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-rw-r--r--wqflask/base/trait.py194
1 files changed, 117 insertions, 77 deletions
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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 14:54:28 +0000