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-rw-r--r--wqflask/base/data_set.py40
-rw-r--r--wqflask/base/trait.py194
-rw-r--r--wqflask/tests/wqflask/test_collect.py57
-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/docs.py4
-rw-r--r--wqflask/wqflask/resource_manager.py20
-rw-r--r--wqflask/wqflask/static/new/javascript/search_results.js10
-rw-r--r--wqflask/wqflask/templates/collections/view.html30
-rw-r--r--wqflask/wqflask/templates/correlation_matrix.html2
-rw-r--r--wqflask/wqflask/templates/correlation_page.html32
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html10
-rw-r--r--wqflask/wqflask/templates/search_result_page.html21
-rw-r--r--wqflask/wqflask/views.py4
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py181
16 files changed, 376 insertions, 279 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 8f8b5b70..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"
@@ -504,8 +539,10 @@ 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 str(description_string or "") != "" and description_string != 'None':
description_display = description_string
@@ -514,7 +551,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if (str(description_display or "") != "" and
description_display != 'N/A' and
- str(target_string or "") != "" and target_string != 'None'):
+ str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
@@ -522,15 +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 = ""
@@ -601,10 +640,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
trait.locus = trait.lrs = trait.additive = ""
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))
+ 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.'
-
+ raise KeyError, `trait.name`+ ' information is not found in the database.'
+
return trait
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/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/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/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/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 61134a88..86660126 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -261,6 +261,12 @@ $(function() {
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 ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) {
return 0;
@@ -276,10 +282,10 @@ $(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)
}
});
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index ca8aece3..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 }}">
@@ -85,7 +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>
@@ -97,7 +97,7 @@
<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 style="font-size: small; color: #FF0000;"> ?</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>
@@ -164,13 +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">
@@ -185,22 +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/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/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 487c6980..2318bfb8 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -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>
@@ -274,10 +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>'
}
@@ -291,7 +289,6 @@
{
'title': "Description",
'type': "natural",
- 'width': "500px",
'data': null,
'render': function(data, type, row, meta) {
try {
@@ -304,7 +301,7 @@
{
'title': "Location",
'type': "natural-minus-na",
- 'width': "120px",
+ 'width': "125px",
'data': "location"
},
{
@@ -315,23 +312,23 @@
'orderSequence': [ "desc", "asc"]
},
{
- '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>",
+ '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': "Peak Location",
'type': "natural-minus-na",
- 'width': "120px",
+ 'width': "125px",
'data': "lrs_location"
},
{
'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' %},
{
@@ -367,17 +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) {
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 42a10c7a..94ec7137 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -50,7 +50,7 @@ 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
+from wqflask.docs import Docs, update_text
from wqflask.db_info import InfoPage
from utility import temp_data
@@ -350,7 +350,7 @@ def environments():
@app.route("/update_text", methods=('POST',))
def update_page():
- docs.update_text(request.form)
+ update_text(request.form)
doc = Docs(request.form['entry_type'], request.form)
return render_template("docs.html", **doc.__dict__)
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))
-
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 21:11:00 +0000