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driver.py
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#!/usr/bin/env python
import os
import argparse
import logging
import xml.etree.cElementTree as ET
import sys
import read_records as rr
import extract as x
from db_info import *
log_levels = { "DEBUG" : logging.DEBUG,
"INFO" : logging.INFO,
"WARNING" : logging.WARNING,
"ERROR" : logging.ERROR,
"CRITICAL": logging.CRITICAL
}
def main (sourcefile, year, datadir, data_format):
count = 0
logging.debug("Starting processing {0}".format(sourcefile))
Pubs_list = []
Lang_list = []
Head_list = []
Subh_list = []
Subj_list = []
Publ_list = []
Auth_list = []
Inst_list = []
NaIn_list = []
Edit_list = []
Refs_list = []
Ftxt_list = []
Fund_list = []
Keyw_list = []
Keyp_list = []
Conf_list = []
CoSp_list = []
with open(args.sourcefile, 'r') as data:
while True:
count += 1
record = rr.get_record(data)
if not record:
logging.debug("Completed processing {0}".format(sourcefile))
print "Processed {0} records".format(count-1)
break
try :
#context = extract.load_data(record)
REC = ET.fromstring(record)
wos_id = list(REC.iterfind('UID'))[0].text
Pub, Languages, Headings, Subheadings, Subjects = x.extract_pub_info(wos_id, REC)
Pubs_list.extend(Pub)
Lang_list.extend(Languages)
Head_list.extend(Headings)
Subh_list.extend(Subheadings)
Subj_list.extend(Subjects)
"""
#print pub
Publishers = x.extract_publisher(wos_id, REC)
Publ_list.extend(Publishers)
#print publisher
Authors = x.extract_authors(wos_id, REC)
Auth_list.extend(Authors)
##print authors
Institutions, Name_inst_relation = x.extract_addresses(wos_id, REC)
Inst_list.extend(Institutions)
NaIn_list.extend(Name_inst_relation)
#print len(Inst_list), Institutions
#print len(NaIn_list), Name_inst_relation
Editions = x.extract_editions(wos_id, REC)
Edit_list.extend(Editions)
References = x.extract_references(wos_id, REC)
Refs_list.extend(References)
Ftext, Funding = x.extract_funding(wos_id, REC)
Ftxt_list.extend(Ftext)
Fund_list.extend(Funding)
Conf, Sponsor = x.extract_conferences(wos_id, REC)
Conf_list.extend(Conf)
CoSp_list.extend(Sponsor)
#print len(Conf_list), Conf
#print len(CoSp_list), Sponsor
Keywords, Keywords_plus = x.extract_keywords(wos_id, REC)
Keyw_list.extend(Keywords)
Keyp_list.extend(Keywords_plus)
#print Keywords
"""
except Exception as e:
print "[ERROR:{0}] Caught an exception : {1}".format(wos_id, e)
pass
try :
x.dump(Pubs_list, h_source, t_source, year+'source', '{0}/source.{1}'.format(datadir, data_format), data_format=data_format)
"""
x.dump(Edit_list, h_editions, t_editions, year+'editions', '{0}/editions.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Ftxt_list, h_fundingtexts, t_fundingtexts, year+'fundingtext', '{0}/fundingtext.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Fund_list, h_funding, t_funding, year+'funding', '{0}/funding.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Keyw_list, h_keywords, t_keywords, year+'keywords', '{0}/keywords.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Keyp_list, h_keywords_plus, t_keywords_plus, year+'keywords_plus', '{0}/keywords_plus.{1}'.format(datadir, data_format),data_format=data_format)
x.dump(Conf_list, h_conferences, t_conferences, year+'conferences', '{0}/conferences.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(CoSp_list, h_conf_sponsors, t_conf_sponsors, year+'confSponsors', '{0}/confSponsors.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Refs_list, h_references, t_references, year+'refs', '{0}/references.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Pubs_list, h_publications, t_publications, year+'publications', '{0}/publications.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Lang_list, h_languages, t_languages, year+'languages', '{0}/langauges.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Head_list, h_headings, t_headings, year+'headings', '{0}/headings.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Subh_list, h_subheadings, t_subheadings, year+'subheadings', '{0}/subheadings.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Subj_list, h_subjects, t_subjects, year+'subjects', '{0}/subjects.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Publ_list, h_publishers, t_publishers, year+'publishers', '{0}/publishers.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Auth_list, h_contributors, t_contributors, year+'contributors', '{0}/contributors.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(Inst_list, h_institutions, t_institutions, year+'institutions', '{0}/institutions.{1}'.format(datadir, data_format), data_format=data_format)
x.dump(NaIn_list, h_name_inst, t_name_inst, year+'affiliations', '{0}/affiliations.{1}'.format(datadir, data_format), data_format=data_format)
"""
except Exception as e:
print "[ERROR] Dumping failed for {0}".format(sourcefile)
logging.error("[ERROR] Dumping failed for {0}".format(sourcefile))
exit(-1)
return
if __name__ == "__main__" :
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--sourcefile", default="sample.xml", help="Path to data file")
parser.add_argument("-v", "--verbosity", default="DEBUG", help="set level of verbosity, DEBUG, INFO, WARN")
parser.add_argument("-l", "--logfile", default="./extract.log", help="Logfile path. Defaults to ./tabulator.log")
parser.add_argument("-d", "--dir", default=".", help="Folder to write data to, Default is current folder")
parser.add_argument("-f", "--format", default="sql", help="Output format to dump into")
args = parser.parse_args()
print "Processing : {0}".format(args.sourcefile)
logging.basicConfig(filename=args.logfile, level=log_levels[args.verbosity],
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
datefmt='%m-%d %H:%M')
logging.debug("Document processing starts")
if not os.path.exists(args.dir):
os.makedirs(args.dir)
logging.debug("Data output folder confirmed : {0}".format(args.dir))
year = ''
if os.path.basename(args.sourcefile).startswith('WR'):
s = args.sourcefile.split('_')
year = s[1] + "_"
print args.sourcefile.replace('.xml', '')
print "[DEBUG] Processing year : {0}".format(year)
main(args.sourcefile, year, args.dir, args.format)