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publication.py
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# -*- coding: utf-8 -*-
"""Functions for publication."""
__copyright__ = 'Copyright (c) 2019-2023, Utrecht University'
__license__ = 'GPLv3, see LICENSE'
from datetime import datetime
import genquery
from requests.exceptions import ReadTimeout
import datacite
import json_datacite
import json_landing_page
import meta
import provenance
import schema
import vault
from util import *
__all__ = ['rule_process_publication',
'rule_process_depublication',
'rule_process_republication',
'rule_update_publication',
'rule_lift_embargos_on_data_access']
def get_publication_config(ctx):
"""Get all publication config keys and their values and report any missing keys."""
zone = user.zone(ctx)
system_coll = "/" + zone + constants.UUSYSTEMCOLLECTION
attr2keys = {"public_host": "publicHost",
"public_vhost": "publicVHost",
"moai_host": "moaiHost",
"yoda_prefix": "yodaPrefix",
"datacite_prefix": "dataCitePrefix",
"random_id_length": "randomIdLength",
"yoda_instance": "yodaInstance",
"davrods_vhost": "davrodsVHost",
"davrods_anonymous_vhost": "davrodsAnonymousVHost",
"publication_verbose_mode": "verboseMode"}
optional_keys = ["publication_verbose_mode"]
configKeys = {}
found_attrs = []
prefix_length = len(constants.UUORGMETADATAPREFIX)
iter = genquery.row_iterator(
"META_COLL_ATTR_NAME, META_COLL_ATTR_VALUE",
"COLL_NAME = '" + system_coll + "' AND META_COLL_ATTR_NAME like '" + constants.UUORGMETADATAPREFIX + "%'",
genquery.AS_LIST, ctx
)
for row in iter:
# Strip prefix From attribute names
attr = row[0][prefix_length:]
val = row[1]
try:
found_attrs.append(attr)
configKeys[attr2keys[attr]] = val
except KeyError:
continue
# Any differences between
for key in attr2keys:
if key not in found_attrs and key not in optional_keys:
log.write(ctx, 'Missing config key ' + key)
return configKeys
def generate_combi_json(ctx, publication_config, publication_state):
"""Join system metadata with the user metadata in yoda-metadata.json.
:param ctx: Combined type of a callback and rei struct
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
temp_coll = "/" + user.zone(ctx) + constants.IIPUBLICATIONCOLLECTION
davrodsAnonymousVHost = publication_config["davrodsAnonymousVHost"]
vaultPackage = publication_state["vaultPackage"]
randomId = publication_state["randomId"]
combiJsonPath = temp_coll + "/" + randomId + "-combi.json"
versionDOI = publication_state["versionDOI"]
lastModifiedDateTime = publication_state["lastModifiedDateTime"]
publicationDate = publication_state["publicationDate"]
openAccessLink = ''
if publication_state["accessRestriction"].startswith("Open"):
split_string = '/home/'
subPath = vaultPackage[len(split_string) + vaultPackage.find(split_string):]
openAccessLink = 'https://' + davrodsAnonymousVHost + "/" + subPath
licenseUri = ""
if "licenseUri" in publication_state:
licenseUri = publication_state["licenseUri"]
# metadataJsonPath contains latest json
metadataJsonPath = meta.get_latest_vault_metadata_path(ctx, vaultPackage)
# Combine content of current *metadataJsonPath with system info and creates a new file in *combiJsonPath:
json_datacite.json_datacite_create_combi_metadata_json(ctx, metadataJsonPath, combiJsonPath, lastModifiedDateTime, versionDOI, publicationDate, openAccessLink, licenseUri)
publication_state["combiJsonPath"] = combiJsonPath
def generate_system_json(ctx, publication_state):
"""Overwrite combi metadata json with system-only metadata.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
"""
temp_coll = "/" + user.zone(ctx) + constants.IIPUBLICATIONCOLLECTION
randomId = publication_state["randomId"]
system_json_path = temp_coll + "/" + randomId + "-combi.json"
doi = publication_state["versionDOI"]
system_json_data = {
"System": {
"Last_Modified_Date": publication_state["lastModifiedDateTime"],
"Persistent_Identifier_Datapackage": {
"Identifier_Scheme": "DOI",
"Identifier": doi,
},
"Publication_Date": publication_state["publicationDate"]
}
}
data_object.write(ctx, system_json_path, jsonutil.dump(system_json_data))
publication_state["combiJsonPath"] = system_json_path
def get_publication_state(ctx, vault_package):
"""The publication state is kept as metadata on the vault package.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:returns: Dict with state of the publication process
"""
publication_state = {
"status": "Unknown",
"accessRestriction": "Closed"
}
publ_metadata = get_collection_metadata(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'publication_')
# Take over all actual values as saved earlier.
for key in publ_metadata.keys():
publication_state[key] = publ_metadata[key]
