,89 @@
-{% extends "base.html" %}
-{% block title %}Group Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
- <div class="container">
- <div class="page-header">
- <h1>Create Group</h1>
- </div>
- <form action="/groups/create" method="POST">
- <input type="hidden" name="admin_emails_to_add" value="">
- <input type="hidden" name="member_emails_to_add" value="">
- <fieldset>
- <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
- <div class="form-group" style="padding-left: 20px;">
- <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-12">
- <input name="group_name" type="text" style="width:100%;"></input>
- </div>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Add User Email:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-12">
- <input name="user_email" type="text" style="width:100%;"></input>
- </div>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label class="col-xs-3"></label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-6">
- <button type="button" id="add_to_admins" class="btn btn-default">Add to Admins</button>
- </div>
- <div class="col-xs-6">
- <button type="button" id="add_to_members" class="btn btn-default">Add to Members</button>
- </div>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label class="col-xs-3" style="font-size: 18px;">Members to be added:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-6">
- <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_admins"></textarea>
- </div>
- <div class="col-xs-6">
- <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_members"></textarea>
- </div>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label class="col-xs-3"></label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-6">
- <button type="button" id="clear_admins" class="btn btn-default">Clear</button>
- </div>
- <div class="col-xs-6">
- <button type="button" id="clear_members" class="btn btn-default">Clear</button>
- </div>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="create_group" class="col-xs-3" style="float: left; font-size: 18px;"></label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <div class="col-xs-6">
- <button type="button" id="create_group" class="btn btn-primary">Create Group</button>
- </div>
- </div>
- </div>
- </div>
- </fieldset>
- </form>
- </div>
-
-
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
- <script type="text/javascript" charset="utf-8">
- </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Group Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Create Group</h1>
+ </div>
+ <form action="/groups/create" method="POST">
+ <input type="hidden" name="admin_emails_to_add" value="">
+ <input type="hidden" name="member_emails_to_add" value="">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-12">
+ <input name="group_name" type="text" style="width:100%;"></input>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Add User Email:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-12">
+ <input name="user_email" type="text" style="width:100%;"></input>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="button" id="add_to_admins" class="btn btn-default">Add to Admins</button>
+ </div>
+ <div class="col-xs-6">
+ <button type="button" id="add_to_members" class="btn btn-default">Add to Members</button>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="font-size: 18px;">Members to be added:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_admins"></textarea>
+ </div>
+ <div class="col-xs-6">
+ <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_members"></textarea>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="button" id="clear_admins" class="btn btn-default">Clear</button>
+ </div>
+ <div class="col-xs-6">
+ <button type="button" id="clear_members" class="btn btn-default">Clear</button>
+ </div>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="create_group" class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <div class="col-xs-6">
+ <button type="submit" id="create_group" class="btn btn-primary">Create Group</button>
+ </div>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ </form>
+ </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index 23d8205a..70d55684 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -23,7 +23,7 @@
<br>
<button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
{% else %}
- <div><h3>Admin Groups</h3></div>
+ <div style="margin-top: 20px;"><h2>Admin Groups</h2></div>
<hr>
{% if admin_groups|length == 0 %}
<h4>You currently aren't the administrator of any groups.</h4>
@@ -45,8 +45,8 @@
<tr>
<td><input type="checkbox" name="group_id" value="{{ group.id }}"></td>
<td align="right">{{ loop.index }}</td>
- <td>{{ group.name }}</td>
- <td align="right">{{ group.admins|length + group.users|length }}</td>
+ <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td>
+ <td align="right">{{ group.admins|length + group.members|length }}</td>
<td>{{ group.created_timestamp }}</td>
<td>{{ group.changed_timestamp }}</td>
<td>{{ group.id }}</td>
@@ -58,7 +58,7 @@
</div>
<hr>
<div style="min-width: 800px; max-width: 1000px;">
- <div><h3>User Groups</h3></div>
+ <div><h2>User Groups</h2></div>
<hr>
{% if user_groups|length == 0 %}
<h4>You currently aren't a member of any groups.</h4>
@@ -80,7 +80,7 @@
<td><input type="checkbox" name="read" value="{{ group.id }}"></td>
<td>{{ loop.index }}</td>
<td>{{ group.name }}</td>
- <td>{{ group.admins|length + group.users|length }}</td>
+ <td>{{ group.admins|length + group.members|length }}</td>
<td>{{ group.created_timestamp }}</td>
<td>{{ group.changed_timestamp }}</td>
</tr>
@@ -103,10 +103,14 @@
<script type="text/javascript" charset="utf-8">
$(document).ready( function () {
{% if admin_groups|length != 0 %}
- $('#admin_groups').dataTable();
+ $('#admin_groups').dataTable({
+ 'sDom': 'tr'
+ });
{% endif %}
{% if user_groups|length != 0 %}
- $('#user_groups').dataTable();
+ $('#user_groups').dataTable({
+ 'sDom': 'tr'
+ });
{% endif %}
submit_special = function(url) {
$("#groups_form").attr("action", url);
diff --git a/wqflask/wqflask/templates/admin/manage_resource.html b/wqflask/wqflask/templates/admin/manage_resource.html
index a47f47ad..0b12eaae 100644
--- a/wqflask/wqflask/templates/admin/manage_resource.html
+++ b/wqflask/wqflask/templates/admin/manage_resource.html
@@ -1,92 +1,108 @@
-{% extends "base.html" %}
-{% block title %}Resource Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
- <div class="container">
- <div class="page-header">
- <h1>Resource Manager</h1>
- </div>
- <form id="manage_resource" action="/resources/manage" method="POST">
- <input type="hidden" name="resource_id" value="{{ resource_id }}">
- <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
- <fieldset>
- <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
- <div class="form-group" style="padding-left: 20px;">
- <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Resource Name:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- {{ resource_info.name }}
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Open to Public:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <label class="radio-inline">
- <input type="radio" name="default_mask" value="True" checked="">
- Yes
- </label>
- <label class="radio-inline">
- <input type="radio" name="default_mask" value="False">
- No
- </label>
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <button id="save_changes" class="btn btn-primary">Save Changes</button>
- </div>
- </div>
- </div>
- </fieldset>
- </div>
- <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
- <button id="add_group_to_resource" class="btn btn-primary" style="margin-bottom: 30px;" data-url="/resources/add_group">Add Group</button>
- <br>
- {% if group_masks|length > 0 %}
- <h3>Current Group Permissions</h3>
- <table>
- <thead>
- <tr>
- <th>Name</th>
- <th>Data</th>
- <th>Metadata</th>
- <th>Admin</th>
- </tr>
- </thead>
- <tbody>
- {% for key, value in group_masks.iteritems() %}
- <tr>
- <td>{{ value.name }}</td>
- <td>{{ value.data }}</td>
- <td>{{ value.metadata }}</td>
- <td>{{ value.admin }}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- {% else %}
- <h3>No groups are currently added to this resource.</h3>
- {% endif %}
- </div>
- </form>
- </div>
-
-
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
- <script type="text/javascript" charset="utf-8">
- $('#add_group_to_resource').click(function(){
- url = $(this).data("url");
- $('#manage_resource').attr("action", url)
- $('#manage_resource').submit()
- })
- </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ {{ flash_me() }}
+ <div class="page-header" style="display: inline-block;">
+ <h1>Resource Manager</h1>
+ <h3>{% if owner_name is not none %}Current Owner: {{ owner_name }}{% endif %} {% if admin_status == "owner" %}<button id="change_owner" class="btn btn-danger" data-url="/resources/change_owner" style="margin-left: 20px;">Change Owner</button>{% endif %}</h3>
+ </div>
+ <form id="manage_resource" action="/resources/manage" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Resource Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ {{ resource_info.name }}
+ </div>
+ </div>
+ {% if admin_status == "owner" %}
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Open to Public:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <label class="radio-inline">
+ <input type="radio" name="open_to_public" value="True" {% if default_mask != 'no-access' %}checked{% endif %}>
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="open_to_public" value="False" {% if default_mask == 'no-access' %}checked{% endif %}>
+ No
+ </label>
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <button id="save_changes" class="btn btn-primary" data-url="/resources/change_default_privileges">Save Changes</button>
+ </div>
+ </div>
+ {% endif %}
+ </div>
+ </fieldset>
+ </div>
+ {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+ <div style="min-width: 600px; max-width: 800px;">
+ <hr>
+ <button id="add_group_to_resource" class="btn btn-primary" style="margin-bottom: 30px;" data-url="/resources/add_group">Add Group</button>
+ <br>
+ {% if group_masks|length > 0 %}
+ <h2>Current Group Permissions</h2>
+ <hr>
+ <table id="groups_table" class="table-hover table-striped cell-border">
+ <thead>
+ <tr>
+ <th>Name</th>
+ <th>Data</th>
+ <th>Metadata</th>
+ <th>Admin</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for key, value in group_masks.iteritems() %}
+ <tr>
+ <td>{{ value.name }}</td>
+ <td>{{ value.data }}</td>
+ <td>{{ value.metadata }}</td>
+ <td>{{ value.admin }}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% else %}
+ <h3>No groups are currently added to this resource.</h3>
+ {% endif %}
+ </div>
+ {% endif %}
+ </form>
+ </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ $('#add_group_to_resource, #save_changes, #change_owner').click(function(){
+ url = $(this).data("url");
+ $('#manage_resource').attr("action", url)
+ $('#manage_resource').submit()
+ })
+
+ {% if group_masks|length > 0 %}
+ $('#groups_table').dataTable({
+ 'sDom': 'tr',
+ });
+ {% endif %}
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
index 89eb11dd..f304a172 100644
--- a/wqflask/wqflask/templates/admin/search_for_groups.html
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -1,64 +1,134 @@
-{% extends "base.html" %}
-{% block title %}Resource Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
- <div class="container">
- <div class="page-header">
- <h1>Find Groups</h1>
- </div>
- <form id="find_groups" action="/resources/add_group" method="POST">
- <input type="hidden" name="resource_id" value="{{ resource_id }}">
- <div style="min-width: 600px; max-width: 800px;">
- <fieldset>
- <div class="form-horizontal" style="width: 900px;">
- <div style="margin-bottom: 30px;">
- <h2>Search by:</h2>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group ID:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <input name="group_id" type="text" value="">
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <input name="group_name" type="text" value="">
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User Name:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <input name="user_name" type="text" value="">
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User E-mail:</label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <input name="user_email" type="text" value="">
- </div>
- </div>
- <div class="form-group" style="padding-left: 20px;">
