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-rwxr-xr-xweb/webqtl/search/PubmedSearch.py94
1 files changed, 0 insertions, 94 deletions
diff --git a/web/webqtl/search/PubmedSearch.py b/web/webqtl/search/PubmedSearch.py
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--- a/web/webqtl/search/PubmedSearch.py
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@@ -1,94 +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
-
-import re
-
-from dbFunction import webqtlDatabaseFunction
-
-import logging
-logging.basicConfig(filename="/tmp/gn_log_leiyan", level=logging.INFO)
-_log = logging.getLogger("PubmedSearch")
-
-#########################################
-# name=megan inst=washington
-#########################################
-
-class PubmedSearch:
-
-		def __init__(self, s, ProbeSetFreezeId):
-				cursor = webqtlDatabaseFunction.getCursor()
-				if (not cursor):
-						return
-				self.olds = s
-				self.news = s
-				sql = "SELECT ProbeSet.Symbol FROM pubmedsearch,ProbeSet,ProbeSetXRef WHERE "
-				#
-				pattern_name = re.compile('\s*name\s*[:=]((\s*\(.+?\)\s*)|(\s*\S+\s*))', re.I)
-				search_name = pattern_name.search(self.news)
-				if search_name:
-					self.news = self.news.replace(search_name.group(), ' ')
-					keywords = search_name.group(1)
-					keywords = keywords.strip()
-					keywords = keywords.strip('(')
-					keywords = keywords.strip(')')
-					keywords = keywords.strip()
-					keywords = keywords.split()
-					for keyword in keywords:
-						sql += "(MATCH (pubmedsearch.authorfullname,authorshortname) AGAINST ('%s' IN BOOLEAN MODE)) AND " % keyword
-				_log.info("news_1: "+self.news)
-				#
-				pattern_inst = re.compile('\s*inst\s*[:=]((\s*\(.+?\)\s*)|(\s*\S+\s*))', re.I)
-				search_inst = pattern_inst.search(self.news)
-				if search_inst:
-					self.news = self.news.replace(search_inst.group(), ' ')
-					keywords = search_inst.group(1)
-					keywords = keywords.strip()
-					keywords = keywords.strip('(')
-					keywords = keywords.strip(')')
-					keywords = keywords.strip()
-					keywords = keywords.split()
-					for keyword in keywords:
-						sql += "(MATCH (pubmedsearch.institute) AGAINST ('%s' IN BOOLEAN MODE)) AND " % keyword
-				_log.info("news_2: "+self.news)
-				#
-				if search_name or search_inst:
-					sql += "pubmedsearch.geneid=ProbeSet.GeneId AND "
-					sql += "ProbeSet.Id=ProbeSetXRef.ProbeSetId AND "
-					sql += "ProbeSetXRef.ProbeSetFreezeId=%d " % ProbeSetFreezeId
-					sql += "GROUP BY ProbeSet.Symbol;"
-					_log.info("sql: "+sql)
-					cursor.execute(sql)
-					symbols1 = cursor.fetchall()
-					symbols2 = ''
-					for symbol in symbols1:
-						symbols2 += (symbol[0]+' ')
-					self.news = symbols2 + self.news
-					_log.info("symbols2: "+symbols2)
-				else:
-					self.news = self.olds
-
-		def getNewS(self):
-				return self.news
\ No newline at end of file