# Handle access restriction.
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"META_COLL_ATTR_NAME like '%Data_Access_Restriction' AND COLL_NAME = '" + vault_package + "'",
genquery.AS_LIST, ctx
)
for row in iter:
publication_state["accessRestriction"] = row[0]
# Handle license.
license = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"META_COLL_ATTR_NAME like '%License' AND COLL_NAME = '" + vault_package + "'",
genquery.AS_LIST, ctx
)
for row in iter:
license = row[0]
if license != "":
publication_state["license"] = license
license_uri = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"META_COLL_ATTR_NAME like '" + constants.UUORGMETADATAPREFIX + "license_uri" + "' AND COLL_NAME = '" + vault_package + "'",
genquery.AS_LIST, ctx
)
for row in iter:
license_uri = row[0]
if license_uri != "":
publication_state["licenseUri"] = license_uri
publication_state["vaultPackage"] = vault_package
return publication_state
def save_publication_state(ctx, vault_package, publication_state):
"""Save the publication state key-value-pairs to AVU's on the vault package.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:param publication_state: Dict with state of the publication process
"""
ctx.msi_rmw_avu("-C", vault_package, constants.UUORGMETADATAPREFIX + 'publication_%', "%", "%")
for key in publication_state.keys():
if publication_state[key] != "":
avu.set_on_coll(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'publication_' + key, publication_state[key])
def set_update_publication_state(ctx, vault_package):
"""Routine to set publication state of vault package pending to update.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:returns: String with state of publication state update
"""
# check permissions - rodsadmin only
if user.user_type(ctx) != 'rodsadmin':
log.write(ctx, "User is no rodsadmin")
return 'Insufficient permissions - should only be called by rodsadmin'
# check current status, perhaps transitioned already
coll_status = vault.get_coll_vault_status(ctx, vault_package).value
if coll_status not in [str(constants.vault_package_state.PUBLISHED), str(constants.vault_package_state.PENDING_DEPUBLICATION), str(constants.vault_package_state.PENDING_REPUBLICATION)]:
return "NotAllowed"
publication_state = get_publication_state(ctx, vault_package)
if publication_state["status"] != "OK":
return "PublicationNotOK"
# Set publication status
publication_state["status"] = "Unknown"
# Generate new JSONs
publication_state["combiJsonPath"] = ""
publication_state["dataCiteJsonPath"] = ""
# Post metadata to DataCite
publication_state["dataCiteMetadataPosted"] = ""
# Generate new landingpage
publication_state["landingPagePath"] = ""
publication_state["landingPageUploaded"] = ""
# Update OAI-PMH metadata
publication_state["oaiUploaded"] = ""
# Update anonymous access
publication_state["anonymousAccess"] = ""
# Save state
save_publication_state(ctx, vault_package, publication_state)
return ""
def get_publication_date(ctx, vault_package):
"""Determine the time of publication as a datetime with UTC offset.
First try action_log. Then icat-time.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:return: Publication date in ISO8601 format
"""
iter = genquery.row_iterator(
"order_desc(META_COLL_MODIFY_TIME), META_COLL_ATTR_VALUE",
"COLL_NAME = '" + vault_package + "' AND META_COLL_ATTR_NAME = '" + constants.UUORGMETADATAPREFIX + 'action_log' + "'",
genquery.AS_LIST, ctx
)
for row in iter:
# row contains json encoded [str(int(time.time())), action, actor]
log_item_list = jsonutil.parse(row[1])
if log_item_list[1] == "published":
publication_timestamp = datetime.fromtimestamp(int(log_item_list[0]))
# ISO8601-fy
return publication_timestamp.strftime('%Y-%m-%dT%H:%M:%S.%f%z')
my_date = datetime.now()
return my_date.strftime('%Y-%m-%dT%H:%M:%S.%f%z')
def get_last_modified_datetime(ctx, vault_package):
"""Determine the time of last modification as a datetime with UTC offset.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:return: Last modified date in ISO8601 format
"""
iter = genquery.row_iterator(
"order_desc(META_COLL_MODIFY_TIME), META_COLL_ATTR_VALUE",
"COLL_NAME = '" + vault_package + "' AND META_COLL_ATTR_NAME = '" + constants.UUORGMETADATAPREFIX + 'action_log' + "'",
genquery.AS_LIST, ctx
)
for row in iter:
log_item_list = jsonutil.parse(row[1])
my_date = datetime.fromtimestamp(int(log_item_list[0]))
return my_date.strftime('%Y-%m-%dT%H:%M:%S.%f%z')
def generate_preliminary_DOI(ctx, publication_config, publication_state):
"""Generate a Preliminary DOI. Preliminary, because we check for collision later.
