refextract_daemon.py
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refextract_daemon.py
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	# -- coding: utf-8 --
	##
	## This file is part of Invenio.
	## Copyright (C) 2011 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.

	"""Initialise Refextract task
	"""
	import sys, os, time
	from shutil import copyfile
	from invenio.bibtask import task_init, task_set_option, \
	task_get_option, write_message, \
	task_has_option, task_get_task_param
	from invenio.config import CFG_VERSION, CFG_TMPDIR, CFG_BINDIR, CFG_ETCDIR
	from invenio.dbquery import run_sql
	## Used to create a new record object, to obtain fulltexts
	from invenio.bibdocfile import BibRecDocs
	## Used to obtain the fulltexts for a given collection
	from invenio.search_engine import get_collection_reclist
	## begin_extraction() is the beginning method of extracting references,
	## given that either standalone or non-standlone methods have been selected
	from invenio.refextract import begin_extraction
	## Help message is the usage() print out of how to use Refextract
	from invenio.refextract import help_message
	from invenio.refextract_config import CFG_REFEXTRACT_JOB_FILE_PARAMS

	from tempfile import mkstemp

	try:
	## Used to obtain the file-type of input documents
	from invenio.config import CFG_PATH_GFILE
	except ImportError:
	CFG_PATH_GFILE='/usr/bin/file'

	def _task_name_exists(name):
	"""Check if the task name is registered in the database."""
	res = run_sql("SELECT id, name, last_updated FROM xtrJOB WHERE name=%s", (name, ))
	if res:
	return res
	return False

	def _collection_exists(collection_name):
	"""Check if the collection name is registered in the database."""
	res = run_sql("SELECT name FROM collection WHERE name=%s",
	(collection_name,))
	if res:
	return res
	return False

	def _recid_exists(recid):
	"""Check if the recid number is registered in the database."""
	if run_sql("SELECT id FROM bibrec WHERE id=%s",
	(recid,)):
	return True
	return False

	## What differs here from the extraction-job params: collections and recids
	possible_task_option_keys = ('collections', 'recids', 'raw-references',
	'output-raw-refs', 'xmlfile', 'dictfile',
	'inspire', 'kb-journal', 'kb-report-number', 'verbose')

	def _task_submit_elaborate_specific_parameter(key, value, opts, args):
	""" Must be defined for bibtask to create a task """
	if args and len(args) > 0:
	## There should be no standalone arguments for any refextract job
	## This will catch args before the job is shipped to Bibsched
	raise StandardError("Error: Unrecognised argument '%s'.\n" % args[0])

	## Task name specified
	if key in ('-e', '--extraction-job'):

	## Make sure that the user is not mixing job name with other defined
	## Refextract flags on the command line
	if filter(lambda p: task_get_option(p), possible_task_option_keys):
	write_message("Error: cli and extraction-job extraction parameters specified together.")
	write_message("The extraction-job flag cannot be mixed with other cli flags.")
	return False

	## ---- Get the task file with this name
	task_file_dir = os.path.join(CFG_ETCDIR, 'refextract')
	## The job file name
	task_file = value + '.cfg'
	abs_path = os.path.join(task_file_dir, task_file)
	try:
	## Open and readlines from file
	file_hdl = open(abs_path, 'r')
	file_params = file_hdl.readlines()
	file_hdl.close()
	except IOError:
	write_message("Error: Unable to read job file '%s'" % \
	abs_path, stream=sys.stdout, verbose=0)
	return False
	## ---- Get the database 'last_updated' value for this name
	xtrJOB_row = _task_name_exists(value)
	## Build the information for this extraction job
	## These dictionaries will be extended with extra file parameters
	if xtrJOB_row:
	task_info = {'id' : xtrJOB_row[0][0],
	'name' : xtrJOB_row[0][1],
	'last_updated' : xtrJOB_row[0][2],
	'collections' : [],
	'recids' : [],}
	else:
	## Save the name as the input argument for this job
	task_info = {'name' : value,
	'last_updated' : None,
	'collections' : [],
	'recids' : [],}
	## ---- Save job parameters
	for p in file_params:
	p = p.strip()
	## Ignore comments and titles, and skip blank lines
	if (not p) or p.startswith('#') or p.startswith("["):
	continue
	## Split arguments just once
	p_args = map(lambda x: x.strip(), p.split("=", 1))
	## Check cfg file param against list of vaild params
	if not (p_args[0] in CFG_REFEXTRACT_JOB_FILE_PARAMS):
	write_message("Error: Unknown task param '%s' inside '%s'." \
	% (p_args[0], task_file),
	stream=sys.stdout, verbose=0)
	return False

