Homec4science
Diffusion invenio-infoscience (maint-1.0) Browse

R3600/modules/bibharvest/lib/oai_harvest_daemon.py
382bd1377cbfmaint-1.0

Last Change
Raw File

oai_harvest_daemon.py
View Options

# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 CERN.
##
## 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.
##
## 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 Invenio; if not, write to the Free Software Foundation, Inc.,
## 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA.
"""
OAI Harvest daemon - harvest records from OAI repositories.
If started via CLI with --verb parameters, starts a manual single-shot
harvesting. Otherwise starts a BibSched task for periodical harvesting
of repositories defined in the OAI Harvest admin interface
"""
__revision__ = "$Id$"
import os
import sys
import getopt
import getpass
import re
import time
import calendar
import shutil
import tempfile
import urlparse
from invenio.config import \
CFG_BINDIR, \
CFG_TMPDIR
from invenio.oai_harvest_config import CFG_OAI_POSSIBLE_POSTMODES
from invenio.dbquery import run_sql
from invenio.bibtask import \
task_get_task_param, \
task_get_option, \
task_set_option, \
write_message, \
task_init, \
task_sleep_now_if_required, \
task_update_progress, \
task_low_level_submission
from invenio.bibrecord import record_extract_oai_id, create_records
from invenio import oai_harvest_getter
from invenio.plotextractor_getter import harvest_single, make_single_directory
from invenio.plotextractor import process_single
## precompile some often-used regexp for speed reasons:
re_subfields = re.compile('\$\$\w')
re_datetime_shift = re.compile("([-\+]{0, 1})([\d]+)([dhms])")
re_record = re.compile('<record>(.*?<datafield tag="035" ind1=" " ind2=" ">' + \
'<subfield code="9">arXiv<\/subfield>' + \
'<subfield code="z">(.*?)<\/subfield>' + \
'<\/datafield>.*?)<\/record>', re.DOTALL)
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 oaiharvest task
queue row, containing if, arguments, etc.
Return 1 in case of success and 0 in case of failure.
"""
reposlist = []
datelist = []
dateflag = 0
possible_postmodes = [code for code, dummy in CFG_OAI_POSSIBLE_POSTMODES]
filepath_prefix = tmpHARVESTpath + "_" + str(task_get_task_param("task_id"))
### 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()
reponame = str(repos[0][6])
postmode = str(repos[0][9])
setspecs = str(repos[0][10])
harvested_files_list = []
if postmode in possible_postmodes:
# Harvest phase
harvestpath = filepath_prefix + "_" + str(j) + "_" + \
time.strftime("%Y%m%d%H%M%S") + "_harvested"
if dateflag == 1:
task_update_progress("Harvesting %s from %s to %s (%i/%i)" % \
(reponame, \
str(datelist[0]),
str(datelist[1]),
j, \
len(reposlist)))
exit_code, file_list = oai_harvest_get(prefix = repos[0][2],
baseurl = repos[0][1],
harvestpath = harvestpath,
fro = str(datelist[0]),
until = str(datelist[1]),
setspecs = setspecs)
if exit_code == 1 :
write_message("source " + reponame + \
" was harvested from " + str(datelist[0]) \
+ " to " + str(datelist[1]))
harvested_files_list = file_list
else:
write_message("an error occurred while harvesting "
"from source " +
reponame + " 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 " + reponame + \
" was never harvested before - harvesting whole "
"repository")
task_update_progress("Harvesting %s (%i/%i)" % \
(reponame,
j, \
len(reposlist)))
exit_code, file_list = oai_harvest_get(prefix = repos[0][2],
baseurl = repos[0][1],
harvestpath = harvestpath,
setspecs = setspecs)
if exit_code == 1 :
update_lastrun(repos[0][0])
harvested_files_list = file_list
else :
write_message("an error occurred while harvesting from "
"source " + reponame)
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 " + reponame +
" 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)" % \
(reponame,
j, \
len(reposlist)))
exit_code, file_list = oai_harvest_get(prefix = repos[0][2],
baseurl = repos[0][1],
harvestpath = harvestpath,
fro = fromdate,
setspecs = setspecs)
if exit_code == 1 :
update_lastrun(repos[0][0])
harvested_files_list = file_list
else :
write_message("an error occurred while harvesting "
"from source " + reponame)
error_happened_p = True
continue
else:
