diff options
Diffstat (limited to 'wqflask/base/trait.py')
| -rw-r--r-- | wqflask/base/trait.py | 32 |
1 files changed, 22 insertions, 10 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 4bce25ac..9566c192 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -9,7 +9,7 @@ from htmlgen import HTMLgen2 as HT from base import webqtlConfig from base.webqtlCaseData import webqtlCaseData from base.data_set import create_dataset -from dbFunction import webqtlDatabaseFunction +from db import webqtlDatabaseFunction from utility import webqtlUtil from wqflask import app @@ -20,6 +20,9 @@ from pprint import pformat as pf from flask import Flask, g, request +from utility.logger import getLogger +logger = getLogger(__name__ ) + def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss print("{}: {}".format(stage, mem/1024)) @@ -253,6 +256,7 @@ class GeneralTrait(object): PublishFreeze.Id = %s """ % (self.name, self.dataset.id) + logger.sql(query) trait_info = g.db.execute(query).fetchone() @@ -272,6 +276,7 @@ class GeneralTrait(object): """ % (escape(display_fields_string), escape(self.dataset.name), escape(str(self.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. @@ -289,9 +294,11 @@ class GeneralTrait(object): """ % (escape(display_fields_string), escape(self.dataset.name), escape(self.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(self.dataset.display_fields,','), self.dataset.type, self.name)).fetchone() @@ -362,6 +369,7 @@ class GeneralTrait(object): InbredSet.SpeciesId = Species.Id AND Species.TaxonomyId = Homologene.TaxonomyId """ % (escape(str(self.geneid)), escape(self.dataset.group.name)) + logger.sql(query) result = g.db.execute(query).fetchone() #else: # result = None @@ -423,6 +431,7 @@ class GeneralTrait(object): ProbeSet.Name = "{}" AND ProbeSetXRef.ProbeSetFreezeId ={} """.format(self.name, self.dataset.id) + logger.sql(query) trait_qtl = g.db.execute(query).fetchone() if trait_qtl: self.locus, self.lrs, self.pvalue, self.mean, self.additive= trait_qtl @@ -433,6 +442,7 @@ class GeneralTrait(object): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(self.dataset.group.species, self.locus) + logger.sql(query) result = g.db.execute(query).fetchone() if result: self.locus_chr = result[0] @@ -446,7 +456,7 @@ class GeneralTrait(object): if self.dataset.type == 'Publish': - trait_qtl = g.db.execute(""" + query = """ SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive FROM @@ -455,7 +465,9 @@ class GeneralTrait(object): PublishXRef.Id = %s AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND PublishFreeze.Id =%s - """, (self.name, self.dataset.id)).fetchone() + """ % (self.name, self.dataset.id) + logger.sql(query) + trait_qtl = g.db.execute(query).fetchone() if trait_qtl: self.locus, self.lrs, self.additive = trait_qtl if self.locus: @@ -465,6 +477,7 @@ class GeneralTrait(object): Geno.Name = '{}' and Geno.SpeciesId = Species.Id """.format(self.dataset.group.species, self.locus) + logger.sql(query) result = g.db.execute(query).fetchone() if result: self.locus_chr = result[0] @@ -651,12 +664,12 @@ class GeneralTrait(object): """ if self.cellid: - self.cursor.execute(""" - select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze - where - ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND - ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id) - probeDBName = self.cursor.fetchone()[0] + query = """ select ProbeFreeze.Name from ProbeFreeze, ProbeSetFreeze where + ProbeFreeze.Id = + ProbeSetFreeze.ProbeFreezeId AND + ProbeSetFreeze.Id = %d""" % thisTrait.dataset.id + logger.sql(query) + probeDBName = g.db.execute(query).fetchone()[0] return dict(name = probeDBName, url = None) else: @@ -724,4 +737,3 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data - |