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-rw-r--r--wqflask/base/data_set.py40
-rw-r--r--wqflask/base/trait.py206
-rw-r--r--wqflask/tests/base/test_data_set.py10
-rw-r--r--wqflask/tests/base/test_trait.py235
-rw-r--r--wqflask/tests/utility/test_authentication_tools.py193
-rw-r--r--wqflask/tests/utility/test_hmac.py39
-rw-r--r--wqflask/tests/wqflask/test_collect.py57
-rw-r--r--wqflask/utility/authentication_tools.py41
-rw-r--r--wqflask/utility/hmac.py9
-rw-r--r--wqflask/utility/redis_tools.py120
-rw-r--r--wqflask/wqflask/__init__.py21
-rw-r--r--wqflask/wqflask/collect.py37
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py11
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/db_info.py127
-rw-r--r--wqflask/wqflask/docs.py4
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py10
-rw-r--r--wqflask/wqflask/resource_manager.py20
-rw-r--r--wqflask/wqflask/static/new/css/marker_regression.css4
-rw-r--r--wqflask/wqflask/static/new/css/show_trait.css4
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js36
-rw-r--r--wqflask/wqflask/templates/base.html12
-rw-r--r--wqflask/wqflask/templates/collections/add.html2
-rw-r--r--wqflask/wqflask/templates/collections/view.html40
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html2
-rw-r--r--wqflask/wqflask/templates/correlation_page.html32
-rw-r--r--wqflask/wqflask/templates/gsearch_gene.html16
-rw-r--r--wqflask/wqflask/templates/gsearch_pheno.html17
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html10
-rw-r--r--wqflask/wqflask/templates/info_page.html92
-rw-r--r--wqflask/wqflask/templates/mapping_results.html139
-rw-r--r--wqflask/wqflask/templates/search_result_page.html52
-rw-r--r--wqflask/wqflask/templates/show_trait.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_calculate_correlations.html12
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html32
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html4
-rw-r--r--wqflask/wqflask/templates/show_trait_statistics.html4
-rw-r--r--wqflask/wqflask/templates/tutorials.html1
-rw-r--r--wqflask/wqflask/user_login.py4
-rw-r--r--wqflask/wqflask/views.py64
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py181
42 files changed, 1388 insertions, 558 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index afffe780..2f1549ae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -150,10 +150,12 @@ Publish or ProbeSet. E.g.
"geno": "Geno",
}
+ group_name = name
if t in ['pheno', 'other_pheno']:
- name = name.replace("Publish", "")
+ group_name = name.replace("Publish", "")
- if bool(len(g.db.execute(sql_query_mapping[t].format(name)).fetchone())):
+ results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+ if results:
self.datasets[name] = dataset_name_mapping[t]
self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
return True
@@ -1173,40 +1175,6 @@ class TempDataSet(DataSet):
self.fullname = 'Temporary Storage'
self.shortname = 'Temp'
- @staticmethod
- def handle_pca(desc):
- if 'PCA' in desc:
- # Todo: Modernize below lines
- desc = desc[desc.rindex(':')+1:].strip()
- else:
- desc = desc[:desc.index('entered')].strip()
- return desc
-
- def get_desc(self):
- query = 'SELECT description FROM Temp WHERE Name=%s' % self.name
- logger.sql(query)
- g.db.execute(query)
- desc = g.db.fetchone()[0]
- desc = self.handle_pca(desc)
- return desc
-
- def retrieve_sample_data(self, trait):
- query = """
- SELECT
- Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
- FROM
- TempData, Temp, Strain
- WHERE
- TempData.StrainId = Strain.Id AND
- TempData.Id = Temp.DataId AND
- Temp.name = '%s'
- Order BY
- Strain.Name
- """ % escape(trait.name)
-
- logger.sql(query)
- results = g.db.execute(query).fetchall()
-
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7666348e..7ebbc4bb 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,4 +1,10 @@
from __future__ import absolute_import, division, print_function
+from utility.logger import getLogger
+from flask import Flask, g, request, url_for, redirect, make_response, render_template
+from pprint import pformat as pf
+from MySQLdb import escape_string as escape
+import simplejson as json
+from wqflask import app
import os
import string
@@ -16,22 +22,19 @@ from utility import webqtlUtil
from utility import hmac
from utility.authentication_tools import check_resource_availability
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 utility.redis_tools import get_redis_conn
+from utility.redis_tools import get_resource_id
+from utility.redis_tools import get_resource_info
-from wqflask import app
+Redis = get_redis_conn()
-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, make_response, render_template
+logger = getLogger(__name__)
-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";
+ assert bool(kw.get('dataset')) != bool(
+ kw.get('dataset_name')), "Needs dataset ob. or name"
permitted = True
if kw.get('name'):
@@ -43,18 +46,21 @@ def create_trait(**kw):
if kw.get('dataset_name') != "Temp":
if dataset.type == 'Publish':
- permissions = check_resource_availability(dataset, kw.get('name'))
+ permissions = check_resource_availability(
+ dataset, kw.get('name'))
else:
permissions = check_resource_availability(dataset)
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'))
+ the_trait = retrieve_trait_info(
+ the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
return the_trait
else:
return None
+
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -64,12 +70,15 @@ class GeneralTrait(object):
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
- assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
- self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
+ assert bool(kw.get('dataset')) != bool(
+ kw.get('dataset_name')), "Needs dataset ob. or name"
+ # Trait ID, ProbeSet ID, Published ID, etc.
+ self.name = kw.get('name')
if kw.get('dataset_name'):
if kw.get('dataset_name') == "Temp":
temp_group = self.name.split("_")[2]
- self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ self.dataset = create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name=temp_group)
else:
self.dataset = create_dataset(kw.get('dataset_name'))
else:
@@ -77,7 +86,8 @@ class GeneralTrait(object):
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
- self.sequence = kw.get('sequence') # Blat sequence, available for ProbeSet
+ # Blat sequence, available for ProbeSet
+ self.sequence = kw.get('sequence')
self.data = kw.get('data', {})
self.view = True
@@ -125,11 +135,11 @@ class GeneralTrait(object):
vals.append(sample_data.value)
the_vars.append(sample_data.variance)
sample_aliases.append(sample_data.name2)
- return samples, vals, the_vars, sample_aliases
+ return samples, vals, the_vars, sample_aliases
@property
def description_fmt(self):
- '''Return a text formated description'''
+ """Return a text formated description"""
if self.dataset.type == 'ProbeSet':
if self.description:
formatted = self.description
@@ -149,7 +159,7 @@ class GeneralTrait(object):
@property
def alias_fmt(self):
- '''Return a text formatted alias'''
+ """Return a text formatted alias"""
alias = 'Not available'
if getattr(self, "alias", None):
@@ -160,16 +170,20 @@ class GeneralTrait(object):
@property
def wikidata_alias_fmt(self):
- '''Return a text formatted alias'''
+ """Return a text formatted alias"""
alias = 'Not available'
if self.symbol:
- human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
- mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
- other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+ human_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+ mouse_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+ other_response = requests.get(
+ GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
if human_response and mouse_response and other_response:
- alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+ alias_list = json.loads(human_response.content) + json.loads(
+ mouse_response.content) + json.loads(other_response.content)
filtered_aliases = []
seen = set()
@@ -183,31 +197,31 @@ class GeneralTrait(object):
return alias
-
@property
def location_fmt(self):
- '''Return a text formatted location
+ """Return a text formatted location
While we're at it we set self.location in case we need it later (do we?)
- '''
+ """
if self.chr and self.mb:
- self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb)
+ self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
elif self.chr:
self.location = 'Chr %s @ Unknown position' % (self.chr)
else:
self.location = 'Not available'
fmt = self.location
- ##XZ: deal with direction
+ # XZ: deal with direction
if self.strand_probe == '+':
fmt += (' on the plus strand ')
elif self.strand_probe == '-':
fmt += (' on the minus strand ')
return fmt
-
+
+
def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist == None:
samplelist = []
@@ -225,16 +239,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
all_samples_ordered = dataset.group.all_samples_ordered()
for i, item in enumerate(results):
try:
- trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+ trait.data[all_samples_ordered[i]] = webqtlCaseData(
+ all_samples_ordered[i], float(item))
except:
pass
else:
for item in results:
name, value, variance, num_cases, name2 = item
if not samplelist or (samplelist and name in samplelist):
- trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
+ # name, value, variance, num_cases)
+ trait.data[name] = webqtlCaseData(*item)
return trait
+
@app.route("/trait/get_sample_data")
def get_sample_data():
params = request.args
@@ -250,7 +267,8 @@ def get_sample_data():
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['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
@@ -260,22 +278,24 @@ def get_sample_data():
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() }])
+ 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
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
-
+ dataset = create_dataset(dataset_name=trait.dataset.name,
+ dataset_type=trait.dataset.type, group_name=trait.dataset.group.name)
+
if dataset.type == "ProbeSet":
return dict(name=trait.name,
symbol=trait.symbol,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
mean=trait.mean,
location=trait.location_repr,
@@ -287,7 +307,7 @@ def jsonable(trait):
if trait.pubmed_id:
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
@@ -300,7 +320,7 @@ def jsonable(trait):
else:
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
@@ -312,19 +332,20 @@ def jsonable(trait):
elif dataset.type == "Geno":
return dict(name=trait.name,
dataset=dataset.name,
- dataset_name = dataset.shortname,
+ dataset_name=dataset.shortname,
location=trait.location_repr
)
else:
return dict()
+
def jsonable_table_row(trait, dataset_name, index):
"""Return a list suitable for json and intended to be displayed in a table
Actual turning into json doesn't happen here though"""
dataset = create_dataset(dataset_name)
-
+
if dataset.type == "ProbeSet":
if trait.mean == "":
mean = "N/A"
@@ -336,11 +357,13 @@ def jsonable_table_row(trait, dataset_name, index):
additive = "%.3f" % round(float(trait.additive), 2)
return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
- '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+ '<a href="/show_trait?trait_id=' +
+ str(trait.name)+'&dataset='+dataset.name +
+ '">'+str(trait.name)+'</a>',
trait.symbol,
trait.description_display,
trait.location_repr,
- mean,
+ mean,
trait.LRS_score_repr,
trait.LRS_location_repr,
additive]
@@ -352,7 +375,9 @@ def jsonable_table_row(trait, dataset_name, index):
if trait.pubmed_id:
return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
- '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+ '<a href="/show_trait?trait_id=' +
+ str(trait.name)+'&dataset='+dataset.name +
+ '">'+str(trait.name)+'</a>',
trait.description_display,
trait.authors,
'<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
@@ -362,7 +387,9 @@ def jsonable_table_row(trait, dataset_name, index):
else:
return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
- '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+ '<a href="/show_trait?trait_id=' +
+ str(trait.name)+'&dataset='+dataset.name +
+ '">'+str(trait.name)+'</a>',
trait.description_display,
trait.authors,
trait.pubmed_text,
@@ -372,7 +399,9 @@ def jsonable_table_row(trait, dataset_name, index):
elif dataset.type == "Geno":
return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
- '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+ '<a href="/show_trait?trait_id=' +
+ str(trait.name)+'&dataset='+dataset.name +
+ '">'+str(trait.name)+'</a>',
trait.location_repr]
else:
return dict()
@@ -383,14 +412,16 @@ 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: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)
+ 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
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
+ 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
@@ -419,8 +450,8 @@ 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.
+ # 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
@@ -433,14 +464,15 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
ProbeSetFreeze.Name = '%s' AND
ProbeSet.Name = '%s'
""" % (escape(display_fields_string),
- escape(dataset.name),
- escape(str(trait.name)))
+ 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
+ # 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 = string.join(
+ dataset.display_fields, ',Geno.')
display_fields_string = 'Geno.' + display_fields_string
query = """
SELECT %s
@@ -451,21 +483,21 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
GenoFreeze.Name = '%s' AND
Geno.Name = '%s'
""" % (escape(display_fields_string),
- escape(dataset.name),
- escape(trait.name))
+ escape(dataset.name),
+ escape(trait.name))
logger.sql(query)
trait_info = g.db.execute(query).fetchone()
- else: #Temp type
+ 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()
+ (string.join(dataset.display_fields, ','),
+ dataset.type, trait.name)).fetchone()
if trait_info:
trait.haveinfo = True
for i, field in enumerate(dataset.display_fields):
- holder = trait_info[i]
+ holder = trait_info[i]
setattr(trait, field, holder)
if dataset.type == 'Publish':
@@ -478,9 +510,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
description = trait.post_publication_description
- #If the dataset is confidential and the user has access to confidential
- #phenotype traits, then display the pre-publication description instead
- #of the post-publication description
+ # If the dataset is confidential and the user has access to confidential
+ # phenotype traits, then display the pre-publication description instead
+ # of the post-publication description
if trait.confidential:
trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
@@ -491,9 +523,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
trait.description_display = ""
- trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
- trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
- trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.abbreviation = unicode(str(trait.abbreviation).strip(
+ codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.description_display = unicode(str(trait.description_display).strip(
+ codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.authors = unicode(str(trait.authors).strip(
+ codecs.BOM_UTF8), 'utf-8', errors="replace")
if not trait.year.isdigit():
trait.pubmed_text = "N/A"
@@ -504,16 +539,19 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
if dataset.type == 'ProbeSet' and dataset.group:
- description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+ description_string = unicode(
+ str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
+ target_string = unicode(
+ str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
- if len(description_string) > 1 and description_string != 'None':
+ if str(description_string or "") != "" and description_string != 'None':
description_display = description_string
else:
description_display = trait.symbol
- if (len(description_display) > 1 and description_display != 'N/A' and
- len(target_string) > 1 and target_string != 'None'):
+ if (str(description_display or "") != "" and
+ description_display != 'N/A' and
+ str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
@@ -521,15 +559,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
- trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+ trait.location_repr = 'Chr%s: %.6f' % (
+ trait.chr, float(trait.mb))
elif dataset.type == "Geno":
trait.location_repr = 'N/A'
if trait.chr and trait.mb:
- trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+ trait.location_repr = 'Chr%s: %.6f' % (
+ trait.chr, float(trait.mb))
if get_qtl_info:
- #LRS and its location
+ # LRS and its location
trait.LRS_score_repr = "N/A"
trait.LRS_location_repr = "N/A"
trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
@@ -599,12 +639,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.lrs = trait.additive = ""
-
- if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
- trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
- if trait.lrs != "":
+ if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and str(trait.locus_chr or "") != "" and str(trait.locus_mb or "") != "":
+ trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+ trait.locus_chr, float(trait.locus_mb))
+ if str(trait.lrs or "") != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
- raise KeyError, `trait.name`+' information is not found in the database.'
