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, 0 insertions, 157 deletions

diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
deleted file mode 100755
index 933077fd..00000000
--- a/wqflask/base/webqtlDataset.py
+++ /dev/null
@@ -1,157 +0,0 @@
-# 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 webqtlDataset:
-    """
-    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:
-            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'
-        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")