Update of /cvsroot/pymerase/pymerase/examples/ncbi
In directory sc8-pr-cvs1:/tmp/cvs-serv11587
Added Files:
pubmed-test.py
Log Message:
example command-line program which allows you to do a search and saves
the results to a local postgresql database.
--- NEW FILE: pubmed-test.py ---
#!/usr/bin/env python2.2
###########################################################################
# #
# C O P Y R I G H T N O T I C E #
# Copyright (c) 2003 by: #
# * California Institute of Technology #
# #
# All Rights Reserved. #
# #
# Permission is hereby granted, free of charge, to any person #
# obtaining a copy of this software and associated documentation files #
# (the "Software"), to deal in the Software without restriction, #
# including without limitation the rights to use, copy, modify, merge, #
# publish, distribute, sublicense, and/or sell copies of the Software, #
# and to permit persons to whom the Software is furnished to do so, #
# subject to the following conditions: #
# #
# The above copyright notice and this permission notice shall be #
# included in all copies or substantial portions of the Software. #
# #
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, #
# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF #
# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND #
# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS #
# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN #
# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN #
# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE #
# SOFTWARE. #
###########################################################################
#
# Authors: Brandon King
# Last Modified: $Date: 2003/06/05 23:33:32 $
#
import os
import sys
import getopt
import time
from PubMedAPI import DBSession
from Bio import PubMed
from Bio import Medline
rev = "$Revision: 1.1 $"
rev = rev.replace('$Revision: ', '')
rev = rev.replace(' $', '')
VERSION = 'v0.%s' % (rev)
def printUseage():
useage = """
Welcome to PubMed-Test!
Useage:
pubmed-test.py -s [search]
pubmed-test.py --search=[search]
Options:
-s, --search=[foo] Pubmed Search you would like to try.
-v, --version Displays version number
-h, --help Displays this help page
"""
print useage
def parseCommandLine():
"""
Processes Command Line Arguments
return (source, inputModule, destination, outputModule)
"""
try:
opts, args = getopt.getopt(sys.argv[1:], "s:hv",
["search=",
"version",
"help"])
except getopt.GetoptError:
print "-------------------------------"
print "- Invalid Command Line Option -"
print "-------------------------------"
printUseage()
sys.exit(2)
if len(sys.argv) <= 1:
printUseage()
sys.exit(2)
search = None
for arg, val in opts:
if arg in ('-h', '--help'):
printUseage()
sys.exit()
if arg in ('-v', '--version'):
print ''
print 'pubmed-test.py %s' % (VERSION)
print ''
sys.exit()
if arg in ('-s', '--search'):
print "SEARCH: %s" % (val)
search = val
return search
if __name__ == '__main__':
search = parseCommandLine()
print 'Searching Now... please wait. %s' % (time.ctime())
pubmedList = PubMed.search_for(search)
print 'Search Complete! %s' % (time.ctime())
print pubmedList
print ''
print 'Preparing Local Database %s' % (time.ctime())
dbs = DBSession(dsn='localhost', database='pubmed', user='king')
print 'Local Database Connection Complete %s' % (time.ctime())
print ''
print 'Creating GroupLabel(%s) %s' % (search, time.ctime())
grpList = dbs.GroupList()
grpList.setName(search)
print 'Created GroupLabel(%s) %s' % (search, time.ctime())
print ''
print 'Retrieving Records %s' % (time.ctime())
rec_parser = Medline.RecordParser()
medline_dict = PubMed.Dictionary(parser=rec_parser)
counter = 0
for rec in pubmedList:
myRec = dbs.PubMedRecord()
pmRec = medline_dict[rec]
print pmRec.title
myRec.setTitle(pmRec.title)
myRec.setAbstract(pmRec.abstract)
myRec.setPubmedAccess(pmRec.pubmed_id)
grpList.appendPubMedRec(myRec)
myRec.commit()
counter += 1
print 'Retrieved %s Records. %s' % (counter, time.ctime())
print 'Saving Search to Local Database. %s' % (time.ctime())
grpList.commit()
print 'Records saved to Local Database. %s' % (time.ctime())
print 'DONE'
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