Created subclass for each main data set type and moved the code

for getting trait info that was in search_results.py into its respective class

Renamed webqtlDataset to DataSet/create_dataset in webqtlTrait.py,
webqtlDatabaseFunction.py, and CorrelationPage.py

Got search page running again for mRNA assay data sets with these changes

1 files changed, 454 insertions, 102 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 992c673e..9e3e6d81 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -19,64 +19,64 @@
 #
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
+
+from __future__ import print_function, division
 
 from htmlgen import HTMLgen2 as HT
 
 import webqtlConfig
 
+from pprint import pformat as pf
 
+# Used by create_database to instantiate objects
+DS_NAME_MAP = {}
+
+def create_dataset(db_conn, dataset_name):
+    cursor = db_conn.cursor()
+    cursor.execute("""
+        SELECT DBType.Name
+        FROM DBList, DBType
+        WHERE DBList.Name = %s and
+              DBType.Id = DBList.DBTypeId
+        """, (dataset_name))
+    print("dataset_name:", dataset_name)
+    dataset_type = cursor.fetchone()[0]
+    print("dataset_type:", pf(dataset_type))
+    
+    dataset_ob = DS_NAME_MAP[dataset_type]
+    #dataset_class = getattr(data_set, dataset_ob)
+    
+    print("DS_NAME_MAP:", pf(DS_NAME_MAP))
+    
+    dataset_class = globals()[dataset_ob]
+    return dataset_class(dataset_name, db_conn)
 
 class DataSet(object):
     """
-    Dataset class defines a dataset in webqtl, can be either Microarray,
+    DataSet class defines a dataset in webqtl, can be either Microarray,
     Published phenotype, genotype, or user input dataset(temp)
 
     """
 
-    def __init__(self, dbName, cursor=None):
-
-        assert dbName
-        self.id = 0
-        self.name = ''
-        self.type = ''
-        self.group = ''
-        self.cursor = cursor
-
-        #temporary storage
-        if dbName.find('Temp') >= 0:
-            self.searchfield = ['name','description']
-            self.disfield = ['name','description']
-            self.type = 'Temp'
-            self.id = 1
-            self.fullname = 'Temporary Storage'
-            self.shortname = 'Temp'
-        elif dbName.find('Publish') >= 0:
-            pass
-        elif dbName.find('Geno') >= 0:
-            self.searchfield = ['name','chr']
-            self.disfield = ['name','chr','mb', 'source2', 'sequence']
-            self.type = 'Geno'
-        else: #ProbeSet
-            self.searchfield = ['name','description','probe_target_description',
-                    'symbol','alias','genbankid','unigeneid','omim',
-                    'refseq_transcriptid','probe_set_specificity', 'probe_set_blat_score']
-            self.disfield = ['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']
-            self.type = 'ProbeSet'
-        self.name = dbName
-        if self.cursor and self.id == 0:
-            self.retrieveName()
-            
-    
+    def __init__(self, name, db_conn):
+
+        assert name
+        self.name = name
+        self.db_conn = db_conn
+        self.cursor = self.db_conn.cursor()
+        self.id = None
+        self.type = None
+        self.group = None
+
+        #if self.cursor and self.id == 0:
+        self.setup()
+        
+        self.check_confidentiality()
+        
+        self.retrieve_name()
+        self.get_group()
+        
+
     # Delete this eventually
     @property
     def riset():
@@ -85,8 +85,93 @@ class DataSet(object):
 
