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R3600/modules/bibharvest/lib/oaiharvestlib.py
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oaiharvestlib.py
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# -*- coding: utf-8 -*-
##
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 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.
"""
oaiharvest implementation. See oaiharvest executable for entry point.
"""
__revision__ = "$Id$"
import os
import re
import time
import calendar
import shutil
import tempfile
from invenio.config import \
CFG_BINDIR, \
CFG_TMPDIR
from invenio.dbquery import run_sql
from invenio.bibtask import \
task_get_option, \
task_set_option, \
write_message, \
task_update_status, \
task_init, \
task_sleep_now_if_required, \
task_update_progress, \
task_low_level_submission
from invenio.bibrecord import record_extract_oai_id, create_records
## precompile some often-used regexp for speed reasons:
re_subfields = re.compile('\$\$\w')
re_html = re.compile("(?s)<[^>]*>|&#?\w+;")
re_datetime_shift = re.compile("([-\+]{0, 1})([\d]+)([dhms])")
tmpHARVESTpath = CFG_TMPDIR + '/oaiharvest'
def get_nb_records_in_file(filename):
"""
Return number of record in FILENAME that is either harvested or converted
file. Useful for statistics.
"""
try:
nb = open(filename, 'r').read().count("</record>")
except IOError:
nb = 0 # file not exists and such
except:
nb = -1
return nb
def task_run_core():
"""Run the harvesting task. The row argument is the Bibharvest task
queue row, containing if, arguments, etc.
Return 1 in case of success and 0 in case of failure.
"""
reposlist = []
datelist = []
dateflag = 0
### go ahead: build up the reposlist
if task_get_option("repository") is not None:
### user requests harvesting from selected repositories
write_message("harvesting from selected repositories")
for reposname in task_get_option("repository"):
row = get_row_from_reposname(reposname)
if row == []:
write_message("source name " + reposname + " is not valid")
continue
else:
reposlist.append(get_row_from_reposname(reposname))
else:
### user requests harvesting from all repositories
write_message("harvesting from all repositories in the database")
reposlist = get_all_rows_from_db()
### go ahead: check if user requested from-until harvesting
if task_get_option("dates"):
### for each repos simply perform a from-until date harvesting...
### no need to update anything
dateflag = 1
for element in task_get_option("dates"):
datelist.append(element)
error_happened_p = False
j = 0
for repos in reposlist:
j += 1
task_sleep_now_if_required()
postmode = str(repos[0][9])
setspecs = str(repos[0][10])
harvested_files = []
if postmode == "h" or postmode == "h-c" or \
postmode == "h-u" or postmode == "h-c-u" or \
postmode == "h-c-f-u":
harvestpath = CFG_TMPDIR + "/oaiharvest" + str(os.getpid()) + '_' + str(j)
if dateflag == 1:
task_update_progress("Harvesting %s from %s to %s (%i/%i)" % \
(str(repos[0][6]),\
str(datelist[0]),
str(datelist[1]),
j, \
len(reposlist)))
res = call_bibharvest(prefix=repos[0][2],
baseurl=repos[0][1],
harvestpath=harvestpath,
fro=str(datelist[0]),
until=str(datelist[1]),
setspecs=setspecs)
if res[0] == 1 :
write_message("source " + str(repos[0][6]) + \
" was harvested from " + str(datelist[0]) \
+ " to " + str(datelist[1]))
harvested_files = res[1]
else:
write_message("an error occurred while harvesting "
"from source " +
str(repos[0][6]) + " for the dates chosen")
error_happened_p = True
continue
elif dateflag != 1 and repos[0][7] is None and repos[0][8] != 0:
write_message("source " + str(repos[0][6]) + \
" was never harvested before - harvesting whole "
"repository")
task_update_progress("Harvesting %s (%i/%i)" % \
(str(repos[0][6]),
j, \
len(reposlist)))
res = call_bibharvest(prefix=repos[0][2],
baseurl=repos[0][1],
harvestpath=harvestpath,
setspecs=setspecs)
if res[0] == 1 :
update_lastrun(repos[0][0])
harvested_files = res[1]
else :
write_message("an error occurred while harvesting from "
"source " + str(repos[0][6]))
error_happened_p = True
continue
elif dateflag != 1 and repos[0][8] != 0:
### check that update is actually needed,
### i.e. lastrun+frequency>today
timenow = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
lastrundate = re.sub(r'\.[0-9]+$', '',
str(repos[0][7])) # remove trailing .00
timeinsec = int(repos[0][8])*60*60
updatedue = add_timestamp_and_timelag(lastrundate, timeinsec)
proceed = compare_timestamps_with_tolerance(updatedue, timenow)
if proceed == 0 or proceed == -1 : #update needed!
