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authorZachary Sloan2013-01-11 23:59:41 +0000
committerZachary Sloan2013-01-11 23:59:41 +0000
commit2b2970d167c5b555e0e0ad0b34b72f817c1fac91 (patch)
tree36fa8c708138fff03593e0f50cc933bcb62b5592 /wqflask/base/data_set.py
parent1db9237a05fd27c80dc963db9916072594156198 (diff)
parentd39b691994a395c45fa242de6d64d12a5470af10 (diff)
downloadgenenetwork2-2b2970d167c5b555e0e0ad0b34b72f817c1fac91.tar.gz
Merge branch 'flask' of http://github.com/zsloan/genenetwork
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+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License
+# as published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the GNU Affero General Public License for more details.
+#
+# This program is available from Source Forge: at GeneNetwork Project
+# (sourceforge.net/projects/genenetwork/).
+#
+# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
+# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
+#
+#we
+#
+# This module is used by GeneNetwork project (www.genenetwork.org)
+
+from __future__ import absolute_import, print_function, division
+import os
+
+from flask import Flask, g
+
+from htmlgen import HTMLgen2 as HT
+
+import reaper
+
+from base import webqtlConfig
+from base import species
+from dbFunction import webqtlDatabaseFunction
+from utility import webqtlUtil
+
+from MySQLdb import escape_string as escape
+from pprint import pformat as pf
+
+# Used by create_database to instantiate objects
+DS_NAME_MAP = {}
+
+def create_dataset(dataset_name):
+ #cursor = db_conn.cursor()
+ print("dataset_name:", dataset_name)
+
+ query = """
+ SELECT DBType.Name
+ FROM DBList, DBType
+ WHERE DBList.Name = '%s' and
+ DBType.Id = DBList.DBTypeId
+ """ % (escape(dataset_name))
+ print("query is: ", pf(query))
+ dataset_type = g.db.execute(query).fetchone().Name
+
+ #dataset_type = cursor.fetchone()[0]
+ print("[blubber] dataset_type:", pf(dataset_type))
+
+ dataset_ob = DS_NAME_MAP[dataset_type]
+ #dataset_class = getattr(data_set, dataset_ob)
+ print("dataset_ob:", dataset_ob)
+ print("DS_NAME_MAP:", pf(DS_NAME_MAP))
+
+ dataset_class = globals()[dataset_ob]
+ return dataset_class(dataset_name)
+
+
+class DatasetGroup(object):
+ """
+ Each group has multiple datasets; each species has multiple groups.
+
+ For example, Mouse has multiple groups (BXD, BXA, etc), and each group
+ has multiple datasets associated with it.
+
+ """
+ def __init__(self, dataset):
+ """This sets self.group and self.group_id"""
+ self.name, self.id = g.db.execute(dataset.query_for_group).fetchone()
+ if self.name == 'BXD300':
+ self.name = "BXD"
+
+ self.species = webqtlDatabaseFunction.retrieve_species(self.name)
+
+ self.incparentsf1 = False
+ self.f1list = None
+ self.parlist = None
+ self.allsamples = None
+
+
+ #def read_genotype(self):
+ # self.read_genotype_file()
+ #
+ # if not self.genotype: # Didn'd succeed, so we try method 2
+ # self.read_genotype_data()
+
+ def read_genotype_file(self):
+ '''read genotype from .geno file instead of database'''
+ #if self.group == 'BXD300':
+ # self.group = 'BXD'
+ #
+ #assert self.group, "self.group needs to be set"
+
+ #genotype_1 is Dataset Object without parents and f1
+ #genotype_2 is Dataset Object with parents and f1 (not for intercross)
+
+ genotype_1 = reaper.Dataset()
+
+ # reaper barfs on unicode filenames, so here we ensure it's a string
+ full_filename = str(os.path.join(webqtlConfig.GENODIR, self.name + '.geno'))
+ genotype_1.read(full_filename)
+
+ print("Got to after read")
+
+ try:
+ # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
+ f1, f12, maternal, paternal = webqtlUtil.ParInfo[self.name]
+ except KeyError:
+ f1 = f12 = maternal = paternal = None
+
+
+ if genotype_1.type == "group" and maternal and paternal:
+ genotype_2 = genotype_1.add(Mat=maternal, Pat=paternal) #, F1=_f1)
+ else:
+ genotype_2 = genotype_1
+
+ #determine default genotype object
+ if self.incparentsf1 and genotype_1.type != "intercross":
+ self.genotype = genotype_2
+ else:
+ self.incparentsf1 = 0