write_message("source " + reponame +
" does not need updating")
continue
elif dateflag != 1 and repos[0][8] == 0:
write_message("source " + reponame + \
" has frequency set to 'Never' so it will not be updated")
continue
# Harvesting done, now convert/extract/filter/upload as requested
if len(harvested_files_list) < 1:
write_message("No records harvested for %s" % (reponame,))
continue
active_files_list = harvested_files_list
# Convert phase
if 'c' in postmode:
converted_files_list = []
i = 0
for active_file in active_files_list:
i += 1
task_sleep_now_if_required()
task_update_progress("Converting material harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
converted_file = filepath_prefix + "_" + str(i) + "_" + \
time.strftime("%Y%m%d%H%M%S") + "_converted"
converted_files_list.append(converted_file)
(exitcode, err_msg) = call_bibconvert(config = str(repos[0][5]),
harvestpath = active_file,
convertpath = converted_file)
if exitcode == 0:
write_message("material harvested from source " +
reponame + " was successfully converted")
else:
write_message("an error occurred while converting from " +
reponame + ': \n' + err_msg)
error_happened_p = True
continue
# print stats:
for converted_file in converted_files_list:
write_message("File %s contains %i records." % \
(converted_file,
get_nb_records_in_file(converted_file)))
active_files_list = converted_files_list
if 'e' in postmode:
# Download tarball for each harvested/converted record, then run plotextrator.
# Update converted xml files with generated xml or add it for upload
extracted_files_list = []
i = 0
for active_file in active_files_list:
i += 1
task_sleep_now_if_required()
task_update_progress("Extracting material harvested from %s (%i/%i)" % \
(reponame, i, len(active_files_list)))
extracted_file = filepath_prefix + "_" + str(i) + "_" + \
time.strftime("%Y%m%d%H%M%S") + "_extracted"
extracted_files_list.append(extracted_file)
(exitcode, err_msg) = call_plotextractor(active_file,
extracted_file)
if exitcode == 0:
write_message("material harvested from source " +
reponame + " was successfully extracted")
else:
write_message("an error occurred while extracting from " +
reponame + ': \n' + err_msg)
error_happened_p = True
continue
# print stats:
for extracted_file in extracted_files_list:
write_message("File %s contains %i records." % \
(extracted_file,
get_nb_records_in_file(extracted_file)))
active_files_list = extracted_files_list
# Filter-phase
if 'f' in postmode:
# first call bibfilter:
res = 0
uploaded = False
i = 0
for active_file in active_files_list:
i += 1
task_sleep_now_if_required()
task_update_progress("Filtering material harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibfilter(str(repos[0][11]), active_file)
if len(active_files_list) > 0:
if res == 0:
write_message("material harvested from source " +
reponame + " was successfully bibfiltered")
else:
write_message("an error occurred while bibfiltering "
"harvest from " + reponame)
error_happened_p = True
continue
# print stats:
for active_file in active_files_list:
write_message("File %s contains %i records." % \
(active_file + ".insert.xml",
get_nb_records_in_file(active_file + ".insert.xml")))
write_message("File %s contains %i records." % \
(active_file + ".correct.xml",
get_nb_records_in_file(active_file + ".correct.xml")))
write_message("File %s contains %i records." % \
(active_file + ".append.xml",
get_nb_records_in_file(active_file + ".append.xml")))
write_message("File %s contains %i records." % \
(active_file + ".holdingpen.xml",
get_nb_records_in_file(active_file + ".holdingpen.xml")))
# Upload files
if "u" in postmode:
if 'f' in postmode:
# upload filtered files
i = 0
for active_file in active_files_list:
task_sleep_now_if_required()
i += 1
if get_nb_records_in_file(active_file + ".insert.xml") > 0:
task_update_progress("Uploading new records harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibupload(active_file + ".insert.xml", \
["-i"], oai_src_id = repos[0][0])
uploaded = True
task_sleep_now_if_required()
if get_nb_records_in_file(active_file + ".correct.xml") > 0:
task_update_progress("Uploading corrections for records harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibupload(active_file + ".correct.xml", \
