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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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