:param ctx: Combined type of a callback and rei struct
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
dataCitePrefix = publication_config["dataCitePrefix"]
yodaPrefix = publication_config["yodaPrefix"]
randomId = datacite.generate_random_id(ctx, publication_config["randomIdLength"])
publication_state["randomId"] = randomId
publication_state["versionDOI"] = dataCitePrefix + "/" + yodaPrefix + "-" + randomId
def generate_base_DOI(ctx, publication_config, publication_state):
"""Generate a base DOI.
:param ctx: Combined type of a callback and rei struct
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
dataCitePrefix = publication_config["dataCitePrefix"]
yodaPrefix = publication_config["yodaPrefix"]
randomId = datacite.generate_random_id(ctx, publication_config["randomIdLength"])
publication_state["baseRandomId"] = randomId
publication_state["baseDOI"] = dataCitePrefix + "/" + yodaPrefix + "-" + randomId
def generate_datacite_json(ctx, publication_state):
"""Generate a DataCite compliant JSON based on yoda-metadata.json.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
"""
combiJsonPath = publication_state["combiJsonPath"]
randomId = publication_state["randomId"]
temp_coll, coll = pathutil.chop(combiJsonPath)
datacite_json_path = temp_coll + "/" + randomId + "-dataCite.json"
# Based on content of *combiJsonPath, get DataciteJson as string
datacite_json = json_datacite.json_datacite_create_datacite_json(ctx, publication_state["landingPageUrl"], combiJsonPath)
data_object.write(ctx, datacite_json_path, jsonutil.dump(datacite_json))
publication_state["dataCiteJsonPath"] = datacite_json_path
def post_metadata_to_datacite(ctx, publication_state, doi, send_method):
"""Upload DataCite JSON to DataCite. This will register the DOI, without minting it.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
:param doi: DataCite DOI to update metadata
:param send_method: http verb (either 'post' or 'put')
"""
datacite_json_path = publication_state["dataCiteJsonPath"]
datacite_json = data_object.read(ctx, datacite_json_path)
try:
if send_method == 'post':
httpCode = datacite.metadata_post(ctx, datacite_json)
else:
httpCode = datacite.metadata_put(ctx, doi, datacite_json)
if (send_method == 'post' and httpCode == 201) or (send_method == 'put' and httpCode == 200):
publication_state["dataCiteMetadataPosted"] = "yes"
elif httpCode in [401, 403, 500, 503, 504]:
# Unauthorized, Forbidden, Precondition failed, Internal Server Error
log.write(ctx, "post_metadata_to_datacite: httpCode " + str(httpCode) + " received. Will be retried later")
publication_state["status"] = "Retry"
else:
log.write(ctx, "post_metadata_to_datacite: httpCode " + str(httpCode) + " received. Unrecoverable error.")
publication_state["status"] = "Unrecoverable"
except ReadTimeout:
# DataCite timeout.
log.write(ctx, "post_metadata_to_datacite: timeout received. Will be retried later")
publication_state["status"] = "Retry"
def post_draft_doi_to_datacite(ctx, publication_state):
"""Upload DOI to DataCite. This will register the DOI as a draft.
This function is also a draft, and will have to be reworked!