-
- return trait \ No newline at end of file
+ raise KeyError, `trait.name`+ ' information is not found in the database.'
+
+ return trait
diff --git a/wqflask/tests/base/test_data_set.py b/wqflask/tests/base/test_data_set.py
index 94780a5d..dd7f5051 100644
--- a/wqflask/tests/base/test_data_set.py
+++ b/wqflask/tests/base/test_data_set.py
@@ -66,7 +66,7 @@ class TestDataSetTypes(unittest.TestCase):
@mock.patch('base.data_set.g')
def test_set_dataset_key_mrna(self, db_mock):
with app.app_context():
- db_mock.db.execute.return_value = [1, 2, 3]
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
redis_mock = mock.Mock()
redis_mock.get.return_value = self.test_dataset
data_set = DatasetType(redis_mock)
@@ -84,7 +84,7 @@ class TestDataSetTypes(unittest.TestCase):
@mock.patch('base.data_set.g')
def test_set_dataset_key_pheno(self, db_mock):
with app.app_context():
- db_mock.db.execute.return_value = [1, 2, 3]
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
redis_mock = mock.Mock()
redis_mock.get.return_value = self.test_dataset
data_set = DatasetType(redis_mock)
@@ -93,7 +93,6 @@ class TestDataSetTypes(unittest.TestCase):
redis_mock.set.assert_called_once_with(
"dataset_structure",
'{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
- expected_db_call = """"""
db_mock.db.execute.assert_called_with(
("SELECT InfoFiles.GN_AccesionId " +
"FROM InfoFiles, PublishFreeze, InbredSet " +
@@ -105,7 +104,7 @@ class TestDataSetTypes(unittest.TestCase):
@mock.patch('base.data_set.g')
def test_set_dataset_other_pheno(self, db_mock):
with app.app_context():
- db_mock.db.execute.return_value = [1, 2, 3]
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
redis_mock = mock.Mock()
redis_mock.get.return_value = self.test_dataset
data_set = DatasetType(redis_mock)
@@ -114,7 +113,6 @@ class TestDataSetTypes(unittest.TestCase):
redis_mock.set.assert_called_once_with(
"dataset_structure",
'{"Aging-Brain-UCIPublish": "Publish", "AKXDGeno": "Geno", "B139_K_1206_M": "ProbeSet", "AD-cases-controls-MyersGeno": "Geno", "AD-cases-controls-MyersPublish": "Publish", "All Phenotypes": "Publish", "Test": "Publish", "AXBXAPublish": "Publish", "B139_K_1206_R": "ProbeSet", "AXBXAGeno": "Geno"}')
- expected_db_call = """"""
db_mock.db.execute.assert_called_with(
("SELECT PublishFreeze.Name " +
"FROM PublishFreeze, InbredSet " +
@@ -125,7 +123,7 @@ class TestDataSetTypes(unittest.TestCase):
@mock.patch('base.data_set.g')
def test_set_dataset_geno(self, db_mock):
with app.app_context():
- db_mock.db.execute.return_value = [1, 2, 3]
+ db_mock.db.execute.return_value.fetchone.return_value = [1, 2, 3]
redis_mock = mock.Mock()
redis_mock.get.return_value = self.test_dataset
data_set = DatasetType(redis_mock)
diff --git a/wqflask/tests/base/test_trait.py b/wqflask/tests/base/test_trait.py
new file mode 100644
index 00000000..1a3820f2
--- /dev/null
+++ b/wqflask/tests/base/test_trait.py
@@ -0,0 +1,235 @@
+# -*- coding: utf-8 -*-
+"""Tests wqflask/base/trait.py"""
+import unittest
+import mock
+
+from base.trait import GeneralTrait
+from base.trait import retrieve_trait_info
+
+
+class TestResponse:
+ """Mock Test Response after a request"""
+ @property
+ def content(self):
+ """Mock the content from Requests.get(params).content"""
+ return "[1, 2, 3, 4]"
+
+
+class TestNilResponse:
+ """Mock Test Response after a request"""
+ @property
+ def content(self):
+ """Mock the content from Requests.get(params).content"""
+ return "{}"
+
+
+class MockTrait(GeneralTrait):
+ @property
+ def wikidata_alias_fmt(self):
+ return "Mock alias"
+
+
+class TestRetrieveTraitInfo(unittest.TestCase):
+ """Tests for 'retrieve_trait_info'"""
+ def test_retrieve_trait_info_with_empty_dataset(self):
+ """Test that an exception is raised when dataset is empty"""
+ with self.assertRaises(AssertionError):
+ retrieve_trait_info(trait=mock.MagicMock(),
+ dataset={})
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ def test_retrieve_trait_info_with_empty_trait_info(self,
+ g_mock,
+ requests_mock):
+ """Empty trait info"""
+ requests_mock.return_value = TestNilResponse()
+ with self.assertRaises(KeyError):
+ retrieve_trait_info(trait=mock.MagicMock(),
+ dataset=mock.MagicMock())
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ def test_retrieve_trait_info_with_non_empty_trait_info(self,
+ g_mock,
+ requests_mock):
+ """Test that attributes are set"""
+ mock_dataset = mock.MagicMock()
+ requests_mock.return_value = TestResponse()
+ type(mock_dataset).display_fields = mock.PropertyMock(
+ return_value=["a", "b", "c", "d"])
+ test_trait = retrieve_trait_info(trait=MockTrait(dataset=mock_dataset),
+ dataset=mock_dataset)
+ self.assertEqual(test_trait.a, 1)
+ self.assertEqual(test_trait.b, 2)
+ self.assertEqual(test_trait.c, 3)
+ self.assertEqual(test_trait.d, 4)
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ def test_retrieve_trait_info_utf8_parsing(self,
+ g_mock,
+ requests_mock):
+ """Test that utf-8 strings are parsed correctly"""
+ utf_8_string = "test_string"
+ mock_dataset = mock.MagicMock()
+ requests_mock.return_value = TestResponse()
+ type(mock_dataset).display_fields = mock.PropertyMock(
+ return_value=["a", "b", "c", "d"])
+ type(mock_dataset).type = 'Publish'
+
+ mock_trait = MockTrait(
+ dataset=mock_dataset,
+ pre_publication_description=utf_8_string
+ )
+ trait_attrs = {
+ "group_code": "test_code",
+ "pre_publication_description": "test_pre_pub",
+ "pre_publication_abbreviation": "ファイルを画面毎に見て行くには、次のコマンドを使います。",
+ "post_publication_description": None,
+ "pubmed_id": None,
+ 'year': "2020",
+ "authors": "Jane Doe かいと",
+ }
+ for key, val in list(trait_attrs.items()):
+ setattr(mock_trait, key, val)
+ test_trait = retrieve_trait_info(trait=mock_trait,
+ dataset=mock_dataset)
+ self.assertEqual(test_trait.abbreviation,
+ "ファイルを画面毎に見て行くには、次のコマンドを使います。".decode('utf-8'))
+ self.assertEqual(test_trait.authors,
+ "Jane Doe かいと".decode('utf-8'))
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ @mock.patch('base.trait.get_resource_id')
+ def test_retrieve_trait_info_with_non_empty_lrs(self,
+ resource_id_mock,
+ g_mock,
+ requests_mock):
+ """Test """
+ resource_id_mock.return_value = 1
+ g_mock.db.execute.return_value.fetchone = mock.Mock()
+ g_mock.db.execute.return_value.fetchone.side_effect = [
+ [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone()
+ [1, 2.37, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone()
+ [2.7333, 2.1204] # trait_info = g.db.execute(query).fetchone()
+ ]
+ requests_mock.return_value = None
+
+ mock_dataset = mock.MagicMock()
+ type(mock_dataset).display_fields = mock.PropertyMock(
+ return_value=["a", "b", "c", "d"])
+ type(mock_dataset).type = "ProbeSet"
+ type(mock_dataset).name = "RandomName"
+
+ mock_trait = MockTrait(
+ dataset=mock_dataset,
+ pre_publication_description="test_string"
+ )
+ trait_attrs = {
+ "description": "some description",
+ "probe_target_description": "some description",
+ "cellid": False,
+ "chr": 2.733,
+ "mb": 2.1204
+ }
+
+ for key, val in list(trait_attrs.items()):
+ setattr(mock_trait, key, val)
+ test_trait = retrieve_trait_info(trait=mock_trait,
+ dataset=mock_dataset,
+ get_qtl_info=True)
+ self.assertEqual(test_trait.LRS_score_repr,
+ "2.4")
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ @mock.patch('base.trait.get_resource_id')
+ def test_retrieve_trait_info_with_empty_lrs_field(self,
+ resource_id_mock,
+ g_mock,
+ requests_mock):
+ """Test retrieve trait info with empty lrs field"""
+ resource_id_mock.return_value = 1
+ g_mock.db.execute.return_value.fetchone = mock.Mock()
+ g_mock.db.execute.return_value.fetchone.side_effect = [
+ [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone()
+ [1, None, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone()
+ [2, 3] # trait_info = g.db.execute(query).fetchone()
+ ]
+ requests_mock.return_value = None
+
+ mock_dataset = mock.MagicMock()
+ type(mock_dataset).display_fields = mock.PropertyMock(
+ return_value=["a", "b", "c", "d"])
+ type(mock_dataset).type = "ProbeSet"
+ type(mock_dataset).name = "RandomName"
+
+ mock_trait = MockTrait(
+ dataset=mock_dataset,
+ pre_publication_description="test_string"
+ )
+ trait_attrs = {
+ "description": "some description",
+ "probe_target_description": "some description",
+ "cellid": False,
+ "chr": 2.733,
+ "mb": 2.1204
+ }
+
+ for key, val in list(trait_attrs.items()):
+ setattr(mock_trait, key, val)
+ test_trait = retrieve_trait_info(trait=mock_trait,
+ dataset=mock_dataset,
+ get_qtl_info=True)
+ self.assertEqual(test_trait.LRS_score_repr,
+ "N/A")
+ self.assertEqual(test_trait.LRS_location_repr,
+ "Chr2: 3.000000")
+
+ @mock.patch('base.trait.requests.get')
+ @mock.patch('base.trait.g')
+ @mock.patch('base.trait.get_resource_id')
+ def test_retrieve_trait_info_with_empty_chr_field(self,
+ resource_id_mock,
+ g_mock,
+ requests_mock):
+ """Test retrieve trait info with empty chr field"""
+ resource_id_mock.return_value = 1
+ g_mock.db.execute.return_value.fetchone = mock.Mock()
+ g_mock.db.execute.return_value.fetchone.side_effect = [
+ [1, 2, 3, 4], # trait_info = g.db.execute(query).fetchone()
+ [1, 2, 3, 4, 5], # trait_qtl = g.db.execute(query).fetchone()
+ [None, 3] # trait_info = g.db.execute(query).fetchone()
+ ]
+
+ requests_mock.return_value = None
+
+ mock_dataset = mock.MagicMock()
+ type(mock_dataset).display_fields = mock.PropertyMock(
+ return_value=["a", "b", "c", "d"])
+ type(mock_dataset).type = "ProbeSet"
+ type(mock_dataset).name = "RandomName"
+
+ mock_trait = MockTrait(
+ dataset=mock_dataset,
+ pre_publication_description="test_string"
+ )
+ trait_attrs = {
+ "description": "some description",
+ "probe_target_description": "some description",
+ "cellid": False,
+ "chr": 2.733,
+ "mb": 2.1204
+ }
+
+ for key, val in list(trait_attrs.items()):
+ setattr(mock_trait, key, val)
+ test_trait = retrieve_trait_info(trait=mock_trait,
+ dataset=mock_dataset,
+ get_qtl_info=True)
+ self.assertEqual(test_trait.LRS_score_repr,
+ "N/A")
+ self.assertEqual(test_trait.LRS_location_repr,
+ "N/A")
diff --git a/wqflask/tests/utility/test_authentication_tools.py b/wqflask/tests/utility/test_authentication_tools.py
new file mode 100644
index 00000000..99c74245
--- /dev/null
+++ b/wqflask/tests/utility/test_authentication_tools.py
@@ -0,0 +1,193 @@
+"""Tests for authentication tools"""
+import unittest
+import mock
+
+from utility.authentication_tools import check_resource_availability
+from utility.authentication_tools import add_new_resource
+
+
+class TestResponse:
+ """Mock Test Response after a request"""
+ @property
+ def content(self):
+ """Mock the content from Requests.get(params).content"""
+ return '["foo"]'
+
+
+class TestUser:
+ """Mock user"""
+ @property
+ def user_id(self):
+ """Mockes user id. Used in Flask.g.user_session.user_id"""
+ return "Jane"
+
+
+class TestUserSession:
+ """Mock user session"""
+ @property
+ def user_session(self):
+ """Mock user session. Mocks Flask.g.user_session object"""
+ return TestUser()
+
+
+def mock_add_resource(resource_ob, update=False):
+ return resource_ob
+
+
+class TestCheckResourceAvailability(unittest.TestCase):
+ """Test methods related to checking the resource availability"""
+ @mock.patch('utility.authentication_tools.add_new_resource')
+ @mock.patch('utility.authentication_tools.Redis')
+ @mock.patch('utility.authentication_tools.g')
+ @mock.patch('utility.authentication_tools.get_resource_id')
+ def test_check_resource_availability_default_mask(
+ self,
+ resource_id_mock,
+ g_mock,
+ redis_mock,
+ add_new_resource_mock):
+ """Test the resource availability with default mask"""
+ resource_id_mock.return_value = 1
+ g_mock.return_value = mock.Mock()
+ redis_mock.smembers.return_value = []
+ test_dataset = mock.MagicMock()
+ type(test_dataset).type = mock.PropertyMock(return_value="Test")
+ add_new_resource_mock.return_value = {"default_mask": 2}
+ self.assertEqual(check_resource_availability(test_dataset), 2)
+
+ @mock.patch('utility.authentication_tools.requests.get')