+ self.genotype = genotype_1
+
+ self.samplelist = list(self.genotype.prgy)
+
+ if f1 and f12:
+ self.f1list = [f1, f12]
+ if maternal and paternal:
+ self.parlist = [maternal, paternal]
+
+
+class DataSet(object):
+ """
+ DataSet class defines a dataset in webqtl, can be either Microarray,
+ Published phenotype, genotype, or user input dataset(temp)
+
+ """
+
+ def __init__(self, name):
+
+ assert name, "Need a name"
+ self.name = name
+ self.id = None
+ self.type = None
+
+ self.setup()
+
+ self.check_confidentiality()
+
+ self.retrieve_other_names()
+
+ self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ self.species = species.TheSpecies(self)
+
+
+
+ def get_desc(self):
+ """Gets overridden later, at least for Temp...used by trait's get_given_name"""
+ return None
+
+ #@staticmethod
+ #def get_by_trait_id(trait_id):
+ # """Gets the dataset object given the trait id"""
+ #
+ #
+ #
+ # name = g.db.execute(""" SELECT
+ #
+ # """)
+ #
+ # return DataSet(name)
+
+ # Delete this eventually
+ @property
+ def riset():
+ Weve_Renamed_This_As_Group
+
+
+ #@property
+ #def group(self):
+ # if not self._group:
+ # self.get_group()
+ #
+ # return self._group
+
+
+
+ def retrieve_other_names(self):
+ """
+ If the data set name parameter is not found in the 'Name' field of the data set table,
+ check if it is actually the FullName or ShortName instead.
+
+ This is not meant to retrieve the data set info if no name at all is passed.
+
+ """
+
+ query_args = tuple(escape(x) for x in (
+ (self.type + "Freeze"),
+ str(webqtlConfig.PUBLICTHRESH),
+ self.name,
+ self.name,
+ self.name))
+ print("query_args are:", query_args)
+
+ print("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args))
+
+ self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+ SELECT Id, Name, FullName, ShortName
+ FROM %s
+ WHERE public > %s AND
+ (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+ """ % (query_args)).fetchone()
+
+ #self.cursor.execute(query)
+ #self.id, self.name, self.fullname, self.shortname = self.cursor.fetchone()
+
+
+ #def genHTML(self, Class='c0dd'):
+ # return HT.Href(text = HT.Span('%s Database' % self.fullname, Class= "fwb " + Class),
+ # url= webqtlConfig.INFOPAGEHREF % self.name,target="_blank")
+
+class PhenotypeDataSet(DataSet):
+ DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
+
+ def setup(self):
+ # Fields in the database table
+ self.search_fields = ['Phenotype.Post_publication_description',
+ 'Phenotype.Pre_publication_description',
+ 'Phenotype.Pre_publication_abbreviation',
+ 'Phenotype.Post_publication_abbreviation',
+ 'Phenotype.Lab_code',
+ 'Publication.PubMed_ID',
+ 'Publication.Abstract',
+ 'Publication.Title',
+ 'Publication.Authors',
+ 'PublishXRef.Id']
+
+ # Figure out what display_fields is
+ self.display_fields = ['name',
+ 'pubmed_id',
+ 'pre_publication_description',
+ 'post_publication_description',
+ 'original_description',
+ 'pre_publication_abbreviation',
+ 'post_publication_abbreviation',
+ 'lab_code',
+ 'submitter', 'owner',
+ 'authorized_users',
+ 'authors', 'title',
+ 'abstract', 'journal',
+ 'volume', 'pages',
+ 'month', 'year',
+ 'sequence', 'units', 'comments']
+
+ # Fields displayed in the search results table header
+ self.header_fields = ['',
+ 'ID',
+ 'Description',
+ 'Authors',
+ 'Year',
+ 'Max LRS',
+ 'Max LRS Location']
+
+ self.type = 'Publish'
+
+ self.query_for_group = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, PublishFreeze
+ WHERE
+ PublishFreeze.InbredSetId = InbredSet.Id AND
+ PublishFreeze.Name = "%s"
+ ''' % escape(self.name)
+
+ def check_confidentiality(self):
+ # (Urgently?) Need to write this
+ pass
+
+ def get_trait_info(self, trait_list, species = ''):
+ for this_trait in trait_list:
+ if not this_trait.haveinfo:
+ this_trait.retrieveInfo(QTL=1)
+
+ description = this_trait.post_publication_description
+ if this_trait.confidential:
+ continue # for now
+ if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
+ description = this_trait.pre_publication_description
+ this_trait.description_display = description
+