	if p_args[0] == 'collection':
	## Separate and strip collections
	collections = map(lambda c: c.strip(), p_args[1].split(','))
	task_info['collections'].extend([c for c in collections if c.strip()])

	#FIXME add author extraction functionality
	# elif p_args[0] == 'extraction-mode':
	# if p_args[0] == 'authors':
	# task_set_option('authors', p_args[1])

	elif p_args[0] == 'recid':
	recids = p_args[1].split(",")
	task_info['recids'].extend([r for r in recids if r.strip()])
	elif len(p_args) == 2:
	## All other flags
	task_info[p_args[0]] = p_args[1]
	else:
	## Standalone flag
	task_info[p_args[0]] = 1

	if not ('xmlfile' in task_info):
	task_info['xmlfile'] = _generate_default_xml_out()

	## Used to flag the creation of a bibupload task
	task_set_option('extraction-job', task_info)

	## using the extraction-job options...
	## set the task options
	for option, value in task_info.items():
	if option == 'collections':
	for collection in value:
	collection_row = _collection_exists(collection)
	if not collection_row:
	write_message("Error: '%s' is not a valid collection." % collection,
	stream=sys.stdout, verbose=0)
	return 0
	## Use the collection name matched from the database
	task_get_option(option).append(collection_row[0][0])
	elif option == 'recids':
	for recid in value:
	if not _recid_exists(recid):
	write_message("Error: '%s' is not a valid record id." % recid,
	stream=sys.stdout, verbose=0)
	return 0
	## Add this valid record id to the list of record ids
	task_get_option(option).append(recid)
	elif option not in ('id', 'name', 'last_updated'):
	## Usual way of setting options, but this time from the extraction-job file
	task_set_option(option, value)

	else:
	## Quick check to see if an extraction job has also been specified
	if task_has_option('extraction-job'):
	write_message("Error: cli and extraction-job extraction parameters specified together.")
	write_message("The extraction-job flag cannot be mixed with other cli flags.")
	return False

	# Recid option
	elif key in ("-i", "--recid"):
	split_recids = value.split(":")
	if len(split_recids) == 2:
	first = last = valid_range = None
	try:
	first = int(split_recids[0])
	last = int(split_recids[1])
	valid_range = first < last
	except ValueError:
	write_message("Error: Range values for --recid must be integers, "
	"not '%s'." % value, stream=sys.stdout, verbose=0)
	if first is None or last is None:
	return False
	if not _recid_exists(first) or not _recid_exists(last) or not valid_range:
	write_message("Error: '%s' is not a valid range of record ID's." % value,
	stream=sys.stdout, verbose=0)
	return False
	task_get_option('recids').extend(range(first, last))
	else:
	int_val = None
	try:
	int_val = int(value)
	except ValueError:
	write_message("Error: The value specified for --recid must be a "
	"valid integer, not '%s'." % value, stream=sys.stdout,
	verbose=0)
	if not _recid_exists(value) or int_val is None:
	write_message("Error: '%s' is not a valid record ID." % value,
	stream=sys.stdout, verbose=0)
	return False
	task_get_option('recids').append(value)
	# Collection option
	elif key in ("-c", "--collection"):
	collection_row = _collection_exists(value)
	if not collection_row:
	write_message("Error: '%s' is not a valid collection." % value,
	stream=sys.stdout, verbose=0)
	return False
	task_get_option('collections').append(collection_row[0][0])
	elif key in ('-z', '--raw-references'):
	task_set_option('raw-references', True)
	elif key in ('-r', '--output-raw-refs'):
	task_set_option('output-raw-refs', True)
	elif key in ('-x', '--xmlfile'):
	task_set_option('xmlfile', value)
	elif key in ('-d', '--dictfile'):
	task_set_option('dictfile', value)
	elif key in ('-p', '--inspire'):
	task_set_option('inspire', True)
	elif key in ('-j', '--kb-journal'):
	task_set_option('kb-journal', value)
	elif key in ('-n', '--kb-report-number'):
	task_set_option('kb-report-number', value)
	return True