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
"""
datacite_json_path = publication_state["dataCiteJsonPath"]
datacite_json = data_object.read(ctx, datacite_json_path)
try:
# post the DOI only
httpCode = datacite.metadata_post(ctx, {
'data': {
'type': 'dois',
'attributes': {
'doi': datacite_json['data']['attributes']['doi']
}
}
})
if httpCode == 201:
publication_state["dataCiteMetadataPosted"] = "no"
elif httpCode in [401, 403, 500, 503, 504]:
# Unauthorized, Forbidden, Precondition failed, Internal Server Error
log.write(ctx, "post_draft_doi_to_datacite: httpCode " + str(httpCode) + " received. Will be retried later")
publication_state["status"] = "Retry"
else:
log.write(ctx, "post_draft_doi_to_datacite: httpCode " + str(httpCode) + " received. Unrecoverable error.")
publication_state["status"] = "Unrecoverable"
except ReadTimeout:
# DataCite timeout.
log.write(ctx, "post_draft_doi_to_datacite: timeout received. Will be retried later")
publication_state["status"] = "Retry"
def remove_metadata_from_datacite(ctx, publication_state, type_flag):
"""Remove metadata XML from DataCite.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
:param type_flag: Determine whether it is base DOI or version DOI
"""
import json
payload = json.dumps({"data": {"attributes": {"event": "hide"}}})
try:
httpCode = datacite.metadata_put(ctx, publication_state[type_flag + "DOI"], payload)
if httpCode == 200:
publication_state["dataCiteMetadataPosted"] = "yes"
elif httpCode in [401, 403, 412, 500, 503, 504]:
# Unauthorized, Forbidden, Precondition failed, Internal Server Error
log.write(ctx, "remove metadata from datacite: httpCode " + str(httpCode) + " received. Will be retried later")
publication_state["status"] = "Retry"
elif httpCode == 404:
# Invalid DOI
log.write(ctx, "remove metadata from datacite: 404 Not Found - Invalid DOI")
publication_state["status"] = "Unrecoverable"
else:
log.write(ctx, "remove metadata from datacite: httpCode " + str(httpCode) + " received. Unrecoverable error.")
publication_state["status"] = "Unrecoverable"
except ReadTimeout:
# DataCite timeout.
log.write(ctx, "remove_metadata_from_datacite: timeout received. Will be retried later")
publication_state["status"] = "Retry"
def mint_doi(ctx, publication_state, type_flag):
"""Announce the landing page URL for a DOI to dataCite. This will mint the DOI.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
:param type_flag: Flag indicating DOI type ('version' or 'base')
"""
import json
payload = json.dumps({"data": {"attributes": {"url": publication_state["landingPageUrl"]}}})
try:
httpCode = datacite.metadata_put(ctx, publication_state[type_flag + "DOI"], payload)
if httpCode == 200: # 201:
publication_state[type_flag + "DOIMinted"] = "yes"
elif httpCode in [401, 403, 412, 500, 503, 504]:
# Unauthorized, Forbidden, Precondition failed, Internal Server Error
log.write(ctx, "mint_doi: httpCode " + str(httpCode) + " received. Could be retried later")
publication_state["status"] = "Retry"
elif httpCode == 400:
log.write(ctx, "mint_doi: 400 Bad Request - request body must be exactly two lines: DOI and URL; wrong domain, wrong prefix")
publication_state["status"] = "Unrecoverable"
else:
log.write(ctx, "mint_doi: httpCode " + str(httpCode) + " received. Unrecoverable error.")
publication_state["status"] = "Unrecoverable"
except ReadTimeout:
# DataCite timeout.
log.write(ctx, "mint_doi: timeout received. Will be retried later")
publication_state["status"] = "Retry"
def generate_landing_page_url(ctx, publication_config, publication_state):
"""Generate a URL for the landing page.