     def get_group(self):
         assert self.cursor
-        if self.type == 'Publish':
-            query = '''
+        self.cursor.execute(self.query)
+        self.group, self.group_id = self.cursor.fetchone()
+        if self.group == 'BXD300':
+            self.group = "BXD"
+        #return group
+
+
+    def retrieve_name(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(self.db_conn.escape_string(x) for x in (
+            (self.type + "Freeze"),
+            str(webqtlConfig.PUBLICTHRESH),
+            self.name,
+            self.name,
+            self.name))
+        print("query_args are:", query_args)
+        
+        query = '''
+                SELECT
+                        Id, Name, FullName, ShortName
+                FROM
+                        %s
+                WHERE
+                        public > %s AND
+                        (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
+          ''' % (query_args)
+            
+        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 = '''
                             SELECT
                                     InbredSet.Name, InbredSet.Id
                             FROM
@@ -94,69 +179,336 @@ class DataSet(object):
                             WHERE
                                     PublishFreeze.InbredSetId = InbredSet.Id AND
                                     PublishFreeze.Name = "%s"
-                    ''' % self.name
-        elif self.type == 'Geno':
-            query = '''
-                            SELECT
-                                    InbredSet.Name, InbredSet.Id
-                            FROM
-                                    InbredSet, GenoFreeze
-                            WHERE
-                                    GenoFreeze.InbredSetId = InbredSet.Id AND
-                                    GenoFreeze.Name = "%s"
-                    ''' % self.name
-        elif self.type == 'ProbeSet':
-            query = '''
-                            SELECT
-                                    InbredSet.Name, InbredSet.Id
-                            FROM
-                                    InbredSet, ProbeSetFreeze, ProbeFreeze
-                            WHERE
-                                    ProbeFreeze.InbredSetId = InbredSet.Id AND
-                                    ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
-                                    ProbeSetFreeze.Name = "%s"
-                    ''' % self.name
-        else:
-            return ""
-        self.cursor.execute(query)
-        group, RIID = self.cursor.fetchone()
-        if group == 'BXD300':
-            group = "BXD"
-        self.group = group
-        self.group_id = RIID
-        return group
+                    ''' % self.db_conn.escape_string(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:
+                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:
+                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]
 
-    def retrieveName(self):
-        assert self.id == 0 and self.cursor
+                        #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) )    
+        
+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'
+        
         query = '''
                 SELECT
-                        Id, Name, FullName, ShortName
+                        InbredSet.Name, InbredSet.Id
                 FROM
-                        %sFreeze
+                        InbredSet, GenoFreeze
                 WHERE
-                        public > %d AND
-                        (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
-          '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
-        try:
+                        GenoFreeze.InbredSetId = InbredSet.Id AND
+                        GenoFreeze.Name = "%s"
+                ''' % self.db_conn.escape_string(self.name)
+                
+    def check_confidentiality(self):
+        return geno_mrna_confidentiality(self)
+    
+    def get_trait_info(self, trait_list):
+        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    
+    
+                
+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 = '''
+                        SELECT
+                                InbredSet.Name, InbredSet.Id
+                        FROM
+                                InbredSet, ProbeSetFreeze, ProbeFreeze
+                        WHERE
+                                ProbeFreeze.InbredSetId = InbredSet.Id AND
+                                ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND
+                                ProbeSetFreeze.Name = "%s"
+                ''' % self.db_conn.escape_string(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 tablet
+            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'
+            """ % (self.db_conn.escape_string(str(this_trait.db.id)),
+                   self.db_conn.escape_string(this_trait.name)))
+
+            print("query is:", pf(query))
+            
             self.cursor.execute(query)
-            self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
-        except:
-            raise KeyError, `self.name`+' doesn\'t exist.'
+            result = self.cursor.fetchone()
 
+            if result:
+                if result[0]:
+                    mean = result[0]
+                else:
+                    mean=0
+            else:
+                mean = 0
 
-    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")
+            #XZ, 06/05/2009: It is neccessary to turn on nowrap
+            this_trait.mean = repr = "%2.3f" % mean
 
-class PhenotypeDataSet(DataSet):
+            #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) )    
+
+
+class TempDataSet(DataSet):
+    '''Temporary user-generated data set'''
     
-    def __init__(self):
-        self.searchfield = ['name','post_publication_description','abstract','title','authors']
-        self.disfield = ['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']
-        self.type = 'Publish'
\ No newline at end of file
+    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'
+        
+        
+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)
+
+    ob.cursor.execute(query, ob.name)
+
+    (dataset_id,
+     name,
+     full_name,
+     confidential,
+     authorized_users) = ob.cursor.fetchall()[0]
+
+    if confidential:
+        # Allow confidential data later
+        NoConfindetialDataForYouTodaySorry
+    
\ No newline at end of file