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diff --git a/web/webqtl/base/webqtlDataset.py b/web/webqtl/base/webqtlDataset.py
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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
-#
-#
-#
-# 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:
- """
- Database class defines a database in webqtl, can be either Microarray,
- Published phenotype, genotype, or user input database(temp)
- """
-
- def __init__(self, dbName, cursor=None):
-
- assert dbName
- self.id = 0
- self.name = ''
- self.type = ''
- self.riset = ''
- 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()
-
- def __str__(self):
- return self.name
-
- __repr__ = __str__
-
-
- def getRISet(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)
- RISet, RIID = self.cursor.fetchone()
- if RISet == 'BXD300':
- RISet = "BXD"
- self.riset = RISet
- self.risetid = RIID
- return RISet
-
-
- 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")
-
-
-
-
-