:param ctx: Combined type of a callback and rei struct
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
publicVHost = publication_config["publicVHost"]
yodaInstance = publication_config["yodaInstance"]
yodaPrefix = publication_config["yodaPrefix"]
randomId = publication_state["randomId"]
publicPath = yodaInstance + "/" + yodaPrefix + "/" + randomId + ".html"
landingPageUrl = "https://" + publicVHost + "/" + publicPath
publication_state["landingPageUrl"] = landingPageUrl
def generate_landing_page(ctx, publication_state, publish):
"""Generate a dataCite compliant XML based up yoda-metadata.json.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
:param publish: Publication or depublication
"""
combiJsonPath = publication_state["combiJsonPath"]
randomId = publication_state["randomId"]
vaultPackage = publication_state["vaultPackage"]
json_schema = schema.get_active_schema(ctx, vaultPackage)
temp_coll, coll = pathutil.chop(combiJsonPath)
landing_page_path = temp_coll + "/" + randomId + ".html"
# Get all DOI versions
if "baseDOI" in publication_state:
base_doi = publication_state["baseDOI"]
versions = get_all_versions(ctx, vaultPackage, publication_state["baseDOI"])[0]
else:
base_doi = ''
versions = []
if publish == "publish":
template_name = 'landingpage.html.j2'
else:
template_name = 'emptylandingpage.html.j2'
landing_page_html = json_landing_page.json_landing_page_create_json_landing_page(ctx, user.zone(ctx), template_name, combiJsonPath, json_schema, base_doi, versions)
data_object.write(ctx, landing_page_path, landing_page_html)
publication_state["landingPagePath"] = landing_page_path
def copy_landingpage_to_public_host(ctx, random_id, publication_config, publication_state):
"""Copy the resulting landing page to configured public host.
:param ctx: Combined type of a callback and rei struct
:param random_id: Random ID part of DOI used for landingpage file
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
publicHost = publication_config["publicHost"]
landingPagePath = publication_state["landingPagePath"]
yodaInstance = publication_config["yodaInstance"]
yodaPrefix = publication_config["yodaPrefix"]
publicPath = yodaInstance + "/" + yodaPrefix + "/" + random_id + ".html"
argv = publicHost + " inbox /var/www/landingpages/" + publicPath
copy_result = ctx.iiGenericSecureCopy(argv, landingPagePath, '')
error = copy_result['arguments'][2]
if int(error) >= 0:
publication_state["landingPageUploaded"] = "yes"
else:
publication_state["status"] = "Retry"
log.write(ctx, "copy_landingpage_to_public: " + error)
def copy_metadata_to_moai(ctx, random_id, publication_config, publication_state):
"""Copy the metadata json file to configured MOAI.
:param ctx: Combined type of a callback and rei struct
:param random_id: Random ID part of DOI used for MOAI metadata file
:param publication_config: Dict with publication configuration
:param publication_state: Dict with state of the publication process
"""
publicHost = publication_config["publicHost"]
yodaInstance = publication_config["yodaInstance"]
yodaPrefix = publication_config["yodaPrefix"]
# randomId = publication_state["randomId"] ##### in case of base? ###### revert to original
combiJsonPath = publication_state["combiJsonPath"]
argv = publicHost + " inbox /var/www/moai/metadata/" + yodaInstance + "/" + yodaPrefix + "/" + random_id + ".json"
copy_result = ctx.iiGenericSecureCopy(argv, combiJsonPath, '')
error = copy_result['arguments'][2]
if int(error) >= 0:
publication_state["oaiUploaded"] = "yes"
else:
publication_state["status"] = "Retry"
log.write(ctx, "copy_metadata_to_public: " + error)
def set_access_restrictions(ctx, vault_package, publication_state):
"""Set access restriction for vault package.
This function is called when (re)publishing a vault package.
The embargo date of a package is essential determining access.
If current date < embargo end date, then set end date in `ord_lift_embargo_date`
to be picked up by lift embargo cronjob.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:param publication_state: Dict with state of the publication process
:returns: None
"""
# Embargo handling
combiJsonPath = publication_state["combiJsonPath"]
dictJsonData = jsonutil.read(ctx, combiJsonPath, want_bytes=False)
# Remove empty lists, empty dicts, or None elements
# to prevent empty fields on landingpage.
dictJsonData = jsonutil.remove_empty(dictJsonData)
active_embargo = False
# Check whether lift_embargo_date is present already
iter = genquery.row_iterator(
"COLL_NAME, META_COLL_ATTR_VALUE",
"COLL_NAME = '" + vault_package + "' AND META_COLL_ATTR_NAME = '" + constants.UUORGMETADATAPREFIX + "lift_embargo_date'",
genquery.AS_LIST, ctx
)
for row in iter:
# Just get rid of the previous lift_embargo_date.
# Will be introduced again if required in below code but will keep the code more focused whether lift_date must be introduced or not.
