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bibreformat.py
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bibreformat.py
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# -*- mode: python; coding: utf-8; -*-
#
# This file is part of Invenio.
# Copyright (C) 2007, 2008, 2010, 2011, 2012, 2014, 2016 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.
"""Call BibFormat engine and create HTML brief (and other) formats cache for
bibliographic records."""
__revision__ = "$Id$"
import os
from datetime import datetime
from invenio.dbquery import run_sql
from invenio.intbitset import intbitset
from invenio.search_engine import perform_request_search, search_pattern
from invenio.bibrank_citation_searcher import get_cited_by
from invenio.bibrank_citation_indexer import get_bibrankmethod_lastupdate
from invenio.bibformat_dblayer import save_preformatted_record
from invenio.shellutils import split_cli_ids_arg
from invenio.bibfield import get_record
from invenio.bibtask import task_init, \
write_message, \
task_set_option, \
task_get_option, \
task_update_progress, \
task_has_option, \
task_sleep_now_if_required
from invenio.bibformat_engine import format_record_1st_pass
def fetch_last_updated(fmt):
select_sql = "SELECT last_updated FROM format WHERE code = %s"
row = run_sql(select_sql, (fmt.lower(), ))
# Fallback in case we receive None instead of a valid date
last_date = row[0][0] or datetime(year=1900, month=1, day=1)
return last_date
def store_last_updated(fmt, iso_date):
sql = "UPDATE format SET last_updated = %s " \
"WHERE code = %s AND (last_updated < %s or last_updated IS NULL)"
run_sql(sql, (iso_date, fmt.lower(), iso_date))
### run the bibreformat task bibsched scheduled
###
def bibreformat_task(fmt, recids, without_fmt, process):
"""BibReformat main task.
@param fmt: output format to use
@param process:
@param recids: a list of record IDs to reformat
@return: None
"""
write_message("Processing format %s" % fmt)
t1 = os.times()[4]
start_date = datetime.now().strftime("%Y-%m-%d %H:%M:%S")
latest_bibrank_run = get_bibrankmethod_lastupdate('citation')
def related_records(recids, recids_processed):
if fmt == "HDREF" and recids:
# HDREF represents the references tab
# the tab needs to be recomputed not only when the record changes
# but also when one of the citations changes
sql = """SELECT id, modification_date FROM bibrec
WHERE id in (%s)""" % ','.join(str(r) for r in recids)
def check_date(mod_date):
return mod_date.strftime(
"%Y-%m-%d %H:%M:%S") < latest_bibrank_run
rel_recids = intbitset([recid for recid, mod_date in run_sql(sql)
if check_date(mod_date)])
for r in rel_recids:
recids |= intbitset(get_cited_by(r))
# To not process recids twice
recids -= recids_processed
# Adds to the set of processed recids
recids_processed += recids
return recids
def recid_chunker(recids):
recids_processed = intbitset()
chunk = intbitset()
for recid in recids:
if len(chunk) == 5000:
for r in related_records(chunk, recids_processed):
yield r
recids_processed += chunk
chunk = intbitset()
if recid not in recids_processed:
chunk.add(recid)
if chunk:
for r in related_records(chunk, recids_processed):
yield r
recIDs = list(recid_chunker(recids))
### list of corresponding record IDs was retrieved
### now format the selected records
if without_fmt:
write_message("Records to be processed: %d" % len(recIDs))
write_message("Out of it records without existing cache: %d" %
len(without_fmt))
else:
write_message("Records to be processed: %d" % len(recIDs))
### Initialize main loop
total_rec = 0 # Total number of records
tbibformat = 0 # time taken up by external call
tbibupload = 0 # time taken up by external call
### Iterate over all records prepared in lists I (option)
if process:
total_rec_1, tbibformat_1, tbibupload_1 = iterate_over_new(recIDs, fmt)
total_rec += total_rec_1
tbibformat += tbibformat_1
tbibupload += tbibupload_1
### Store last run time
if task_has_option("last"):
write_message("storing run date to %s" % start_date)
store_last_updated(fmt, start_date)
### Final statistics
t2 = os.times()[4]
elapsed = t2 - t1
message = "total records processed: %d" % total_rec
write_message(message)
message = "total processing time: %2f sec" % elapsed
write_message(message)
message = "Time spent on external call (os.system):"
write_message(message)
message = " bibformat: %2f sec" % tbibformat
write_message(message)
message = " bibupload: %2f sec" % tbibupload
write_message(message)
def check_validity_input_formats(input_formats):
"""Check the validity of every input format.
@param input_formats: list of given formats
@type input_formats: list
@return: if there is any invalid input format it returns this value
@rtype: string
"""
from invenio.search_engine import get_available_output_formats
valid_formats = get_available_output_formats()
# let's to extract the values of the available formats
format_values = []
for aformat in valid_formats:
format_values.append(aformat['value'])
invalid_format = ''
for aformat in input_formats:
if aformat.lower() not in format_values:
invalid_format = aformat.lower()
break
return invalid_format
### Bibreformat all selected records (using new python bibformat)
### (see iterate_over_old further down)
def _update_recjson_format(recid, *args, **kwargs):
"""Update RECJSON cache.