- <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
- <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
- <button type="submit" id="find_groups" class="btn btn-primary">Search</button>
- </div>
- </div>
- </div>
- </fieldset>
- </div>
- </form>
- </div>
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
- <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
- <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
- <script type="text/javascript" charset="utf-8">
- </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>Find Groups</h1>
+ </div>
+ <form id="add_group" action="/resources/add_group" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <fieldset>
+ <div class="form-horizontal" style="width: 900px;">
+ <div style="margin-bottom: 30px;">
+ <h2>Search by:</h2>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group ID:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="group_id" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="group_name" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User Name:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_name" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User E-mail:</label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <input name="user_email" type="text" value="">
+ </div>
+ </div>
+ <div class="form-group" style="padding-left: 20px;">
+ <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+ <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+ <button type="button" id="find_groups" class="btn btn-primary">Search</button>
+ <button style="margin-left: 20px; display: none;" type="submit" id="submit_group" class="btn btn-success">Add Privileges for Selected Group</button>
+ </div>
+ </div>
+ </div>
+ </fieldset>
+ <hr>
+ <div id="group_results">
+ </div>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+ <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+ <script type="text/javascript" charset="utf-8">
+
+ $('#find_groups').click(function() {
+ $.ajax({
+ method: "POST",
+ url: "/search_for_groups",
+ data: {
+ group_id: $('input[name=group_id]').val(),
+ group_name: $('input[name=group_name]').val(),
+ user_name: $('input[name=user_name]').val(),
+ user_email: $('input[name=user_email]').val()
+ },
+ success: populate_groups
+ });
+ })
+
+ populate_groups = function(json_group_list){
+ console.log(json_group_list)
+ var group_list = JSON.parse(json_group_list)
+
+ var the_html = ""
+ if (group_list.length > 0){
+ the_html += "<table id='groups_table' style='padding-top: 10px; width: 100%;' class='table-hover table-striped cell-border'>";
+ the_html += "<thead><tr><th></th><th>Index</th><th>Name</th><th># Admins</th><th># Members</th></tr></thead>";
+ the_html += "<tbody>";
+ for (_i = 0, _len = group_list.length; _i < _len; _i++) {
+ this_group = group_list[_i]
+ the_html += "<tr>";
+ the_html += "<td align='center' class='select_group'><input type='radio' name='selected_group' value='" + this_group.id + "'></td>";
+ the_html += "<td>" + (_i + 1).toString() + "</td>"
+ if ("name" in this_group) {
+ the_html += "<td>" + this_group.name + "</td>";
+ } else {
+ the_html += "<td>N/A</td>"
+ }
+ if ("admins" in this_group) {
+ the_html += "<td>" + this_group.admins.length + "</td>";
+ } else {
+ the_html += "<td>0</td>"
+ }
+ if ("members" in this_group) {
+ the_html += "<td>" + this_group.members.length + "</td>";
+ } else {
+ the_html += "<td>0</td>"
+ }
+ the_html += "</tr>"
+ }
+ the_html += "</tbody>";
+ the_html += "</table>";
+ } else {
+ the_html = "<span>No groups were found matching the entered criteria.</span>"
+ }
+
+ $('#group_results').html(the_html)
+ if (group_list.length > 0){
+ $('#groups_table').dataTable({
+ 'order': [[1, "asc" ]],
+ 'sDom': 'tr'
+ });
+ $('input[name=selected_group]:eq(0)').prop("checked", true)
+ $('#submit_group').css("display", "inline-block")
+ }
+ }
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/select_group_to_add.html b/wqflask/wqflask/templates/admin/select_group_to_add.html
deleted file mode 100644
index df70fb2f..00000000
--- a/wqflask/wqflask/templates/admin/select_group_to_add.html
+++ /dev/null
@@ -1,54 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Matched Groups{% endblock %}
-{% block css %}
- <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
- <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
- <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
-{% endblock %}
-{% block content %}
-<!-- Start of body -->
- <div class="container">
- <h1>The following groups were found:</h1>
- <br>
- <form id="add_groups">
- <input type="hidden" name="resource_id" value="{{ resource_id }}">
- <div id="groups_list" style="min-width: 600px; max-width: 800px;">
- {% if group_list|length > 0 %}
- <button type="submit" class="btn btn-primary" style="margin-bottom: 40px;">Add Selected Group</button>
- <table id="groups_table" class="table-hover table-striped cell-border" style="float: left;">
- <thead>
- <tr>
- <th></th>
- <th>Name</th>
- <th>Created</th>
- <th>Last Changed</th>
- </tr>
- </thead>
- <tbody>
- {% for group in group_list %}
- <tr>
- <td align="center" style="padding: 0px;"><input type="radio" name="selected_group" VALUE="{{ group.id }}"></td>
- <td>{% if 'name' in group %}{{ group.name }}{% else %}N/A{% endif %}</td>
- <td>{% if 'created_timestamp' in group %}{{ group.created_timestamp }}{% else %}N/A{% endif %}</td>
- <td>{% if 'changed_timestamp' in group %}{{ group.changed_timestamp }}{% else %}N/A{% endif %}</td>
- </tr>
- {% endfor %}
- </tbody>
- </table>
- {% else %}
- <h2>No matching groups were found.</h2>
- {% endif %}
- </div>
- </form>
- </div>
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
- <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
- <script>
- $('#groups_table').dataTable();
- </script>
-{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html
new file mode 100644
index 00000000..bc52788f
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/set_group_privileges.html
@@ -0,0 +1,102 @@
+{% extends "base.html" %}
+{% block title %}Set Group Privileges{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <h1>Group Privileges</h1>
+ <br>
+ <form id="set_group_privileges" action="/resources/add_group" method="POST">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <input type="hidden" name="group_id" value="{{ group_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <button type="submit" class="btn btn-primary" style="margin-bottom: 10px;">Add Group</button>
+ <hr>
+ <h2>Data and Metadata Privileges</h2>
+ <table id="data_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>No-Access</th>
+ <th>View</th>
+ <th>Edit</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Data:</td>
+ {% if 'data' in default_privileges %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" {% if default_privileges.data == "no-access" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view" {% if default_privileges.data == "view" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit" {% if default_privileges.data == "edit" %}checked{% endif %}></td>
+ {% else %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit"></td>
+ {% endif %}
+ </tr>
+ <tr>
+ <td>Metadata:</td>
+ {% if 'metadata' in default_privileges %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" {% if default_privileges.metadata == "no-access" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view" {% if default_privileges.metadata == "view" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit" {% if default_privileges.metadata[-1] == "edit" %}checked{% endif %}></td>
+ {% else %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit"></td>
+ {% endif %}
+ </tr>
+ </tbody>
+ </table>
+ <hr>
+ <h2>Admin Privileges</h2>
+ <table id="admin_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Not Admin</th>
+ <th>Edit Access</th>
+ <th>Edit Admins</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Admin:</td>
+ {% if 'admin' in default_privileges %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" {% if default_privileges.admin == "not-admin" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access" {% if default_privileges.admin == "edit-access" %}checked{% endif %}></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins" {% if default_privileges.admin == "edit-admins" %}checked{% endif %}></td>
+ {% else %}
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins"></td>
+ {% endif %}
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script>
+ $('#data_privileges_table').dataTable({
+ 'sDom': 'tr',
+ 'bSort': false
+ });
+ $('#admin_privileges_table').dataTable({
+ 'sDom': 'tr',
+ 'bSort': false
+ });
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html
new file mode 100644
index 00000000..b797cd70
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/view_group.html
@@ -0,0 +1,238 @@
+{% extends "base.html" %}
+{% block title %}View and Edit Group{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <div class="page-header">
+ <h1>
+ <span id="group_name">{{ group_info.name }}</span>
+ <input type="text" name="new_group_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ group_info.name }}">
+ <button class="btn btn-default" style="display: inline;" id="change_group_name">Change Group Name</button>
+ </h1>
+ {% if user_is_admin == true %}
+ <div style="display: inline;">
+ <button type="button" id="remove_users" class="btn btn-danger" data-url="/groups/remove_users">Remove Selected Users from Group</button>
+ </div>
+ {% endif %}
+ </div>
+ <form id="group_form" action="/groups/view" method="POST">
+ <input type="hidden" name="group_id" value="{{ group_info.id }}">
+ <input type="hidden" name="selected_admin_ids" value="">
+ <input type="hidden" name="selected_member_ids" value="">
+ <div class="row">
+ <div id="groups_div" class="col-xs-6" style="margin-right: 30px; min-width: 600px; max-width: 800px;">
+ <div>
+ <div style="margin-top: 20px;"><h2>Admins</h2></div>
+ <hr>
+ <table id="group_admins" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Index</th>
+ <th>Name</th>
+ <th>Email Address</th>
+ <th>Organization</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for admin in admins %}
+ <tr>
+ <td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="admin_id" value="{{ admin.user_id }}"></td>
+ <td align="right">{{ loop.index }}</td>
+ <td>{% if 'full_name' in admin %}{{ admin.full_name }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'email_address' in admin %}{{ admin.email_address }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'organization' in admin %}{{ admin.organization }}{% else %}N/A{% endif %}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% if user_is_admin == true %}
+ <div style="margin-top: 20px;">
+ <span>E-mail of user to add to admins (multiple e-mails can be added separated by commas):</span>
+ <input type="text" size="60" name="admin_emails_to_add" placeholder="Enter E-mail(s)" value="">
+ </div>
+ <div style="margin-bottom: 30px; margin-top: 20px;">
+ <button type="button" id="add_admins" class="btn btn-primary" data-usertype="admin" data-url="/groups/add_admins">Add Admin(s)</button>
+ </div>
+ {% endif %}
+ </div>
+ <hr>
+ <div>
+ {% if members|length > 0 %}
+ <div><h2>Members</h2></div>
+ <hr>
+ <table id="group_members" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Index</th>
+ <th>Name</th>
+ <th>Email Address</th>
+ <th>Organization</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for member in members %}
+ <tr>
+ <td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="member_id" value="{{ member.user_id }}"></td>
+ <td align="right">{{ loop.index }}</td>
+ <td>{% if 'full_name' in member %}{{ member.full_name }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'organization' in member %}{{ member.organization }}{% else %}N/A{% endif %}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% if user_is_admin == true %}
+ <div style="margin-top: 20px;">
+ <span>E-mail of user to add to members (multiple e-mails can be added separated by commas):</span>
+ <input type="text" size="60" name="member_emails_to_add" placeholder="Enter E-mail(s)" value="">
+ </div>
+ <div style="margin-bottom: 30px; margin-top: 20px;">
+ <button type="button" id="add_members" class="btn btn-primary" data-usertype="member" data-url="/groups/add_members">Add Member(s)</button>
+ </div>
+ {% endif %}
+ {% else %}
+ There are currently no members in this group.
