From 218576a04f90cc0bc9e53685323e1caa8cffe986 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 4 Jun 2020 15:50:56 -0500
Subject: Added back in trait info queries for situations where the proxy isn't
running
---
wqflask/base/trait.py | 94 +++++++++++++++++++++++++++++++++++++++++++--------
1 file changed, 80 insertions(+), 14 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index b133bf21..405c4ebf 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,9 +1,11 @@
from __future__ import absolute_import, division, print_function
+import os
import string
import resource
import codecs
import requests
+import random
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
@@ -12,8 +14,8 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility import hmac
from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL
-from utility.redis_tools import get_redis_conn
+from utility.tools import GN2_BASE_URL, GN_VERSION
+from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
Redis = get_redis_conn()
from wqflask import app
@@ -22,7 +24,7 @@ import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g, request, url_for, redirect
+from flask import Flask, g, request, url_for, redirect, make_response, render_template
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -45,7 +47,10 @@ def create_trait(**kw):
permitted = check_resource_availability(dataset)
if permitted:
- return GeneralTrait(**kw)
+ the_trait = GeneralTrait(**kw)
+ if the_trait.dataset.type != "Temp":
+ the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
+ return the_trait
else:
return None
@@ -99,9 +104,6 @@ class GeneralTrait(object):
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
- if self.dataset.type != "Temp":
- self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
-
if get_sample_info != False:
self = retrieve_sample_data(self, self.dataset)
@@ -373,17 +375,15 @@ def jsonable_table_row(trait, dataset_name, index):
else:
return dict()
+
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
+ resource_id = get_resource_id(dataset, trait.name)
if dataset.type == 'Publish':
- resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait.name))
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
- elif dataset.type == 'ProbeSet':
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
- the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
else:
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+
the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
try:
@@ -394,11 +394,77 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
except:
resource_info = get_resource_info(resource_id)
default_permissions = resource_info['default_mask']['data']
- if 'view' not in default_persmissions:
+ if 'view' not in default_permissions:
trait.view = False
return trait
- trait_info = json.loads(response)
+ if dataset.type == 'Publish':
+ query = """
+ SELECT
+ PublishXRef.Id, Publication.PubMed_ID,
+ Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
+ Publication.Authors, Publication.Title, Publication.Abstract,
+ Publication.Journal, Publication.Volume, Publication.Pages,
+ Publication.Month, Publication.Year, PublishXRef.Sequence,
+ Phenotype.Units, PublishXRef.comments
+ FROM
+ PublishXRef, Publication, Phenotype, PublishFreeze
+ WHERE
+ PublishXRef.Id = %s AND
+ Phenotype.Id = PublishXRef.PhenotypeId AND
+ Publication.Id = PublishXRef.PublicationId AND
+ PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishFreeze.Id = %s
+ """ % (trait.name, dataset.id)
+
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+
+
+ #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+ #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+ elif dataset.type == 'ProbeSet':
+ display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
+ display_fields_string = 'ProbeSet.' + display_fields_string
+ query = """
+ SELECT %s
+ FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSet.Name = '%s'
+ """ % (escape(display_fields_string),
+ escape(dataset.name),
+ escape(str(trait.name)))
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+ #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+ # to avoid the problem of same marker name from different species.
+ elif dataset.type == 'Geno':
+ display_fields_string = string.join(dataset.display_fields,',Geno.')
+ display_fields_string = 'Geno.' + display_fields_string
+ query = """
+ SELECT %s
+ FROM Geno, GenoFreeze, GenoXRef
+ WHERE
+ GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+ GenoXRef.GenoId = Geno.Id AND
+ GenoFreeze.Name = '%s' AND
+ Geno.Name = '%s'
+ """ % (escape(display_fields_string),
+ escape(dataset.name),
+ escape(trait.name))
+ logger.sql(query)
+ trait_info = g.db.execute(query).fetchone()
+ else: #Temp type
+ query = """SELECT %s FROM %s WHERE Name = %s"""
+ logger.sql(query)
+ trait_info = g.db.execute(query,
+ (string.join(dataset.display_fields,','),
+ dataset.type, trait.name)).fetchone()
if trait_info:
trait.haveinfo = True
--
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