write_message("source " + str(repos[0][6]) +
" is going to be updated")
fromdate = str(repos[0][7])
fromdate = fromdate.split()[0] # get rid of time
# of the day for the moment
task_update_progress("Harvesting %s (%i/%i)" % \
(str(repos[0][6]),
j, \
len(reposlist)))
res = call_bibharvest(prefix=repos[0][2],
baseurl=repos[0][1],
harvestpath=harvestpath,
fro=fromdate,
setspecs=setspecs)
if res[0] == 1 :
update_lastrun(repos[0][0])
harvested_files = res[1]
else :
write_message("an error occurred while harvesting "
"from source " + str(repos[0][6]))
error_happened_p = True
continue
else:
write_message("source " + str(repos[0][6]) +
" does not need updating")
continue
elif dateflag != 1 and repos[0][8] == 0:
write_message("source " + str(repos[0][6]) +
" has frequency set to 'Never' so it will not be updated")
continue
# print stats:
for harvested_file in harvested_files:
write_message("File %s contains %i records." % \
(harvested_file,
get_nb_records_in_file(harvested_file)))
if postmode == "h-u":
res = 0
i = 0
for harvested_file in harvested_files:
i += 1
task_sleep_now_if_required()
task_update_progress("Uploading records harvested from %s (%i/%i)" % \
(str(repos[0][6]),\
i, \
len(harvested_files)))
res += call_bibupload(harvested_file, oai_src_id = repos[0][0])
if res == 0:
write_message("material harvested from source " +
str(repos[0][6]) + " was successfully uploaded")
else:
write_message("an error occurred while uploading "
"harvest from " + str(repos[0][6]))
error_happened_p = True
continue
if postmode == "h-c" or postmode == "h-c-u" or postmode == "h-c-f-u":
convert_dir = CFG_TMPDIR
convertpath = convert_dir + os.sep + "bibconvertrun" + \
str(os.getpid()) + '_' + str(j)
converted_files = []
i = 0
for harvested_file in harvested_files:
i += 1
task_sleep_now_if_required()
converted_file = convertpath+".%07d" % i
converted_files.append(converted_file)
task_update_progress("Converting material harvested from %s (%i/%i)" % \
(str(repos[0][6]), \
i, \
len(harvested_files)))
(exitcode, err_msg) = call_bibconvert(config=str(repos[0][5]),
harvestpath=harvested_file,
convertpath=converted_file)
if exitcode == 0:
write_message("material harvested from source " +
str(repos[0][6]) + " was successfully converted")
else:
write_message("an error occurred while converting from " +
str(repos[0][6]) + ': \n' + err_msg)
error_happened_p = True
continue
# print stats:
for converted_file in converted_files:
write_message("File %s contains %i records." % \
(converted_file,
get_nb_records_in_file(converted_file)))
if postmode == "h-c-u":
res = 0
i = 0
uploaded = False
for converted_file in converted_files:
i += 1
task_sleep_now_if_required()
if get_nb_records_in_file(converted_file) > 0:
task_update_progress("Uploading records harvested from %s (%i/%i)" % \
(str(repos[0][6]),\
i, \
len(converted_files)))
res += call_bibupload(converted_file, oai_src_id = repos[0][0])
uploaded = True
if len(converted_files) > 0:
if res == 0:
if uploaded:
write_message("material harvested from source " +
str(repos[0][6]) + " was successfully uploaded")
else:
write_message("nothing to upload")
else:
write_message("an error occurred while uploading "
"harvest from " + str(repos[0][6]))
error_happened_p = True
continue
elif postmode == "h-c-f-u":
# first call bibfilter:
res = 0
uploaded = False
i = 0
for converted_file in converted_files:
i += 1
task_sleep_now_if_required()
task_update_progress("Filtering material harvested from %s (%i/%i)" % \
(str(repos[0][6]), \
i,\
len(converted_files)))
res += call_bibfilter(str(repos[0][11]), converted_file)
if len(converted_files) > 0:
if res == 0:
write_message("material harvested from source " +
str(repos[0][6]) + " was successfully bibfiltered")
else:
write_message("an error occurred while bibfiltering "
"harvest from " + str(repos[0][6]))
error_happened_p = True
continue
# print stats:
for converted_file in converted_files:
write_message("File %s contains %i records." % \
(converted_file + ".insert.xml",
get_nb_records_in_file(converted_file + ".insert.xml")))