	def _get_fulltext_args_from_recids(recids, task_info):
	"""Get list of fulltext locations for input recids
	@param recids: (list) list of recids
	@return: (list) list of strings of the form 'recid:fulltext dir'
	"""
	fulltext_arguments = []
	last_updated = None
	if task_info:
	last_updated = task_info['last_updated']

	if recids:
	if last_updated:
	q_get_outdated = "SELECT id FROM bibrec WHERE id IN (%s) AND " \
	"modification_date > '%s';" % \
	(",".join(map(lambda r: str(r), recids)), last_updated)
	## Get records for reference extraction
	changed_records = run_sql(q_get_outdated)
	else:
	## Make list of lists of input recids
	changed_records = [[r] for r in recids]
	if changed_records:
	for record_row in changed_records:
	record = record_row[0]
	bibrecdoc = BibRecDocs(record)
	## Get the latest 'document items' for this record
	bibdocfiles = bibrecdoc.list_latest_files()
	if bibdocfiles:
	doc_types = {'pdf' : [],
	'pdfa' : [],
	'text' : [],}

	bibdoc = bibrecdoc.list_bibdocs()
	## Get the text file for this record
	if bibdoc and bibdoc[0].has_text():
	doc_types['text'].append(bibdoc[0].get_text_path())

	## For each file, of a record
	for doc in bibdocfiles:
	pipe_gfile = \
	os.popen("%s '%s'" \
	% (CFG_PATH_GFILE, doc.get_full_path().replace("'", "\\'")), "r")
	res_gfile = pipe_gfile.readline()
	pipe_gfile.close()

	## Look for : 1. Unstamped, original uploaded-by-user, pdf files
	## 2. Stamped, processed, pdf files
	## 3. Text files
	if (res_gfile.lower().find('pdfa') != -1):
	doc_types['pdfa'].append(doc.get_full_path())
	elif (res_gfile.lower().find('pdf') != -1):
	doc_types['pdf'].append(doc.get_full_path())

	## Choose the type in this order of priority
	type_of_choice = doc_types['text'] or doc_types['pdf'] or doc_types['pdfa']
	if type_of_choice:
	fulltext_arguments.append(str(record).rstrip(".")+':'+type_of_choice[0])
	else:
	write_message("W: No pdf/text file for recid %s" % \
	str(record), stream=sys.stdout, verbose=0)
	else:
	write_message("W: No files exist for recid %s" % \
	str(record), stream=sys.stdout, verbose=0)
	elif task_info:
	## In the event that no records have been modified since the
	## last reference extraction
	write_message("No newly modified records for extraction-job '%s'." \
	% task_info['name'], stream=sys.stdout, verbose=0)
	return fulltext_arguments

	def _task_run_core():
	"""calls extract_references in refextract"""

	def _append_recid_collection_list(collection, current_recids):
	"""Updated list of recids with new recids from collection
	@param collection: (string) collection name to use to obtain record
	ids
	@param current_recids: (list) list of current record ids
	which have already been obtained from previous collection or
	recid flags
	@return: (list) current record ids with newly appended recids
	from input collection
	"""
	records = get_collection_reclist(collection)
	for r in records:
	if r not in current_recids:
	current_recids.append(r)
	return current_recids

	daemon_cli_opts = { 'treat_as_reference_section' : 0,
	'fulltext' : [],
	'output_raw' : 0,
	'verbosity' : 0,
	'xmlfile' : 0,
	'dictfile' : 0,
	'inspire' : 0,
	'kb-journal' : 0,
	'kb-report-number' : 0,
	'extraction-mode' : 'ref',
	'authors' : 0,
	'affiliations' : 0,
	'treat_as_raw_section' : 0,
	}

