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-rw-r--r--wqflask/base/trait.py68
1 files changed, 53 insertions, 15 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6fecf725..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -3,6 +3,7 @@ from __future__ import absolute_import, division, print_function
import string
import resource
import codecs
+import requests
import redis
Redis = redis.StrictRedis()
@@ -12,6 +13,7 @@ from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from db import webqtlDatabaseFunction
from utility import webqtlUtil
+from utility import hmac
from wqflask import app
@@ -24,8 +26,6 @@ from flask import Flask, g, request, url_for
from utility.logger import getLogger
logger = getLogger(__name__ )
-from wqflask import user_manager
-
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -60,6 +60,7 @@ class GeneralTrait(object):
self.num_overlap = None
self.strand_probe = None
self.symbol = None
+ self.display_name = self.name
self.LRS_score_repr = "N/A"
self.LRS_location_repr = "N/A"
@@ -120,11 +121,36 @@ class GeneralTrait(object):
@property
def alias_fmt(self):
'''Return a text formatted alias'''
+
+ alias = 'Not available'
if self.alias:
alias = string.replace(self.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
- else:
- alias = 'Not available'
+
+ return alias
+
+ @property
+ def wikidata_alias_fmt(self):
+ '''Return a text formatted alias'''
+
+ alias = 'Not available'
+ if self.symbol:
+ human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper())
+ mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize())
+ other_response = requests.get("http://gn2.genenetwork.org/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)
+
+ filtered_aliases = []
+ seen = set()
+ for item in alias_list:
+ if item in seen:
+ continue
+ else:
+ filtered_aliases.append(item)
+ seen.add(item)
+ alias = "; ".join(filtered_aliases)
return alias
@@ -277,7 +303,7 @@ def jsonable_table_row(trait, dataset_name, index):
additive = "N/A"
else:
additive = "%.3f" % round(float(trait.additive), 2)
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ 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>',
trait.symbol,
@@ -293,7 +319,7 @@ def jsonable_table_row(trait, dataset_name, index):
else:
additive = "%.2f" % round(float(trait.additive), 2)
if trait.pubmed_id:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ 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>',
trait.description_display,
@@ -303,7 +329,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
else:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ 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>',
trait.description_display,
@@ -313,7 +339,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
elif dataset.type == "Geno":
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ 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>',
trait.location_repr]
@@ -326,21 +352,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if dataset.type == 'Publish':
query = """
SELECT
- PublishXRef.Id, Publication.PubMed_ID,
+ PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
- PublishXRef, Publication, Phenotype, PublishFreeze
+ PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
@@ -390,17 +417,25 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait_info = g.db.execute(query,
(string.join(dataset.display_fields,','),
dataset.type, trait.name)).fetchone()
+
if trait_info:
trait.haveinfo = True
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
+ # if isinstance(trait_info[i], basestring):
+ # logger.debug("HOLDER:", holder)
+ # logger.debug("HOLDER2:", holder.decode(encoding='latin1'))
+ # holder = unicode(trait_info[i], "utf-8", "ignore")
if isinstance(trait_info[i], basestring):
- holder = unicode(trait_info[i], "utf-8", "ignore")
+ holder = holder.encode('latin1')
setattr(trait, field, holder)
if dataset.type == 'Publish':
+ if trait.group_code:
+ trait.display_name = trait.group_code + "_" + str(trait.name)
+
trait.confidential = 0
if trait.pre_publication_description and not trait.pubmed_id:
trait.confidential = 1
@@ -427,6 +462,10 @@ 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")
+
if not trait.year.isdigit():
trait.pubmed_text = "N/A"
else:
@@ -464,7 +503,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#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 = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
+ trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
@@ -495,9 +536,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
- else:
- trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
-
if dataset.type == 'Publish':
query = """
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-28 04:40:32 +0000