From 527bb0459cf488e5021696e326dc10d28ecdd74c Mon Sep 17 00:00:00 2001
From: Sam Ockman
Date: Thu, 24 May 2012 02:18:20 -0400
Subject: Trying to get stuff working under new structure

---
 wqflask/base/webqtlDataset.py | 160 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 160 insertions(+)
 create mode 100755 wqflask/base/webqtlDataset.py

(limited to 'wqflask/base/webqtlDataset.py')

diff --git a/wqflask/base/webqtlDataset.py b/wqflask/base/webqtlDataset.py
new file mode 100755
index 00000000..da1b8601
--- /dev/null
+++ b/wqflask/base/webqtlDataset.py
@@ -0,0 +1,160 @@
+# 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")
+
+
+
+
+	
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