avu.rm_from_coll(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'lift_embargo_date', row[1])
# Datapackage under embargo?
embargo_end_date = dictJsonData.get('Embargo_End_Date', None)
if embargo_end_date is not None and len(embargo_end_date):
# String comparison is possible as both are in same string format YYYY-MM-DD
active_embargo = (datetime.now().strftime('%Y-%m-%d') < embargo_end_date)
access_restriction = publication_state["accessRestriction"]
# Lift embargo handling is only interesting when package has open access.
if access_restriction.startswith('Open'):
if active_embargo:
# datapackage data is under embargo.
# Add indication to metadata on vault_package so cronjob can pick it up and sets acls when embargo date is passed in the FUTURE
avu.set_on_coll(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'lift_embargo_date', embargo_end_date)
# Now handle the data access taking possible embargo into account
access_level = "null"
# Only without an active embargo date AND open access is it allowed to read data!
if access_restriction.startswith('Open') and not active_embargo:
access_level = "read"
try:
msi.set_acl(ctx, "recursive", access_level, "anonymous", vault_package)
except Exception as e:
log.write(ctx, "set_access_restrictions for {} failed: {}".format(vault_package, str(e)))
publication_state["status"] = "Unrecoverable"
return
# We cannot set "null" as value in a kvp as this will crash msi_json_objops if we ever perform a uuKvp2JSON on it.
if access_level == "null":
publication_state["anonymousAccess"] = "no"
else:
publication_state["anonymousAccess"] = "yes"
def check_doi_availability(ctx, publication_state, type_flag):
"""Request DOI to check on availability. We want a 404 as return code.
:param ctx: Combined type of a callback and rei struct
:param publication_state: Dict with state of the publication process
:param type_flag: Flag indicating DOI type ('version' or 'base')
"""
DOI = publication_state[type_flag + "DOI"]
try:
httpCode = datacite.metadata_get(ctx, DOI)
if httpCode == 404:
publication_state[type_flag + "DOIAvailable"] = "yes"
elif httpCode in [401, 403, 500, 503, 504]:
# request failed, worth a retry
publication_state["status"] = "Retry"
elif httpCode in [200, 204]:
# DOI already in use
publication_state[type_flag + "DOIAvailable"] = "no"
publication_state["status"] = "Retry"
except ReadTimeout:
# DataCite timeout.
log.write(ctx, "check_doi_availability: timeout received. Will be retried later")
publication_state["status"] = "Retry"
def process_publication(ctx, vault_package):
"""Handling of publication of vault_package.
:param ctx: Combined type of a callback and rei struct
:param vault_package: Path to the package in the vault
:return: "OK" if all went ok
"""
publication_state = {}
log.write(ctx, "Process publication of vault package <{}>".format(vault_package))
# check permissions - rodsadmin only
if user.user_type(ctx) != 'rodsadmin':
log.write(ctx, "User is no rodsadmin")
return 'Insufficient permissions - should only be called by rodsadmin'
# check current status, perhaps transitioned already
vault_status = vault.get_coll_vault_status(ctx, vault_package).value
if vault_status not in [str(constants.vault_package_state.PUBLISHED), str(constants.vault_package_state.APPROVED_FOR_PUBLICATION)]:
return "InvalidPackageStatusForPublication" + ": " + vault_status
# get publication configuration
publication_config = get_publication_config(ctx)
# get state of all related to the publication
publication_state = get_publication_state(ctx, vault_package)
status = publication_state['status']
# Check if verbose mode is enabled
verbose = True if "verboseMode" in publication_config else False
if verbose:
log.write(ctx, "Running process_publication in verbose mode.")
# Publication status check and handling
if verbose:
log.write(ctx, "Initial publication status is: " + publication_state['status'])
if status in ["Unrecoverable", "Processing"]:
return "publication status: " + status
elif status in ["Unknown", "Retry"]:
status = "Processing"
publication_state['status'] = status
# Set flag to update base DOI when this data package is the latest version.
update_base_doi = False
if "previous_version" in publication_state and "next_version" not in publication_state:
if verbose:
log.write(ctx, "In branch for updating base DOI")
update_base_doi = True
# Get previous publication state
previous_vault_package = publication_state["previous_version"]
previous_publication_state = get_publication_state(ctx, previous_vault_package)
if "baseDOI" in previous_publication_state:
# Set the link to previous publication state
publication_state["baseDOI"] = previous_publication_state["baseDOI"]
publication_state["baseRandomId"] = previous_publication_state["baseRandomId"]
