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daemon.py
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# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014 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
"""
from __future__ import print_function
import sys
import getopt
import getpass
import time
from six.moves import urllib
from sqlalchemy import orm
from invenio.config import (CFG_OAI_FAILED_HARVESTING_STOP_QUEUE,
CFG_OAI_FAILED_HARVESTING_EMAILS_ADMIN,
CFG_SITE_SUPPORT_EMAIL)
from invenio.modules.oaiharvester.models import OaiHARVEST
from invenio.legacy.bibsched.bibtask import (task_get_task_param,
task_get_option, task_set_option,
write_message, task_init)
from invenio.legacy.oaiharvest.config import InvenioOAIHarvestWarning
from invenio.legacy.oaiharvest import getter
from invenio.ext.logging import register_exception
from invenio.base.factory import with_app_context
from invenio.legacy.oaiharvest.utils import (compare_timestamps_with_tolerance,
generate_harvest_report,
create_ticket)
from invenio.legacy.webuser import email_valid_p
from invenio.ext.email import send_email
from invenio.modules.workflows.models import (BibWorkflowEngineLog, Workflow,
BibWorkflowObjectLog)
from invenio.modules.workflows.registry import workflows as registry_workflows
from invenio.modules.workflows.api import start
from invenio.modules.workflows.errors import WorkflowError
import invenio.legacy.template
oaiharvest_templates = invenio.legacy.template.load('oaiharvest')
def task_run_core():
"""Core task of oaiharvest.
This function will run all the operations needed
to run an oaiharvest task into bibsched.
:return: :raise InvenioOAIHarvestWarning:
"""
workflow_id_preservation = 0
workflow = None
start_time = time.time()
list_of_workflow_without_repository = []
list_of_repository_per_workflow = {}
repository = task_get_option("repository")
if not repository:
workflow_option = task_get_option("workflow")
if isinstance(workflow_option, list):
for name in workflow_option:
if name not in list_of_workflow_without_repository:
list_of_workflow_without_repository.append(name)
else:
list_of_workflow_without_repository.append(workflow_option)
else:
if task_get_option("workflow"):
workflow_option = task_get_option("workflow")
if isinstance(workflow_option, list):
for name in workflow_option:
if name not in list_of_repository_per_workflow:
list_of_repository_per_workflow[name] = repository
else:
list_of_repository_per_workflow[workflow_option] = repository
elif isinstance(repository, list):
for name_repository in repository:
name_workflow = OaiHARVEST.get(
OaiHARVEST.name == name_repository).one().workflows
if name_workflow not in list_of_repository_per_workflow:
list_of_repository_per_workflow[name_workflow] = [
name_repository]
else:
list_of_repository_per_workflow[name_workflow].append(
name_repository)
else:
workflow_found = OaiHARVEST.get(
OaiHARVEST.name == repository).one().workflows
list_of_repository_per_workflow[workflow_found] = repository
try:
if list_of_repository_per_workflow:
for workflow_to_launch in list_of_repository_per_workflow:
options = task_get_option(None)
options["repository"] = list_of_repository_per_workflow[
workflow_to_launch]
workflow = start(workflow_to_launch,
data=[""],
stop_on_error=True,
options=options)
else:
for workflow_to_launch in list_of_workflow_without_repository:
workflow = start(workflow_to_launch,
data=[""],
stop_on_error=True,
options=task_get_option(None))
if workflow:
workflow_id_preservation = workflow.uuid
workflowlog = BibWorkflowEngineLog.query.filter(
BibWorkflowEngineLog.id_object == workflow.uuid
).all()
for log in workflowlog:
write_message(log.message)
execution_time = round(time.time() - start_time, 2)
write_message("Execution time :" + str(execution_time))
except WorkflowError as e:
write_message("ERRORS HAPPENED")
write_message("____________Workflow log output____________")
workflow_id_preservation = e.id_workflow
workflowlog = BibWorkflowEngineLog.query.filter(
BibWorkflowEngineLog.id_object == e.id_workflow
).filter(BibWorkflowEngineLog.log_type >= 40).all()
for log in workflowlog:
write_message(log.message)
for i in e.payload:
write_message("\n\n____________Workflow " + i + " log output____________")
workflowlog = BibWorkflowEngineLog.query.filter(
BibWorkflowEngineLog.id_object == i
).filter(BibWorkflowEngineLog.log_type >= 40).all()
for log in workflowlog:
write_message(log.message)
write_message("____________Object log output____________")
objectlog = BibWorkflowObjectLog.query.filter(
BibWorkflowObjectLog.id_object == e.id_object
).filter(BibWorkflowEngineLog.log_type >= 40).all()
for log in objectlog:
write_message(log.message)
execution_time = round(time.time() - start_time, 2)
write_message("Execution time :" + str(execution_time))
# Generate reports
ticket_queue = task_get_option("create-ticket-in")
notification_email = task_get_option("notify-email-to")
workflow_main = Workflow.query.filter(
Workflow.uuid == workflow_id_preservation
).one()
if ticket_queue or notification_email:
subject, text = generate_harvest_report(
workflow_main,
current_task_id=task_get_task_param("task_id")
)
# Create ticket for finished harvest?
if ticket_queue:
ticketid = create_ticket(ticket_queue, subject=subject, text=text)
if ticketid:
write_message("Ticket %s submitted." % (str(ticketid),))
# Send e-mail for finished harvest?
if notification_email:
send_email(fromaddr=CFG_SITE_SUPPORT_EMAIL,
toaddr=notification_email,
subject=subject,
content=text)
if workflow_main.counter_error:
if CFG_OAI_FAILED_HARVESTING_STOP_QUEUE == 0 or \
not task_get_task_param("sleeptime") or \
workflow_main.counter_error > 1:
# Admin want BibSched to stop, or the task is not set to
# run at a later date: we must stop the queue.
write_message("An error occurred. Task is configured to stop")
return False
else:
# An error happened, but it can be recovered at next run
# (task is re-scheduled) and admin set BibSched to
# continue even after failure.
write_message("Error occurred, but task is configured to continue")
if CFG_OAI_FAILED_HARVESTING_EMAILS_ADMIN:
try:
raise InvenioOAIHarvestWarning(
"OAIHarvest (task #%s) failed at fully harvesting."