+ {% endif %}
+ </div>
+ </div>
+ <div id="resources_div" class="col-xs-6" style="border-left: 1px solid #eee; margin-right: 30px; min-width: 600px; max-width: 800px;">
+ <div style="margin-top: 20px;"><h2>Resources</h2></div>
+ <hr>
+ {% if resources|length > 0 %}
+ <table id="resources" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th>Index</th>
+ <th>Name</th>
+ <th>Data</th>
+ <th>Metadata</th>
+ <th>Admin</th>
+ </tr>
+ </thead>
+ <tbody>
+ {% for resource in resources %}
+ <tr>
+ <td align="right">{{ loop.index }}</td>
+ <td>{% if 'name' in resource %}<a href="/resources/manage?resource_id={{ resource.id }}">{{ resource.name }}</a>{% else %}N/A{% endif %}</td>
+ <td>{% if 'data' in resource %}{{ resource.data }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'metadata' in resource %}{{ resource.metadata }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'admin' in resource %}{{ resource.admin }}{% else %}N/A{% endif %}</td>
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
+ {% else %}
+ There are currently no resources associated with this group.
+ {% endif %}
+ </div>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+ <script type="text/javascript" charset="utf-8">
+ $(document).ready( function () {
+ $('#group_admins').dataTable({
+ 'order': [[1, "asc" ]],
+ 'columns': [
+ { "type": "natural", "width": "25px"},
+ { "type": "natural", "width": "30px" },
+ { "type": "natural", "width": "150px" },
+ { "type": "natural" },
+ { "type": "natural" }
+ ],
+ 'sDom': 'tr'
+ });
+ {% if members|length > 0 %}
+ $('#group_members').dataTable({
+ 'order': [[1, "asc" ]],
+ 'columns': [
+ { "type": "natural", "width": "25px"},
+ { "type": "natural", "width": "30px" },
+ { "type": "natural", "width": "150px" },
+ { "type": "natural" },
+ { "type": "natural" }
+ ],
+ 'sDom': 'tr'
+ });
+ {% endif %}
+ {% if resources|length > 0 %}
+ $('#resources').dataTable({
+ 'order': [[0, "asc" ]],
+ 'columns': [
+ { "type": "natural", "width": "30px" },
+ { "type": "natural", "width": "150px" },
+ { "type": "natural" },
+ { "type": "natural" },
+ { "type": "natural" }
+ ],
+ 'sDom': 'tr'
+ });
+ {% endif %}
+
+ $('#resources_div').css('height', $('#groups_div').css('height'))
+
+ submit_special = function(url) {
+ $("#group_form").attr("action", url);
+ return $("#group_form").submit();
+ };
+
+ $("#remove_users").on("click", function() {
+ url = $(this).data("url");
+ admins = [];
+ $("input[name=admin_id]:checked").each(function() {
+ admins.push($(this).val());
+ });
+ admins_string = admins.join(":")
+ $("input[name=selected_admin_ids]").val(admins_string)
+
+ members = [];
+ $("input[name=member_id]:checked").each(function() {
+ members.push($(this).val());
+ });
+ members_string = members.join(":")
+ $("input[name=selected_member_ids]").val(members_string)
+ return submit_special(url)
+ });
+
+ $("#add_admins, #add_members").on("click", function() {
+ url = $(this).data("url");
+ return submit_special(url)
+ });
+
+ $("#change_group_name").on("click", function() {
+ if ($('input[name=new_group_name]').css('display') == 'none') {
+ $('input[name=new_group_name]').css('display', 'inline');
+ $('#group_name').css('display', 'none');
+ } else {
+ new_name = $('input[name=new_group_name]').val()
+ $.ajax({
+ type: "POST",
+ url: "/groups/change_name",
+ data: {
+ group_id: $('input[name=group_id]').val(),
+ new_name: new_name
+ }
+ });
+ $('input[name=new_group_name]').css('display', 'none');
+ $('input[name=group_name]').val(new_name);
+ $('#group_name').text(new_name)
+ $('#group_name').css('display', 'inline');
+ }
+ });
+ });
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 07c1b48e..262d9ee5 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -94,6 +94,11 @@
<a id="login_in" href="/n/login">Sign in</a>
{% endif %}
</li>
+ {% if g.user_session.logged_in %}
+ <li class="">
+ <a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a>
+ </li>
+ {% endif %}
{% endif %}
<!--
<li style="margin-left: 20px;">
diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/wqflask/wqflask/templates/set_group_privileges.html
new file mode 100644
index 00000000..98b0cc12
--- /dev/null
+++ b/wqflask/wqflask/templates/set_group_privileges.html
@@ -0,0 +1,77 @@
+{% extends "base.html" %}
+{% block title %}Set Group Privileges{% endblock %}
+{% block css %}
+ <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+ <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+ <div class="container">
+ <h1>Group Privileges</h1>
+ <br>
+ <form id="set_group_privileges">
+ <input type="hidden" name="resource_id" value="{{ resource_id }}">
+ <div style="min-width: 600px; max-width: 800px;">
+ <button type="submit" class="btn btn-primary" style="margin-bottom: 40px;">Add Group</button>
+ <hr>
+ <h2>Data and Metadata Privileges</h2>
+ <table id="data_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>No-Access</th>
+ <th>View</th>
+ <th>Edit</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Data:</td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit"></td>
+ </tr>
+ <tr>
+ <td>Metadata:</td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit"></td>
+ </tr>
+ </tbody>
+ </table>
+ <hr>
+ <h2>Admin Privileges</h2>
+ <table id="admin_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Not Admin</th>
+ <th>Edit Access</th>
+ <th>Edit Admins</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Admin:</td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" checked></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access"></td>
+ <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins"></td>
+ </tr>
+ </tbody>
+ </table>
+ </div>
+ </form>
+ </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+ <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+ <script>
+ $('#data_privileges_table').dataTable();
+ $('#admin_privileges_table').dataTable();
+ </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 5c315878..5e0bae79 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -248,8 +248,8 @@
<a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
<button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
</a>
- {% if resource_id %}
- <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
+ {% if admin_status[1] == "owner" or admin_status[1] == "edit-admins" or admin_status[1] == "edit-access" %}
+ <a target="_blank" href="./resources/manage?resource_id={{ admin_status[0] }}">
<button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
</a>
{% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ee827ba3..dc431aa9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -102,7 +102,7 @@ def check_access_permissions():
else:
available = check_resource_availability(dataset)
- if not available:
+ if available == "no-access":
return redirect(url_for("no_access_page"))
@app.teardown_appcontext
--
cgit v1.2.3
From 15f5df7fe795a32e2d61dd11f825e53b1a1175ec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 15:21:41 -0500
Subject: Fixed issue where removing traits from collection didn't work;
previous fix wasn't working for some reason
---
wqflask/wqflask/collect.py | 2 +-
.../static/new/javascript/search_results.js | 34 ----------------------
wqflask/wqflask/templates/collections/view.html | 5 ++++
3 files changed, 6 insertions(+), 35 deletions(-)
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index e8459821..42a09fed 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -157,7 +157,7 @@ def remove_traits():
params = request.form
uc_id = params['uc_id']
- traits_to_remove = params.getlist('traits[]')
+ traits_to_remove = params['trait_list']
traits_to_remove = process_traits(traits_to_remove)
members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove)
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 115dac13..39aae113 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -137,40 +137,6 @@ $(function() {
}
};
- remove = function() {
- var traits, uc_id;
- checked_traits = $("#trait_table input:checked");
- traits = checked_traits.map(function() {
- return $(this).val();
- }).get();
- console.log("checked length is:", traits.length);
- console.log("checked is:", traits);
- if ( $("#uc_id").length ) {
- uc_id = $("#uc_id").val();
- return $.ajax({
- type: "POST",
- url: "/collections/remove",
- data: {
- uc_id: uc_id,
- traits: traits
- },
- success: removed_traits
- });
- }
- else {
- collection_name = $("#collection_name").val();
- return $.ajax({
- type: "POST",
- url: "/collections/remove",
- data: {
- collection_name: collection_name,
- traits: traits
- },
- success: removed_traits
- });
- }
- };
-
submit_bnw = function() {
trait_data = get_traits_from_table("trait_table", "submit_bnw")
}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ec0e0220..b56a89da 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -232,6 +232,11 @@
$("#remove").on("click", function() {
url = $(this).data("url")
+ traits = $("#trait_table input:checked").map(function() {
+ return $(this).val();
+ }).get();
+ $("#trait_list").val(traits)
+
return submit_special(url)
});
--
cgit v1.2.3
From fcb3cb1105cf2a1d97c1a08fa636b118ed231ffa Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 16:28:15 -0500
Subject: A user's id is now set as a parameter if it doesn't already exist
---
wqflask/maintenance/set_resource_defaults.py | 8 +++---
wqflask/utility/authentication_tools.py | 30 ++++++++++++----------
wqflask/utility/redis_tools.py | 4 +++
wqflask/wqflask/group_manager.py | 4 +--
wqflask/wqflask/templates/admin/group_manager.html | 16 +++++++-----
5 files changed, 36 insertions(+), 26 deletions(-)
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 344e6a23..0c221bbf 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -27,8 +27,9 @@ sys.path.insert(0,'./')
# NEW: import app to avoid a circular dependency on utility.tools
from wqflask import app
+from utility import hmac
from utility.tools import SQL_URI
-from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources
+from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
Redis = get_redis_conn()
import MySQLdb
@@ -117,7 +118,7 @@ def insert_geno_resources(default_owner_id):
resource_ob = {}
resource_ob['name'] = resource[1]
if resource[1] == "HET3-ITPGeno":
- resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e"
+ resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
else:
resource_ob['owner_id'] = default_owner_id
resource_ob['data'] = { "dataset" : str(resource[0]) }
@@ -145,7 +146,8 @@ def main():
Redis.delete("resources")
- owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com")
+ owner_id = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
+
insert_resources(owner_id)
if __name__ == '__main__':
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 07ceacc0..dfa0e2d9 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -7,6 +7,7 @@ from base import data_set
from utility import hmac
from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+Redis = get_redis_conn()
from flask import Flask, g, redirect, url_for
@@ -14,8 +15,12 @@ import logging
logger = logging.getLogger(__name__ )
