Latest version of GN source codes

1 files changed, 94 insertions, 0 deletions

diff --git a/web/webqtl/search/PubmedSearch.py b/web/webqtl/search/PubmedSearch.py
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+++ b/web/webqtl/search/PubmedSearch.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
+
+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
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