+ @mock.patch('utility.authentication_tools.add_new_resource')
+ @mock.patch('utility.authentication_tools.Redis')
+ @mock.patch('utility.authentication_tools.g')
+ @mock.patch('utility.authentication_tools.get_resource_id')
+ def test_check_resource_availability_non_default_mask(
+ self,
+ resource_id_mock,
+ g_mock,
+ redis_mock,
+ add_new_resource_mock,
+ requests_mock):
+ """Test the resource availability with default mask"""
+ resource_id_mock.return_value = 1
+ g_mock.return_value = mock.Mock()
+ redis_mock.smembers.return_value = []
+ add_new_resource_mock.return_value = {"default_mask": 2}
+ requests_mock.return_value = TestResponse()
+ test_dataset = mock.MagicMock()
+ type(test_dataset).type = mock.PropertyMock(return_value="Test")
+ self.assertEqual(check_resource_availability(test_dataset),
+ ['foo'])
+
+ @mock.patch('utility.authentication_tools.webqtlConfig.SUPER_PRIVILEGES',
+ "SUPERUSER")
+ @mock.patch('utility.authentication_tools.requests.get')
+ @mock.patch('utility.authentication_tools.add_new_resource')
+ @mock.patch('utility.authentication_tools.Redis')
+ @mock.patch('utility.authentication_tools.g', TestUserSession())
+ @mock.patch('utility.authentication_tools.get_resource_id')
+ def test_check_resource_availability_of_super_user(
+ self,
+ resource_id_mock,
+ redis_mock,
+ add_new_resource_mock,
+ requests_mock):
+ """Test the resource availability if the user is the super user"""
+ resource_id_mock.return_value = 1
+ redis_mock.smembers.return_value = ["Jane"]
+ add_new_resource_mock.return_value = {"default_mask": 2}
+ requests_mock.return_value = TestResponse()
+ test_dataset = mock.MagicMock()
+ type(test_dataset).type = mock.PropertyMock(return_value="Test")
+ self.assertEqual(check_resource_availability(test_dataset),
+ "SUPERUSER")
+
+ @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+ "John Doe")
+ def test_check_resource_availability_string_dataset(self):
+ """Test the resource availability if the dataset is a string"""
+ self.assertEqual(check_resource_availability("Test"),
+ "John Doe")
+
+ @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+ "John Doe")
+ def test_check_resource_availability_temp(self):
+ """Test the resource availability if the dataset is a string"""
+ test_dataset = mock.MagicMock()
+ type(test_dataset).type = mock.PropertyMock(return_value="Temp")
+ self.assertEqual(check_resource_availability(test_dataset),
+ "John Doe")
+
+
+class TestAddNewResource(unittest.TestCase):
+ """Test cases for add_new_resource method"""
+ @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+ "John Doe")
+ @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+ @mock.patch('utility.authentication_tools.get_group_code')
+ def test_add_new_resource_if_publish_datatype(self, group_code_mock):
+ """Test add_new_resource if dataset type is 'publish'"""
+ group_code_mock.return_value = "Test"
+ test_dataset = mock.MagicMock()
+ type(test_dataset).type = mock.PropertyMock(return_value="Publish")
+ type(test_dataset).id = mock.PropertyMock(return_value=10)
+ expected_value = {
+ "owner_id": "none",
+ "default_mask": "John Doe",
+ "group_masks": {},
+ "name": "Test_None",
+ "data": {
+ "dataset": 10,
+ "trait": None
+ },
+ "type": "dataset-publish"
+ }
+ self.assertEqual(add_new_resource(test_dataset),
+ expected_value)
+
+ @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+ "John Doe")
+ @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+ @mock.patch('utility.authentication_tools.get_group_code')
+ def test_add_new_resource_if_geno_datatype(self, group_code_mock):
+ """Test add_new_resource if dataset type is 'geno'"""
+ group_code_mock.return_value = "Test"
+ test_dataset = mock.MagicMock()
+ type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+ type(test_dataset).type = mock.PropertyMock(return_value="Geno")
+ type(test_dataset).id = mock.PropertyMock(return_value=20)
+ expected_value = {
+ "owner_id": "none",
+ "default_mask": "John Doe",
+ "group_masks": {},
+ "name": "Geno",
+ "data": {
+ "dataset": 20,
+ },
+ "type": "dataset-geno"
+ }
+ self.assertEqual(add_new_resource(test_dataset),
+ expected_value)
+
+ @mock.patch('utility.authentication_tools.webqtlConfig.DEFAULT_PRIVILEGES',
+ "John Doe")
+ @mock.patch('utility.authentication_tools.add_resource', mock_add_resource)
+ @mock.patch('utility.authentication_tools.get_group_code')
+ def test_add_new_resource_if_other_datatype(self, group_code_mock):
+ """Test add_new_resource if dataset type is not 'geno' or 'publish'"""
+ group_code_mock.return_value = "Test"
+ test_dataset = mock.MagicMock()
+ type(test_dataset).name = mock.PropertyMock(return_value="Geno")
+ type(test_dataset).type = mock.PropertyMock(return_value="other")
+ type(test_dataset).id = mock.PropertyMock(return_value=20)
+ expected_value = {
+ "owner_id": "none",
+ "default_mask": "John Doe",
+ "group_masks": {},
+ "name": "Geno",
+ "data": {
+ "dataset": 20,
+ },
+ "type": "dataset-probeset"
+ }
+ self.assertEqual(add_new_resource(test_dataset),
+ expected_value)
diff --git a/wqflask/tests/utility/test_hmac.py b/wqflask/tests/utility/test_hmac.py
new file mode 100644
index 00000000..16b50771
--- /dev/null
+++ b/wqflask/tests/utility/test_hmac.py
@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+"""Test hmac utility functions"""
+
+import unittest
+import mock
+
+from utility.hmac import data_hmac
+from utility.hmac import url_for_hmac
+from utility.hmac import hmac_creation
+
+
+class TestHmacUtil(unittest.TestCase):
+ """Test Utility method for hmac creation"""
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ def test_hmac_creation(self):
+ """Test hmac creation with a utf-8 string"""
+ self.assertEqual(hmac_creation("ファイ"), "7410466338cfe109e946")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ def test_data_hmac(self):
+ """Test data_hmac fn with a utf-8 string"""
+ self.assertEqual(data_hmac("ファイ"), "ファイ:7410466338cfe109e946")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ @mock.patch("utility.hmac.url_for")
+ def test_url_for_hmac_with_plain_url(self, mock_url):
+ """Test url_for_hmac without params"""
+ mock_url.return_value = "https://mock_url.com/ファイ/"
+ self.assertEqual(url_for_hmac("ファイ"),
+ "https://mock_url.com/ファイ/?hm=05bc39e659b1948f41e7")
+
+ @mock.patch("utility.hmac.app.config", {'SECRET_HMAC_CODE': "secret"})
+ @mock.patch("utility.hmac.url_for")
+ def test_url_for_hmac_with_param_in_url(self, mock_url):
+ """Test url_for_hmac with params"""
+ mock_url.return_value = "https://mock_url.com/?ファイ=1"
+ self.assertEqual(url_for_hmac("ファイ"),
+ "https://mock_url.com/?ファイ=1&hm=4709c1708270644aed79")
diff --git a/wqflask/tests/wqflask/test_collect.py b/wqflask/tests/wqflask/test_collect.py
new file mode 100644
index 00000000..6b8d7931
--- /dev/null
+++ b/wqflask/tests/wqflask/test_collect.py
@@ -0,0 +1,57 @@
+"""Test cases for some methods in collect.py"""
+
+import unittest
+import mock
+
+from flask import Flask
+from wqflask.collect import process_traits
+
+app = Flask(__name__)
+
+
+class MockSession:
+ """Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+ def __init__(self, is_logged_in=False):
+ self.is_logged_in = is_logged_in
+
+ @property
+ def logged_in(self):
+ return self.is_logged_in
+
+
+class MockFlaskG:
+ """Helper class for mocking wqflask.collect.g.user_session"""
+ def __init__(self, is_logged_in=False):
+ self.is_logged_in = is_logged_in
+
+ @property
+ def user_session(self):
+ if self.is_logged_in:
+ return MockSession(is_logged_in=True)
+ return MockSession()
+
+
+class TestCollect(unittest.TestCase):
+
+ def setUp(self):
+ self.app_context = app.app_context()
+ self.app_context.push()
+
+ def tearDown(self):
+ self.app_context.pop()
+
+ @mock.patch("wqflask.collect.g", MockFlaskG())
+ def test_process_traits_when_user_is_logged_out(self):
+ """
+ Test that the correct traits are returned when the user is logged
+ out
+ """
+ self.assertEqual(process_traits(
+ b'1452452_at:HC_M2_0606_P:163d04f7db7c9e110de6,'
+ b'1452447_at:HC_M2_0606_P:eeece8fceb67072debea,'
+ b'1451401_a_at:HC_M2_0606_P:a043d23b3b3906d8318e,'
+ b'1429252_at:HC_M2_0606_P:6fa378b349bc9180e8f5'),
+ set(['1429252_at:HC_M2_0606_P',
+ '1451401_a_at:HC_M2_0606_P',
+ '1452447_at:HC_M2_0606_P',
+ '1452452_at:HC_M2_0606_P']))
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 3553b92b..239b08e3 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,4 +1,6 @@
from __future__ import absolute_import, print_function, division
+import logging
+from flask import Flask, g, redirect, url_for
import json
import requests
@@ -9,33 +11,31 @@ from utility import hmac
from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
Redis = get_redis_conn()
-from flask import Flask, g, redirect, url_for
-import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
+
def check_resource_availability(dataset, trait_id=None):
- #At least for now assume temporary entered traits are accessible
- if type(dataset) == str:
- return webqtlConfig.DEFAULT_PRIVILEGES
- if dataset.type == "Temp":
+ # At least for now assume temporary entered traits are accessible
+ if type(dataset) == str or dataset.type == "Temp":
return webqtlConfig.DEFAULT_PRIVILEGES
resource_id = get_resource_id(dataset, trait_id)
- if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+ if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
resource_info = get_resource_info(resource_id)
- if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
+ if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges
resource_info = add_new_resource(dataset, trait_id)
- #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+ # 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 webqtlConfig.SUPER_PRIVILEGES
+ return webqtlConfig.SUPER_PRIVILEGES
response = None
- the_url = "http://localhost:8080/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:
@@ -43,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None):
return response
+
def add_new_resource(dataset, trait_id=None):
resource_ob = {
- 'owner_id' : "none", # webqtlConfig.DEFAULT_OWNER_ID,
+ 'owner_id': "none", # webqtlConfig.DEFAULT_OWNER_ID,
'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
- 'group_masks' : {}
+ 'group_masks': {}
}
if dataset.type == "Publish":
resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
resource_ob['data'] = {
'dataset': dataset.id,
- 'trait' : trait_id
+ 'trait': trait_id
}
resource_ob['type'] = 'dataset-publish'
elif dataset.type == "Geno":
@@ -74,15 +75,19 @@ def add_new_resource(dataset, trait_id=None):
return resource_info
+
def get_group_code(dataset):
- results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+ results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
+ dataset.group.name)).fetchone()
if results[0]:
return results[0]
else:
return ""
+
def check_admin(resource_id=None):
- the_url = "http://localhost:8080/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:
@@ -96,6 +101,7 @@ def check_admin(resource_id=None):
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)
@@ -110,6 +116,7 @@ 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 not resource_id:
if dataset.type == "Temp":
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..fd75803e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -7,11 +7,11 @@ from flask import url_for
from wqflask import app
+
def hmac_creation(stringy):
"""Helper function to create the actual hmac"""
secret = app.config['SECRET_HMAC_CODE']
-
hmaced = hmac.new(secret, stringy, hashlib.sha1)
hm = hmaced.hexdigest()
# ZS: Leaving the below comment here to ask Pjotr about
@@ -20,10 +20,12 @@ def hmac_creation(stringy):
hm = hm[:20]
return hm
+
def data_hmac(stringy):
- """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
+ """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with"""
return stringy + ":" + hmac_creation(stringy)
+
def url_for_hmac(endpoint, **values):
"""Like url_for but adds an hmac at the end to insure the url hasn't been tampered with"""
@@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values):
combiner = "?"