def check_resource_availability(dataset, trait_id=None):
- resource_id = get_resource_id(dataset, trait_id)
+ #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+ if g.user_session.user_id in Redis.smembers("super_users"):
+ return "edit"
+
+ resource_id = get_resource_id(dataset, trait_id)
response = None
if resource_id:
resource_info = get_resource_info(resource_id)
@@ -68,19 +73,16 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
return False
def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
- if resource_id:
- resource_info = get_resource_info(resource_id)
- if g.user_session.user_id == resource_info['owner_id']:
- return [resource_id, "owner"]
- else:
- return [resource_id, check_admin(resource_id)]
- else:
+ if not resource_id:
resource_id = get_resource_id(dataset, trait_id)
- if resource_id:
- resource_info = get_resource_info(resource_id)
- if g.user_session.user_id == resource_info['owner_id']:
- return [resource_id, "owner"]
- else:
- return [resource_id, check_admin(resource_id)]
+
+ if g.user_session.user_id in Redis.smembers("super_users"):
+ return [resource_id, "owner"]
+
+ resource_info = get_resource_info(resource_id)
+ if g.user_session.user_id == resource_info['owner_id']:
+ return [resource_id, "owner"]
+ else:
+ return [resource_id, check_admin(resource_id)]
return [resource_id, "not-admin"]
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index c6d221ff..9d09a66b 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -30,6 +30,7 @@ def is_redis_available():
def get_user_id(column_name, column_value):
user_list = Redis.hgetall("users")
+ key_list = []
for key in user_list:
user_ob = json.loads(user_list[key])
if column_name in user_ob and user_ob[column_name] == column_value:
@@ -62,6 +63,9 @@ def get_users_like_unique_column(column_name, column_value):
if column_name != "user_id":
for key in user_list:
user_ob = json.loads(user_list[key])
+ if "user_id" not in user_ob:
+ set_user_attribute(key, "user_id", key)
+ user_ob["user_id"] = key
if column_name in user_ob:
if column_value in user_ob[column_name]:
matched_users.append(user_ob)
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 9afc016b..24848ed8 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -19,8 +19,8 @@ def manage_groups():
if "add_new_group" in params:
return redirect(url_for('add_group'))
else:
- admin_groups, user_groups = get_user_groups(g.user_session.user_id)
- return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
+ admin_groups, member_groups = get_user_groups(g.user_session.user_id)
+ return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
@app.route("/groups/view", methods=('GET', 'POST'))
def view_group():
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index 70d55684..c8ed6851 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -10,18 +10,20 @@
<div class="container">
<div class="page-header">
<h1>Manage Groups</h1>
+ {% if admin_groups|length != 0 or member_groups|length != 0 %}
<div style="display: inline;">
<button type="button" id="create_group" class="btn btn-primary" data-url="/groups/create">Create Group</button>
<button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
</div>
+ {% endif %}
</div>
<form id="groups_form" action="/groups/manage" method="POST">
<input type="hidden" name="selected_group_ids" value="">
<div style="min-width: 800px; max-width: 1000px;">
- {% if admin_groups|length == 0 and user_groups|length == 0 %}
+ {% if admin_groups|length == 0 and member_groups|length == 0 %}
<h4>You currently aren't a member or admin of any groups.</h4>
<br>
- <button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
+ <button type="button" id="create_group" class="btn btn-primary" data-url="/groups/create">Create a new group</button>
{% else %}
<div style="margin-top: 20px;"><h2>Admin Groups</h2></div>
<hr>
@@ -60,10 +62,10 @@
<div style="min-width: 800px; max-width: 1000px;">
<div><h2>User Groups</h2></div>
<hr>
- {% if user_groups|length == 0 %}
+ {% if member_groups|length == 0 %}
<h4>You currently aren't a member of any groups.</h4>
{% else %}
- <table id="user_groups" class="table-hover table-striped cell-border" style="float: left;">
+ <table id="member_groups" class="table-hover table-striped cell-border" style="float: left;">
<thead>
<tr>
<th></th>
@@ -75,7 +77,7 @@
</tr>
</thead>
<tbody>
- {% for group in user_groups %}
+ {% for group in member_groups %}
<tr>
<td><input type="checkbox" name="read" value="{{ group.id }}"></td>
<td>{{ loop.index }}</td>
@@ -107,8 +109,8 @@
'sDom': 'tr'
});
{% endif %}
- {% if user_groups|length != 0 %}
- $('#user_groups').dataTable({
+ {% if member_groups|length != 0 %}
+ $('#member_groups').dataTable({
'sDom': 'tr'
});
{% endif %}
--
cgit v1.2.3
From 75802ed1f9e5d955987bf5f5eb78a9cb120116ec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:33:22 -0500
Subject: Added some admin functionality and fixed issue with temp traits
---
wqflask/base/trait.py | 17 ++++--
wqflask/base/webqtlConfig.py | 4 ++
wqflask/maintenance/set_resource_defaults.py | 20 +++++--
wqflask/utility/authentication_tools.py | 79 +++++++++++++++-------------
wqflask/wqflask/resource_manager.py | 6 +--
wqflask/wqflask/views.py | 20 ++++---
6 files changed, 90 insertions(+), 56 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7700ecd5..c2b8b910 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -42,11 +42,11 @@ def create_trait(**kw):
if kw.get('dataset_name') != "Temp":
if dataset.type == 'Publish':
- permitted = check_resource_availability(dataset, kw.get('name'))
+ permissions = check_resource_availability(dataset, kw.get('name'))
else:
- permitted = check_resource_availability(dataset)
+ permissions = check_resource_availability(dataset)
- if permitted != "no-access":
+ if "view" in permissions['data']:
the_trait = GeneralTrait(**kw)
if the_trait.dataset.type != "Temp":
@@ -382,9 +382,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
else:
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+ the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+
+ response = requests.get(the_url).content
+ if response.strip() == "no-access":
+ trait.view = False
+ return trait
+ else:
+ trait_info = json.loads(response)
try:
response = requests.get(the_url).content
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 55407123..3d86bc22 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -17,6 +17,10 @@ DEBUG = 1
#USER privilege
USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
+#Set privileges
+SUPER_PRIVILEGES = {'data': ['no-access', 'view', 'edit'], 'metadata': ['no-access', 'view', 'edit'], 'admin': ['not-admin', 'edit-access', 'edit-admins']}
+DEFAULT_PRIVILEGES = {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']}
+
#minimum number of informative strains
KMININFORMATIVE = 5
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 0c221bbf..ddb3b17b 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -68,9 +68,13 @@ def insert_probeset_resources(default_owner_id):
resource_ob['data'] = { "dataset" : str(resource[0])}
resource_ob['type'] = "dataset-probeset"
if resource[2] < 1 and resource[3] > 0:
- resource_ob['default_mask'] = { "data": "view" }
+ resource_ob['default_mask'] = { "data": "view",
+ "metadata": "view",
+ "admin": "not-admin"}
else:
- resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['default_mask'] = { "data": "no-access",
+ "metadata": "no-access",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob)
@@ -98,7 +102,9 @@ def insert_publish_resources(default_owner_id):
resource_ob['data'] = { "dataset" : str(resource[1]) ,
"trait" : str(resource[0])}
resource_ob['type'] = "dataset-publish"
- resource_ob['default_mask'] = { "data": "view" }
+ resource_ob['default_mask'] = { "data": "view",
+ "metadata": "view",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
@@ -124,9 +130,13 @@ def insert_geno_resources(default_owner_id):
resource_ob['data'] = { "dataset" : str(resource[0]) }
resource_ob['type'] = "dataset-geno"
if resource[2] < 1:
- resource_ob['default_mask'] = { "data": "view" }
+ resource_ob['default_mask'] = { "data": "view",
+ "metadata": "view",
+ "admin": "not-admin"}
else:
- resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['default_mask'] = { "data": "no-access",
+ "metadata": "no-access",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob)
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index dfa0e2d9..6c88949b 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division
import json
import requests
-from base import data_set
+from base import data_set, webqtlConfig
from utility import hmac
from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
@@ -18,45 +18,47 @@ def check_resource_availability(dataset, trait_id=None):
#ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
if g.user_session.user_id in Redis.smembers("super_users"):
- return "edit"
+ return webqtlConfig.SUPER_PRIVILEGES
- resource_id = get_resource_id(dataset, trait_id)
response = None
- if resource_id:
- resource_info = get_resource_info(resource_id)
-
- the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
- try:
- response = json.loads(requests.get(the_url).content)['data']
- except:
- response = resource_info['default_mask']['data']
- if 'edit' in response:
- return "edit"
- elif 'view' in response:
- return "view"
- else:
- return "no-access"
+ #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible
+ if type(dataset) == str:
+ return webqtlConfig.DEFAULT_PRIVILEGES
+ if dataset.type == "Temp":
+ return webqtlConfig.DEFAULT_PRIVILEGES
- return False
+ resource_id = get_resource_id(dataset, trait_id)
-def check_admin(resource_id=None):
+ if resource_id:
+ resource_info = get_resource_info(resource_id)
+ else:
+ return response #ZS: Need to substitute in something that creates the resource in Redis later
- return "not-admin"
+ the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ try:
+ response = json.loads(requests.get(the_url).content)
+ except:
+ response = resource_info['default_mask']
- # ZS: commented out until proxy can return this
- # the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
- # try:
- # response = json.loads(requests.get(the_url).content)
- # except:
- # response = resource_info['default_mask']['admin']
+ if response:
+ return response
+ else: #ZS: No idea how this would happen, but just in case
+ return False
- # if 'edit-admins' in response:
- # return "edit-admins"
- # elif 'edit-access' in response:
- # return "edit-access"
- # else:
- # return "not-admin"
+def check_admin(resource_id=None):
+ the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ try:
+ response = json.loads(requests.get(the_url).content)['admin']
+ except:
+ response = resource_info['default_mask']['admin']
+
+ if 'edit-admins' in response:
+ return "edit-admins"
+ elif 'edit-access' in response:
+ return "edit-access"
+ else:
+ return "not-admin"
def check_owner(dataset=None, trait_id=None, resource_id=None):
if resource_id:
@@ -74,15 +76,18 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