["-c"], oai_src_id = repos[0][0])
uploaded = True
if get_nb_records_in_file(active_file + ".append.xml") > 0:
task_update_progress("Uploading additions for records harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibupload(active_file + ".append.xml", \
["-a"], oai_src_id = repos[0][0])
uploaded = True
if get_nb_records_in_file(active_file + ".holdingpen.xml") > 0:
task_update_progress("Uploading records harvested from %s to holding pen (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibupload(active_file + ".holdingpen.xml", \
["-o"], oai_src_id = repos[0][0])
uploaded = True
if len(active_files_list) > 0:
if res == 0:
if uploaded:
write_message("material harvested from source " +
reponame + " was successfully uploaded")
else:
write_message("nothing to upload")
else:
write_message("an error occurred while uploading "
"harvest from " + reponame)
error_happened_p = True
continue
else:
# upload files normally
res = 0
i = 0
uploaded = False
for active_file in active_files_list:
i += 1
task_sleep_now_if_required()
if get_nb_records_in_file(active_file) > 0:
task_update_progress("Uploading records harvested from %s (%i/%i)" % \
(reponame, \
i, \
len(active_files_list)))
res += call_bibupload(active_file, oai_src_id = repos[0][0])
uploaded = True
if res == 0:
if uploaded:
write_message("material harvested from source " +
reponame + " was successfully uploaded")
else:
write_message("nothing to upload")
else:
write_message("an error occurred while uploading "
"harvest from " + reponame)
error_happened_p = True
continue
else: ### 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 oai_harvest_get(prefix, baseurl, harvestpath,
fro = None, until = None, setspecs = None,
user = None, password = None, cert_file = None,
key_file = None, method = "POST"):
"""
Retrieve OAI records from given repository, with given arguments
"""
try:
(addressing_scheme, network_location, path, parameters, \
query, fragment_identifier) = urlparse.urlparse(baseurl)
secure = (addressing_scheme == "https")
http_param_dict = {'verb': "ListRecords",
'metadataPrefix': prefix}
if fro:
http_param_dict['from'] = fro
if until:
http_param_dict['until'] = until
sets = None
if setspecs:
sets = [set.strip() for set in setspecs.split(' ')]
print "Start harvesting"
oai_harvest_getter.harvest(network_location, path, http_param_dict, method, harvestpath,
sets, secure, user, password, cert_file, key_file)
harvest_dir, harvest_filename = os.path.split(harvestpath)
files = os.listdir(harvest_dir)
files.sort()
harvested_files = [harvest_dir + os.sep + filename for \
filename in files \
if filename.startswith(harvest_filename)]
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 call_plotextractor(active_file, extracted_file):
"""
Function that generates proper MARCXML containing harvested material
such as plots and fulltext for each record.
@param active_file: path to the currently processed file
@param extracted_file: path to the file to be extracted in which the
final resulting MARCXML will be saved
@return: exitcode and any error messages as: (exitcode, err_msg)
"""
err_msg = ""
exitcode = 0
# Read in active file
recs_fd = open(active_file, 'r')
records = recs_fd.read()
recs_fd.close()
# Find all records mapped with identifier
record_xmls = re_record.findall(records)
updated_xml = '<?xml version="1.0" encoding="UTF-8"?><collection>'
for record_xml, identifier in record_xmls:
updated_xml += "<record>%s" % (record_xml,)
exitcode, err_msg, extracted_fulltext_xml, plotextracted_xml = \
plotextractor_harvest(identifier, active_file)
if plotextracted_xml != None:
# Strip tags. Expecting:
# <?xml version="1.0" encoding="UTF-8"?>
# <collection><record>
# ...
# </record></collection>
plotextracted_xml = plotextracted_xml[58:-22]
updated_xml += plotextracted_xml
if extracted_fulltext_xml != None:
updated_xml += extracted_fulltext_xml
updated_xml += "</record>"
# Write to file
file_fd = open(extracted_file, 'w')
file_fd.write(updated_xml + '</collection>')
file_fd.close()
return exitcode, err_msg
def plotextractor_harvest(identifier, active_file):
"""
Function that calls plotextractor library to download and extract tarball
and fulltext pdf for each record.
