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bibclassify_daemon.py
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Thu, May 9, 20:16

bibclassify_daemon.py
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# -*- coding: utf-8 -*-
##
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your option) any later version.
##
## CDS Invenio 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
## General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with CDS Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""
BibClassify daemon.
FIXME: the code below requires collection table to be updated to add column:
clsMETHOD_fk mediumint(9) unsigned NOT NULL,
This is not clean and should be fixed.
"""
__revision__ = "$Id$"
import sys
from invenio.dbquery import run_sql
from invenio.bibtask import task_init, write_message, get_datetime, \
task_set_option, task_get_option, task_get_task_param, task_update_status, \
task_update_progress
from invenio.bibclassifylib import generate_keywords_rdf
from invenio.config import *
from os import popen, remove, listdir
import sys
from invenio.intbitset import intbitset
from invenio.search_engine import get_collection_reclist
from invenio.bibdocfile import BibRecDocs
import time
import os
def get_recids_foreach_ontology():
"""Returns an array containing hash objects containing the collection, its
corresponding ontology and the records belonging to the given collection."""
rec_onts = []
res = run_sql("""SELECT clsMETHOD.name, last_updated, collection.name
FROM clsMETHOD JOIN collection_clsMETHOD ON clsMETHOD.id=id_clsMETHOD
JOIN collection ON id_collection=collection.id""")
for ontology, date_last_run, collection in res:
recs = get_collection_reclist(collection)
if recs:
if not date_last_run:
date_last_run = '0000-00-00'
modified_records = intbitset(run_sql("SELECT id FROM bibrec WHERE modification_date >=%s", (date_last_run, )))
recs &= modified_records
if recs:
rec_onts.append({
'ontology' : ontology,
'collection' : collection,
'recIDs' : recs
})
return rec_onts
def update_date_of_last_run():
"""
Update bibclassify daemon table information about last run time.
"""
run_sql("UPDATE clsMETHOD SET last_updated=NOW()")
def task_run_core():
"""Runs anayse_documents for each ontology,collection,record ids set."""
outfilename = CFG_TMPDIR + "/bibclassifyd_%s.xml" % time.strftime("%Y%m%dH%M%S", time.localtime())
outfiledesc = open(outfilename, "w")
coll_counter = 0
print >> outfiledesc, """<?xml version="1.0" encoding="UTF-8"?>"""
print >> outfiledesc, """<collection xmlns="http://www.loc.gov/MARC21/slim">"""
for onto_rec in get_recids_foreach_ontology():
write_message('Applying taxonomy %s to collection %s (%s records)' % (onto_rec['ontology'], onto_rec['collection'], len(onto_rec['recIDs'])))
if onto_rec['recIDs']:
coll_counter += analyse_documents(onto_rec['recIDs'], onto_rec['ontology'], onto_rec['collection'], outfilename, outfiledesc)
print >> outfiledesc, '</collection>'
outfiledesc.close()
if coll_counter:
cmd = "%s/bibupload -n -c '%s' " % (CFG_BINDIR, outfilename)
errcode = 0
try:
errcode = os.system(cmd)
except OSError, e:
print 'command' + cmd + ' failed ',e
if errcode != 0:
write_message("WARNING, %s failed, error code is %s" % (cmd,errcode))
return 0
update_date_of_last_run()
return 1
def analyse_documents(recs, ontology, collection, outfilename, outfiledesc):
"""For each collection, parse the documents attached to the records in collection with the corresponding ontology."""
time_now = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
did_something = False
counter = 1
max = len(recs)
# store running time:
# see which records we'll have to process:
#recIDs = get_recIDs_of_modified_records_since_last_run()
temp_text = None
if recs:
# process records:
cmd = None
path = None
temp_text = CFG_TMPDIR + '/bibclassify.pdftotext.' + str(os.getpid())
for rec in recs:
bibdocfiles = BibRecDocs(rec).list_latest_files()
found_one_pdf = False
for bibdocfile in bibdocfiles:
if bibdocfile.get_format() == '.pdf':
found_one_pdf = True
if found_one_pdf:
did_something = True
print >> outfiledesc, '<record>'
print >> outfiledesc, """<controlfield tag="001">%(recID)s</controlfield>""" % ({'recID':rec})
for f in bibdocfiles:
if f.get_format() == '.pdf':
cmd = "%s '%s' '%s'" % (CFG_PATH_PDFTOTEXT, f.get_full_path(), temp_text)
else:
write_message("Can't parse file %s." % f.get_full_path(), verbose=3)
continue
errcode = os.system(cmd)
if errcode != 0 or not os.path.exists("%s" % temp_text):
write_message("Error while executing command %s Error code was: %s " % (cmd, errcode))
write_message('Generating keywords for %s' % f.get_full_path())
print >> outfiledesc, generate_keywords_rdf(temp_text, CFG_ETCDIR + '/bibclassify/' + ontology + '.rdf', 2, 70, 25, 0, False, verbose=0, ontology=ontology)
print >> outfiledesc, '</record>'
task_update_progress("Done %s of %s for collction %s." % (counter, max, collection))
counter += 1
else:
write_message("Nothing to be done, move along")
return did_something
def cleanup_tmp():
"""Remove old temporary files created by this module"""
for f in listdir(CFG_TMPDIR):
if 'bibclassify' in f: remove(CFG_TMPDIR + '/' +f)
def main():
"""Constructs the bibclassifyd bibtask."""
cleanup_tmp()
task_init(authorization_action='runbibclassify',
authorization_msg="BibClassify Task Submission",
description="""Examples:
%s -u admin
""" % (sys.argv[0],),
version=__revision__,
task_run_fnc = task_run_core)
if __name__ == '__main__':
main()
# FIXME: one can have more than one ontologies in clsMETHOD.
# bibclassifyd -w HEP,Pizza
# FIXME: add more CLI options like bibindex ones, e.g.
# bibclassifyd -a -i 10-20
# FIXME: outfiledesc can be multiple files, e.g. when processing
# 100000 records it is good to store results by 1000 records
# (see oaiharvest)

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