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R3600/modules/bibharvest/lib/oaiarchive_engine.py
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oaiarchive_engine.py
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## $Id$
## OAI repository archive and management tool
## 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.
"""OAI repository archive and management tool
TODO: - Enable -c ('correct' or mode == 4) mode once correctly tested.
- Fix problem of zombie records (records that are in not set, and
can therefore not be removed) that can occurs with -c mode.
"""
__revision__ = "$Id$"
import os
import time
from stat import ST_SIZE
from invenio.config import \
CFG_OAI_ID_FIELD, \
CFG_OAI_ID_PREFIX, \
CFG_OAI_SET_FIELD, \
CFG_BINDIR, \
CFG_SITE_NAME, \
CFG_TMPDIR
from invenio.search_engine import perform_request_search
from invenio.dbquery import run_sql
from invenio.bibtask import task_get_option, task_set_option, write_message, \
task_update_progress, task_init, task_sleep_now_if_required
def all_sets():
"""
Returns a list of sets.
Each set is [id, setName, setSpec, setCollection,
setDescription, setDefinition, setRecList,
p1, f1, m1, p2, f2, m2, p3, f3, m3]
but parameters p1, f1, m1, p2, f2, m2, p3, f3, m3 should not be used.
Use parse_set_definition(setDefinition) instead.
"""
sets = []
query = """SELECT id, setName, setSpec, setCollection, setDescription,
setDefinition, setRecList,
p1, f1, m1, p2, f2, m2, p3, f3, m3
FROM oaiARCHIVE"""
res = run_sql(query)
for (setID, setName, setSpec, setCollection, setDescription,
setDefinition, setRecList, p1, f1, m1, p2, f2, m2, p3, f3, m3) in res:
params = parse_set_definition(setDefinition)
set = [setID,
setName,
setSpec,
setCollection,
setDescription,
setDefinition,
setRecList,
params['p1'],
params['f1'],
params['m1'],
params['p2'],
params['f2'],
params['m2'],
params['p3'],
params['f3'],
params['m3']]
sets.append(set)
return sets
def parse_set_definition(set_definition):
"""
Returns the parameters for the given set definition
The returned structure is a dictionary with keys being
c, p1, f1, m1, p2, f2, m2, p3, f3, m3 and corresponding values
@param set_definition a string as returned by the database for column 'setDefinition'
@return a dictionary
"""
params = {'c':'',
'p1':'', 'f1':'', 'm1':'',
'p2':'', 'f2':'', 'm2':'',
'p3':'', 'f3':'', 'm3':'',
'op1':'a', 'op2':'a'}
definitions = set_definition.split(';')
for definition in definitions:
arguments = definition.split('=')
if len(arguments) == 2:
params[arguments[0]] = arguments[1]
return params
def repository_size():
"Read repository size"
return len(perform_request_search(p1="oai:*", f1=CFG_OAI_ID_FIELD, m1="e", ap=0))
def get_set_descriptions(setSpec):
"Retrieve set descriptions from oaiARCHIVE table"
set_descriptions = []
query = "select setName, setDefinition from oaiARCHIVE where setSpec=%s"
res = run_sql(query, (setSpec, ))
for (set_name, set_definition) in res:
params = parse_set_definition(set_definition)
params['setSpec'] = setSpec
params['setName'] = set_name
set_descriptions.append(params)
return set_descriptions
def get_recID_list(oai_set_descriptions, set):
"""Returns the list of records ID belonging to 'set'
@param set The set object from which to retrieve the records
(as in list returned by all_sets())
@param oai_set_descriptions The list of descriptions for the set
(as returned by get_set_descriptions())
"""
setSpec = ""
setName = ""
setCoverage = ""
#list_of_sets = []