return url + combiner + "hm=" + hm
+
app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
- data_hmac=data_hmac) \ No newline at end of file
+ data_hmac=data_hmac)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 81ba04ea..ef02268e 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -4,23 +4,21 @@ import uuid
import simplejson as json
import datetime
-import redis # used for collections
-
-import logging
-
-from flask import (render_template, flash)
-
-from utility import hmac
+import redis # used for collections
+from utility.hmac import hmac_creation
from utility.logger import getLogger
logger = getLogger(__name__)
+
def get_redis_conn():
Redis = redis.StrictRedis(port=6379)
return Redis
+
Redis = get_redis_conn()
+
def is_redis_available():
try:
Redis.ping()
@@ -28,6 +26,7 @@ def is_redis_available():
return False
return True
+
def get_user_id(column_name, column_value):
user_list = Redis.hgetall("users")
key_list = []
@@ -38,6 +37,7 @@ def get_user_id(column_name, column_value):
return None
+
def get_user_by_unique_column(column_name, column_value):
item_details = None
@@ -52,9 +52,11 @@ 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
+ """Like previous function, but this only checks if the input is a
+ subset of a field and can return multiple results
+
"""
matched_users = []
@@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, 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))
@@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value):
Redis.hset("users", user_id, json.dumps(user_info))
+
def get_user_collections(user_id):
collections = None
collections = Redis.hget("collections", user_id)
@@ -91,22 +93,27 @@ def get_user_collections(user_id):
else:
return []
+
def save_user(user, user_id):
Redis.hset("users", user_id, json.dumps(user))
+
def save_collections(user_id, collections_ob):
Redis.hset("collections", user_id, collections_ob)
+
def save_verification_code(user_email, code):
Redis.hset("verification_codes", code, user_email)
+
def check_verification_code(code):
email_address = None
user_details = None
email_address = Redis.hget("verification_codes", code)
if email_address:
- user_details = get_user_by_unique_column('email_address', email_address)
+ user_details = get_user_by_unique_column(
+ 'email_address', email_address)
if user_details:
return user_details
else:
@@ -114,10 +121,12 @@ def check_verification_code(code):
else:
return None
+
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
+ # 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:
try:
@@ -142,6 +151,7 @@ def get_user_groups(user_id):
return admin_groups, user_groups
+
def get_group_info(group_id):
group_json = Redis.hget("groups", group_id)
group_info = None
@@ -150,6 +160,7 @@ 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 """
@@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value):
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
+ # ZS: Since these fields are lists, search in the list
+ if column_name == "admins" or column_name == "members":
if column_value in group_info[column_name]:
matched_groups.append(group_info)
else:
@@ -167,9 +179,11 @@ 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
+ """Like previous function, but this only checks if the input is a
+ subset of a field and can return multiple results
+
"""
matched_groups = []
@@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value):
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
+ # ZS: Since these fields are lists, search in the list
+ if column_name == "admins" or column_name == "members":
if column_value in group_info[column_name]:
matched_groups.append(group_info)
else:
@@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value):
return matched_groups
-def create_group(admin_user_ids, member_user_ids = [], group_name = "Default 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,
+ "id": group_id,
"admins": admin_user_ids,
- "members" : member_user_ids,
- "name" : group_name,
+ "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')
}
@@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro
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
+ # 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)
@@ -214,9 +232,15 @@ def delete_group(user_id, group_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
+
+# ZS "admins" is just to indicate whether the users should be added to
+# the groups admins or regular users set
+def add_users_to_group(user_id, group_id, user_emails=[], admins=False):
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
+ # 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 user_id in group_info["admins"]:
if admins:
group_users = set(group_info["admins"])
else:
@@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
else:
group_info["members"] = list(group_users)
- group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ 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 = "members"): #ZS: User type is because I assume admins can remove other admins
+
+# 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"):
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
+ # 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
+ if user_type == "admins" and user_id in users_to_remove_set:
users_to_remove_set.remove(user_id)
group_users = set(group_info[user_type])
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')
+ 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"]:
@@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name):
else:
return None
+
def get_resources():
resource_list = Redis.hgetall("resources")
return resource_list
+
def get_resource_id(dataset, trait_id=None):
resource_id = False
if dataset.type == "Publish":
if trait_id:
- resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+ resource_id = hmac_creation("{}:{}:{}".format(
+ 'dataset-publish', dataset.id, trait_id))
elif dataset.type == "ProbeSet":
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+ resource_id = hmac_creation(
+ "{}:{}".format('dataset-probeset', dataset.id))
elif dataset.type == "Geno":
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+ resource_id = hmac_creation(
+ "{}:{}".format('dataset-geno', dataset.id))
return resource_id
+
def get_resource_info(resource_id):
resource_info = Redis.hget("resources", resource_id)
if resource_info:
@@ -282,17 +323,23 @@ def get_resource_info(resource_id):
else:
return None
+
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'])))
+ resource_id = 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'])))
+ resource_id = hmac_creation('{}:{}'.format(
+ str(resource_info['type']), str(resource_info['data']['dataset'])))
if update or not Redis.hexists("resources", resource_id):
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
@@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask):
return the_resource
+
def change_resource_owner(resource_id, new_owner_id):
- the_resource= get_resource_info(resource_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
+ Redis.hset("resources", resource_id, json.dumps(the_resource))
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..7ed9c7b8 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -12,13 +12,24 @@ logging.basicConfig(level=logging.INFO)
app = Flask(__name__)
-app.config.from_envvar('GN2_SETTINGS') # See http://flask.pocoo.org/docs/config/#configuring-from-files
+# See http://flask.pocoo.org/docs/config/#configuring-from-files
# Note no longer use the badly named WQFLASK_OVERRIDES (nyi)
-
+app.config.from_envvar('GN2_SETTINGS')
app.jinja_env.globals.update(
- undefined = jinja2.StrictUndefined,
- numify = formatting.numify
-)
+ undefined=jinja2.StrictUndefined,
+ numify=formatting.numify)
from wqflask.api import router
+from wqflask import group_manager
+from wqflask import resource_manager
+from wqflask import search_results
+from wqflask import export_traits
+from wqflask import gsearch
+from wqflask import update_search_results
+from wqflask import docs
+from wqflask import news
+from wqflask import db_info
+from wqflask import user_login
+from wqflask import user_session
+
import wqflask.views
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 42a09fed..4c558bfe 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,41 +1,30 @@
from __future__ import print_function, division, absolute_import
-
-import os
-import hashlib
import datetime
-import time
-
-import uuid
-import hashlib
-import base64
-
-import urlparse
-
import simplejson as json
-from flask import (Flask, g, render_template, url_for, request, make_response,
- redirect, flash, jsonify)
+from flask import g
+from flask import render_template
+from flask import url_for
+from flask import request
+from flask import redirect
+from flask import flash
from wqflask import app
-
-from pprint import pformat as pf
-
-from wqflask.database import db_session
-
-from wqflask import model
-
-from utility import Bunch, Struct, hmac
+from utility import hmac
from utility.formatting import numify
from utility.redis_tools import get_redis_conn
-Redis = get_redis_conn()
-from base.trait import create_trait, retrieve_trait_info, jsonable
+from base.trait import create_trait
+from base.trait import retrieve_trait_info
+from base.trait import jsonable
from base.data_set import create_dataset
-import logging
from utility.logger import getLogger
+
logger = getLogger(__name__)
+Redis = get_redis_conn()
+
def process_traits(unprocessed_traits):
if isinstance(unprocessed_traits, basestring):
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 819836b1..0f3d455c 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,8 +17,15 @@ class CorrScatterPlot(object):
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
- self.dataset_1 = data_set.create_dataset(params['dataset_1'])
- self.dataset_2 = data_set.create_dataset(params['dataset_2'])
+ if "Temp" in params['dataset_1']:
+ self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+ else:
+ self.dataset_1 = data_set.create_dataset(params['dataset_1'])
+ if "Temp" in params['dataset_2']:
+ self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+ else:
+ 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)
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 0ac94139..3beee84f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -147,7 +147,7 @@ class CorrelationMatrix(object):
if num_overlap < self.lowest_overlap:
self.lowest_overlap = num_overlap
- if num_overlap == 0:
+ if num_overlap < 2:
corr_result_row.append([target_trait, 0, num_overlap])
pca_corr_result_row.append(0)
else:
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
new file mode 100644
index 00000000..f04e38bf
--- /dev/null
+++ b/wqflask/wqflask/db_info.py
@@ -0,0 +1,127 @@
+import httplib, urllib2
+import re
+
+from flask import Flask, g
+
+from utility.logger import getLogger
+logger = getLogger(__name__ )
+
+class InfoPage(object):
+ def __init__(self, start_vars):
+ self.info = None
+ self.gn_accession_id = None
+ if 'gn_accession_id' in start_vars:
+ self.gn_accession_id = start_vars['gn_accession_id']
+ self.info_page_name = start_vars['info_page_name']
+
+ self.get_info()
+ self.get_datasets_list()
+
+ def get_info(self, create=False):
+ query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
+ "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
+ "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
+ "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
+ "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
+ "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
+ "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
+ "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
+ "FROM InfoFiles " +
+ "LEFT JOIN Species USING (SpeciesId) " +
+ "LEFT JOIN Tissue USING (TissueId) " +
+ "LEFT JOIN InbredSet USING (InbredSetId) " +
+ "LEFT JOIN GeneChip USING (GeneChipId) " +
+ "LEFT JOIN AvgMethod USING (AvgMethodId) " +
+ "LEFT JOIN Datasets USING (DatasetId) " +
+ "LEFT JOIN Investigators USING (InvestigatorId) " +
+ "LEFT JOIN Organizations USING (OrganizationId) " +
+ "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+
+ if self.gn_accession_id:
+ final_query = query_base + "GN_AccesionId = {}".format(self.gn_accession_id)
+ results = g.db.execute(final_query).fetchone()
+ if self.info_page_name and not results:
+ final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+ elif self.info_page_name:
+ final_query = query_base + "InfoPageName={}".format(self.info_page_name)
+ results = g.db.execute(final_query).fetchone()
+ else:
+ raise 'No correct parameter found'
+
+ if results:
+ self.info = process_query_results(results)
+
+ if (not results or len(results) < 1) and self.info_page_name and create:
+ insert_sql = "INSERT INTO InfoFiles SET InfoFiles.InfoPageName={}".format(self.info_page_name)
+ return self.get_info()
+
+ if not self.gn_accession_id and self.info:
+ self.gn_accession_id = self.info['accession_id']
+ if not self.info_page_name and self.info:
+ self.info_page_name = self.info['info_page_name']
+
+ def get_datasets_list(self):
+ self.filelist = []
+ try:
+ response = urllib2.urlopen("http://datafiles.genenetwork.org/download/GN%s" % self.gn_accession_id)
+ data = response.read()
+
+ matches = re.findall(r"<tr>.+?</tr>", data, re.DOTALL)
+ for i, match in enumerate(matches):
+ if i == 0:
+ continue
+ cells = re.findall(r"<td.+?>.+?</td>", match, re.DOTALL)
+ full_filename = re.search(r"<a href=\"(.+?)\"", cells[1], re.DOTALL).group(1).strip()
+ filename = full_filename.split("/")[-1]
+ filesize = re.search(r">(.+?)<", cells[2]).group(1).strip()
+ filedate = "N/A" #ZS: Since we can't get it for now
+
+ self.filelist.append([filename, filedate, filesize])
+ except Exception, e:
+ pass
+
+def process_query_results(results):
+ info_ob = {
+ 'info_page_name': results[0],