	## holds the name of the extraction job, and if it's already in the db
	task_info = task_get_option('extraction-job')

	## Now set the cli options, from the set task options list
	if task_has_option('verbose'):
	v = task_get_option('verbose')
	if not v.isdigit():
	daemon_cli_opts['verbosity'] = 0
	elif int(v) not in xrange(0, 10):
	daemon_cli_opts['verbosity'] = 0
	else:
	daemon_cli_opts['verbosity'] = int(v)
	if task_has_option('raw-references'):
	daemon_cli_opts['treat_as_reference_section'] = 1
	if task_has_option('output-raw-refs'):
	daemon_cli_opts['output_raw'] = 1
	if task_has_option('xmlfile'):
	daemon_cli_opts['xmlfile'] = task_get_option('xmlfile')
	if task_has_option('dictfile'):
	daemon_cli_opts['dictfile'] = task_get_option('dictfile')
	if task_has_option('inspire'):
	daemon_cli_opts['inspire'] = 1
	if task_has_option('kb-journal'):
	daemon_cli_opts['kb-journal'] = task_get_option('kb-journal')
	if task_has_option('kb-report-number'):
	daemon_cli_opts['kb-report-number'] = task_get_option('kb-report-number')
	if task_get_option('recids'):
	## Construct the fulltext argument equivalent from record id's
	## (records, and arguments, which have valid files)
	try:
	fulltexts_for_collection = \
	_get_fulltext_args_from_recids(task_get_option('recids'), task_info)
	daemon_cli_opts['fulltext'].extend(fulltexts_for_collection)
	except Exception, err:
	write_message('Error: Unable to obtain fulltexts for recid %s. %s' \
	% (str(task_get_option('recids')), err), \
	stream=sys.stdout, verbose=0)
	raise StandardError
	if task_get_option('collections'):
	## Construct the fulltext argument equivalent from record id's
	recids_from_collection = []
	for collection in task_get_option('collections'):
	recids_from_collection = \
	_append_recid_collection_list(collection, recids_from_collection)
	## Construct the fulltext argument equivalent for collection recid's
	## (records, and arguments, which have valid files)
	fulltexts_for_collection = \
	_get_fulltext_args_from_recids(recids_from_collection, task_info)
	daemon_cli_opts['fulltext'].extend(fulltexts_for_collection)

	## If some records exist which actually need to have their references extracted
	if daemon_cli_opts['fulltext']:
	begin_extraction(daemon_cli_options=daemon_cli_opts)

	try:
	## Always move contents of file holding xml into a file
	## with a timestamp
	perm_file_fd, perm_file_name = \
	mkstemp(suffix='.xml', prefix="refextract_%s_" % \
	time.strftime("%Y-%m-%d_%H:%M:%S"), \
	dir=os.path.join(CFG_TMPDIR, "refextract"))
	copyfile(daemon_cli_opts['xmlfile'], perm_file_name)
	os.close(perm_file_fd)
	except IOError, err:
	write_message("Error: Unable to copy content to timestamped XML file, %s" \
	% err)
	return 0

