diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/mrna_assay_tissue_data.py | 7 | ||||
| -rw-r--r-- | wqflask/base/species.py | 16 | ||||
| -rw-r--r-- | wqflask/base/trait.py | 18 |
3 files changed, 30 insertions, 11 deletions
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py index 039f5d1f..5511af06 100644 --- a/wqflask/base/mrna_assay_tissue_data.py +++ b/wqflask/base/mrna_assay_tissue_data.py @@ -11,6 +11,9 @@ from MySQLdb import escape_string as escape from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + class MrnaAssayTissueData(object): def __init__(self, gene_symbols=None): @@ -54,7 +57,7 @@ class MrnaAssayTissueData(object): as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol and t.Mean = x.maxmean; '''.format(in_clause) - + logger.sql(query) results = g.db.execute(query).fetchall() lower_symbols = [] @@ -99,6 +102,7 @@ class MrnaAssayTissueData(object): TissueProbeSetXRef.DataId = TissueProbeSetData.Id""".format(db_tools.create_in_clause(id_list)) print("TISSUE QUERY:", query) + logger.sql(query) results = g.db.execute(query).fetchall() for result in results: @@ -157,4 +161,3 @@ class MrnaAssayTissueData(object): # # if len(tissue_data.gene_symbols): # return get_symbol_values_pairs(tissue_data) - diff --git a/wqflask/base/species.py b/wqflask/base/species.py index 79d867c8..ce763fc3 100644 --- a/wqflask/base/species.py +++ b/wqflask/base/species.py @@ -10,6 +10,9 @@ from utility import Bunch from pprint import pformat as pf +from utility.logger import getLogger +logger = getLogger(__name__ ) + class TheSpecies(object): def __init__(self, dataset): self.dataset = dataset @@ -48,16 +51,17 @@ class Chromosomes(object): self.dataset = dataset self.chromosomes = collections.OrderedDict() - results = g.db.execute(""" + + query = """ Select Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet where Chr_Length.SpeciesId = InbredSet.SpeciesId AND - InbredSet.Name = %s + InbredSet.Name = '%s' Order by OrderId - """, self.dataset.group.name).fetchall() - #print("group: ", self.dataset.group.name) - #print("bike:", results) + """ % self.dataset.group.name + logger.sql(query) + results = g.db.execute(query).fetchall() for item in results: self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) @@ -120,4 +124,4 @@ class Chromosomes(object): # Testing #if __name__ == '__main__': -# foo = dict(bar=dict(length))
\ No newline at end of file +# foo = dict(bar=dict(length)) diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 3dc4ddda..4d4d1a42 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -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)) @@ -259,6 +262,7 @@ class GeneralTrait(object): PublishFreeze.Id = %s """ % (self.name, self.dataset.id) + logger.sql(query) trait_info = g.db.execute(query).fetchone() @@ -278,6 +282,7 @@ 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. @@ -295,9 +300,11 @@ 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() @@ -368,6 +375,7 @@ 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 @@ -429,6 +437,7 @@ 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 @@ -439,6 +448,7 @@ 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] @@ -452,7 +462,7 @@ class GeneralTrait(object): if self.dataset.type == 'Publish': - trait_qtl = g.db.execute(""" + query = """ SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive FROM @@ -461,7 +471,9 @@ 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: @@ -471,6 +483,7 @@ 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] @@ -730,4 +743,3 @@ def get_sample_data(): # jsonable_sample_data[sample] = trait_ob.data[sample].value # #return jsonable_sample_data - |