+ 'accession_id': results[1],
+ 'menu_name': results[2],
+ 'taxonomy_id': results[3],
+ 'tissue_name': results[4],
+ 'group_name': results[5],
+ 'gene_chip_name': results[6],
+ 'geo_platform': results[7],
+ 'avg_method_name': results[8],
+ 'dataset_name': results[9],
+ 'geo_series': results[10],
+ 'publication_title': results[11],
+ 'dataset_status_name': results[12],
+ 'dataset_summary': results[13],
+ 'about_cases': results[14],
+ 'about_tissue': results[15],
+ 'about_data_processing': results[16],
+ 'acknowledgement': results[17],
+ 'experiment_design': results[18],
+ 'contributors': results[19],
+ 'citation': results[20],
+ 'notes': results[21],
+ 'investigator_firstname': results[22],
+ 'investigator_lastname': results[23],
+ 'investigator_address': results[24],
+ 'investigator_city': results[25],
+ 'investigator_state': results[26],
+ 'investigator_zipcode': results[27],
+ 'investigator_country': results[28],
+ 'investigator_phone': results[29],
+ 'investigator_email': results[30],
+ 'investigator_url': results[31],
+ 'organization_name': results[32],
+ 'investigator_id': results[33],
+ 'dataset_id': results[34],
+ 'dataset_status_is': results[35],
+ 'about_platform': results[36],
+ 'info_file_title': results[37],
+ 'specifics': results[38]
+ }
+
+ return info_ob
+ \ No newline at end of file
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..9fad1cf1 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -11,7 +11,7 @@ class Docs(object):
def __init__(self, entry, start_vars={}):
sql = """
- SELECT Docs.title, Docs.content
+ SELECT Docs.title, CAST(Docs.content AS BINARY)
FROM Docs
WHERE Docs.entry LIKE %s
"""
@@ -22,7 +22,7 @@ class Docs(object):
self.content = ""
else:
self.title = result[0]
- self.content = result[1].encode("latin1")
+ self.content = result[1]
self.editable = "false"
# ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 9bde343c..8a44b3fd 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -401,9 +401,7 @@ class RunMapping(object):
rs = marker['name'],
pos = this_ps
)
- #if 'p_value' in marker:
- # logger.debug("P EXISTS:", marker['p_value'])
- #else:
+
if 'lrs_value' in marker and marker['lrs_value'] > 0:
browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61)
elif 'lod_score' in marker and marker['lod_score'] > 0:
@@ -417,6 +415,12 @@ class RunMapping(object):
if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
highest_chr = marker['chr']
if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
+ if 'Mb' in marker.keys():
+ marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['Mb'])
+ elif 'cM' in marker.keys():
+ marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM'])
+ else:
+ marker['display_pos'] = "N/A"
self.qtl_results.append(marker)
with Bench("Exporting Results"):
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 39a07310..14ff2183 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -25,16 +25,16 @@ def manage_resource():
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
+
+ owner_display_name = None
+ if owner_id != "none":
+ 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']
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)
diff --git a/wqflask/wqflask/static/new/css/marker_regression.css b/wqflask/wqflask/static/new/css/marker_regression.css
index f1a26a83..e0a5ceea 100644
--- a/wqflask/wqflask/static/new/css/marker_regression.css
+++ b/wqflask/wqflask/static/new/css/marker_regression.css
@@ -62,6 +62,10 @@ table.dataTable tbody td {
padding: 4px 20px 2px 10px;
}
+table.dataTable tbody tr.selected {
+ background-color: #ffee99;
+}
+
table.dataTable.cell-border tbody th, table.dataTable.cell-border tbody td {
border-top: 1px solid #ccc;
border-right: 1px solid #ccc;
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index 853819ea..7a7f5455 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -54,4 +54,8 @@ table.dataTable.cell-border tbody tr td:first-child {
.trait_value_input {
text-align: right;
+
+.glyphicon {
+ position: relative;
+ top: 2px;
} \ 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 4e87d67a..86660126 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -93,7 +93,7 @@ $(function() {
});
- add = function() {
+ add_to_collection = function() {
var traits;
traits = $("#trait_table input:checked").map(function() {
return $(this).val();
@@ -250,7 +250,7 @@ $(function() {
$("#select_all").click(select_all);
$("#deselect_all").click(deselect_all);
$("#invert").click(invert);
- $("#add").click(add);
+ $("#add").click(add_to_collection);
$("#submit_bnw").click(submit_bnw);
$("#export_traits").click(export_traits);
$('.trait_checkbox, .btn').click(change_buttons);
@@ -259,14 +259,22 @@ $(function() {
let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"]
let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"]
+ let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A
+
+ function extract_inner_text(the_string){
+ var span = document.createElement('span');
+ span.innerHTML = the_string;
+ return span.textContent || span.innerText;
+ }
+
function sort_NAs(a, b, sort_function){
- if (a === "N/A" && b === "N/A") {
+ if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
return 0;
}
- if (a === "N/A"){
+ if (na_equivalent_vals.includes(a)){
return 1
}
- if (b === "N/A") {
+ if (na_equivalent_vals.includes(b)) {
return -1;
}
return sort_function(a, b)
@@ -274,11 +282,25 @@ $(function() {
$.extend( $.fn.dataTableExt.oSort, {
"natural-minus-na-asc": function (a, b) {
- return sort_NAs(a, b, naturalAsc)
+ return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalAsc)
},
"natural-minus-na-desc": function (a, b) {
- return sort_NAs(a, b, naturalDesc)
+ return sort_NAs(extract_inner_text(a), extract_inner_text(b), naturalDesc)
}
});
+ $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
+ {
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $('input', td).prop('checked') ? '1' : '0';
+ } );
+ };
+
+ $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
+ {
+ return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
+ return $(td).text();
+ } );
+ }
+
}); \ No newline at end of file
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 50562200..b44538cf 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -4,7 +4,9 @@
<head>
<meta charset="utf-8">
- <title>{% block title %}{% endblock %}</title>
+
+ <title>{% block title %}{% endblock %} GeneNetwork 2</title>
+
<meta name="description" content="">
<meta name="author" content="">
<link rel="icon" type="image/png" sizes="64x64" href="/static/new/images/CITGLogo.png">
@@ -19,6 +21,14 @@
{% block css %}
{% endblock %}
+ <style>
+ table.dataTable thead .sorting_asc {
+ background-image: url({{ url_for("js", filename="DataTables/images/sort_asc_disabled.png") }});
+ }
+ table.dataTable thead .sorting_desc {
+ background-image: url({{ url_for("js", filename="DataTables/images/sort_desc_disabled.png") }});
+ }
+ </style>
</head>
<body style="width: 100%">
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index 825dfb84..62b6abb5 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -5,7 +5,7 @@
or add to an existing collection.</p>
</div>
<div class="modal-body" style="margin-left: 20px;">
- <form action="/collections/new" data-validate="parsley" id="add_form">
+ <form action="/collections/new" target="_blank" data-validate="parsley" id="add_form">
{% if traits is defined %}
<input type="hidden" name="traits" value="{{ traits }}" />
{% else %}
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index dce814dd..d1a97310 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: 2050px;">
+ <div class="container">
<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 }}">
@@ -16,8 +16,6 @@
</h1>
<h3>This collection has {{ '{}'.format(numify(trait_obs|count, "record", "records")) }}</h3>
- <!--<hr style="height: 1px; background-color: #A9A9A9;">-->
-
<div>
<form id="collection_form" action="/delete" method="post">
<input type="hidden" name="uc_id" id="uc_id" value="{{ uc.id }}" />
@@ -77,7 +75,7 @@
<input type="hidden" name="database_name" id="database_name" value="None">
<input type="hidden" name="export_data" id="export_data" value="">
<input type="hidden" name="file_name" id="file_name" value="collection_table">
- <button class="btn btn-default" id="export_traits">Download CSV</button>
+ <button class="btn btn-default" id="export_traits">Download</button>
<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>
@@ -87,7 +85,7 @@
<div style="margin-top: 10px; margin-bottom: 5px;">
<b>Show/Hide Columns:</b>
</div>
- <div>
+ <div style="min-width: 1500px;">
<table class="table-hover table-striped cell-border" id='trait_table' style="float: left;">
<thead>
<tr>
@@ -99,9 +97,9 @@
<th data-export="Description">Description</th>
<th data-export="Location">Location</th>
<th data-export="Mean">Mean</th>
- <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup>?</sup></a></th>
- <th data-export="Max LRS Location">Max LRS Location</th>
- <th data-export="Add. Eff.">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup>?</sup></a></th>
+ <th data-export="Max LRS">High P <a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
+ <th data-export="Peak Location">Peak Location</th>
+ <th data-export="Add. Eff.">Effect Size <a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="font-size: small; color: #FF0000;"> ?</sup></a></th>
</tr>
</thead>
@@ -144,7 +142,7 @@
<TD data-export="{{ this_trait.LRS_score_repr }}" align="right">N/A</TD>
{% endif %}
<TD data-export="{{ this_trait.LRS_location_repr }}">{{ this_trait.LRS_location_repr }}</TD>
- {% if this_trait.additive|float > 0 %}
+ {% if this_trait.additive|float != 0 %}
<TD data-export="{{ this_trait.additive }}" align="right">{{ '%0.3f' % this_trait.additive|float }}</TD>
{% else %}
<TD data-export="{{ this_trait.additive }}" align="right">N/A</TD>
@@ -166,13 +164,13 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script>
- <script type="text/javascript" src="/static/new/javascript/search_results.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="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colResize/dataTables.colResize.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/colReorder/js/dataTables.colReorder.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script>
<script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/buttons.colVis.min.js') }}"></script>
+ <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
<script language="javascript" type="text/javascript">
@@ -187,22 +185,22 @@
console.time("Creating table");
$('#trait_table').dataTable( {
"columns": [
- { "type": "natural", "width": 10 },
+ {
+ "orderDataType": "dom-checkbox",
+ "orderSequence": [ "desc", "asc"],
+ "width": 10
+ },
{ "type": "natural", "width": 50 },
{ "type": "natural" },
- { "type": "natural", "width": 120 },
+ { 'type': "natural-minus-na", "width": 120 },
{ "type": "natural" },
{ "type": "natural" },
- { "type": "natural", "width": 130 },
- { "type": "natural", "width": 35 },
- { "type": "natural", "width": 35 },
- { "type": "natural", "width": 130 },
- { "type": "natural" }
+ { "type": "natural", "width": 125 },
+ { "type": "natural", "width": 60 },
+ { "type": "natural", "width": 60 },
+ { "type": "natural", "width": 125 },
+ { "type": "natural", "width": 85 }
],
- "columnDefs": [ {
- "targets": 0,
- "orderable": false
- } ],
"order": [[1, "asc" ]],
buttons: [
{
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index 9b96de1c..d556f31a 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -51,7 +51,7 @@
{% if result[0].name == trait.name and result[0].dataset == trait.dataset %}
<td nowrap="ON" align="center" bgcolor="#cccccc" style="padding: 3px; line-height: 1.1;"><a href="/show_trait?trait_id={{ trait.name }}&dataset={{ trait.dataset.name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><em>n</em><br>{{ result[2] }}</font></a></td>
{% else %}
- <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={{ trait.dataset.name }}&dataset_2={{ result[0].dataset.name }}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
+ <td nowrap="ON" align="middle" class="corr_cell" style="padding: 3px; line-height: 1.1;"><a href="/corr_scatter_plot?dataset_1={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&dataset_2={% if result[0].dataset.name == 'Temp' %}Temp_{{ result[0].dataset.group.name }}{% else %}{{ result[0].dataset.name }}{% endif %}&trait_1={{ trait.name }}&trait_2={{ result[0].name }}"><font style="font-size: 12px; color: #3071a9; font-weight: bold;" ><span class="corr_value">{{ '%0.2f' % result[1] }}</span><br>{{ result[2] }}</font></a></td>
{% endif %}
{% endfor %}
</tr>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index e597bea9..fb218e29 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -144,7 +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={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&dataset_2={% if trait.dataset.name == 'Temp' %}Temp_{{ trait.dataset.group.name }}{% else %}{{ trait.dataset.name }}{% endif %}&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 %}
@@ -164,22 +164,26 @@
<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>
+ <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="N/A">N/A</TD>
+ <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>
+ <td data-export="N/A">N/A</td>
{% endif %}
<td data-export="{{ trait.pubmed_text }}">
+ {% if trait.pubmed_text != "N/A" %}
<a href="{{ trait.pubmed_link }}">
{{ trait.pubmed_text }}
</a>
+ {% else %}
+ {{ trait.pubmed_text }}
+ {% endif %}
</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={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&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>
<td data-export="{{ trait.LRS_score_repr }}" align="right">{{ trait.LRS_score_repr }}</td>
@@ -187,7 +191,7 @@