processed_sets = []
recID_list = []
for oai in oai_set_descriptions:
if oai['setSpec'] in processed_sets :
pass
else:
#list_of_sets.append(oai)
processed_sets.append(oai['setSpec'])
if(oai['setSpec'] == set):
setSpec = oai['setSpec']
setName = oai['setName']
setCoverage += oai['c']
setCoverage += " "
recID_list_ = perform_request_search(c=[coll.strip()
for coll in oai['c'].split(',')],
p1=oai['p1'],
f1=oai['f1'],
m1=oai['m1'],
op1=oai['op1'],
p2=oai['p2'],
f2=oai['f2'],
m2=oai['m2'],
op2=oai['op2'],
p3=oai['p3'],
f3=oai['f3'],
m3=oai['m3'],
ap=0)
for recID in recID_list_:
if recID in recID_list:
pass
else:
recID_list.append(recID)
if (setSpec == "global"):
setCoverage = CFG_SITE_NAME
return (setSpec, setName, setCoverage, recID_list)
### MAIN ###
def oaiarchive_task():
"""Main business logic code of oai_archive"""
upload = task_get_option("upload")
mode = task_get_option("mode")
nice = task_get_option("nice")
sets = task_get_option("oaiset")
if(mode == 3):
# Print repository status
all_oai_sets = all_sets()
repository_size_s = "%d" % repository_size()
write_message(CFG_SITE_NAME)
write_message(" OAI Repository Status")
write_message("=" * 73)
write_message(" setSpec" + " " * 16 + " setName" +
" " * 29 + " Volume")
write_message("-" * 73)
for _set in all_oai_sets:
task_sleep_now_if_required(can_stop_too=True)
oai_sets = get_set_descriptions(_set[2])
setSpec, setName, setCoverage, recID_list = \
get_recID_list(oai_sets, _set)
oai_has_list = perform_request_search(c=CFG_SITE_NAME, p1=_set[2],
f1=CFG_OAI_SET_FIELD, m1="e", ap=0)
oai_has_list_len = "%d" % len(oai_has_list)
set_name = "%s" % _set[1][:32]
if (len(set_name) == 32):
set_name = "%s..." % set_name
write_message(" " + _set[2] + " " * (25 - len(_set[2])) + set_name +
" " * (35 - len(set_name)) +
" " * (9 - len(oai_has_list_len)) +
oai_has_list_len)
write_message("=" * 73)
write_message(" Total" + " " * 55 +
" " * (9 - len(repository_size_s)) + repository_size_s)
return True
# Mode 1, 2 and 4
if isinstance(sets, str):
# Backward compatibility with old way of storing 'oaiset' parameter
sets = list(sets)
set_number = 0
for set in sets:
task_sleep_now_if_required(can_stop_too=True)
set_number += 1
# Reset some variables
oaisetentrycount = 0
oaiIDentrycount = 0
i = 0
if(mode == 0):
oai_sets = get_set_descriptions(set)
setSpec, setName, setCoverage, recID_list = \
get_recID_list(oai_sets, set)
if(set == ""):
raise StandardError
else:
oai_has_list = perform_request_search(c=CFG_SITE_NAME, p1=set,
f1=CFG_OAI_SET_FIELD, m1="e", ap=0)
write_message(" setSpec : %s" % setSpec)
write_message(" setName : %s" % setName)
write_message(" setDescription : %s" % setCoverage)
write_message(" Coverage : %d records" %
(len(recID_list)))
write_message(" OAI repository has : %d records" %
(len(oai_has_list)))
write_message(" To be uploaded : %d records" %
(len(recID_list) - len(oai_has_list)))
else:
task_update_progress("[%i/%i] Fetching records in %s." % \
(set_number, len(sets), set))
if mode == 1 or mode == 4:
filename = CFG_TMPDIR + "/oai_archive_%s" % time.strftime(
"%Y%m%d_%H%M%S", time.localtime())
oai_out = open(filename,"w")
if mode == 2 or mode == 4:
filename2 = CFG_TMPDIR + "/oai_archive_%s_2" % time.strftime(
"%Y%m%d_H%M%S", time.localtime())
oai_out2 = open(filename2,"w")
oai_sets = get_set_descriptions(set)
setSpec, setName, setCoverage, recID_list = \
get_recID_list(oai_sets, set)
i = 0
for recID in recID_list:
task_update_progress("[%i/%i] Set %s: done %s out of %s records." % \
(set_number, len(sets), setSpec, i, len(recID_list)))
i += 1
time.sleep(int(nice)/10)
ID = "%d" % recID
### oaiIDentry validation
### Check if OAI identifier is already in the record or not
add_ID_entry = True
oaiIDentry = "<subfield code=\"%s\">oai:%s:%s</subfield>\n" % \
(CFG_OAI_ID_FIELD[5:6], CFG_OAI_ID_PREFIX,ID)
query = "select b3.value from bibrec_bib%sx as br " \
"left join bib%sx as b3 on br.id_bibxxx=b3.id " \
"where b3.tag=%%s and br.id_bibrec=%%s" % \
(CFG_OAI_ID_FIELD[0:2], CFG_OAI_ID_FIELD[0:2])
res = run_sql(query, (CFG_OAI_ID_FIELD, recID))
if(res):
# No need to add identifier if already exists. (Check
# that it INDEED exist, i.e. that field is not empty)
for value in res:
if len(value) > 0 and value[0] != '':
add_ID_entry = False
if add_ID_entry:
oaiIDentrycount += 1
datafield_set_head = \
"<datafield tag=\"%s\" ind1=\"%s\" ind2=\"%s\">" % \
(CFG_OAI_SET_FIELD[0:3],
CFG_OAI_SET_FIELD[3:4].replace('_', ' '),
CFG_OAI_SET_FIELD[4:5].replace('_', ' '))
datafield_id_head = \
"<datafield tag=\"%s\" ind1=\"%s\" ind2=\"%s\">" % \
(CFG_OAI_ID_FIELD[0:3],
CFG_OAI_ID_FIELD[3:4].replace('_', ' '),
CFG_OAI_ID_FIELD[4:5].replace('_', ' '))
oaisetentry = "<subfield code=\"%s\">%s</subfield>\n" % \
(CFG_OAI_SET_FIELD[5:6], set)
oaisetentrycount += 1
### oaisetentry validation
### Check to which sets this record belongs
query = "select b3.value from bibrec_bib%sx as br " \
"left join bib%sx as b3 on br.id_bibxxx=b3.id " \
"where b3.tag=%%s and br.id_bibrec=%%s" % \
(CFG_OAI_SET_FIELD[0:2], CFG_OAI_SET_FIELD[0:2])
res = run_sql(query, (CFG_OAI_SET_FIELD, recID))
remaining_sets = []
if(res):
for item in res:
if (item[0]==set):
# No need to add set to metadata if already there
oaisetentry = ''
oaisetentrycount -= 1
elif item[0]:
# Collect name of the other sets to which the
# record must also belong (in case we are in
# mode == 2)
remaining_sets.append(item[0])
if (mode==2):
# Delete mode
oaisetentry = ''
# Build sets that the record is still part of
for remaining_set in remaining_sets:
oaisetentry += "<subfield code=\"%s\">%s</subfield>\n" % \
(CFG_OAI_SET_FIELD[5:6], remaining_set)
if (CFG_OAI_ID_FIELD[0:5] == CFG_OAI_SET_FIELD[0:5]):
# Put set and OAI ID in the same datafield
oai_out2.write("<record>\n")
oai_out2.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
oai_out2.write(datafield_id_head)
oai_out2.write("\n")
if oaisetentry:
# Record is still part of some sets
oai_out2.write(oaiIDentry)
oai_out2.write(oaisetentry)
else:
# Remove record from OAI repository
oai_out2.write("<subfield code=\"")
oai_out2.write(CFG_OAI_ID_FIELD[5:6])
oai_out2.write("\"></subfield>\n")
oai_out2.write("<subfield code=\"")
oai_out2.write(CFG_OAI_SET_FIELD[5:6])
oai_out2.write("\"></subfield>\n")
oai_out2.write("</datafield>\n")
oai_out2.write("</record>\n")
else:
oai_out2.write("<record>\n")
oai_out2.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
if oaisetentry:
# Record is still part of some set
# Keep the OAI ID as such
pass
else:
# Remove record from OAI repository
# i.e. remove OAI ID
oai_out2.write(datafield_id_head)
oai_out2.write("\n")
oai_out2.write("<subfield code=\"")
oai_out2.write(CFG_OAI_ID_FIELD[5:6])
oai_out2.write("\"></subfield>\n")
oai_out2.write("</datafield>\n")
oai_out2.write(datafield_set_head)
oai_out2.write("\n")
if oaisetentry:
# Record is still part of some set
oai_out2.write(oaisetentry)
else:
# Remove record from OAI repository
oai_out2.write("<subfield code=\"")
oai_out2.write(CFG_OAI_SET_FIELD[5:6])
oai_out2.write("\"></subfield>\n")
oai_out2.write("</datafield>\n")
oai_out2.write("</record>\n")
elif (mode==1) or mode == 4:
# Add mode (1)
# or clean mode (4)
if ((add_ID_entry)or(oaisetentry)):
if (CFG_OAI_ID_FIELD[0:5] == CFG_OAI_SET_FIELD[0:5]):
# Put set and OAI ID in the same datafield
oai_out.write("<record>\n")
oai_out.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
oai_out.write(datafield_id_head)
oai_out.write("\n")
if(add_ID_entry):
oai_out.write(oaiIDentry)
if(oaisetentry):
oai_out.write(oaisetentry)
oai_out.write("</datafield>\n")
oai_out.write("</record>\n")
else:
oai_out.write("<record>\n")
oai_out.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
if(add_ID_entry):
oai_out.write(datafield_id_head)
oai_out.write("\n")
oai_out.write(oaiIDentry)
oai_out.write("</datafield>\n")
if(oaisetentry):
oai_out.write(datafield_set_head)
oai_out.write("\n")
oai_out.write(oaisetentry)
oai_out.write("</datafield>\n")
oai_out.write("</record>\n")
if mode == 4:
# Update records that should no longer be in this set
# Fetch records that are currently marked with this set in
# the database
oai_has_list = perform_request_search(c=CFG_SITE_NAME, p1=set,
f1=CFG_OAI_SET_FIELD, m1="e", ap=0)
# Fetch records that should not be in this set
# (oai_has_list - recID_list)
records_to_update = [rec_id for rec_id in oai_has_list \
if not rec_id in recID_list]
datafield_set_head = "<datafield tag=\"%s\" ind1=\"%s\"" \
" ind2=\"%s\">" % (CFG_OAI_SET_FIELD[0:3], \
CFG_OAI_SET_FIELD[3:4].replace('_', ' '), \
CFG_OAI_SET_FIELD[4:5].replace('_', ' '))
datafield_id_head = "<datafield tag=\"%s\" ind1=\"%s\"" \
" ind2=\"%s\">" % (CFG_OAI_ID_FIELD[0:3], \
CFG_OAI_ID_FIELD[3:4].replace('_', ' '), \
CFG_OAI_ID_FIELD[4:5].replace('_', ' '))
for recID in records_to_update:
oaiIDentry = "<subfield code=\"%s\">oai:%s:%s</subfield>\n" % \
(CFG_OAI_ID_FIELD[5:6], CFG_OAI_ID_PREFIX, recID)
### Check to which sets this record belongs
query = "select b3.value from bibrec_bib%sx as br " \
"left join bib%sx as b3 on br.id_bibxxx=b3.id " \
"where b3.tag=%%s and br.id_bibrec=%%s" % \
(CFG_OAI_SET_FIELD[0:2], CFG_OAI_SET_FIELD[0:2])
res = run_sql(query, (CFG_OAI_SET_FIELD, recID))
oaisetentry = ''
for in_set in res:
if in_set[0] != set:
oaisetentry += "<subfield code=\"%s\">%s" \
"</subfield>\n" % \
(CFG_OAI_SET_FIELD[5:6], in_set[0])
if (CFG_OAI_ID_FIELD[0:5] == CFG_OAI_SET_FIELD[0:5]):
# Put set and OAI ID in the same datafield
oai_out2.write("<record>\n")
oai_out2.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
oai_out2.write(datafield_id_head)
oai_out2.write("\n")
# if oaisetentry:
# Record is still part of some sets
oai_out2.write(oaiIDentry)
oai_out2.write(oaisetentry)
## else:
## # Remove record from OAI repository
## oai_out.write("<subfield code=\"")
## oai_out.write(CFG_OAI_ID_FIELD[5:6])
## oai_out.write("\"></subfield>\n")
## oai_out.write("<subfield code=\"")
## oai_out.write(CFG_OAI_SET_FIELD[5:6])
## oai_out.write("\"></subfield>\n")
oai_out2.write("</datafield>\n")
oai_out2.write("</record>\n")
else:
oai_out2.write("<record>\n")
oai_out2.write("<controlfield tag=\"001\">%s"
"</controlfield>\n" % recID)
## if oaisetentry:
## # Record is still part of some set
## # Keep the OAI ID as such
## pass
## else:
## # Remove record from OAI repository
## # i.e. remove OAI ID
## oai_out.write(datafield_id_head)
## oai_out.write("\n")
## oai_out.write("<subfield code=\"")
## oai_out.write(CFG_OAI_ID_FIELD[5:6])
## oai_out.write("\"></subfield>\n")
## oai_out.write("</datafield>\n")
oai_out2.write(datafield_set_head)