+ if not this_trait.year.isdigit():
+ this_trait.pubmed_text = "N/A"
+
+ if this_trait.pubmed_id:
+ this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
+
+ #LRS and its location
+ this_trait.LRS_score_repr = "N/A"
+ this_trait.LRS_score_value = 0
+ this_trait.LRS_location_repr = "N/A"
+ this_trait.LRS_location_value = 1000000
+
+ if this_trait.lrs:
+ result = g.db.execute("""
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = %s and
+ Geno.Name = %s and
+ Geno.SpeciesId = Species.Id
+ """, (species, this_trait.locus)).fetchone()
+ #result = self.cursor.fetchone()
+
+ if result:
+ if result[0] and result[1]:
+ LRS_Chr = result[0]
+ LRS_Mb = result[1]
+
+ #XZ: LRS_location_value is used for sorting
+ try:
+ LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
+ except:
+ if LRS_Chr.upper() == 'X':
+ LRS_location_value = 20*1000 + float(LRS_Mb)
+ else:
+ LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
+
+ this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
+ this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb))
+
+ def retrieve_sample_data(self, trait):
+ query = """
+ SELECT
+ Strain.Name, PublishData.value, PublishSE.error, NStrain.count
+ FROM
+ (PublishData, Strain, PublishXRef, PublishFreeze)
+ left join PublishSE on
+ (PublishSE.DataId = PublishData.Id AND PublishSE.StrainId = PublishData.StrainId)
+ left join NStrain on
+ (NStrain.DataId = PublishData.Id AND
+ NStrain.StrainId = PublishData.StrainId)
+ WHERE
+ PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishData.Id = PublishXRef.DataId AND PublishXRef.Id = %s AND
+ PublishFreeze.Id = %d AND PublishData.StrainId = Strain.Id
+ Order BY
+ Strain.Name
+ """ % (trait.name, self.id)
+ results = g.db.execute(query).fetchall()
+ return results
+
+
+class GenotypeDataSet(DataSet):
+ DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
+
+ def setup(self):
+ # Fields in the database table
+ self.search_fields = ['Name',
+ 'Chr']
+
+ # Find out what display_fields is
+ self.display_fields = ['name',
+ 'chr',
+ 'mb',
+ 'source2',
+ 'sequence']
+
+ # Fields displayed in the search results table header
+ self.header_fields = ['',
+ 'ID',
+ 'Location']
+
+ # Todo: Obsolete or rename this field
+ self.type = 'Geno'
+
+ self.query_for_group = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, GenoFreeze
+ WHERE
+ GenoFreeze.InbredSetId = InbredSet.Id AND
+ GenoFreeze.Name = "%s"
+ ''' % escape(self.name)
+
+ def check_confidentiality(self):
+ return geno_mrna_confidentiality(self)
+
+ def get_trait_info(self, trait_list, species=None):
+ for this_trait in trait_list:
+ if not this_trait.haveinfo:
+ this_trait.retrieveInfo()
+
+ #XZ: trait_location_value is used for sorting
+ trait_location_repr = 'N/A'
+ trait_location_value = 1000000
+
+ if this_trait.chr and this_trait.mb:
+ try:
+ trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+ except:
+ if this_trait.chr.upper() == 'X':
+ trait_location_value = 20*1000 + this_trait.mb
+ else:
+ trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
+
+ this_trait.location_repr = 'Chr%s: %.4f' % (this_trait.chr, float(this_trait.mb) )
+ this_trait.location_value = trait_location_value
+
+ def retrieve_sample_data(self, trait):
+ query = """
+ SELECT
+ Strain.Name, GenoData.value, GenoSE.error, GenoData.Id
+ FROM
+ (GenoData, GenoFreeze, Strain, Geno, GenoXRef)
+ left join GenoSE on
+ (GenoSE.DataId = GenoData.Id AND GenoSE.StrainId = GenoData.StrainId)
+ WHERE
+ Geno.SpeciesId = %s AND Geno.Name = '%s' AND GenoXRef.GenoId = Geno.Id AND
+ GenoXRef.GenoFreezeId = GenoFreeze.Id AND
+ GenoFreeze.Name = '%s' AND
+ GenoXRef.DataId = GenoData.Id AND
+ GenoData.StrainId = Strain.Id
+ Order BY
+ Strain.Name
+ """ % (webqtlDatabaseFunction.retrieve_species_id(self.group.name), trait.name, self.name)
+ results = g.db.execute(query).fetchall()
+ return results
+
+
+class MrnaAssayDataSet(DataSet):
+ '''
+ An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait
+
+ This used to be called ProbeSet, but that term only refers specifically to the Affymetrix
+ platform and is far too specific.
