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Diffstat (limited to 'web/webqtl/search/PubmedSearch.py')
| -rwxr-xr-x | web/webqtl/search/PubmedSearch.py | 94 |
1 files changed, 0 insertions, 94 deletions
diff --git a/web/webqtl/search/PubmedSearch.py b/web/webqtl/search/PubmedSearch.py deleted file mode 100755 index 17c1d1ec..00000000 --- a/web/webqtl/search/PubmedSearch.py +++ /dev/null @@ -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
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