if not resource_id:
- resource_id = get_resource_id(dataset, trait_id)
+ if dataset.type == "Temp":
+ return "not-admin"
+ else:
+ resource_id = get_resource_id(dataset, trait_id)
if g.user_session.user_id in Redis.smembers("super_users"):
- return [resource_id, "owner"]
+ return "owner"
resource_info = get_resource_info(resource_id)
if g.user_session.user_id == resource_info['owner_id']:
- return [resource_id, "owner"]
+ return "owner"
else:
- return [resource_id, check_admin(resource_id)]
+ return check_admin(resource_id)
- return [resource_id, "not-admin"]
\ No newline at end of file
+ return "not-admin"
\ No newline at end of file
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 0f9f5c9d..39a07310 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -18,7 +18,7 @@ def manage_resource():
params = request.form if request.form else request.args
if 'resource_id' in request.args:
resource_id = request.args['resource_id']
- admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+ admin_status = check_owner_or_admin(resource_id=resource_id)
resource_info = get_resource_info(resource_id)
group_masks = resource_info['group_masks']
@@ -67,7 +67,7 @@ def search_for_groups():
def change_owner():
resource_id = request.form['resource_id']
if 'new_owner' in request.form:
- admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+ admin_status = check_owner_or_admin(resource_id=resource_id)
if admin_status == "owner":
new_owner_id = request.form['new_owner']
change_resource_owner(resource_id, new_owner_id)
@@ -100,7 +100,7 @@ def change_default_privileges():
@app.route("/resources/add_group", methods=('POST',))
def add_group_to_resource():
resource_id = request.form['resource_id']
- admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+ admin_status = check_owner_or_admin(resource_id=resource_id)
if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access":
if 'selected_group' in request.form:
group_id = request.form['selected_group']
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index dc431aa9..bc01839b 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -96,13 +96,21 @@ def check_access_permissions():
pass
else:
if 'dataset' in request.args:
- dataset = create_dataset(request.args['dataset'])
- if 'trait_id' in request.args:
- available = check_resource_availability(dataset, request.args['trait_id'])
+ if request.args['dataset'] == "Temp":
+ permissions = check_resource_availability("Temp")
else:
- available = check_resource_availability(dataset)
-
- if available == "no-access":
+ dataset = create_dataset(request.args['dataset'])
+
+ if dataset.type == "Temp":
+ permissions = False
+ if 'trait_id' in request.args:
+ permissions = check_resource_availability(dataset, request.args['trait_id'])
+ elif dataset.type != "Publish":
+ permissions = check_resource_availability(dataset)
+ else:
+ return None
+
+ if 'view' not in permissions['data']:
return redirect(url_for("no_access_page"))
@app.teardown_appcontext
--
cgit v1.2.3
From 51417c06061246bc92be89db198b3e74e7126035 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:47:38 -0500
Subject: Fixed ports for proxy (though I need to add the port to global
variables) and also simplified the check_owner_or_admin function a little
---
wqflask/base/trait.py | 4 ++--
wqflask/utility/authentication_tools.py | 4 ++--
wqflask/wqflask/show_trait/show_trait.py | 3 ++-
wqflask/wqflask/templates/show_trait_details.html | 4 ++--
4 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index c2b8b910..0e26ca2c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -382,9 +382,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
- the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
else:
- the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+ the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
response = requests.get(the_url).content
if response.strip() == "no-access":
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 6c88949b..06b2854a 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -35,7 +35,7 @@ def check_resource_availability(dataset, trait_id=None):
else:
return response #ZS: Need to substitute in something that creates the resource in Redis later
- the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
try:
response = json.loads(requests.get(the_url).content)
except:
@@ -47,7 +47,7 @@ def check_resource_availability(dataset, trait_id=None):
return False
def check_admin(resource_id=None):
- the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
try:
response = json.loads(requests.get(the_url).content)['admin']
except:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index ed4ff0ad..4698807a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -72,7 +72,8 @@ class ShowTrait(object):
cellid=None)
self.trait_vals = Redis.get(self.trait_id).split()
- self.admin_status = check_owner_or_admin(self.dataset, self.trait_id)
+ self.resource_id = get_resource_id(self.dataset, self.trait_id)
+ self.admin_status = check_owner_or_admin(resource_id=self.resource_id)
#ZS: Get verify/rna-seq link URLs
try:
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 5e0bae79..965c0340 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -248,8 +248,8 @@
<a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
<button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
</a>
- {% if admin_status[1] == "owner" or admin_status[1] == "edit-admins" or admin_status[1] == "edit-access" %}
- <a target="_blank" href="./resources/manage?resource_id={{ admin_status[0] }}">
+ {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+ <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
<button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
</a>
{% endif %}
--
cgit v1.2.3
From a13e2c5856acd05610a5966d3f8ecc17038e4735 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:53:51 -0500
Subject: Missed one issue introduced by last commit
---
wqflask/wqflask/show_trait/show_trait.py | 10 +++++++---
1 file changed, 7 insertions(+), 3 deletions(-)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 4698807a..5fc69cab 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -49,18 +49,23 @@ class ShowTrait(object):
self.temp_trait = False
self.trait_id = kw['trait_id']
helper_functions.get_species_dataset_trait(self, kw)
+ self.resource_id = get_resource_id(self.dataset, self.trait_id)
+ self.admin_status = check_owner_or_admin(resource_id=self.resource_id)
elif 'group' in kw:
self.temp_trait = True
self.trait_id = "Temp_"+kw['species']+ "_" + kw['group'] + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
self.temp_species = kw['species']
self.temp_group = kw['group']
self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = self.temp_group)
+
# Put values in Redis so they can be looked up later if added to a collection
Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR)
self.trait_vals = kw['trait_paste'].split()
self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
+
+ self.admin_status = check_owner_or_admin(dataset=self.dataset, trait_id=self.trait_id)
else:
self.temp_trait = True
self.trait_id = kw['trait_id']
@@ -70,10 +75,9 @@ class ShowTrait(object):
self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
cellid=None)
- self.trait_vals = Redis.get(self.trait_id).split()
- self.resource_id = get_resource_id(self.dataset, self.trait_id)
- self.admin_status = check_owner_or_admin(resource_id=self.resource_id)
+ self.trait_vals = Redis.get(self.trait_id).split()
+ self.admin_status = check_owner_or_admin(dataset=self.dataset, trait_id=self.trait_id)
#ZS: Get verify/rna-seq link URLs
try:
--
cgit v1.2.3
From 01c3acf485de10fb1696fc24471751d4d3ab8e05 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 22 Jun 2020 13:30:01 -0500
Subject: Fixed issue with temp traits not working for trait page functions
like correlation or mapping
---
wqflask/base/data_set.py | 3 +++
wqflask/wqflask/static/new/javascript/show_trait.js | 3 ++-
wqflask/wqflask/views.py | 5 ++++-
3 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 92dc8615..2272b6ee 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -65,6 +65,9 @@ logger = getLogger(__name__ )
DS_NAME_MAP = {}
def create_dataset(dataset_name, dataset_type = None, get_samplelist = True, group_name = None):
+ if dataset_name == "Temp":
+ dataset_type = "Temp"
+
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c0b2e6db..738cd536 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -515,7 +515,8 @@ $('select[name=corr_type]').change(on_corr_method_change);
submit_special = function(url) {
$("#trait_data_form").attr("action", url);
- return $("#trait_data_form").submit();
+ $("#trait_data_form").submit();
+ return false
};
var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index bc01839b..80164a22 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -641,7 +641,10 @@ def loading_page():
if 'num_vals' in start_vars:
num_vals = int(start_vars['num_vals'])
else:
- dataset = create_dataset(start_vars['dataset'])
+ if 'group' in start_vars:
+ dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
+ else:
+ dataset = create_dataset(start_vars['dataset'])
genofile_samplelist = []
samples = start_vars['primary_samples'].split(",")
if 'genofile' in start_vars:
--
cgit v1.2.3
From 10a281056b19ee150b471afdf016251d5f9ead32 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 23 Jun 2020 17:25:54 -0500
Subject: Changed back previous 'fix' that was intended to fix issue where two
tabs were opened when doing mapping/correlations; apparently this is a chrome
specific problem so it will need to be deal twiht differently
---
wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js | 2 +-
wqflask/wqflask/static/new/javascript/show_trait.js | 1 -
wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 1 -
3 files changed, 1 insertion(+), 3 deletions(-)
diff --git a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
index 8cd6dac3..934cc14d 100644
--- a/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
+++ b/wqflask/wqflask/static/new/javascript/get_covariates_from_collection.js
@@ -110,7 +110,7 @@ submit_click = function() {
trait_click = function() {
var dataset, this_trait_url, trait;
trait = $(this).parent().find('.trait').text();
- dataset = $(this).parent().find('.dataset').text();
+ dataset = $(this).parent().find('.dataset').data("dataset");
$("input[name=covariates]").val(trait + ":" + dataset)
$(".selected_covariates").text(trait)
return $.colorbox.close();
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 738cd536..c0784073 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -516,7 +516,6 @@ $('select[name=corr_type]').change(on_corr_method_change);
submit_special = function(url) {
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit();
- return false
};
var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index db17af40..4dce0705 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -5,7 +5,6 @@
submit_special = function(url) {
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit();
- return false;
};