+
+ '''
+ DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
+
+ def setup(self):
+ # Fields in the database table
+ self.search_fields = ['Name',
+ 'Description',
+ 'Probe_Target_Description',
+ 'Symbol',
+ 'Alias',
+ 'GenbankId',
+ 'UniGeneId',
+ 'RefSeq_TranscriptId']
+
+ # Find out what display_fields is
+ self.display_fields = ['name', 'symbol',
+ 'description', 'probe_target_description',
+ 'chr', 'mb',
+ 'alias', 'geneid',
+ 'genbankid', 'unigeneid',
+ 'omim', 'refseq_transcriptid',
+ 'blatseq', 'targetseq',
+ 'chipid', 'comments',
+ 'strand_probe', 'strand_gene',
+ 'probe_set_target_region',
+ 'probe_set_specificity',
+ 'probe_set_blat_score',
+ 'probe_set_blat_mb_start',
+ 'probe_set_blat_mb_end',
+ 'probe_set_strand',
+ 'probe_set_note_by_rw',
+ 'flag']
+
+ # Fields displayed in the search results table header
+ self.header_fields = ['',
+ 'ID',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean Expr',
+ 'Max LRS',
+ 'Max LRS Location']
+
+ # Todo: Obsolete or rename this field
+ self.type = 'ProbeSet'
+
+ self.query_for_group = '''
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, ProbeSetFreeze, ProbeFreeze
+ WHERE
+ ProbeFreeze.InbredSetId = InbredSet.Id AND
+ ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+ ProbeSetFreeze.Name = "%s"
+ ''' % escape(self.name)
+
+
+ def check_confidentiality(self):
+ return geno_mrna_confidentiality(self)
+
+ def get_trait_info(self, trait_list=None, species=''):
+
+ # Note: setting trait_list to [] is probably not a great idea.
+ if not trait_list:
+ trait_list = []
+
+ for this_trait in trait_list:
+
+ if not this_trait.haveinfo:
+ this_trait.retrieveInfo(QTL=1)
+
+ if this_trait.symbol:
+ pass
+ else:
+ this_trait.symbol = "N/A"
+
+ #XZ, 12/08/2008: description
+ #XZ, 06/05/2009: Rob asked to add probe target description
+ description_string = str(this_trait.description).strip()
+ target_string = str(this_trait.probe_target_description).strip()
+
+ description_display = ''
+
+ if len(description_string) > 1 and description_string != 'None':
+ description_display = description_string
+ else:
+ description_display = this_trait.symbol
+
+ if len(description_display) > 1 and description_display != 'N/A' and len(target_string) > 1 and target_string != 'None':
+ description_display = description_display + '; ' + target_string.strip()
+
+ # Save it for the jinja2 template
+ this_trait.description_display = description_display
+ #print(" xxxxdd [%s]: %s" % (type(this_trait.description_display), description_display))
+
+ #XZ: trait_location_value is used for sorting
+ trait_location_repr = 'N/A'
+ trait_location_value = 1000000
+
+ if this_trait.chr and this_trait.mb:
+ try:
+ trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+ except:
+ if this_trait.chr.upper() == 'X':
+ trait_location_value = 20*1000 + this_trait.mb
+ else:
+ trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
+
+ this_trait.location_repr = 'Chr %s: %.4f Mb' % (this_trait.chr, float(this_trait.mb) )
+ this_trait.location_value = trait_location_value
+ #this_trait.trait_location_value = trait_location_value
+
+ #XZ, 01/12/08: This SQL query is much faster.