# Create base DOI if it does not exist in the previous publication state.
elif "baseDOI" not in previous_publication_state:
log.write(ctx, "Creating base DOI for the vault package <{}>".format(vault_package))
try:
generate_base_DOI(ctx, publication_config, publication_state)
check_doi_availability(ctx, publication_state, 'base')
publication_state["baseDOIMinted"] = 'no'
# Set the link to previous publication state
previous_publication_state["baseDOI"] = publication_state["baseDOI"]
previous_publication_state["baseRandomId"] = publication_state["baseRandomId"]
except Exception as e:
log.write(ctx, "Error while checking version DOI availability: " + str(e))
publication_state["status"] = "Retry"
save_publication_state(ctx, previous_vault_package, previous_publication_state)
save_publication_state(ctx, vault_package, publication_state)
if status in ["Retry"]:
if verbose:
log.write(ctx, "Error status for creating base DOI: " + status)
return status
# Publication date
if "publicationDate" not in publication_state:
if verbose:
log.write(ctx, "Setting publication date.")
publication_state["publicationDate"] = get_publication_date(ctx, vault_package)
# DOI handling
if "versionDOI" not in publication_state:
if verbose:
log.write(ctx, "Generating preliminary DOI.")
generate_preliminary_DOI(ctx, publication_config, publication_state)
save_publication_state(ctx, vault_package, publication_state)
elif "versionDOIAvailable" in publication_state:
if publication_state["versionDOIAvailable"] == "no":
if verbose:
log.write(ctx, "Version DOI available: no")
log.write(ctx, "Generating preliminary DOI.")
generate_preliminary_DOI(ctx, publication_config, publication_state)
publication_state["combiJsonPath"] = ""
publication_state["dataCiteJsonPath"] = ""
save_publication_state(ctx, vault_package, publication_state)
# Determine last modification time. Always run, no matter if retry
if verbose:
log.write(ctx, "Updating modification date.")
publication_state["lastModifiedDateTime"] = get_last_modified_datetime(ctx, vault_package)
# Generate Combi Json consisting of user and system metadata
if "combiJsonPath" not in publication_state:
if verbose:
log.write(ctx, "Generating combi JSON.")
try:
generate_combi_json(ctx, publication_config, publication_state)
except Exception as e:
log.write(ctx, "Exception while generating combi JSON: " + str(e))
publication_state["status"] = "Unrecoverable"
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] in ["Unrecoverable", "Retry"]:
if verbose:
log.write(ctx, "Error status after generating combi JSON.")
return publication_state["status"]
# Create Landing page URL
if verbose:
log.write(ctx, "Creating landing page.")
generate_landing_page_url(ctx, publication_config, publication_state)
# Generate DataCite JSON
if "dataCiteJsonPath" not in publication_state:
if verbose:
log.write(ctx, "Generating Datacite JSON.")
try:
generate_datacite_json(ctx, publication_state)
except Exception as e:
log.write(ctx, "Exception while generating Datacite JSON: " + str(e))
publication_state["status"] = "Unrecoverable"
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] in ["Unrecoverable", "Retry"]:
log.write(ctx, "Error status after generating Datacite JSON: " + publication_state["status"])
return publication_state["status"]
# Check if DOI is in use
if "versionDOIAvailable" not in publication_state:
if verbose:
log.write(ctx, "Checking whether version DOI is available.")
try:
check_doi_availability(ctx, publication_state, 'version')
except Exception as e:
log.write(ctx, "Error while checking DOI availability: " + str(e))
publication_state["status"] = "Retry"
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] == "Retry":
log.write(ctx, "Error status after checking version DOI availability: " + publication_state["status"])
return publication_state["status"]
# Determine whether an update ('put') or create ('post') message has to be sent to datacite
datacite_action = 'post'
try:
if publication_state['versionDOIMinted'] == 'yes':
datacite_action = 'put'
except KeyError:
pass
# Send DataCite JSON to metadata end point
if "dataCiteMetadataPosted" not in publication_state:
if verbose:
log.write(ctx, "Uploading metadata to Datacite.")
try:
version_doi = publication_state['versionDOI']
post_metadata_to_datacite(ctx, publication_state, version_doi, datacite_action)
if update_base_doi:
base_doi = None
datacite_action = 'post'
if publication_state['baseDOIMinted'] == 'yes':
datacite_action = 'put'
if verbose:
log.write(ctx, "Updating base DOI.")
