Renamed webqtlDataSet.py to data_set.py

Renamed the class webqtlDataset to DataSet

Finished cisLRS and transLRS search types in d_search.py

Fixed parent/f1 issue in show_trait.py

1 files changed, 162 insertions, 0 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
new file mode 100755
index 00000000..992c673e
--- /dev/null
+++ b/wqflask/base/data_set.py
@@ -0,0 +1,162 @@
+# 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
+#
+#
+#
+# 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 htmlgen import HTMLgen2 as HT
+
+import webqtlConfig
+
+
+
+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, 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()
+            
+    
+    # Delete this eventually
+    @property
+    def riset():
+        Weve_Renamed_This_As_Group
+
+
+    def get_group(self):
+        assert self.cursor
+        if self.type == 'Publish':
+            query = '''
+                            SELECT
+                                    InbredSet.Name, InbredSet.Id
+                            FROM
+                                    InbredSet, PublishFreeze
+                            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
+
+
+    def retrieveName(self):
+        assert self.id == 0 and self.cursor
+        query = '''
+                SELECT
+                        Id, Name, FullName, ShortName
+                FROM
+                        %sFreeze
+                WHERE
+                        public > %d AND
+                        (Name = "%s" OR FullName = "%s" OR ShortName = "%s")
+          '''% (self.type, webqtlConfig.PUBLICTHRESH, self.name, self.name, self.name)
+        try:
+            self.cursor.execute(query)
+            self.id,self.name,self.fullname,self.shortname=self.cursor.fetchone()
+        except:
+            raise KeyError, `self.name`+' doesn\'t exist.'
+
+
+    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):
+    
+    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