:param int recid: record id to process
"""
dummy = get_record(recid, reset_cache=True)
def _update_format(recid, fmt):
"""Usual format update procedure, gets the formatted record and saves it.
:param int recid: record id to process
:param str fmt: format to update/create, i.e. 'HB'
"""
record, needs_2nd_pass = format_record_1st_pass(recID=recid,
of=fmt,
on_the_fly=True,
save_missing=False)
save_preformatted_record(recID=recid,
of=fmt,
res=record,
needs_2nd_pass=needs_2nd_pass,
low_priority=True)
_CFG_BIBFORMAT_UPDATE_FORMAT_FUNCTIONS = {'recjson': _update_recjson_format}
"""Specific functions to be used for each format if needed.
If not set `_update_format` will be used.
"""
def iterate_over_new(recIDs, fmt):
"""Iterate over list of IDs.
@param list: the list of record IDs to format
@param fmt: the output format to use
@return: tuple (total number of records, time taken to format, time taken
to insert)
"""
tbibformat = 0 # time taken up by external call
tbibupload = 0 # time taken up by external call
tot = len(recIDs)
reformat_function = _CFG_BIBFORMAT_UPDATE_FORMAT_FUNCTIONS.get(
fmt.lower(), _update_format)
for count, recID in enumerate(recIDs):
t1 = os.times()[4]
reformat_function(recID, fmt)
t2 = os.times()[4]
tbibformat += t2 - t1
if count % 100 == 0:
write_message(" ... formatted %s records out of %s" %
(count, tot))
task_update_progress('Formatted %s out of %s' % (count, tot))
task_sleep_now_if_required(can_stop_too=True)
if tot % 100 != 0:
write_message(" ... formatted %s records out of %s" % (tot, tot))
return tot, tbibformat, tbibupload
def all_records():
"""Produce record IDs for all available records."""
return intbitset(run_sql("SELECT id FROM bibrec"))
def outdated_caches(fmt, last_updated, chunk_size=5000):
sql = """SELECT br.id
FROM bibrec AS br
INNER JOIN bibfmt AS bf ON bf.id_bibrec = br.id
WHERE bf.format = %s
AND bf.last_updated < br.modification_date
AND br.id BETWEEN %s AND %s"""
last_updated_str = last_updated.strftime('%Y-%m-%d %H:%M:%S')
recids = intbitset()
max_id = run_sql("SELECT max(id) FROM bibrec")[0][0] or 0
for start in xrange(1, max_id + 1, chunk_size):
end = start + chunk_size
recids += intbitset(run_sql(sql, (fmt, start, end)))
return recids
def missing_caches(fmt, chunk_size=100000):
"""Produce record IDs to be formated, because their fmt cache is missing.
@param fmt: format to query for
@return: record IDs generator without pre-created format cache
"""
write_message("Querying database for records without cache...")
all_recids = intbitset()
max_id = run_sql("SELECT max(id) FROM bibrec")[0][0] or 0
for start in xrange(1, max_id + 1, chunk_size):
end = start + chunk_size
sql = "SELECT id FROM bibrec WHERE id BETWEEN %s AND %s"
recids = intbitset(run_sql(sql, (start, end)))
sql = """SELECT id_bibrec FROM bibfmt
WHERE id_bibrec BETWEEN %s AND %s
AND format = %s"""
without_fmt = intbitset(run_sql(sql, (start, end, fmt)))
all_recids += recids - without_fmt
return all_recids
def query_records(params):
"""Produce record IDs from given query parameters.
By passing the appriopriate CLI options, we can query here for additional
records.
"""
write_message("Querying database (records query)...")
res = intbitset()
if params['field'] or params['collection'] or params['pattern']:
if not params['collection']:
# use search_pattern() whenever possible, as it can search
# even in private collections
res = search_pattern(p=params['pattern'],
f=params['field'],
m=params['matching'])
else:
# use perform_request_search when '-c' argument has been
# defined, as it is not supported by search_pattern()
res = intbitset(perform_request_search(req=None,
of='id',
c=params['collection'],
p=params['pattern'],
f=params['field']))
return res
def task_run_core():
"""Run the task by fetching arguments from the BibSched task queue.
This is what BibSched will be invoking via daemon call.