@param identifier: OAI identifier of the record to harvest
@param active_file: path to the currently processed file
@return: exitcode, errormessages and paths to generated MARCXML for plots and fulltext as a tuple
(exitcode, err_msg, fulltext_xml, plotextracted_xml)
"""
err_msg = ""
exitcode = 0
plotextracted_xml = None
fulltext_xml = None
active_dir, active_name = os.path.split(active_file)
extract_path = make_single_directory(active_dir, active_name + \
"_plotextraction")
tarball, pdf = harvest_single(identifier, extract_path)
if tarball != None:
plotextracted_xml_path = process_single(tarball, clean = True)
if plotextracted_xml_path != None:
plotsxml_fd = open(plotextracted_xml_path, 'r')
plotextracted_xml = plotsxml_fd.read()
plotsxml_fd.close()
else:
err_msg += "Error extracting plots from id: %s %s\n" % \
(identifier, tarball)
exitcode = 1
else:
err_msg += "Error harvesting plots from id: %s %s\n" % \
(identifier, extract_path)
exitcode = 1
if pdf != None:
fulltext_xml = '<datafield tag="FFT" ind1=" " ind2=" ">' + \
'<subfield code="a">' + pdf + '</subfield>' + \
'<subfield code="t"></subfield>' + \
'</datafield>'
else:
err_msg += "Error harvesting fulltext from id: %s %s\n" % \
(identifier, extract_path)
exitcode = 1
return exitcode, err_msg, fulltext_xml, plotextracted_xml
def create_oaiharvest_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_oaiharvest_log_str(task_id, oai_src_id, xml_content)
def create_oaiharvest_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
args.append(marcxmlfile)
task_id = task_low_level_submission("bibupload", "oaiharvest", *tuple(args))
create_oaiharvest_log(task_id, oai_src_id, marcxmlfile)
except Exception, msg:
write_message("An exception during submitting oaiharvest 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, which is usually
run before uploading records.
The bibfilter should produce up to four files called MARCXMLFILE.insert.xml,
MARCXMLFILE.correct.xml, MARCXMLFILE.append.xml and MARCXMLFILE.holdingpen.xml.
The first file contains parts of MARCXML to be uploaded in insert mode,
the second file is uploaded in correct mode, third in append mode and the last file
contains MARCXML to be uploaded into the holding pen.
@param bibfilterprogram: path to bibfilter script to run
@param marcxmlfile: base-marcxmlfilename
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 usage(exitcode = 0, msg = ""):
"Print out info. Only used when run in 'manual' harvesting mode"
sys.stderr.write("*Manual single-shot harvesting mode*\n")
if msg:
sys.stderr.write(msg + "\n")
sys.exit(exitcode)
def main():
"""Starts the tool.
If the command line arguments are those of the 'manual' mode, then
starts a manual one-time harvesting. Else trigger a BibSched task
for automated harvesting based on the OAIHarvest admin settings.
"""
# Let's try to parse the arguments as used in manual harvesting:
try:
opts, args = getopt.getopt(sys.argv[1:], "o:v:m:p:i:s:f:u:r:x:c:k:w:l:",
["output=",
"verb=",
"method=",
"metadataPrefix=",
"identifier=",
"set=",
"from=",
"until=",
"resumptionToken=",
"certificate=",
"key=",
"user=",
"password="]
)
# So everything went smoothly: start harvesting in manual mode
if len([opt for opt, opt_value in opts if opt in ['-v', '--verb']]) > 0:
# verb parameter is given
http_param_dict = {}
method = "POST"
output = ""
user = None
password = None
cert_file = None
key_file = None
sets = []
# get options and arguments
for opt, opt_value in opts:
if opt in ["-v", "--verb"]:
http_param_dict['verb'] = opt_value
elif opt in ["-m", '--method']:
if opt_value == "GET" or opt_value == "POST":
method = opt_value
elif opt in ["-p", "--metadataPrefix"]:
http_param_dict['metadataPrefix'] = opt_value
elif opt in ["-i", "--identifier"]:
http_param_dict['identifier'] = opt_value
elif opt in ["-s", "--set"]:
sets = opt_value.split()
elif opt in ["-f", "--from"]:
http_param_dict['from'] = opt_value
elif opt in ["-u", "--until"]:
http_param_dict['until'] = opt_value
elif opt in ["-r", "--resumptionToken"]:
http_param_dict['resumptionToken'] = opt_value
elif opt in ["-o", "--output"]:
output = opt_value
elif opt in ["-c", "--certificate"]:
cert_file = opt_value
elif opt in ["-k", "--key"]:
key_file = opt_value
elif opt in ["-l", "--user"]:
user = opt_value
elif opt in ["-w", "--password"]:
password = opt_value