" BibSched has NOT been stopped, and OAIHarvest will"
" try to recover at next run" %
(task_get_task_param("task_id"),)
)
except InvenioOAIHarvestWarning:
register_exception(stream='warning', alert_admin=True)
return True
else:
return True
def get_dates(dates):
"""Validate and process the dates input by the user."""
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 the repository names input by the user."""
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 get_identifier_names(identifier):
""" Return processed identifier list."""
if identifier:
# Let's see if the user had a comma-separated list of OAI ids.
stripped_idents = []
for ident in identifier.split(","):
if not ident.startswith("oai:arXiv.org"):
if "oai:arxiv.org" in ident.lower():
ident = ident.replace("oai:arxiv.org", "oai:arXiv.org")
elif "arXiv" in ident:
# New style arXiv ID
ident = ident.replace("arXiv", "oai:arXiv.org")
elif "/" in ident:
# Old style arXiv ID?
ident = "%s%s" % ("oai:arXiv.org:", ident)
stripped_idents.append(ident.strip())
return stripped_idents
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)
@with_app_context()
def main():
"""Start 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:c:k:l:w:",
["output=",
"verb=",
"method=",
"metadataPrefix=",
"identifier=",
"set=",
"from=",
"until=",
"resumptionToken=",
"certificate=",
"key=",
"user=",
"password=",
"workflow=",
])
# 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, dummy1,
dummy2, dummy3) = urllib.parse(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 as error:
sys.stderr.write("\n%s\n" % (error,))
sys.exit(0)
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([opt for opt, opt_value in opts if
opt in ['-i', '--identifier']]) == 0 \
and len(args) > 1 or \
(len(args) == 1 and not args[0].isdigit()):
usage(1, "You must specify the --verb parameter")
except getopt.error:
# 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.
num_of_critical_parameter = 0
num_of_critical_parameterb = 0
repositories = []
for opt in sys.argv[1:]:
if opt in "-r" or opt in "--repository":
num_of_critical_parameter += 1
elif opt in "--workflow":
num_of_critical_parameterb += 1
if num_of_critical_parameter > 1 or num_of_critical_parameterb > 1:
usage(1, "You can't specify twice -r or --workflow")
if num_of_critical_parameter == 1:
if "-r" in sys.argv:
position = sys.argv.index("-r")
else:
position = sys.argv.index("--repository")
repositories = sys.argv[position + 1].split(",")
if len(repositories) > 1 and \
("-i" in sys.argv or "--identifier" in sys.argv):
usage(1,
"It is impossible to harvest an identifier from several "
"repositories.")
if num_of_critical_parameterb == 1:
position = sys.argv.index("--workflow")
workflows = sys.argv[position + 1].split(",")
for workflow_candidate in workflows:
if workflow_candidate not in registry_workflows:
usage(1, "The workflow %s doesn't exist." % workflow_candidate)
if num_of_critical_parameter == 1 and num_of_critical_parameterb == 0:
for name_repository in repositories:
try:
oaiharvest_instance = OaiHARVEST.get(
OaiHARVEST.name == name_repository).one()
if oaiharvest_instance.workflows not in registry_workflows:
usage(1,
"The repository %s doesn't have a valid workflow specified." % name_repository)
except orm.exc.NoResultFound:
usage(1,
"The repository %s doesn't exist in our database." % name_repository)
elif num_of_critical_parameter == 1 and num_of_critical_parameterb == 1:
for name_repository in repositories:
try:
OaiHARVEST.get(OaiHARVEST.name == name_repository).one()
except orm.exc.NoResultFound:
usage(1,
"The repository %s doesn't exist in our database." % name_repository)
print("A workflow has been specified, overriding the repository one.")
task_set_option("repository", None)
task_set_option("dates", None)
task_set_option("workflow", None)
task_set_option("identifiers", 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://cds.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'
'Deamon mode (periodical or one-shot 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'
' -i, --identifier OAI identifier if wished to run in as a task.\n'
' --notify-email-to Receive notifications on given email on successful upload and/or finished harvest.\n'
' --workflow specify the workflow to execute.\n'
' --create-ticket-in Provide desired ticketing queue to create a ticket in it on upload and/or finished harvest.\n'
' Requires a configured ticketing system (BibCatalog).\n',
specific_params=(
"r:i:d:W",
["repository=", "identifier=", "dates=", "workflow=",
"notify-email-to=", "create-ticket-in="]),
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 ("--workflow"):
task_set_option('workflow', get_repository_names(value))
elif key in ("-i", "--identifier"):
task_set_option('identifiers', get_identifier_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.")
elif key in ("--notify-email-to",):
if email_valid_p(value):
task_set_option('notify-email-to', value)
else:
raise StandardError("E-mail format not valid.")
elif key in ("--create-ticket-in",):
task_set_option('create-ticket-in', value)
else:
return False
return True

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