write_message("File %s contains %i records." % \
(converted_file + ".correct.xml",
get_nb_records_in_file(converted_file + ".correct.xml")))
write_message("File %s contains %i records." % \
(converted_file + ".holdingpen.xml",
get_nb_records_in_file(converted_file + ".holdingpen.xml")))
# only then call upload:
i = 0
for converted_file in converted_files:
task_sleep_now_if_required()
i += 1
if get_nb_records_in_file(converted_file + ".insert.xml") > 0:
task_update_progress("Uploading new records harvested from %s (%i/%i)" % \
(str(repos[0][6]),\
i, \
len(converted_files)))
res += call_bibupload(converted_file + ".insert.xml", ["-i"], oai_src_id = repos[0][0])
uploaded = True
task_sleep_now_if_required()
if get_nb_records_in_file(converted_file + ".correct.xml") > 0:
task_update_progress("Uploading corrections for records harvested from %s (%i/%i)" % \
(str(repos[0][6]),\
i, \
len(converted_files)))
res += call_bibupload(converted_file + ".correct.xml", ["-c"], oai_src_id = repos[0][0])
uploaded = True
if get_nb_records_in_file(converted_file + ".holdingpen.xml") > 0:
task_update_progress("Uploading records harvested from %s to holding pen (%i/%i)" % \
(str(repos[0][6]),\
i, \
len(converted_files)))
res += call_bibupload(converted_file + ".holdingpen.xml", ["-o"], oai_src_id = repos[0][0])
uploaded = True
if len(converted_files) > 0:
if res == 0:
if uploaded:
write_message("material harvested from source " +
str(repos[0][6]) + " was successfully uploaded")
else:
write_message("nothing to upload")
else:
write_message("an error occurred while uploading "
"harvest from " + str(repos[0][6]))
error_happened_p = True
continue
elif postmode not in ["h", "h-c", "h-u",
"h-c-u", "h-c-f-u"]: ### this should not happen
write_message("invalid postprocess mode: " + postmode +
" skipping repository")
error_happened_p = True
continue
if error_happened_p:
return False
else:
return True
def add_timestamp_and_timelag(timestamp,
timelag):
""" Adds a time lag in seconds to a given date (timestamp).
Returns the resulting date. """
# remove any trailing .00 in timestamp:
timestamp = re.sub(r'\.[0-9]+$', '', timestamp)
# first convert timestamp to Unix epoch seconds:
timestamp_seconds = calendar.timegm(time.strptime(timestamp,
"%Y-%m-%d %H:%M:%S"))
# now add them:
result_seconds = timestamp_seconds + timelag
result = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime(result_seconds))
return result
def update_lastrun(index):
""" A method that updates the lastrun of a repository
successfully harvested """
try:
today = time.strftime("%Y-%m-%d %H:%M:%S", time.localtime())
sql = 'UPDATE oaiHARVEST SET lastrun=%s WHERE id=%s'
run_sql(sql, (today, index))
return 1
except StandardError, e:
return (0, e)
def call_bibharvest(prefix, baseurl, harvestpath,
fro="", until="", setspecs=""):
""" A method that calls bibharvest and writes harvested output to disk """
try:
command = '%s/bibharvest -o %s -v ListRecords -p %s ' % (CFG_BINDIR,
harvestpath,
prefix)
if fro != "":
command += '-f %s ' % fro
if until != "":
command += '-u %s ' % until
if setspecs != "":
command += '-s "%s" ' % setspecs
command += baseurl
print "Start harvesting"
#print command
os.system(command)
#print "Harvesting finished, merging files"
harvest_dir, harvest_filename = os.path.split(harvestpath)
#print "get files"
files = os.listdir(harvest_dir)
#print "sort file"
files.sort()
harvested_files = [harvest_dir + os.sep + filename for \
filename in files \
if filename.startswith(harvest_filename)]
#print "open dest file"
## hf = file(harvestpath, 'w')
## for f in files:
## if f.startswith(filename)
## print "processing file %s"%f
## rf = file(os.path.join(harvestdir, f), 'r')
## hf.write(rf.read())
## hf.write("\n")
## rf.close()
## #os.remove(os.path.join(harvestdir, f))
## hf.close()
## print "Files merged"
return (1, harvested_files)
except StandardError, e:
print e
return (0, e)
def call_bibconvert(config, harvestpath, convertpath):
""" Call BibConvert to convert file given at 'harvestpath' with
conversion template 'config', and save the result in file at
'convertpath'.