elif opt in ["-V", "--version"]:
print __revision__
sys.exit(0)
else:
usage(1, "Option %s is not allowed" % opt)
if len(args) > 0:
base_url = args[-1]
if not base_url.lower().startswith('http'):
base_url = 'http://' + base_url
(addressing_scheme, network_location, path, parameters, \
query, fragment_identifier) = urlparse.urlparse(base_url)
secure = (addressing_scheme == "https")
if (cert_file and not key_file) or \
(key_file and not cert_file):
# Both are needed if one specified
usage(1, "You must specify both certificate and key files")
if password and not user:
# User must be specified when password is given
usage(1, "You must specify a username")
elif user and not password:
if not secure:
sys.stderr.write("*WARNING* Your password will be sent in clear!\n")
try:
password = getpass.getpass()
except KeyboardInterrupt, e:
sys.stderr.write("\n")
sys.exit(0)
oai_harvest_getter.harvest(network_location, path,
http_param_dict, method,
output, sets, secure, user,
password, cert_file,
key_file)
sys.stderr.write("Harvesting completed at: %s\n\n" %
time.strftime("%Y-%m-%d %H:%M:%S --> ", time.localtime()))
return
else:
usage(1, "You must specify the URL to harvest")
else:
# verb is not given. We will continue with periodic
# harvesting. But first check if URL parameter is given:
# if it is, then warn directly now
if len(args) > 1 or \
(len(args) == 1 and not args[0].isdigit()):
usage(1, "You must specify the --verb parameter")
except getopt.error, e:
# So could it be that we are using different arguments? Try to
# start the BibSched task (automated harvesting) and see if it
# validates
pass
# BibSched mode - periodical harvesting
# Note that the 'help' is common to both manual and automated
# mode.
task_set_option("repository", None)
task_set_option("dates", None)
task_init(authorization_action = 'runoaiharvest',
authorization_msg = "oaiharvest Task Submission",
description = """
Harvest records from OAI sources.
Manual vs automatic harvesting:
- Manual harvesting retrieves records from the specified URL,
with the specified OAI arguments. Harvested records are displayed
on the standard output or saved to a file, but are not integrated
into the repository. This mode is useful to 'play' with OAI
repositories or to build special harvesting scripts.
- Automatic harvesting relies on the settings defined in the OAI
Harvest admin interface to periodically retrieve the repositories
and sets to harvest. It also take care of harvesting only new or
modified records. Records harvested using this mode are converted
and integrated into the repository, according to the settings
defined in the OAI Harvest admin interface.
Examples:
Manual (single-shot) harvesting mode:
Save to /tmp/z.xml records from CDS added/modified between 2004-04-01
and 2004-04-02, in MARCXML:
$ oaiharvest -vListRecords -f2004-04-01 -u2004-04-02 -pmarcxml -o/tmp/z.xml http://cdsweb.cern.ch/oai2d
Automatic (periodical) harvesting mode:
Schedule daily harvesting of all repositories defined in OAIHarvest admin:
$ oaiharvest -s 24h
Schedule daily harvesting of repository 'arxiv', defined in OAIHarvest admin:
$ oaiharvest -r arxiv -s 24h
Harvest in 10 minutes from 'pubmed' repository records added/modified
between 2005-05-05 and 2005-05-10:
$ oaiharvest -r pubmed -d 2005-05-05:2005-05-10 -t 10m
""",
help_specific_usage = 'Manual single-shot harvesting mode:\n'
' -o, --output specify output file\n'
' -v, --verb OAI verb to be executed\n'
' -m, --method http method (default POST)\n'
' -p, --metadataPrefix metadata format\n'
' -i, --identifier OAI identifier\n'
' -s, --set OAI set(s). Whitespace-separated list\n'
' -r, --resuptionToken Resume previous harvest\n'
' -f, --from from date (datestamp)\n'
' -u, --until until date (datestamp)\n'
' -c, --certificate path to public certificate (in case of certificate-based harvesting)\n'
' -k, --key path to private key (in case of certificate-based harvesting)\n'
' -l, --user username (in case of password-protected harvesting)\n'
' -w, --password password (in case of password-protected harvesting)\n'
'Automatic periodical harvesting mode:\n'
' -r, --repository="repo A"[,"repo B"] \t which repositories to harvest (default=all)\n'
' -d, --dates=yyyy-mm-dd:yyyy-mm-dd \t reharvest given dates only\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()
c4science · Help