update_time_remaining = function(percent_complete) {
--
cgit v1.2.3
From 9b1aecdbb51c7cb843ca79ab430d8dc2b9d3767e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 24 Jun 2020 15:35:47 -0500
Subject: Fixed issue where scatterplot had different N than correlation
results + fixed some aesthetic issues with correlatoin results table
---
wqflask/wqflask/correlation/corr_scatter_plot.py | 23 ++++++++++++++++-------
wqflask/wqflask/templates/correlation_page.html | 24 ++++++++----------------
2 files changed, 24 insertions(+), 23 deletions(-)
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 04ec427d..819836b1 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -4,7 +4,7 @@ import math
from flask import g
-from base.trait import create_trait
+from base.trait import create_trait, retrieve_sample_data
from base import data_set
from utility import corr_result_helpers
from scipy import stats
@@ -17,12 +17,21 @@ class CorrScatterPlot(object):
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
- self.data_set_1 = data_set.create_dataset(params['dataset_1'])
- self.data_set_2 = data_set.create_dataset(params['dataset_2'])
- #self.data_set_3 = data_set.create_dataset(params['dataset_3'])
- self.trait_1 = create_trait(name=params['trait_1'], dataset=self.data_set_1)
- self.trait_2 = create_trait(name=params['trait_2'], dataset=self.data_set_2)
- #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.data_set_3)
+ self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+ self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+ #self.dataset_3 = data_set.create_dataset(params['dataset_3'])
+ self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
+ self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
+ #self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3)
+
+ primary_samples = self.dataset_1.group.samplelist
+ if self.dataset_1.group.parlist != None:
+ primary_samples += self.dataset_1.group.parlist
+ if self.dataset_1.group.f1list != None:
+ primary_samples += self.dataset_1.group.f1list
+
+ self.trait_1 = retrieve_sample_data(self.trait_1, self.dataset_1, primary_samples)
+ self.trait_2 = retrieve_sample_data(self.trait_2, self.dataset_2, primary_samples)
samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 71705390..f429948d 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -4,6 +4,7 @@
<link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
<link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+ <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
{% endblock %}
{% block content %}
<div class="container" style="min-width: 1250px;">
@@ -114,8 +115,8 @@
<div style="margin-bottom: 5px;">
<b>Show/Hide Columns:</b>
</div>
- <div style="width: {% if target_dataset.type == "ProbeSet" %}1600px{% elif target_dataset.type == "Publish" %}1400px{% else %}800px{% endif %};">
- <table id="trait_table" class="display dataTable nowrap" style="font-size: 12px; float: left;">
+ <div style="width: 100%; min-width: {% if target_dataset.type == "ProbeSet" %}1700px{% elif target_dataset.type == "Publish" %}1600px{% else %}600px{% endif %};">
+ <table id="trait_table" class="table-hover table-striped cell-border" style="float: left;">
<thead>
<tr>
<th></th>
@@ -143,7 +144,7 @@
<td data-export="{{ trait.description_display }}">{{ trait.description_display }}</TD>
<td data-export="{{ trait.location_repr }}" style="white-space: nowrap;">{{ trait.location_repr }}</td>
<td data-export="{{ '%0.3f' % trait.mean|float }}" align="right">{{ '%0.3f' % trait.mean|float }}</td>
- <td data-export="{{ '%0.3f'|format(trait.sample_r) }} align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
+ <td data-export="{{ '%0.3f'|format(trait.sample_r) }}"" align="right"><a target="_blank" href="corr_scatter_plot?dataset_1={{dataset.name}}&dataset_2={{trait.dataset.name}}&trait_1={{this_trait.name}}&trait_2={{trait.name}}">{{ '%0.3f'|format(trait.sample_r) }}</a></td>
<td data-export="{{ trait.num_overlap }}" align="right">{{ trait.num_overlap }}</td>
<td data-export="{{ '%0.3e'|format(trait.sample_p) }}" align="right">{{ '%0.3e'|format(trait.sample_p) }}</td>
{% if trait.lit_corr == "" or trait.lit_corr == 0.000 %}
@@ -167,8 +168,8 @@
{% else %}
<TD data-export="N/A">N/A</TD>
{% endif %}
- <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 50 %}{{ trait.description_display[:50] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
- <td data-export="{{ trait.authors }}">{{ trait.authors }}</td>
+ <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
+ <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
<td data-export="{{ trait.pubmed_text }}">
<a href="{{ trait.pubmed_link }}">
{{ trait.pubmed_text }}
@@ -211,7 +212,6 @@
</script>
<script type="text/javascript" charset="utf-8">
-
$.fn.dataTable.ext.order['dom-innertext'] = function (settings, col) {
return this.api().column(col, { order: 'index' }).nodes().map(function (td, i) {
return Math.abs(parseFloat($('a', td).text()));
@@ -424,16 +424,8 @@
{ "type": "natural" }
],
"createdRow": function ( row, data, index ) {
- $('td', row).eq(3).attr('title', $('td', row).eq(3).text());
- if ($('td', row).eq(3).text().length > 50) {
- $('td', row).eq(3).text($('td', row).eq(3).text().substring(0, 50));
- $('td', row).eq(3).text($('td', row).eq(3).text() + '...')
- }
- $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
- if ($('td', row).eq(4).text().length > 40) {
- $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 40));
- $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
- }
+ $('td', row).eq(4).text(decodeURIComponent(escape($('td', row).eq(4).text())));
+ $('td', row).eq(5).text(decodeURIComponent(escape($('td', row).eq(5).text())));
},
"order": [[9, "asc" ]],
"sDom": "Btir",
--
cgit v1.2.3
From 645c07b98aae9508e8a0aeedd8eaca815d5daf54 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 24 Jun 2020 17:13:45 -0500
Subject: Temporary partial fix to issue of resources without info; need to add
something that automatically inserts resources with default privileges
---
wqflask/base/trait.py | 12 ++++--------
wqflask/utility/authentication_tools.py | 11 +++++++----
wqflask/utility/redis_tools.py | 5 ++++-
wqflask/wqflask/correlation/show_corr_results.py | 7 +++----
wqflask/wqflask/templates/correlation_page.html | 4 ++++
5 files changed, 22 insertions(+), 17 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 0e26ca2c..7fc016f3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -386,13 +386,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
- response = requests.get(the_url).content
- if response.strip() == "no-access":
- trait.view = False
- return trait
- else:
- trait_info = json.loads(response)
-
try:
response = requests.get(the_url).content
if response.strip() == "no-access":
@@ -402,7 +395,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait_info = json.loads(response)
except:
resource_info = get_resource_info(resource_id)
- default_permissions = resource_info['default_mask']['data']
+ if resource_info:
+ default_permissions = resource_info['default_mask']['data']
+ else:
+ default_permissions = webqtlConfig.DEFAULT_PRIVILEGES
if 'view' not in default_permissions:
trait.view = False
return trait
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 06b2854a..f9028f32 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -32,6 +32,8 @@ def check_resource_availability(dataset, trait_id=None):
if resource_id:
resource_info = get_resource_info(resource_id)
+ if not resource_info:
+ return webqtlConfig.DEFAULT_PRIVILEGES
else:
return response #ZS: Need to substitute in something that creates the resource in Redis later
@@ -85,9 +87,10 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
return "owner"
resource_info = get_resource_info(resource_id)
- if g.user_session.user_id == resource_info['owner_id']:
- return "owner"
- else:
- return check_admin(resource_id)
+ if resource_info:
+ if g.user_session.user_id == resource_info['owner_id']:
+ return "owner"
+ else:
+ return check_admin(resource_id)
return "not-admin"
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 9d09a66b..8a5f95ee 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -280,7 +280,10 @@ def get_resource_id(dataset, trait_id=None):
def get_resource_info(resource_id):
resource_info = Redis.hget("resources", resource_id)
- return json.loads(resource_info)
+ if resource_info:
+ return json.loads(resource_info)
+ else:
+ return None
def add_resource(resource_info):
if 'trait' in resource_info['data']:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7eab7184..bc2912f2 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -200,8 +200,6 @@ class CorrelationResults(object):
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
- if not trait_object:
- continue
if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
#ZS: Convert trait chromosome to an int for the location range option
@@ -237,9 +235,8 @@ class CorrelationResults(object):
trait_object.tissue_pvalue = tissue_corr_data[trait][2]
elif self.corr_type == "lit":
trait_object.lit_corr = lit_corr_data[trait][1]
- self.correlation_results.append(trait_object)
- self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species)
+ self.correlation_results.append(trait_object)
if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
self.do_lit_correlation_for_trait_list()
@@ -498,6 +495,8 @@ def do_bicor(this_trait_vals, target_trait_vals):
def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False):
results_list = []
for i, trait in enumerate(corr_results):
+ if trait.view == False:
+ continue
results_dict = {}
if not for_api:
results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + hmac.hmac_creation('{}:{}'.format(trait.name, trait.dataset.name)) + "'>"
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index f429948d..3d750bea 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -169,7 +169,11 @@
<TD data-export="N/A">N/A</TD>
{% endif %}
<td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
+ {% if trait.authors %}
<td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
+ {% else %}
+ <TD data-export="N/A">N/A</TD>
+ {% endif %}
<td data-export="{{ trait.pubmed_text }}">
<a href="{{ trait.pubmed_link }}">
{{ trait.pubmed_text }}
--
cgit v1.2.3
From 297391cd25c5ec5bcb72de9636e1a08f32175a6a Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 26 Jun 2020 14:42:08 -0500
Subject: Changed drop-down menus to include type sub-categories
---
wqflask/wqflask/api/gen_menu.py | 8 +++---
.../new/javascript/dataset_select_menu_orig.js | 32 ++++++++++++++++++++++
2 files changed, 36 insertions(+), 4 deletions(-)
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index bdcc3bf7..cfce0c8e 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -68,12 +68,12 @@ def get_types(groups):
types[species] = {}
for group_name, _group_full_name, _family_name in group_dict:
if phenotypes_exist(group_name):
- types[species][group_name] = [("Phenotypes", "Phenotypes")]
+ types[species][group_name] = [("Phenotypes", "Traits and Cofactors", "Phenotypes")]
if genotypes_exist(group_name):