	## Now, given the references have been output to option 'xmlfile'
	## enrich the meta-data of the affected records, via bibupload
	## Only if a named file was given as input
	if task_has_option('extraction-job'):
	cmd = "%s/bibupload -n -c '%s' " % (CFG_BINDIR, perm_file_name)
	errcode = 0
	try:
	errcode = os.system(cmd)
	except OSError, exc:
	write_message('Error: Command %s failed [%s].' % (cmd, exc),
	stream=sys.stdout, verbose=0)
	if errcode != 0:
	write_message("Error: %s failed, error code is %d." %
	(cmd, errcode), stream=sys.stdout, verbose=0)
	return 0
	## Update the extraction_date for each record id,
	## (only those which have been given to Refextract)
	if task_info['last_updated']:
	## If the last updated time exists in the db.. update it
	run_sql("UPDATE xtrJOB SET last_updated = NOW() WHERE name=%s", \
	(task_info['name'],))
	else:
	## This task does not exist in the db, add it
	run_sql("INSERT INTO xtrJOB (name, last_updated) VALUES (%s, NOW())", \
	(task_info['name'],))

	write_message("Reference extraction complete. Saved extraction-job XML file to %s" \
	% (perm_file_name))

	## When not calling a predefined extraction-job, display the
	## directory of the outputted references.
	else:
	write_message("Reference extraction complete. Saved references XML file to %s" \
	% (perm_file_name))

	return True

	def _generate_default_xml_out():
	"""Generates the default output xml file directory, corresponding
	to this refextract task id. This will be called in a user specified
	xml out file has not been provided.
	@return: (string) output xml file directory"""
	results_dir = os.path.join(CFG_TMPDIR, "refextract")
	# Write the changes to a temporary file.
	filename = "refextract_task_%d.xml" % task_get_task_param('task_id', 0)
	abs_path = os.path.join(results_dir, filename)
	## Make the folder, if not exists
	if not os.path.isdir(results_dir):
	os.mkdir(results_dir)
	return abs_path

	def _task_submit_check_options():
	""" Reimplement this method for having the possibility to check options
	before submitting the task, in order for example to provide default
	values. It must return False if there are errors in the options.
	"""
	if not task_get_option('recids') and not task_get_option('collections'):
	write_message('Error: No input file specified', stream=sys.stdout, verbose=0),
	return False
	## Output to a file in tmp, if the user has not specified an output file
	if not task_get_option('xmlfile', default=False):
	abs_path = _generate_default_xml_out()
	## Set the output
	task_set_option('xmlfile', abs_path)
	return True

	def refextract_daemon():
	"""Constructs the refextract bibtask."""
	## Build and submit the task
	task_init(authorization_action='runrefextract',
	authorization_msg="Refextract Task Submission",
	description="Extraction of references from pdf/text files, as XML.\n",
	# get the global help_message variable imported from refextract.py
	help_specific_usage= """Usage: refextract [options] -f recid:file1 [-f recid:file2 ...]
	refextract [options] --collection coll1 [--collection coll2 ...]
	refextract [options] --extraction-job refextract-job-name""" \
	+ help_message + """
	Scheduled (daemon) Refextract options:
	-i, --recid Record id for extraction.
	-c, --collection Entire Collection for extraction.
	-e, --extraction-job Name of a pre-configured Refextract task.

	Examples:
	(run a daemon job)
	refextract --extraction-job refextract-job-preprints
	(run on groups of/specific recids)
	refextract --collection preprints
	(run as standalone)
	refextract -x /home/chayward/refs.xml -f 499:/home/chayward/thesis.pdf

	""",
	version="Invenio v%s" % CFG_VERSION,
	specific_params=("hVv:zrx:d:pj:n:i:c:e:",
	["help",
	"version",
	"verbose=",
	"raw-references",
	"output-raw-refs",
	"xmlfile=",
	"dictfile=",
	"inspire",
	"kb-journal=",
	"kb-report-number=",
	"recid=",
	"collection=",
	"extraction-job=",]),
	task_submit_elaborate_specific_parameter_fnc=\
	_task_submit_elaborate_specific_parameter,
	task_submit_check_options_fnc=_task_submit_check_options,
	task_run_fnc=_task_run_core)

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