Merge branch 'flask' of http://github.com/zsloan/genenetwork

1 files changed, 743 insertions, 0 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
new file mode 100755
index 00000000..50ef8f57
--- /dev/null
+++ b/wqflask/base/data_set.py
@@ -0,0 +1,743 @@
+# 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