<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 == "Geno" %}
<td data-export="{{ trait.location_repr }}" align="right">{{ trait.location_repr }}</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={% if dataset.name == 'Temp' %}Temp_{{ dataset.group.name }}{% else %}{{ dataset.name }}{% endif %}&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>
{% endif %}
@@ -365,9 +369,9 @@
{ "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
{ "type": "numeric-html", 'orderSequence': [ "desc", "asc"] },
{ "type": "scientific" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" }
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" }
],
"createdRow": function ( row, data, index ) {
$('td', row).eq(4).attr('title', $('td', row).eq(4).text());
@@ -419,13 +423,13 @@
{ "type": "natural" },
{ "type": "natural", "width": "20%" },
{ "type": "natural", "width": "12%" },
- { "orderDataType": "dom-innertext" },
+ { "type": "natural-minus-na" },
{ "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
{ "type": "natural" },
{ "type": "scientific" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" }
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" }
],
"order": [[9, "asc" ]],
"sDom": "Btir",
@@ -461,7 +465,7 @@
{ "type": "natural" },
{ "type": "natural" },
{ "orderDataType": "dom-innertext", 'orderSequence': [ "desc", "asc"] },
- { "type": "natural" },
+ { "type": "natural-minus-na" },
{ "type": "scientific" }
],
"order": [[6, "asc" ]],
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 478d6f5f..d2c78d65 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -59,20 +59,6 @@
</script>
<script type="text/javascript" charset="utf-8">
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
@@ -252,7 +238,7 @@
'sDom': "pitirp",
'autoWidth': true,
'iDisplayLength': 500,
- 'deferRender': true,
+ 'deferRender': false,
'paging': true,
'orderClasses': true,
'processing': true,
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index eb998d15..c44231f3 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -59,20 +59,6 @@
</script>
<script type="text/javascript" charset="utf-8">
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
@@ -172,6 +158,7 @@
'title': "Record",
'type': "natural",
'data': null,
+ 'orderDataType': "dom-inner-text",
'render': function(data, type, row, meta) {
return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
}
@@ -252,7 +239,7 @@
'order': [[1, "asc" ]],
'sDom': "pitirp",
'autoWidth': false,
- 'deferRender': true,
+ 'deferRender': false,
'iDisplayLength': 500,
'paging': true,
'orderClasses': true,
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 06b71f53..6b3bec9a 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -17,13 +17,13 @@
</header>
-->
- <div class="container-fluid" style="min-width: 1200px;">
+ <div class="container-fluid" style="min-width: 1210px;">
{{ flash_me() }}
<div class="row" style="width: 100%;">
- <div class="col-xs-5" style="min-width: 530px; max-width: 550px;">
+ <div class="col-xs-4" style="margin-right:50px; min-width: 530px; max-width: 550px;">
<section id="search">
<div>
<h1>Select and search</h1>
@@ -84,7 +84,7 @@
<label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
<div class="col-xs-10 controls" style="padding-left: 20px;">
<div class="col-8">
- <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
+ <textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="or_search"></textarea>
</div>
</div>
</div>
@@ -105,7 +105,7 @@
<label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
<div class="col-xs-10 controls" style="padding-left: 20px;">
<div class="col-8">
- <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
+ <textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="resize: vertical; max-width: 550px; width: 450px !important;" id="and_search"></textarea>
</div>
</div>
</div>
@@ -184,7 +184,7 @@
</section>
</div>
- <div style="padding-left:80px" class="col-xs-4" style="width: 600px !important;">
+ <div class="col-xs-4" style="width: 600px !important;">
<section id="affiliates">
<div class="page-header">
<h1>Affiliates</h1>
diff --git a/wqflask/wqflask/templates/info_page.html b/wqflask/wqflask/templates/info_page.html
new file mode 100644
index 00000000..d8b7d74c
--- /dev/null
+++ b/wqflask/wqflask/templates/info_page.html
@@ -0,0 +1,92 @@
+{% extends "base.html" %}
+{% block title %}Policies{% endblock %}
+{% block content %}
+
+<h1 id="parent-fieldname-title">Data Set Group: {{ info.dataset_name }}
+<!--<a href="/infoshare/manager/member-studies-edit.html?DatasetId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>-->
+<span style="color:red;">{{ info.info_page_name }}</span>
+</h1>
+<table border="0" width="100%">
+<tr>
+<td valign="top" width="50%">
+<table name="info_table" cellSpacing=0 cellPadding=5 width=100% border=0>
+ <tr><td><b>Data Set:</b> {{ info.info_file_title }} <!--<a href="/infoshare/manager/member-infofile-edit.html?GN_AccesionId=%s"><img src="/images/modify.gif" alt="modify this page" border="0" valign="middle"></a>--></td></tr>
+ <tr><td><b>GN Accession:</b> GN{{ gn_accession_id }}</td></tr>
+ <tr><td><b>GEO Series:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_series }}" target="_blank">{{ info.geo_series }}</a></td></tr>
+ <tr><td><b>Title:</b> {{ info.publication_title }}</td></tr>
+ <tr><td><b>Organism:</b> <a href="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id={{ info.taxonomy_id }}" target="_blank">{{ info.menu_name }}</a></td></tr>
+ <tr><td><b>Group:</b> {{ info.group_name }}</td></tr>
+ <tr><td><b>Tissue:</b> {{ info.tissue_name }}</td></tr>
+ <tr><td><b>Dataset Status:</b> {{ info.dataset_status_name }}</td></tr>
+ <tr><td><b>Platforms:</b> <a href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc={{ info.geo_platform }}" target="_blank">{{ info.gene_chip_name }}</a></td></tr>
+ <tr><td><b>Normalization:</b> {{ info.avg_method_name }}</td></tr>
+</table>
+</td>
+<td valign="top" width="50%">
+<table border="0" width="100%">
+ <tr>
+ <td><b>Contact Information</b></td>
+ </tr>
+ <tr>
+ <td>
+ {{ info.investigator_first_name }} {{ info.inveestigator_last_name }}<br>
+ {{ info.organization_name }} <br>
+ {{ info.investigator_address }}<br>
+ {{ info.investigator_city }}, {{ info.investigator_state }} {{ info.investigator_zipcode }} {{ info.investigator_country }}<br>
+ Tel. {{ info.investigator_phone }}<br>
+ {{ info.investigator_email }}<br>
+ <a href="{{ info.investigator_url }}" target="_blank">Website</a>
+ </td>
+ </tr>
+
+<tr>
+ <td><b>Download datasets and supplementary data files</b></td>
+</tr>
+<tr>
+ <td>
+ <ul style="line-height: 160%">
+ {% for file in filelist %}
+ <li><a href="http://datafiles.genenetwork.org/download/GN{{ gn_accession_id }}/{{ file[0] }}">{{ file[0] }} ({{ file[2] }})</a></li>
+ {% endfor %}
+ </ul>
+ </td>
+</tr>
+
+<tr><td>
+</td></tr>
+
+</table>
+</td>
+</tr>
+</table>
+<HR>
+<p>
+<table name="info_table" width="100%" border="0" cellpadding="5" cellspacing="0">
+<tr><td><span style="font-size:115%%;font-weight:bold;">Specifics of this Data Set:</span></td></tr>
+ <tr><td> {{ info.specifics|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%%;font-weight:bold;">Summary:</span></td></tr>
+ <tr><td> {{ info.dataset_summary|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the cases used to generate this set of data:</span></td></tr>
+ <tr><td> {{ info.about_cases|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About the tissue used to generate this set of data:</span></td></tr>
+ <tr><td> {{ info.about_tissue|safe }}<br><br></td></tr>
+ <tr><td><span style="font-size:115%; font-weight:bold;">About the array platform:</span></td></tr>
+ <tr><td> {{ info.about_platform|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">About data values and data processing:</span></td></tr>
+ <tr><td> {{ info.about_data_processing|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Notes:</span></td></tr>
+ <tr><td> {{ info.notes|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Experiment Type:</span></td></tr>
+ <tr><td> {{ info.experiment_design|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Contributor:</span></td></tr>
+ <tr><td> {{ info.contributors|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Citation:</span></td></tr>
+ <tr><td> {{ info.citation|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Data source acknowledgment:</span></td></tr>
+ <tr><td> {{ info.acknowledgement|safe }}<br><br></td></tr>
+<tr><td><span style="font-size:115%; font-weight:bold;">Study Id:</span></td></tr>
+ <tr><td> {{ info.dataset_id }}<br><br></td></tr>
+</table>
+</p>
+
+{% endblock %} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 8edda548..41d760c0 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -228,71 +228,61 @@
<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
<br />
<br />
- <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}500{% else %}470{% endif %}px;">
- <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
- <thead>
- <tr>
- <th></th>
- <th>Row</th>
- <th>Marker</th>
- <th>{{ LRS_LOD }}</th>
- <th>Chr</th>
- {% if plotScale != "physic" %}
- <th>cM</th>
- {% else %}
- <th align="right">Mb</th>
- {% endif %}
- {% if 'additive' in trimmed_markers[0] %}
- <th>Add Eff</th>
- {% endif %}
- {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
- <th>Dom Eff</th>
- {% endif %}
- </tr>
- </thead>
- <tbody>
- {% for marker in trimmed_markers %}
- <tr>
- <td align="center" style="padding: 1px 0px 1px 0px;">
- <input type="checkbox" name="selectCheck"
- class="checkbox trait_checkbox"
- value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
- </td>
- <td align="right">{{ loop.index }}</td>
- <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
- {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
- {% if 'lod_score' in marker %}
- <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
- {% else %}
- <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
- {% endif %}
- {% else %}
- {% if 'lod_score' in marker %}
- <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
- {% else %}
- <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
- {% endif %}
- {% 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 %}
- {% if 'additive' in marker %}
- <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
- {% endif %}
- {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
- <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
- {% endif %}
- </tr>
- {% endfor %}
- </tbody>
- </table>
+ <div id="table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;">
+ <table id="trait_table" class="table-hover table-striped cell-border dataTable no-footer">
+ <thead>
+ <tr>
+ <th></th>
+ <th>Row</th>
+ <th>Marker</th>
+ {% if LRS_LOD == "-log(p)" %}
+ <th>–log(p)</th>
+ {% else %}
+ <th>{{ LRS_LOD }}</th>
+ {% endif %}
+ <th>Position ({% if plotScale == "physic" %}Mb{% else %}cM{% endif %})</th>
+ {% if 'additive' in trimmed_markers[0] %}
+ <th>Add Eff</th>
+ {% endif %}
+ {% if 'dominance' in trimmed_markers[0] and dataset.group.genetic_type != "riset" %}
+ <th>Dom Eff</th>
+ {% endif %}
+ </tr>
+ </thead>
+ <tbody>
+ {% for marker in trimmed_markers %}
+ <tr>
+ <td align="center" style="padding: 1px 0px 1px 0px;">
+ <input type="checkbox" name="selectCheck"
+ class="checkbox trait_checkbox"
+ value="{{ data_hmac('{}:{}Geno'.format(marker.name, dataset.group.name)) }}">
+ </td>
+ <td align="right">{{ loop.index }}</td>
+ <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
+ {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
+ {% if 'lod_score' in marker %}
+ <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
+ {% else %}
+ <td align="right">{{ '%0.2f' | format(marker.lrs_value|float / 4.61) }}</td>
+ {% endif %}
+ {% else %}
+ {% if 'lod_score' in marker %}
+ <td align="right">{{ '%0.2f' | format(marker.lod_score|float * 4.61) }}</td>
+ {% else %}
+ <td align="right">{{ '%0.2f' | format(marker.lrs_value|float) }}</td>
+ {% endif %}
+ {% endif %}
+ <td align="right">{{ marker.display_pos }}</td>
+ {% if 'additive' in marker %}
+ <td align="right">{{ '%0.3f' | format(marker.additive|float) }}</td>
+ {% endif %}
+ {% if 'dominance' in marker and dataset.group.genetic_type != "riset" %}
+ <td align="right">{{ '%0.2f' | format(marker.dominance|float) }}</td>
+ {% endif %}
+ </tr>
+ {% endfor %}
+ </tbody>
+ </table>
</div>
</div>
{% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
@@ -362,8 +352,7 @@
"columns": [
{ "type": "natural", "width": "5%" },
{ "type": "natural", "width": "8%" },
- { "type": "natural", "width": "25%" },
- { "type": "natural" },
+ { "type": "natural", "width": "20%" },
{ "type": "natural" },
{ "type": "natural" }{% if 'additive' in qtlresults[0] %},
{ "type": "natural" }{% endif %}{% if 'dominance' in qtlresults[0] and dataset.group.genetic_type != "riset" %},
@@ -395,16 +384,16 @@
$('td', row).eq(9).attr("align", "right");
},
"columns": [
- { "bSortable": false},
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
- { "type": "natural" },
+ { "orderDataType": "dom-checkbox" },
+ { "type": "natural"},
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
+ { "type": "natural" , "orderDataType": "dom-inner-text" },
{ "type": "natural" },
{ "type": "natural" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" },
+ { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" },
{ "type": "natural" }
],
"columnDefs": [ {
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 53373b41..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -127,7 +127,7 @@
<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-success" 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>
+ <button class="btn btn-default" id="export_traits">Download <span class="glyphicon glyphicon-download"></span></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>