Returns status exit code of the conversion, as well as error
messages, if any
"""
cmd_err_fd, file_cmd_err = tempfile.mkstemp()
command = "%s/bibconvert -c %s < %s > %s 2> %s" % \
(CFG_BINDIR, config, harvestpath, convertpath, file_cmd_err)
exitcode = os.system(command)
cmd_err = ""
if exitcode != 0:
cmd_err_fo = open(file_cmd_err)
cmd_err = cmd_err_fo.read()
cmd_err_fo.close()
os.remove(file_cmd_err)
os.close(cmd_err_fd)
return (exitcode, cmd_err)
def create_bibharvest_log(task_id, oai_src_id, marcxmlfile):
"""
Function which creates the harvesting logs
@param task_id bibupload task id
"""
file = open(marcxmlfile, "r")
xml_content = file.read(-1)
file.close()
create_bibharvest_log_str(task_id, oai_src_id, xml_content)
def create_bibharvest_log_str(task_id, oai_src_id, xml_content):
"""
Function which creates the harvesting logs
@param task_id bibupload task id
"""
try:
records = create_records(xml_content)
for record in records:
oai_id = record_extract_oai_id(record[0])
query = "INSERT INTO oaiHARVESTLOG (id_oaiHARVEST, oai_id, date_harvested, bibupload_task_id) VALUES (%s, %s, NOW(), %s)"
run_sql(query, (str(oai_src_id),str(oai_id), str(task_id)))
except Exception, msg:
print "Logging exception : %s " % (str(msg), )
def call_bibupload(marcxmlfile, mode = None, oai_src_id = -1):
"""Call bibupload in insert mode on MARCXMLFILE."""
if mode is None:
mode = ["-r", "-i"]
if os.path.exists(marcxmlfile):
try:
args = mode
print marcxmlfile
args.append(marcxmlfile)
task_id = task_low_level_submission("bibupload", "oaiharvest", *tuple(args))
create_bibharvest_log(task_id, oai_src_id, marcxmlfile)
except Exception, msg:
write_message("An exception during submitting bibharvest task occured : %s " % (str(msg)))
return 1
return 0
else:
write_message("marcxmlfile %s does not exist" % marcxmlfile)
return 1
def call_bibfilter(bibfilterprogram, marcxmlfile):
"""
Call bibfilter program BIBFILTERPROGRAM on MARCXMLFILE that is a
MARCXML file usually obtained after harvest and convert steps.
The bibfilter should produce two files called MARCXMLFILE.insert.xml
and MARCXMLFILE.correct.xml, the first file containing parts of
MARCXML to be uploaded in insert mode and the second file part of
MARCXML to be uploaded in correct mode.
Return 0 if everything went okay, 1 otherwise.
"""
if bibfilterprogram:
if not os.path.isfile(bibfilterprogram):
write_message("bibfilterprogram %s is not a file" %
bibfilterprogram)
return 1
elif not os.path.isfile(marcxmlfile):
write_message("marcxmlfile %s is not a file" % marcxmlfile)
return 1
else:
return os.system('%s %s' % (bibfilterprogram, marcxmlfile))
else:
try:
write_message("no bibfilterprogram defined, copying %s only" %
marcxmlfile)
shutil.copy(marcxmlfile, marcxmlfile + ".insert.xml")
return 0
except:
write_message("cannot copy %s into %s.insert.xml" % marcxmlfile)
return 1
def get_row_from_reposname(reposname):
""" Returns all information about a row (OAI source)
from the source name """
try:
sql = """SELECT id, baseurl, metadataprefix, arguments,
comment, bibconvertcfgfile, name, lastrun,
frequency, postprocess, setspecs,
bibfilterprogram
FROM oaiHARVEST WHERE name=%s"""
res = run_sql(sql, (reposname, ))
reposdata = []
for element in res:
reposdata.append(element)
return reposdata
except StandardError, e:
return (0, e)
def get_all_rows_from_db():
""" This method retrieves the full database of repositories and returns
a list containing (in exact order):
| id | baseurl | metadataprefix | arguments | comment
| bibconvertcfgfile | name | lastrun | frequency
| postprocess | setspecs | bibfilterprogram
"""
try:
reposlist = []
sql = """SELECT id FROM oaiHARVEST"""
idlist = run_sql(sql)
for index in idlist:
sql = """SELECT id, baseurl, metadataprefix, arguments,
comment, bibconvertcfgfile, name, lastrun,
frequency, postprocess, setspecs,
bibfilterprogram
FROM oaiHARVEST WHERE id=%s""" % index
reposelements = run_sql(sql)
repos = []
for element in reposelements:
repos.append(element)
reposlist.append(repos)
return reposlist
except StandardError, e:
return (0, e)
def compare_timestamps_with_tolerance(timestamp1,
timestamp2,
tolerance=0):
"""Compare two timestamps TIMESTAMP1 and TIMESTAMP2, of the form
'2005-03-31 17:37:26'. Optionally receives a TOLERANCE argument
(in seconds). Return -1 if TIMESTAMP1 is less than TIMESTAMP2
minus TOLERANCE, 0 if they are equal within TOLERANCE limit,
and 1 if TIMESTAMP1 is greater than TIMESTAMP2 plus TOLERANCE.