oai_out2.write("\n")
# if oaisetentry:
# Record is still part of some set
oai_out2.write(oaisetentry)
# else:
# # Remove record from OAI repository
# oai_out.write("<subfield code=\"")
# oai_out.write(CFG_OAI_SET_FIELD[5:6])
# oai_out.write("\"></subfield>\n")
oai_out2.write("</datafield>\n")
oai_out2.write("</record>\n")
if mode == 1 or mode == 4:
oai_out.close()
if mode == 2 or mode == 4:
oai_out2.close()
if upload:
if (mode == 1 or mode == 4) and oaisetentrycount > 0:
# Check if file is empty or not:
len_file = os.stat(filename)[ST_SIZE]
if len_file > 0:
command = "%s/bibupload -a %s" % (CFG_BINDIR, filename)
os.system(command)
if mode == 2 or mode == 4:
# Check if file is empty or not:
len_file = os.stat(filename2)[ST_SIZE]
if len_file > 0:
command = "%s/bibupload -c %s" % (CFG_BINDIR, filename2)
os.system(command)
return True
#########################
def main():
"""Main that construct all the bibtask."""
task_init(authorization_action='runoaiarchive',
authorization_msg="OAI Archive Task Submission",
description="Examples:\n"
" Expose set 'setSpec' via OAI repository gateway\n"
" oaiarchive --oaiset='setSpec' --add --upload\n"
" oaiarchive -apo 'setSpec'\n\n"
" Expose multiple sets via OAI repository gateway\n"
" oaiarchive --oaiset='setSpec1 setSpec2 setSpec3' --add --upload\n"
" oaiarchive -apo 'setSpec1 setSpec2 setSpec3'\n\n"
" Remove records defined by 'setSpec' from OAI repository\n"
" oaiarchive --oaiset='setSpec' --delete --upload\n"
" oaiarchive -dpo 'setSpec'\n\n"
" Expose entire repository via OAI gateway\n"
" oaiarchive --set=global --add --upload\n"
" oaiarchive -apo global\n\n"
" Print OAI set status\n"
" oaiarchive --oaiset='setSpec' --info\n"
" oaiarchive -io 'setSpec'\n\n"
" Print OAI repository status\n"
" oaiarchive -r\n\n",
help_specific_usage="Options:\n"
" -o --oaiset= Specify setSpec(s) (whitespace separated list of setSpecs) to expose via OAI\n"
"Modes\n"
" -a --add Add records to OAI repository\n"
" -d --delete Remove records from OAI repository\n"
" -r --report OAI repository status\n"
" -i --info Give info about OAI set (default)\n"
"Additional parameters:\n"
" -p --upload Upload records\n",
version=__revision__,
specific_params=("ado:pirn", [
"add",
"delete",
"oaiset=",
"upload",
"info",
"report",
"no-process"]),
task_submit_elaborate_specific_parameter_fnc=
task_submit_elaborate_specific_parameter,
task_run_fnc=oaiarchive_task)
def task_submit_elaborate_specific_parameter(key, value, opts, args):
"""Elaborate specific CLI parameters of oaiarchive"""
if key in ("-n", "--nice"):
task_set_option("nice", value)
elif key in ("-o", "--oaiset"):
sets = [set for set in value.split(' ') if set != '']
task_set_option("oaiset", sets)
elif key in ("-a", "--add"):
task_set_option("mode", 1)
elif key in ("-d", "--delete"):
task_set_option("mode", 2)
elif key in ("-c", "--clean"):
task_set_option("mode", 4)
elif key in ("-p", "--upload"):
task_set_option("upload", 1)
elif key in ("-i", "--info"):
task_set_option("mode", 0)
elif key in ("-r", "--report"):
task_set_option("mode", 3)
elif key in ("-n", "--no-process"):
task_set_option("upload", 0)
else:
return False
return True
### okay, here we go:
if __name__ == '__main__':
main()
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