@@ -140,7 +140,6 @@
<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" {% if dataset.type == 'ProbeSet' or dataset.type == 'Publish' %}style="min-width: 1500px;"{% endif %}>
<table class="table-hover table-striped cell-border" id='trait_table' style="float: left; width: {% if dataset.type == 'Geno' %}380px{% else %}100%{% endif %};">
<tbody>
@@ -174,21 +173,6 @@
</script>
<script type="text/javascript" charset="utf-8">
-
- $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $('input', td).prop('checked') ? '1' : '0';
- } );
- };
-
- $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col )
- {
- return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) {
- return $(td).text();
- } );
- }
-
$(document).ready( function () {
$('#trait_table tr').click(function(event) {
@@ -289,10 +273,9 @@
},
{
'title': "Record",
- 'type': "natural",
+ 'type': "natural-minus-na",
'data': null,
'width': "60px",
- 'orderDataType': "dom-inner-text",
'render': function(data, type, row, meta) {
return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset=' + data.dataset + '">' + data.display_name + '</a>'
}
@@ -306,7 +289,6 @@
{
'title': "Description",
'type': "natural",
- 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -319,7 +301,7 @@
{
'title': "Location",
'type': "natural-minus-na",
- 'width': "120px",
+ 'width': "125px",
'data': "location"
},
{
@@ -330,23 +312,23 @@
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+ 'title': "High P<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
'type': "natural-minus-na",
'data': "lrs_score",
- 'width': "80px",
+ 'width': "60px",
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Max LRS Location",
+ 'title': "Peak Location",
'type': "natural-minus-na",
- 'width': "150px",
+ 'width': "125px",
'data': "lrs_location"
},
{
- 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+ 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
'type': "natural-minus-na",
'data': "additive",
- 'width': "120px",
+ 'width': "85px",
'orderSequence': [ "desc", "asc"]
}{% elif dataset.type == 'Publish' %},
{
@@ -382,17 +364,11 @@
author_string = data.authors
}
return author_string
- // try {
- // return decodeURIComponent(escape(author_string))
- // } catch(err){
- // return author_string
- // }
}
},
{
'title': "Year",
'type': "natural-minus-na",
- 'orderDataType': "dom-inner-text",
'data': null,
'width': "80px",
'render': function(data, type, row, meta) {
@@ -405,20 +381,20 @@
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+ 'title': "Max LRS<a href=\"http://genenetwork.org//glossary.html#LRS\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
'type': "natural-minus-na",
'data': "lrs_score",
'width': "80px",
'orderSequence': [ "desc", "asc"]
},
{
- 'title': "Max LRS Location",
+ 'title': "Peak Location",
'type': "natural-minus-na",
- 'width': "150px",
+ 'width': "120px",
'data': "lrs_location"
},
{
- 'title': "Additive Effect<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup>?</sup></a>",
+ 'title': "Effect Size<a href=\"http://genenetwork.org//glossary.html#A\" target=\"_blank\" style=\"color: white;\"><sup style=\"font-size: small; color: #FF0000;\"> ?</sup></a>",
'type': "natural-minus-na",
'width': "120px",
'data': "additive",
@@ -427,7 +403,7 @@
{
'title': "Location",
'type': "natural-minus-na",
- 'width': "140px",
+ 'width': "120px",
'data': "location"
}{% endif %}
],
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 2d65f008..5ed7a90b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -37,7 +37,7 @@
<input type="hidden" name="covariates" value="">
<input type="hidden" name="transform" value="">
- <div class="container" style="min-width: 1450px;">
+ <div class="container" style="min-width: 700px;">
<div class="panel-group" id="accordion">
<div class="panel panel-default">
<div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseOne" aria-expanded="true">
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 1378b91b..9420c9c6 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,5 +1,5 @@
<div>
- <div class="col-xs-7">
+ <div class="col-xs-6" style="min-width: 800px;">
<div style="padding: 20px" class="form-horizontal">
<div class="form-group">
@@ -39,7 +39,7 @@
<div class="form-group">
<label for="corr_return_results" class="col-xs-2 control-label">Return</label>
- <div class="col-xs-3 controls">
+ <div class="col-xs-4 controls">
<select name="corr_return_results" class="form-control">
{% for return_result in corr_tools.return_results_menu %}
<option value="{{ return_result }}"
@@ -55,7 +55,7 @@
<div class="form-group">
<label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
- <div class="col-xs-3 controls">
+ <div class="col-xs-4 controls">
<select name="corr_samples_group" class="form-control">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
@@ -66,7 +66,7 @@
<div id="corr_sample_method" class="form-group">
<label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
- <div class="col-xs-3 controls">
+ <div class="col-xs-4 controls">
<select name="corr_sample_method" class="form-control">
<option value="pearson">Pearson</option>
<option value="spearman">Spearman Rank</option>
@@ -77,7 +77,7 @@
{% if dataset.type != "Publish" %}
<div class="form-group">
<label class="col-xs-2 control-label">Min Expr</label>
- <div class="col-xs-3 controls">
+ <div class="col-xs-4 controls">
<input name="min_expr" value="" type="text" class="form-control" style="width: 70px;">
</div>
</div>
@@ -114,7 +114,7 @@
</div>
</div>
</div>
- <div class="col-xs-5">
+ <div>
<span id="sample_r_desc" class="correlation_desc fs12">
The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
is computed
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 8b3e4907..4aced50c 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -215,43 +215,27 @@
<div style="margin-bottom:15px;" class="btn-toolbar">
<div class="btn-group">
- <a href="#redirect">
- <button type="button" id="add_to_collection" class="btn btn-primary" title="Add to collection">Add</button>
- </a>
+ <button type="button" id="add_to_collection" class="btn btn-success" title="Add to Collection">Add</button>
{% 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&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}">
- <button type="button" class="btn btn-default" title="Find similar expression data">Find</button>
- </a>
+ <button type="button" class="btn btn-default" title="Find similar expression data" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=sch&amp;gene={{ this_trait.symbol }}&amp;alias=1&amp;species={{ dataset.group.species }}', '_blank')">Find</button>
{% endif %}
{% if UCSC_BLAT_URL != "" %}
- <a target="_blank" href="{{ UCSC_BLAT_URL }}">
- <button type="button" class="btn btn-default" title="Check probe locations at UCSC">Verify</button>
- </a>
+ <button type="button" class="btn btn-default" title="Check probe locations at UCSC" onclick="window.open('{{ UCSC_BLAT_URL }}', '_blank')">Verify</button>
{% endif %}
{% if this_trait.symbol != None %}
- <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}">
- <button type="button" class="btn btn-default" title="Write or review comments about this gene">GeneWiki</button>
- </a>
+ <button type="button" class="btn btn-default" title="Write or review comments about this gene" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=geneWiki&symbol={{ this_trait.symbol }}', '_blank')">GeneWiki</button>
{% if dataset.group.species == "mouse" or dataset.group.species == "rat" %}
- <a href="/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on">
- <button type="button" class="btn btn-default" title="View SNPs and Indels">SNPs</button>
- </a>
+ <button type="button" class="btn btn-default" title="View SNPs and Indels" onclick="window.open('/snp_browser?first_run=true&species={{ dataset.group.species }}&gene_name={{ this_trait.symbol }}&limit_strains=on', '_blank')">SNPs</button>
{% endif %}
{% endif %}
{% if show_probes == "True" %}
- <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON">
- <button type="button" class="btn btn-default" title="Check sequence of probes">Probes</button>
- </a>
+ <button type="button" class="btn btn-default" title="Check sequence of probes" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?FormID=showProbeInfo&database={{ this_trait.dataset.name }}&ProbeSetID={{ this_trait.name }}&CellID={{ this_trait.cellid }}&RISet={{ dataset.group.name }}&incparentsf1=ON', '_blank')">Probes</button>
{% endif %}
{% endif %}
- <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>
+ <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1" onclick="window.open('http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}', '_blank')">Go to GN1</button>
{% 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>
+ <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource" onclick="window.open('./resources/manage?resource_id={{ resource_id }}', '_blank')">Edit</button>
{% endif %}
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 05a2be73..a8ed91b1 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -5,7 +5,7 @@
<input type="text" id="{{ sample_type.sample_group_type }}_searchbox" class="form-control" style="width: 200px; display: inline; float: left; vertical-align: top;" placeholder="Search This Table For ...">
</div>
<div style="padding-left: 10px; display: inline;">
- <input type="button" class="btn btn-default export" value="Export">
+ <button class="btn btn-default export">Export <span class="glyphicon glyphicon-download-alt"></span></button>
<select class="select optional span2 export_format">
<option value="excel">Excel</option>
<option value="csv">CSV</option>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 27040045..94388b2f 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -397,8 +397,8 @@
</div>
</div>
</div>
- <div class="col-xs-7">
- <dl style="width: 500px;">
+ <div>
+ <dl>
{% for mapping_method in dataset.group.mapping_names %}
{% if mapping_method == "GEMMA" %}
<dt style="padding-top: 20px;">GEMMA</dt>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 974081d3..7bdb3ef9 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -76,11 +76,13 @@
<i class="icon-signal"></i> Sort By Value
</button>
</div>
+ <!--
<div class="btn-group">
- <button type="button" class="btn btn-default" id="color_by_trait">
+ <button type="button" class="btn btn-default" id="color_by_trait" style="margin-bottom: 5px;">
<i class="icon-tint"></i> Color by Trait
</button>
</div>
+ -->
<div id="bar_chart_container">
<div id="bar_chart"></div>
</div>
diff --git a/wqflask/wqflask/templates/tutorials.html b/wqflask/wqflask/templates/tutorials.html
index 3e6ef01c..f9d12ba5 100644
--- a/wqflask/wqflask/templates/tutorials.html
+++ b/wqflask/wqflask/templates/tutorials.html
@@ -15,3 +15,4 @@ and initial mapping results for Rat GWAS P50 as implemented in GeneNetwork.org</
</TR></TABLE>
{% endblock %}
+
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 9331f369..077a799b 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -453,7 +453,9 @@ def register_user(params):
user_details['confirmed'] = 1
user_details['registration_info'] = basic_info()
- save_user(user_details, user_details['user_id'])
+
+ if len(errors) == 0:
+ save_user(user_details, user_details['user_id'])
return errors
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index fc9949a8..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -29,14 +29,7 @@ import array
import sqlalchemy
from wqflask import app
from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, url_for, send_file
-from wqflask import group_manager
-from wqflask import resource_manager
-from wqflask import search_results
-from wqflask import export_traits
-from wqflask import gsearch
-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 create_dataset, DataSet # Used by YAML in marker_regression
from wqflask.show_trait import show_trait
@@ -53,6 +46,12 @@ 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.search_results import SearchResultPage
+from wqflask.export_traits import export_search_results_csv
+from wqflask.gsearch import GSearch
+from wqflask.update_search_results import GSearch as UpdateGSearch
+from wqflask.docs import Docs, update_text
+from wqflask.db_info import InfoPage
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
@@ -66,9 +65,6 @@ from utility.benchmark import Bench
from pprint import pformat as pf
-from wqflask import user_login
-from wqflask import user_session
-
from wqflask import collect
from wqflask.database import db_session
@@ -215,7 +211,7 @@ def search_page():
logger.info("Skipping Redis cache (USE_REDIS=False)")
logger.info("request.args is", request.args)
- the_search = search_results.SearchResultPage(request.args)
+ the_search = SearchResultPage(request.args)
result = the_search.__dict__
valid_search = result['search_term_exists']
@@ -233,7 +229,7 @@ def search_page():
@app.route("/gsearch", methods=('GET',))
def gsearchact():
logger.info(request.url)
- result = gsearch.GSearch(request.args).__dict__
+ result = GSearch(request.args).__dict__
type = request.args['type']
if type == "gene":
return render_template("gsearch_gene.html", **result)
@@ -244,7 +240,7 @@ def gsearchact():
def gsearch_updating():
logger.info("REQUEST ARGS:", request.values)
logger.info(request.url)
- result = update_search_results.GSearch(request.args).__dict__
+ result = UpdateGSearch(request.args).__dict__
return result['results']
# type = request.args['type']
# if type == "gene":
@@ -257,7 +253,7 @@ def docedit():
logger.info(request.url)
try:
if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
- doc = docs.Docs(request.args['entry'], request.args)
+ doc = Docs(request.args['entry'], request.args)
return render_template("docedit.html", **doc.__dict__)
else:
return "You shouldn't be here!"