if group_name in types[species]:
- types[species][group_name] += [("Genotypes", "Genotypes")]
+ types[species][group_name] += [("Genotypes", "DNA Markers and SNPs", "Genotypes")]
else:
- types[species][group_name] = [("Genotypes", "Genotypes")]
+ types[species][group_name] = [("Genotypes", "DNA Markers and SNPs", "Genotypes")]
if group_name in types[species]:
types_list = build_types(species, group_name)
if len(types_list) > 0:
@@ -134,7 +134,7 @@ def build_types(species, group):
if len(result):
these_datasets = build_datasets(species, group, result[0])
if len(these_datasets) > 0:
- results.append([str(result[0]), str(result[0])])
+ results.append([str(result[0]), str(result[0]), "Molecular Trait Datasets"])
return results
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index ee7be68c..d5711f6d 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -94,6 +94,37 @@ redo_dropdown = function(dropdown, items) {
_results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
}
}
+ } else if (dropdown.attr('id') == "type"){
+ type_family_list = [];
+ for (_i = 0, _len = items.length; _i < _len; _i++) {
+ item = items[_i];
+ type_family_list.push([item[0], item[1], item[2]])
+ }
+
+ current_family = ""
+ this_opt_group = null
+ for (_i = 0, _len = type_family_list.length; _i < _len; _i++) {
+ item = type_family_list[_i];
+ if (item[2] != "None" && current_family == ""){
+ current_family = item[2]
+ this_opt_group = $("<optgroup label=\"" + item[2] + "\">")
+ this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ } else if (current_family != "" && item[2] == current_family){
+ this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == type_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
+ } else if (current_family != "" && item[2] != current_family && item[2] != "None"){
+ current_family = item[2]
+ _results.push(dropdown.append(this_opt_group))
+ this_opt_group = $("<optgroup label=\"" + current_family + "\">")
+ this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ } else {
+ _results.push(dropdown.append(this_opt_group))
+ current_family = ""
+ _results.push(dropdown.append($("<option />").val(item[0]).text(item[1])));
+ }
+ }
} else {
for (_i = 0, _len = items.length; _i < _len; _i++) {
item = items[_i];
@@ -104,6 +135,7 @@ redo_dropdown = function(dropdown, items) {
}
}
}
+
return _results;
};
$('#species').change((function(_this) {
--
cgit v1.2.3
From e100f2dd564044006f09e94276a98607856f1c8f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 26 Jun 2020 14:45:35 -0500
Subject: Fixed issue where option to add members to an existing group was in
the wrong place
---
wqflask/wqflask/templates/admin/view_group.html | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html
index b797cd70..9e3cce7b 100644
--- a/wqflask/wqflask/templates/admin/view_group.html
+++ b/wqflask/wqflask/templates/admin/view_group.html
@@ -44,7 +44,7 @@
<tr>
<td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="admin_id" value="{{ admin.user_id }}"></td>
<td align="right">{{ loop.index }}</td>
- <td>{% if 'full_name' in admin %}{{ admin.full_name }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'full_name' in admin %}{{ admin.full_name }}{% elif 'name' in admin %}{{ admin.name }}{% else %}N/A{% endif %}</td>
<td>{% if 'email_address' in admin %}{{ admin.email_address }}{% else %}N/A{% endif %}</td>
<td>{% if 'organization' in admin %}{{ admin.organization }}{% else %}N/A{% endif %}</td>
</tr>
@@ -81,7 +81,7 @@
<tr>
<td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="member_id" value="{{ member.user_id }}"></td>
<td align="right">{{ loop.index }}</td>
- <td>{% if 'full_name' in member %}{{ member.full_name }}{% else %}N/A{% endif %}</td>
+ <td>{% if 'full_name' in member %}{{ member.full_name }}{% elif 'name' in admin %}{{ admin.name }}{% else %}N/A{% endif %}</td>
<td>{% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %}</td>
<td>{% if 'organization' in member %}{{ member.organization }}{% else %}N/A{% endif %}</td>
</tr>
@@ -99,6 +99,15 @@
{% endif %}
{% else %}
There are currently no members in this group.
+ {% if user_is_admin == true %}
+ <div style="margin-top: 20px;">
+ <span>E-mail of user to add to members (multiple e-mails can be added separated by commas):</span>
+ <input type="text" size="60" name="member_emails_to_add" placeholder="Enter E-mail(s)" value="">
+ </div>
+ <div style="margin-bottom: 30px; margin-top: 20px;">
+ <button type="button" id="add_members" class="btn btn-primary" data-usertype="member" data-url="/groups/add_members">Add Member(s)</button>
+ </div>
+ {% endif %}
{% endif %}
</div>
</div>
--
cgit v1.2.3
From 7e683d7d3f770b2d30c4b2a3c0e1f1c4fd4d75b5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 26 Jun 2020 14:46:28 -0500
Subject: Changed buttons to inputs on trait page to fix issue with Chrome
opening two tabs
---
.../wqflask/templates/show_trait_calculate_correlations.html | 4 +---
wqflask/wqflask/templates/show_trait_mapping_tools.html | 12 +++---------
2 files changed, 4 insertions(+), 12 deletions(-)
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 297d62ce..a9b371b8 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -109,9 +109,7 @@
<div class="form-group">
<label for="corr_sample_method" class="col-xs-2 control-label"></label>
<div class="col-xs-3 controls">
- <button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation">
- <i class="icon-ok-circle icon-white"></i> Compute
- </button>
+ <input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
</div>
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index e851a81e..4d51adff 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -90,9 +90,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
- Compute
- </button>
+ <input type="button" id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">
</div>
</div>
</div>
@@ -226,9 +224,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
- Compute
- </button>
+ <input type="button" id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping" value="Compute">
</div>
</div>
</div>
@@ -391,9 +387,7 @@
<div class="mapping_method_fields form-group">
<label class="col-xs-3 control-label"></label>
<div style="margin-left:20px;" class="col-xs-6">
- <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
- Compute
- </button>
+ <input type="button" id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression" value="Compute">
</div>
</div>
</div>
--
cgit v1.2.3
From aa06c83ecd4d36878ac0aadd75ab2bd461f44344 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 26 Jun 2020 14:47:10 -0500
Subject: Removed collections with zero members from list and count of user
collections
---
wqflask/wqflask/templates/collections/list.html | 2 ++
wqflask/wqflask/user_session.py | 2 +-
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index c8705c7d..94e22c4d 100644
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -42,6 +42,7 @@
<tbody>
{% for uc in collections %}
+ {% if uc.num_members > 0 %}
<tr class="collection_line">
<td align="center" style="padding: 0px;"><INPUT TYPE="checkbox" NAME="collection" class="checkbox trait_checkbox" VALUE="{{ uc.id }}"></td>
<td align="right">{{ loop.index }}
@@ -50,6 +51,7 @@
<td>{{ uc.changed_timestamp }}</td>
<td align="right">{{ uc.num_members }}</td>
</tr>
+ {% endif %}
{% endfor %}
</tbody>
</table>
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index ec6d4ae3..ba659fe5 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -167,7 +167,7 @@ class UserSession(object):
def num_collections(self):
"""Number of user's collections"""
- return len(self.user_collections)
+ return len([item for item in self.user_collections if item['num_members'] > 0])
def add_collection(self, collection_name, traits):
"""Add collection into Redis"""
--
cgit v1.2.3
From cef130716782cf5c06453705bee7ab6aed1dcce0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Jun 2020 12:19:23 -0500
Subject: Change that hopefully fixes some encoding stuff
---
wqflask/base/trait.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7fc016f3..5903fb08 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -6,6 +6,7 @@ import resource
import codecs
import requests
import random
+import urllib
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
@@ -144,6 +145,7 @@ class GeneralTrait(object):
formatted = self.post_publication_description
else:
formatted = "Not available"
+
return formatted
@property
@@ -474,9 +476,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.haveinfo = True
for i, field in enumerate(dataset.display_fields):
- holder = trait_info[i]
- #if isinstance(trait_info[i], basestring):
- # holder = holder.encode('latin1')
+ holder = trait_info[i]
+ if isinstance(trait_info[i], basestring):
+ holder = holder.encode('latin1')
setattr(trait, field, holder)
if dataset.type == 'Publish':
--
cgit v1.2.3
From f1a539098884eb99191809dac7fba823872270ae Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Jun 2020 12:45:47 -0500
Subject: Loading screen should now show correct N when re-mapping or zooming
into a map
---
wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +-
wqflask/wqflask/marker_regression/run_mapping.py | 5 ++++-
wqflask/wqflask/templates/loading.html | 2 +-
wqflask/wqflask/templates/mapping_results.html | 4 ++--
wqflask/wqflask/views.py | 12 ++++++------
5 files changed, 14 insertions(+), 11 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 74fa4329..89f56c30 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -147,7 +147,7 @@ class DisplayMappingResults(object):
self.dataset = start_vars['dataset']
self.this_trait = start_vars['this_trait']
- self.n_samples = start_vars['num_vals']
+ self.n_samples = start_vars['n_samples']
self.species = start_vars['species']
self.genofile_string = ""
if 'genofile_string' in start_vars:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c859fdaa..c9d10f7c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -124,7 +124,10 @@ class RunMapping(object):
self.samples.append(sample)
self.vals.append(value)
- self.num_vals = len(self.vals)
+ if 'n_samples' in start_vars:
+ self.n_samples = start_vars['n_samples']
+ else:
+ self.n_samples = len([val for val in self.vals if val != "x"])
#ZS: Check if genotypes exist in the DB in order to create links for markers
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 49bcbff7..15ab4080 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -11,7 +11,7 @@
{% if start_vars.tool_used == "Mapping" %}
<h1>Computing the Maps</h1>
<br>
- <i>n</i> = {{ start_vars.num_vals }}
+ <i>n</i> = {{ start_vars.n_samples }}
<br>
Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
<br>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index c5d49168..132d5249 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -35,7 +35,7 @@
{% for sample in samples %}
<input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
{% endfor %}
- <input type="hidden" name="num_vals" value="{{ n_samples }}">
+ <input type="hidden" name="n_samples" value="{{ n_samples }}">
<input type="hidden" name="maf" value="{{ maf }}">