+ query = (
+"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
+ where ProbeSetXRef.ProbeSetFreezeId = %s and
+ ProbeSet.Id = ProbeSetXRef.ProbeSetId and
+ ProbeSet.Name = '%s'
+ """ % (escape(str(this_trait.dataset.id)),
+ escape(this_trait.name)))
+
+ print("query is:", pf(query))
+
+ result = g.db.execute(query).fetchone()
+
+ if result:
+ if result[0]:
+ mean = result[0]
+ else:
+ mean=0
+ else:
+ mean = 0
+
+ #XZ, 06/05/2009: It is neccessary to turn on nowrap
+ this_trait.mean = repr = "%2.3f" % mean
+
+ #LRS and its location
+ this_trait.LRS_score_repr = 'N/A'
+ this_trait.LRS_score_value = 0
+ this_trait.LRS_location_repr = 'N/A'
+ this_trait.LRS_location_value = 1000000
+
+ #Max LRS and its Locus location
+ if this_trait.lrs and this_trait.locus:
+ self.cursor.execute("""
+ select Geno.Chr, Geno.Mb from Geno, Species
+ where Species.Name = '%s' and
+ Geno.Name = '%s' and
+ Geno.SpeciesId = Species.Id
+ """ % (species, this_trait.locus))
+ result = self.cursor.fetchone()
+
+ if result:
+ if result[0] and result[1]:
+ LRS_Chr = result[0]
+ LRS_Mb = result[1]
+
+ #XZ: LRS_location_value is used for sorting
+ try:
+ LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
+ except:
+ if LRS_Chr.upper() == 'X':
+ LRS_location_value = 20*1000 + float(LRS_Mb)
+ else:
+ LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
+
+ this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
+ this_trait.LRS_location_repr = LRS_location_repr = 'Chr %s: %.4f Mb' % (LRS_Chr, float(LRS_Mb) )
+
+ def get_sequence(self):
+ query = """
+ SELECT
+ ProbeSet.BlatSeq
+ FROM
+ ProbeSet, ProbeSetFreeze, ProbeSetXRef
+ WHERE
+ ProbeSet.Id=ProbeSetXRef.ProbeSetId and
+ ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
+ ProbeSet.Name = %s
+ ProbeSetFreeze.Name = %s
+ """ % (escape(self.name), escape(self.dataset.name))
+ results = g.db.execute(query).fetchone()
+
+ return results[0]
+
+ def retrieve_sample_data(self, trait):
+ query = """
+ SELECT
+ Strain.Name, ProbeSetData.value, ProbeSetSE.error, ProbeSetData.Id
+ FROM
+ (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
+ left join ProbeSetSE on
+ (ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
+ WHERE
+ ProbeSet.Name = '%s' AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetFreeze.Name = '%s' AND
+ ProbeSetXRef.DataId = ProbeSetData.Id AND
+ ProbeSetData.StrainId = Strain.Id
+ Order BY
+ Strain.Name
+ """ % (escape(trait.name), escape(self.name))
+ results = g.db.execute(query).fetchall()
+ return results
+
+
+class TempDataSet(DataSet):
+ '''Temporary user-generated data set'''
+
+ def setup(self):
+ self.search_fields = ['name',
+ 'description']
+
+ self.display_fields = ['name',
+ 'description']
+
+ self.header_fields = ['Name',
+ 'Description']
+
+ self.type = 'Temp'
+
+ # Need to double check later how these are used
+ self.id = 1
+ self.fullname = 'Temporary Storage'
+ self.shortname = 'Temp'
+
+
+ @staticmethod
+ def handle_pca(desc):
+ if 'PCA' in desc:
+ # Todo: Modernize below lines
+ desc = desc[desc.rindex(':')+1:].strip()
+ else:
+ desc = desc[:desc.index('entered')].strip()
+ return desc
+
+ def get_desc(self):
+ g.db.execute('SELECT description FROM Temp WHERE Name=%s', self.name)
+ desc = g.db.fetchone()[0]
+ desc = self.handle_pca(desc)
+ return desc
+
+ def get_group(self):
+ self.cursor.execute("""
+ SELECT
+ InbredSet.Name, InbredSet.Id
+ FROM
+ InbredSet, Temp
+ WHERE
+ Temp.InbredSetId = InbredSet.Id AND
+ Temp.Name = "%s"
+ """, self.name)
+ self.group, self.group_id = self.cursor.fetchone()
+ #return self.group
+
+ def retrieve_sample_data(self, trait):
+ query = """
+ SELECT
+ Strain.Name, TempData.value, TempData.SE, TempData.NStrain, TempData.Id
+ FROM
+ TempData, Temp, Strain
+ WHERE
+ TempData.StrainId = Strain.Id AND
+ TempData.Id = Temp.DataId AND
+ Temp.name = '%s'
+ Order BY
+ Strain.Name
+ """ % escape(trait.name)
+
+ results = g.db.execute(query).fetchall()
+
+
+def geno_mrna_confidentiality(ob):
+ dataset_table = ob.type + "Freeze"
+ print("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
+
+ query = '''SELECT Id, Name, FullName, confidentiality,
+ AuthorisedUsers FROM %s WHERE Name = %%s''' % (dataset_table)
+
+ result = g.db.execute(query, ob.name)
+
+ (dataset_id,
+ name,
+ full_name,
+ confidential,
+ authorized_users) = result.fetchall()[0]
+
+ if confidential:
+ # Allow confidential data later
+ NoConfindetialDataForYouTodaySorry