"""
fmts = task_get_option('format', 'HB,RECJSON')
for fmt in fmts.split(','):
last_updated = fetch_last_updated(fmt)
write_message("last stored run date is %s" % last_updated)
recids = intbitset()
if task_has_option("all"):
recids += all_records()
if task_has_option("last"):
recids += outdated_caches(fmt, last_updated)
if task_has_option('ignore_without') or \
task_has_option('collection') or \
task_has_option('field') or \
task_has_option('pattern') or \
task_has_option('recids'):
without_fmt = intbitset()
else:
without_fmt = missing_caches(fmt)
recids += without_fmt
cli_recids = split_cli_ids_arg(task_get_option('recids', ''))
recids += cli_recids
query_params = {'collection': task_get_option('collection', ''),
'field': task_get_option('field', ''),
'pattern': task_get_option('pattern', ''),
'matching': task_get_option('matching', '')}
recids += query_records(query_params)
bibreformat_task(fmt,
recids,
without_fmt,
not task_has_option('noprocess'))
return True
def main():
"""Main that construct all the bibtask."""
task_init(authorization_action='runbibformat',
authorization_msg="BibReformat Task Submission",
description="""
BibReformat formats the records and saves the produced outputs for
later retrieval.
BibReformat is usually run periodically via BibSched in order to (1)
format new records in the database and to (2) reformat records for
which the meta data has been modified.
BibReformat has to be run manually when (3) format config files have
been modified, in order to see the changes in the web interface.
Although it is not necessary to run BibReformat to display formatted
records in the web interface, BibReformat allows to improve serving
speed by precreating the outputs. It is suggested to run
BibReformat for 'HB' output.
Option -m cannot be used at the same time as option -c.
Option -c prevents from finding records in private collections.
Examples:
bibreformat Format all new or modified records (in HB and RECJSON).
bibreformat -o HD Format all new or modified records in HD.
bibreformat -o HD,HB Format all new or modified records in HD and HB.
bibreformat -a Force reformatting all records (in HB).
bibreformat -c 'Photos' Force reformatting all records in 'Photos' collection (in HB).
bibreformat -c 'Photos' -o HD Force reformatting all records in 'Photos' collection in HD.
bibreformat -i 15 Force reformatting record 15 (in HB).
bibreformat -i 15:20 Force reformatting records 15 to 20 (in HB).
bibreformat -i 15,16,17 Force reformatting records 15, 16 and 17 (in HB).
bibreformat -n Show how many records are to be (re)formatted.
bibreformat -n -c 'Articles' Show how many records are to be (re)formatted in 'Articles' collection.
bibreformat -oHB -s1h Format all new and modified records every hour, in HB.
""", help_specific_usage=""" -o, --formats \t Specify output format/s (default HB)
-n, --noprocess \t Count records to be formatted (no processing done)
Reformatting options:
-a, --all \t Force reformatting all records
-c, --collection \t Force reformatting records by collection
-f, --field \t Force reformatting records by field
-p, --pattern \t Force reformatting records by pattern
-i, --id \t Force reformatting records by record id(s)
--no-missing \t Ignore reformatting records without format
Pattern options:
-m, --matching \t Specify if pattern is exact (e), regular expression (r),
\t partial (p), any of the words (o) or all of the words (a)
""",
version=__revision__,
specific_params=("ac:f:p:lo:nm:i:",
["all",
"collection=",
"matching=",
"field=",
"pattern=",
"format=",
"noprocess",
"id=",
"no-missing"]),
task_submit_check_options_fnc=task_submit_check_options,
task_submit_elaborate_specific_parameter_fnc=
task_submit_elaborate_specific_parameter,
task_run_fnc=task_run_core)
def task_submit_check_options():
"""Last checks and updating on the options..."""
if not (task_has_option('all') or task_has_option('collection')
or task_has_option('field') or task_has_option('pattern')
or task_has_option('matching') or task_has_option('recids')):
task_set_option('last', 1)
return True
def task_submit_elaborate_specific_parameter(key, value, opts, args): # pylint: disable-msg=W0613
"""
Elaborate specific CLI parameters of BibReformat.
@param key: a parameter key to check
@param value: a value associated to parameter X{Key}
@return: True for known X{Key} else False.
"""
if key in ("-a", "--all"):
task_set_option("all", 1)
elif key in ("--no-missing", ):
task_set_option("ignore_without", 1)
elif key in ("-c", "--collection"):
task_set_option("collection", value)
elif key in ("-n", "--noprocess"):
task_set_option("noprocess", 1)
elif key in ("-f", "--field"):
task_set_option("field", value)
elif key in ("-p", "--pattern"):
task_set_option("pattern", value)
elif key in ("-m", "--matching"):
task_set_option("matching", value)
elif key in ("-o", "--format"):
input_formats = value.split(',')
# check the validity of the given output formats
invalid_format = check_validity_input_formats(input_formats)
if invalid_format:
try:
raise Exception('Invalid output format.')
except Exception: # pylint: disable-msg=W0703
from invenio.errorlib import register_exception
register_exception(
prefix="The given output format '%s' is not available or "
"is invalid. Please try again" %
(invalid_format, ), alert_admin=True)
return
else: # every given format is available
task_set_option("format", value)
elif key in ("-i", "--id"):
task_set_option("recids", value)
else:
return False
return True
### okay, here we go:
if __name__ == '__main__':
main()

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