base_doi = publication_state['baseDOI']
post_metadata_to_datacite(ctx, publication_state, base_doi, datacite_action)
except Exception as e:
log.write(ctx, "Exception while sending metadata to Datacite: " + str(e))
publication_state["status"] = "Retry"
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] in ["Unrecoverable", "Retry"]:
log.write(ctx, "Error status after sending metadata to Datacite: " + publication_state["status"])
return publication_state["status"]
# Create landing page
if "landingPagePath" not in publication_state:
if verbose:
log.write(ctx, "Creating landing page.")
# Create landing page
try:
generate_landing_page(ctx, publication_state, "publish")
except Exception as e:
log.write(ctx, "Error while creating landing page: " + str(e))
publication_state["status"] = "Unrecoverable"
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] == "Unrecoverable":
log.write(ctx, "Error status after creating landing page: " + publication_state["status"])
return publication_state["status"]
# Use secure copy to push landing page to the public host
if "landingPageUploaded" not in publication_state:
if verbose:
log.write(ctx, "Uploading landing page.")
random_id = publication_state["randomId"]
copy_landingpage_to_public_host(ctx, random_id, publication_config, publication_state)
if update_base_doi:
base_random_id = publication_state["baseRandomId"]
if verbose:
log.write(ctx, "Updating base DOI landing page.")
copy_landingpage_to_public_host(ctx, base_random_id, publication_config, publication_state)
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] == "Retry":
log.write(ctx, "Error status after uploading landing page:" + publication_state["status"])
return publication_state["status"]
# Use secure copy to push combi JSON to MOAI server
if "oaiUploaded" not in publication_state:
if verbose:
log.write(ctx, "Uploading to MOAI.")
random_id = publication_state["randomId"]
copy_metadata_to_moai(ctx, random_id, publication_config, publication_state)
if update_base_doi:
base_random_id = publication_state["baseRandomId"]
if verbose:
log.write(ctx, "Updating base DOI at MOAI.")
copy_metadata_to_moai(ctx, base_random_id, publication_config, publication_state)
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] == "Retry":
log.write(ctx, "Error status after uploading to MOAI: " + publication_state["status"])
return publication_state["status"]
# Set access restriction for vault package.
if "anonymousAccess" not in publication_state:
if verbose:
log.write(ctx, "Setting vault access restrictions.")
set_access_restrictions(ctx, vault_package, publication_state)
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] == "Retry":
log.write(ctx, "Error status after setting vault access restrictions." + publication_state["status"])
return publication_state["status"]
# Mint DOI with landing page URL.
if "versionDOIMinted" not in publication_state:
if verbose:
log.write(ctx, "Minting DOI.")
mint_doi(ctx, publication_state, 'version')
if update_base_doi:
if verbose:
log.write(ctx, "Base DOI update.")
base_doi = publication_state['baseDOI']
mint_doi(ctx, publication_state, 'base')
save_publication_state(ctx, vault_package, publication_state)
if publication_state["status"] in ["Unrecoverable", "Retry"]:
if verbose:
log.write(ctx, "Error status during minting DOI.")
return publication_state["status"]
# The publication was a success
publication_state["status"] = "OK"
save_publication_state(ctx, vault_package, publication_state)
avu.set_on_coll(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'vault_status', constants.vault_package_state.PUBLISHED)
if "previous_version" in publication_state:
if verbose:
log.write(ctx, "Updating previous version AVU.")
avu.set_on_coll(ctx, publication_state["previous_version"], constants.UUORGMETADATAPREFIX + 'publication_next_version', vault_package)
if verbose:
log.write(ctx, "Updating previous version landing page.")
previous_versions = get_all_versions(ctx, publication_state["previous_version"], publication_state["baseDOI"])[1]
for item in previous_versions[1:]:
update_publication(ctx, item[1], update_datacite=False, update_landingpage=True, update_moai=False)
else:
# The publication was a success
if verbose:
log.write(ctx, "Publication successful.")
publication_state["status"] = "OK"
save_publication_state(ctx, vault_package, publication_state)
provenance.log_action(ctx, "system", vault_package, "publication updated")
log.write(ctx, "Finished publication of vault package <{}>".format(vault_package))
return publication_state["status"]