<input type="hidden" name="use_loco" value="{{ use_loco }}">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
@@ -435,7 +435,7 @@
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
- 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'num_vals']
+ 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples']
$('input[name=wanted_inputs]').val(mapping_input_list.join(","));
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 80164a22..131345d3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -630,7 +630,7 @@ def loading_page():
logger.info(request.url)
initial_start_vars = request.form
start_vars_container = {}
- num_vals = 0 #ZS: So it can be displayed on loading page
+ n_samples = 0 #ZS: So it can be displayed on loading page
if 'wanted_inputs' in initial_start_vars:
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
@@ -638,8 +638,8 @@ def loading_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- if 'num_vals' in start_vars:
- num_vals = int(start_vars['num_vals'])
+ if 'n_samples' in start_vars:
+ n_samples = int(start_vars['n_samples'])
else:
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
@@ -658,9 +658,9 @@ def loading_page():
for sample in samples:
value = start_vars.get('value:' + sample)
if value != "x":
- num_vals += 1
+ n_samples += 1
- start_vars['num_vals'] = num_vals
+ start_vars['n_samples'] = n_samples
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
start_vars_container['start_vars'] = start_vars
@@ -730,7 +730,7 @@ def mapping_results_page():
'mapmodel_rqtl_geno',
'temp_trait',
'reaper_version',
- 'num_vals',
+ 'n_samples',
'transform'
)
start_vars = {}
--
cgit v1.2.3
From b7d3b90bb9a074200e440eaeb22b782053efc819 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 29 Jun 2020 12:55:13 -0500
Subject: Fixed remaining issue with the logic for creating the type dropdown
option groups for the home page search
---
wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js | 3 +++
1 file changed, 3 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index d5711f6d..d172907a 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -119,6 +119,9 @@ redo_dropdown = function(dropdown, items) {
_results.push(dropdown.append(this_opt_group))
this_opt_group = $("<optgroup label=\"" + current_family + "\">")
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == type_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
} else {
_results.push(dropdown.append(this_opt_group))
current_family = ""
--
cgit v1.2.3
From 0a0d733af4b6c61c381a1c4ec9fa162182a057e9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Jul 2020 14:47:04 -0500
Subject: Fixed some of the logic with how traits are authenticated to avoid
situation where a trait is authenticated twice
---
wqflask/base/trait.py | 30 ++++++++--------------------
wqflask/maintenance/set_resource_defaults.py | 6 +++---
wqflask/utility/redis_tools.py | 5 +++--
3 files changed, 14 insertions(+), 27 deletions(-)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7fc016f3..4c3e790c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -49,7 +49,6 @@ def create_trait(**kw):
if "view" in permissions['data']:
the_trait = GeneralTrait(**kw)
if the_trait.dataset.type != "Temp":
-
the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
return the_trait
else:
@@ -144,6 +143,7 @@ class GeneralTrait(object):
formatted = self.post_publication_description
else:
formatted = "Not available"
+
return formatted
@property
@@ -388,27 +388,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
try:
response = requests.get(the_url).content
- if response.strip() == "no-access":
- trait.view = False
- return trait
- else:
- trait_info = json.loads(response)
- except:
- resource_info = get_resource_info(resource_id)
- if resource_info:
- default_permissions = resource_info['default_mask']['data']
- else:
- default_permissions = webqtlConfig.DEFAULT_PRIVILEGES
- if 'view' not in default_permissions:
- trait.view = False
- return trait
-
+ trait_info = json.loads(response)
+ except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
if dataset.type == 'Publish':
query = """
SELECT
- PublishXRef.Id, Publication.PubMed_ID,
+ PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
@@ -472,11 +459,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait_info:
trait.haveinfo = True
-
for i, field in enumerate(dataset.display_fields):
- holder = trait_info[i]
- #if isinstance(trait_info[i], basestring):
- # holder = holder.encode('latin1')
+ holder = trait_info[i]
+ # if isinstance(trait_info[i], basestring):
+ # holder = unicode(holder.strip(codecs.BOM_UTF8), 'utf-8', "ignore")
setattr(trait, field, holder)
if dataset.type == 'Publish':
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index ddb3b17b..54fd8e7e 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -77,7 +77,7 @@ def insert_probeset_resources(default_owner_id):
"admin": "not-admin"}
resource_ob['group_masks'] = {}
- add_resource(resource_ob)
+ add_resource(resource_ob, update=False)
def insert_publish_resources(default_owner_id):
current_resources = Redis.hgetall("resources")
@@ -108,7 +108,7 @@ def insert_publish_resources(default_owner_id):
resource_ob['group_masks'] = {}
- add_resource(resource_ob)
+ add_resource(resource_ob, update=False)
else:
continue
@@ -139,7 +139,7 @@ def insert_geno_resources(default_owner_id):
"admin": "not-admin"}
resource_ob['group_masks'] = {}
- add_resource(resource_ob)
+ add_resource(resource_ob, update=False)
def insert_resources(default_owner_id):
current_resources = get_resources()
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 8a5f95ee..6c912a23 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -285,13 +285,14 @@ def get_resource_info(resource_id):
else:
return None
-def add_resource(resource_info):
+def add_resource(resource_info, update=True):
if 'trait' in resource_info['data']:
resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
else:
resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
- Redis.hset("resources", resource_id, json.dumps(resource_info))
+ if not Redis.hexists("resources", resource_id):
+ Redis.hset("resources", resource_id, json.dumps(resource_info))
return resource_info
--
cgit v1.2.3
From 445d976eed7dad4f94febe2b6c768ef6aa1e5acd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Jul 2020 14:48:32 -0500
Subject: Fixed issue where the N on the mapping loading page would sometimes
be wrong when reloading the page or zooming in, etc
---
wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +-
wqflask/wqflask/marker_regression/run_mapping.py | 5 ++++-
wqflask/wqflask/templates/loading.html | 2 +-
wqflask/wqflask/templates/mapping_results.html | 4 ++--
wqflask/wqflask/views.py | 12 ++++++------
5 files changed, 14 insertions(+), 11 deletions(-)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 74fa4329..89f56c30 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -147,7 +147,7 @@ class DisplayMappingResults(object):
self.dataset = start_vars['dataset']
self.this_trait = start_vars['this_trait']
- self.n_samples = start_vars['num_vals']
+ self.n_samples = start_vars['n_samples']
self.species = start_vars['species']
self.genofile_string = ""
if 'genofile_string' in start_vars:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c859fdaa..c9d10f7c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -124,7 +124,10 @@ class RunMapping(object):
self.samples.append(sample)
self.vals.append(value)
- self.num_vals = len(self.vals)
+ if 'n_samples' in start_vars:
+ self.n_samples = start_vars['n_samples']
+ else:
+ self.n_samples = len([val for val in self.vals if val != "x"])
#ZS: Check if genotypes exist in the DB in order to create links for markers
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 49bcbff7..15ab4080 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -11,7 +11,7 @@
{% if start_vars.tool_used == "Mapping" %}
<h1>Computing the Maps</h1>
<br>
- <i>n</i> = {{ start_vars.num_vals }}
+ <i>n</i> = {{ start_vars.n_samples }}
<br>
Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
<br>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index c5d49168..132d5249 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -35,7 +35,7 @@
{% for sample in samples %}
<input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
{% endfor %}
- <input type="hidden" name="num_vals" value="{{ n_samples }}">
+ <input type="hidden" name="n_samples" value="{{ n_samples }}">
<input type="hidden" name="maf" value="{{ maf }}">
<input type="hidden" name="use_loco" value="{{ use_loco }}">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
@@ -435,7 +435,7 @@
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
- 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'num_vals']
+ 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples']
$('input[name=wanted_inputs]').val(mapping_input_list.join(","));
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 80164a22..131345d3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -630,7 +630,7 @@ def loading_page():
logger.info(request.url)
initial_start_vars = request.form
start_vars_container = {}
- num_vals = 0 #ZS: So it can be displayed on loading page
+ n_samples = 0 #ZS: So it can be displayed on loading page
if 'wanted_inputs' in initial_start_vars:
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
@@ -638,8 +638,8 @@ def loading_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- if 'num_vals' in start_vars:
- num_vals = int(start_vars['num_vals'])
+ if 'n_samples' in start_vars:
+ n_samples = int(start_vars['n_samples'])
else:
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
@@ -658,9 +658,9 @@ def loading_page():
for sample in samples:
value = start_vars.get('value:' + sample)
if value != "x":
- num_vals += 1
+ n_samples += 1
- start_vars['num_vals'] = num_vals
+ start_vars['n_samples'] = n_samples
start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
start_vars_container['start_vars'] = start_vars
@@ -730,7 +730,7 @@ def mapping_results_page():
'mapmodel_rqtl_geno',
'temp_trait',
'reaper_version',
- 'num_vals',
+ 'n_samples',
'transform'
)
start_vars = {}
--
cgit v1.2.3
From 3a0ee1628b51ee34b7576ba63d9a05674d9d0760 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Jul 2020 14:49:16 -0500
Subject: Fixed remaining issue with the logic for making the categories for
the Type drop-down on the home search page
---
wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js | 3 +++
1 file changed, 3 insertions(+)
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index d5711f6d..d172907a 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -119,6 +119,9 @@ redo_dropdown = function(dropdown, items) {
_results.push(dropdown.append(this_opt_group))
this_opt_group = $("<optgroup label=\"" + current_family + "\">")
this_opt_group.append($("<option />").val(item[0]).text(item[1]));
+ if (_i == type_family_list.length - 1){
+ _results.push(dropdown.append(this_opt_group))
+ }
} else {
_results.push(dropdown.append(this_opt_group))
current_family = ""
--
cgit v1.2.3