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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:
"""
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.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")
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