"""
# remove any trailing .00 in timestamps:
timestamp1 = re.sub(r'\.[0-9]+$', '', timestamp1)
timestamp2 = re.sub(r'\.[0-9]+$', '', timestamp2)
# first convert timestamps to Unix epoch seconds:
timestamp1_seconds = calendar.timegm(time.strptime(timestamp1,
"%Y-%m-%d %H:%M:%S"))
timestamp2_seconds = calendar.timegm(time.strptime(timestamp2,
"%Y-%m-%d %H:%M:%S"))
# now compare them:
if timestamp1_seconds < timestamp2_seconds - tolerance:
return -1
elif timestamp1_seconds > timestamp2_seconds + tolerance:
return 1
else:
return 0
def get_dates(dates):
""" A method to validate and process the dates input by the user
at the command line """
twodates = []
if dates:
datestring = dates.split(":")
if len(datestring)==2:
for date in datestring:
### perform some checks on the date format
datechunks = date.split("-")
if len(datechunks)==3:
try:
if int(datechunks[0]) and int(datechunks[1]) and \
int(datechunks[2]):
twodates.append(date)
except StandardError:
write_message("Dates have invalid format, not "
"'yyyy-mm-dd:yyyy-mm-dd'")
twodates = None
return twodates
else:
write_message("Dates have invalid format, not "
"'yyyy-mm-dd:yyyy-mm-dd'")
twodates = None
return twodates
## final check.. date1 must me smaller than date2
date1 = str(twodates[0]) + " 01:00:00"
date2 = str(twodates[1]) + " 01:00:00"
if compare_timestamps_with_tolerance(date1, date2)!=-1:
write_message("First date must be before second date.")
twodates = None
return twodates
else:
write_message("Dates have invalid format, not "
"'yyyy-mm-dd:yyyy-mm-dd'")
twodates = None
else:
twodates = None
return twodates
def get_repository_names(repositories):
""" A method to validate and process the repository names input by the
user at the command line """
repository_names = []
if repositories:
names = repositories.split(",")
for name in names:
### take into account both single word names and multiple word
### names (which get wrapped around "" or '')
name = name.strip()
if name.startswith("'"):
name = name.strip("'")
elif name.startswith('"'):
name = name.strip('"')
repository_names.append(name)
else:
repository_names = None
return repository_names
def main():
"""Main that construct all the bibtask."""
task_set_option("repository", None)
task_set_option("dates", None)
task_init(authorization_action='runoaiharvest',
authorization_msg="oaiharvest Task Submission",
description="""Examples:
oaiharvest -r arxiv -s 24h
oaiharvest -r pubmed -d 2005-05-05:2005-05-10 -t 10m\n""",
help_specific_usage=' -r, --repository=REPOS_ONE,"REPOS TWO" '
'name of the OAI repositories to be harvested (default=all)\n'
' -d, --dates=yyyy-mm-dd:yyyy-mm-dd '
'harvest repositories between specified dates '
'(overrides repositories\' last updated timestamps)\n',
version=__revision__,
specific_params=("r:d:", ["repository=", "dates=", ]),
task_submit_elaborate_specific_parameter_fnc=
task_submit_elaborate_specific_parameter,
task_run_fnc=task_run_core)
def task_submit_elaborate_specific_parameter(key, value, opts, args):
"""Elaborate specific cli parameters for oaiharvest."""
if key in ("-r", "--repository"):
task_set_option('repository', get_repository_names(value))
elif key in ("-d", "--dates"):
task_set_option('dates', get_dates(value))
if value is not None and task_get_option("dates") is None:
raise StandardError, "Date format not valid."
else:
return False
return True
### okay, here we go:
if __name__ == '__main__':
main()
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