Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 160 deletions

diff --git a/web/webqtl/base/webqtlDataset.py b/web/webqtl/base/webqtlDataset.py
deleted file mode 100755
index da1b8601..00000000
--- a/web/webqtl/base/webqtlDataset.py
+++ /dev/null
@@ -1,160 +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:
-	"""
-	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")
-
-
-
-
-