@@ -273,7 +269,7 @@ def generated_file(filename):
@app.route("/help")
def help():
logger.info(request.url)
- doc = docs.Docs("help", request.args)
+ doc = Docs("help", request.args)
return render_template("docs.html", **doc.__dict__)
@app.route("/wgcna_setup", methods=('POST',))
@@ -308,54 +304,54 @@ def ctl_results():
@app.route("/news")
def news():
- doc = docs.Docs("news", request.args)
+ doc = Docs("news", request.args)
return render_template("docs.html", **doc.__dict__)
@app.route("/references")
def references():
- doc = docs.Docs("references", request.args)
+ doc = Docs("references", request.args)
return render_template("docs.html", **doc.__dict__)
#return render_template("reference.html")
@app.route("/intro")
def intro():
- doc = docs.Docs("intro", request.args)
+ doc = Docs("intro", request.args)
return render_template("docs.html", **doc.__dict__)
@app.route("/policies")
def policies():
- doc = docs.Docs("policies", request.args)
+ doc = Docs("policies", request.args)
#return render_template("policies.html")
return render_template("docs.html", **doc.__dict__)
@app.route("/links")
def links():
- #doc = docs.Docs("links", request.args)
+ #doc = Docs("links", request.args)
#return render_template("docs.html", **doc.__dict__)
return render_template("links.html")
@app.route("/tutorials")
def tutorials():
- #doc = docs.Docs("links", request.args)
+ #doc = Docs("links", request.args)
#return render_template("docs.html", **doc.__dict__)
return render_template("tutorials.html")
@app.route("/credits")
def credits():
- #doc = docs.Docs("links", request.args)
+ #doc = Docs("links", request.args)
#return render_template("docs.html", **doc.__dict__)
return render_template("credits.html")
@app.route("/environments")
def environments():
- doc = docs.Docs("environments", request.args)
+ doc = Docs("environments", request.args)
return render_template("docs.html", **doc.__dict__)
#return render_template("environments.html", **doc.__dict__)
@app.route("/update_text", methods=('POST',))
def update_page():
- docs.update_text(request.form)
- doc = docs.Docs(request.form['entry_type'], request.form)
+ update_text(request.form)
+ doc = Docs(request.form['entry_type'], request.form)
return render_template("docs.html", **doc.__dict__)
@app.route("/submit_trait")
@@ -370,7 +366,7 @@ def create_temp_trait():
#template_vars = submit_trait.SubmitTrait(request.form)
- doc = docs.Docs("links")
+ doc = Docs("links")
return render_template("links.html", **doc.__dict__)
#return render_template("show_trait.html", **template_vars.__dict__)
@@ -425,7 +421,7 @@ def export_traits_csv():
logger.info("In export_traits_csv")
logger.info("request.form:", request.form)
logger.info(request.url)
- file_list = export_traits.export_search_results_csv(request.form)
+ file_list = export_search_results_csv(request.form)
if len(file_list) > 1:
now = datetime.datetime.now()
@@ -908,12 +904,24 @@ def snp_browser_page():
return render_template("snp_browser.html", **template_vars.__dict__)
+@app.route("/db_info", methods=('GET',))
+def db_info_page():
+ template_vars = InfoPage(request.args)
+
+ return render_template("info_page.html", **template_vars.__dict__)
+
@app.route("/tutorial/WebQTLTour", methods=('GET',))
def tutorial_page():
#ZS: Currently just links to GN1
logger.info(request.url)
return redirect("http://gn1.genenetwork.org/tutorial/WebQTLTour/")
+@app.route("/tutorial/security", methods=('GET',))
+def security_tutorial_page():
+ #ZS: Currently just links to GN1
+ logger.info(request.url)
+ return render_template("admin/security_help.html")
+
@app.route("/submit_bnw", methods=('POST',))
def submit_bnw():
logger.info(request.url)
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 880a1cb2..70077703 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -1,5 +1,8 @@
-# WGCNA analysis for GN2
-# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
+WGCNA analysis for GN2
+
+Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
+"""
import sys
from numpy import *
import scipy as sp # SciPy
@@ -17,106 +20,138 @@ from utility import helper_functions
from rpy2.robjects.packages import importr
utils = importr("utils")
-## Get pointers to some common R functions
-r_library = ro.r["library"] # Map the library function
-r_options = ro.r["options"] # Map the options function
-r_read_csv = ro.r["read.csv"] # Map the read.csv function
-r_dim = ro.r["dim"] # Map the dim function
-r_c = ro.r["c"] # Map the c function
-r_cat = ro.r["cat"] # Map the cat function
-r_paste = ro.r["paste"] # Map the paste function
-r_unlist = ro.r["unlist"] # Map the unlist function
-r_unique = ro.r["unique"] # Map the unique function
-r_length = ro.r["length"] # Map the length function
-r_unlist = ro.r["unlist"] # Map the unlist function
-r_list = ro.r.list # Map the list function
-r_matrix = ro.r.matrix # Map the matrix function
-r_seq = ro.r["seq"] # Map the seq function
-r_table = ro.r["table"] # Map the table function
-r_names = ro.r["names"] # Map the names function
-r_sink = ro.r["sink"] # Map the sink function
-r_is_NA = ro.r["is.na"] # Map the is.na function
-r_file = ro.r["file"] # Map the file function
-r_png = ro.r["png"] # Map the png function for plotting
-r_dev_off = ro.r["dev.off"] # Map the dev.off function
+# Get pointers to some common R functions
+r_library = ro.r["library"] # Map the library function
+r_options = ro.r["options"] # Map the options function
+r_read_csv = ro.r["read.csv"] # Map the read.csv function
+r_dim = ro.r["dim"] # Map the dim function
+r_c = ro.r["c"] # Map the c function
+r_cat = ro.r["cat"] # Map the cat function
+r_paste = ro.r["paste"] # Map the paste function
+r_unlist = ro.r["unlist"] # Map the unlist function
+r_unique = ro.r["unique"] # Map the unique function
+r_length = ro.r["length"] # Map the length function
+r_unlist = ro.r["unlist"] # Map the unlist function
+r_list = ro.r.list # Map the list function
+r_matrix = ro.r.matrix # Map the matrix function
+r_seq = ro.r["seq"] # Map the seq function
+r_table = ro.r["table"] # Map the table function
+r_names = ro.r["names"] # Map the names function
+r_sink = ro.r["sink"] # Map the sink function
+r_is_NA = ro.r["is.na"] # Map the is.na function
+r_file = ro.r["file"] # Map the file function
+r_png = ro.r["png"] # Map the png function for plotting
+r_dev_off = ro.r["dev.off"] # Map the dev.off function
+
class WGCNA(object):
def __init__(self):
+ # To log output from stdout/stderr to a file add `r_sink(log)`
print("Initialization of WGCNA")
- #log = r_file("/tmp/genenetwork_wcgna.log", open = "wt")
- #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
- #r_sink(log, type = "message")
- r_library("WGCNA") # Load WGCNA - Should only be done once, since it is quite expensive
- r_options(stringsAsFactors = False)
+
+ # Load WGCNA - Should only be done once, since it is quite expensive
+ r_library("WGCNA")
+ r_options(stringsAsFactors=False)
print("Initialization of WGCNA done, package loaded in R session")
- self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"] # Map the enableWGCNAThreads function
- self.r_pickSoftThreshold = ro.r["pickSoftThreshold"] # Map the pickSoftThreshold function
- self.r_blockwiseModules = ro.r["blockwiseModules"] # Map the blockwiseModules function
- self.r_labels2colors = ro.r["labels2colors"] # Map the labels2colors function
- self.r_plotDendroAndColors = ro.r["plotDendroAndColors"] # Map the plotDendroAndColors function
+ # Map the enableWGCNAThreads function
+ self.r_enableWGCNAThreads = ro.r["enableWGCNAThreads"]
+ # Map the pickSoftThreshold function
+ self.r_pickSoftThreshold = ro.r["pickSoftThreshold"]
+ # Map the blockwiseModules function
+ self.r_blockwiseModules = ro.r["blockwiseModules"]
+ # Map the labels2colors function
+ self.r_labels2colors = ro.r["labels2colors"]
+ # Map the plotDendroAndColors function
+ self.r_plotDendroAndColors = ro.r["plotDendroAndColors"]
print("Obtained pointers to WGCNA functions")
def run_analysis(self, requestform):
print("Starting WGCNA analysis on dataset")
- self.r_enableWGCNAThreads() # Enable multi threading
- self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
- print("Retrieved phenotype data from database", requestform['trait_list'])
+ # Enable multi threading
+ self.r_enableWGCNAThreads()
+ self.trait_db_list = [trait.strip()
+ for trait in requestform['trait_list'].split(',')]
+ print("Retrieved phenotype data from database",
+ requestform['trait_list'])
helper_functions.get_trait_db_obs(self, self.trait_db_list)
- self.input = {} # self.input contains the phenotype values we need to send to R
- strains = [] # All the strains we have data for (contains duplicates)
- traits = [] # All the traits we have data for (should not contain duplicates)
+ # self.input contains the phenotype values we need to send to R
+ self.input = {}
+ # All the strains we have data for (contains duplicates)
+ strains = []
+ # All the traits we have data for (should not contain duplicates)
+ traits = []
for trait in self.trait_list:
traits.append(trait[0].name)
self.input[trait[0].name] = {}
for strain in trait[0].data:
strains.append(strain)
- self.input[trait[0].name][strain] = trait[0].data[strain].value
+ self.input[trait[0].name][strain] = trait[0].data[strain].value
# Transfer the load data from python to R
- uStrainsR = r_unique(ro.Vector(strains)) # Unique strains in R vector
+ # Unique strains in R vector
+ uStrainsR = r_unique(ro.Vector(strains))
uTraitsR = r_unique(ro.Vector(traits)) # Unique traits in R vector
r_cat("The number of unique strains:", r_length(uStrainsR), "\n")
r_cat("The number of unique traits:", r_length(uTraitsR), "\n")
- # rM is the datamatrix holding all the data in R /rows = strains columns = traits
- rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(uTraitsR), dimnames = r_list(uStrainsR, uTraitsR))
+ # rM is the datamatrix holding all the data in
+ # R /rows = strains columns = traits
+ rM = ro.r.matrix(ri.NA_Real, nrow=r_length(uStrainsR), ncol=r_length(
+ uTraitsR), dimnames=r_list(uStrainsR, uTraitsR))
for t in uTraitsR:
- trait = t[0] # R uses vectors every single element is a vector
+ # R uses vectors every single element is a vector
+ trait = t[0]
for s in uStrainsR:
- strain = s[0] # R uses vectors every single element is a vector
- #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
- rM.rx[strain, trait] = self.input[trait].get(strain) # Update the matrix location
+ # R uses vectors every single element is a vector
+ strain = s[0]
+ rM.rx[strain, trait] = self.input[trait].get(
+ strain) # Update the matrix location
sys.stdout.flush()
self.results = {}
- self.results['nphe'] = r_length(uTraitsR)[0] # Number of phenotypes/traits
- self.results['nstr'] = r_length(uStrainsR)[0] # Number of strains
+ # Number of phenotypes/traits
+ self.results['nphe'] = r_length(uTraitsR)[0]
+ self.results['nstr'] = r_length(
+ uStrainsR)[0] # Number of strains
self.results['phenotypes'] = uTraitsR # Traits used
- self.results['strains'] = uStrainsR # Strains used in the analysis
- self.results['requestform'] = requestform # Store the user specified parameters for the output page
+ # Strains used in the analysis
+ self.results['strains'] = uStrainsR
+ # Store the user specified parameters for the output page
+ self.results['requestform'] = requestform
- # Calculate soft threshold if the user specified the SoftThreshold variable
+ # Calculate soft threshold if the user specified the
+ # SoftThreshold variable
if requestform.get('SoftThresholds') is not None:
- powers = [int(threshold.strip()) for threshold in requestform['SoftThresholds'].rstrip().split(",")]
- rpow = r_unlist(r_c(powers))
- print "SoftThresholds: {} == {}".format(powers, rpow)
- self.sft = self.r_pickSoftThreshold(rM, powerVector = rpow, verbose = 5)
-
- print "PowerEstimate: {}".format(self.sft[0])
- self.results['PowerEstimate'] = self.sft[0]
- if self.sft[0][0] is ri.NA_Integer:
- print "No power is suitable for the analysis, just use 1"
- self.results['Power'] = 1 # No power could be estimated
- else:
- self.results['Power'] = self.sft[0][0] # Use the estimated power
+ powers = [int(threshold.strip())
+ for threshold in requestform['SoftThresholds'].rstrip().split(",")]
+ rpow = r_unlist(r_c(powers))
+ print("SoftThresholds: {} == {}".format(powers, rpow))
+ self.sft = self.r_pickSoftThreshold(
+ rM, powerVector=rpow, verbose=5)
+
+ print("PowerEstimate: {}".format(self.sft[0]))
+ self.results['PowerEstimate'] = self.sft[0]
+ if self.sft[0][0] is ri.NA_Integer:
+ print "No power is suitable for the analysis, just use 1"
+ # No power could be estimated
+ self.results['Power'] = 1
+ else:
+ # Use the estimated power
+ self.results['Power'] = self.sft[0][0]
else:
- # The user clicked a button, so no soft threshold selection
- self.results['Power'] = requestform.get('Power') # Use the power value the user gives
+ # The user clicked a button, so no soft threshold selection
+ # Use the power value the user gives
+ self.results['Power'] = requestform.get('Power')
# Create the block wise modules using WGCNA
- network = self.r_blockwiseModules(rM, power = self.results['Power'], TOMType = requestform['TOMtype'], minModuleSize = requestform['MinModuleSize'], verbose = 3)
+ network = self.r_blockwiseModules(
+ rM,
+ power=self.results['Power'],
+ TOMType=requestform['TOMtype'],
+ minModuleSize=requestform['MinModuleSize'],
+ verbose=3)
# Save the network for the GUI
self.results['network'] = network
@@ -130,7 +165,9 @@ class WGCNA(object):
self.results['imgloc'] = GENERATED_IMAGE_DIR + self.results['imgurl']
r_png(self.results['imgloc'], width=1000, height=600, type='cairo-png')
mergedColors = self.r_labels2colors(network[1])
- self.r_plotDendroAndColors(network[5][0], mergedColors, "Module colors", dendroLabels = False, hang = 0.03, addGuide = True, guideHang = 0.05)
+ self.r_plotDendroAndColors(network[5][0], mergedColors,
+ "Module colors", dendroLabels=False,
+ hang=0.03, addGuide=True, guideHang=0.05)
r_dev_off()
sys.stdout.flush()
@@ -146,11 +183,9 @@ class WGCNA(object):
print("Processing WGCNA output")
template_vars = {}
template_vars["input"] = self.input
- template_vars["powers"] = self.sft[1:] # Results from the soft threshold analysis
+ # Results from the soft threshold analysis
+ template_vars["powers"] = self.sft[1:]
template_vars["results"] = self.results
self.render_image(results)
sys.stdout.flush()
- #r_sink(type = "message") # This restores R output to the stdout/stderr
- #r_sink() # We should end the Rpy session more or less
return(dict(template_vars))
-