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vault.py
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# -*- coding: utf-8 -*-
"""Functions to copy packages to the vault and manage permissions of vault packages."""
__copyright__ = 'Copyright (c) 2019-2022, Utrecht University'
__license__ = 'GPLv3, see LICENSE'
import itertools
import os
import re
import subprocess
import time
from datetime import datetime
import genquery
import irods_types
from dateutil import parser
import folder
import groups
import meta
import meta_form
import policies_datamanager
import policies_datapackage_status
from util import *
__all__ = ['api_vault_submit',
'api_vault_approve',
'api_vault_cancel',
'api_vault_depublish',
'api_vault_republish',
'api_vault_preservable_formats_lists',
'api_vault_unpreservable_files',
'rule_vault_copy_original_metadata_to_vault',
'rule_vault_write_license',
'rule_vault_enable_indexing',
'rule_vault_disable_indexing',
'rule_vault_process_status_transitions',
'api_vault_system_metadata',
'api_vault_collection_details',
'api_vault_get_package_by_reference',
'api_vault_copy_to_research',
'api_vault_get_publication_terms',
'api_vault_get_landingpage_data',
'api_grant_read_access_research_group',
'api_revoke_read_access_research_group',
'api_vault_get_published_packages']
@api.make()
def api_vault_submit(ctx, coll, previous_version=None):
"""Submit data package for publication.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to submit
:param previous_version: Path to previous version of data package in the vault
:returns: API status
"""
ret = vault_request_status_transitions(ctx, coll, constants.vault_package_state.SUBMITTED_FOR_PUBLICATION, previous_version)
if ret[0] == '':
log.write(ctx, 'api_vault_submit: iiAdminVaultActions')
ctx.iiAdminVaultActions()
return 'Success'
else:
return api.Error(ret[0], ret[1])
@api.make()
def api_vault_approve(ctx, coll):
"""Approve data package for publication.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to approve
:returns: API status
"""
# Check for previous version.
previous_version = get_previous_version(ctx, coll)
# Add related data package metadata for new and previous version.
if previous_version:
meta_add_new_version(ctx, coll, previous_version)
ret = vault_request_status_transitions(ctx, coll, constants.vault_package_state.APPROVED_FOR_PUBLICATION)
if ret[0] == '':
log.write(ctx, 'api_vault_approve: iiAdminVaultActions')
ctx.iiAdminVaultActions()
return 'Success'
else:
return api.Error(ret[0], ret[1])
@api.make()
def api_vault_cancel(ctx, coll):
"""Cancel submit of data package.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to cancel submit
:returns: API status
"""
ret = vault_request_status_transitions(ctx, coll, constants.vault_package_state.UNPUBLISHED)
if ret[0] == '':
log.write(ctx, 'api_vault_submit: iiAdminVaultActions')
ctx.iiAdminVaultActions()
return 'Success'
else:
return api.Error(ret[0], ret[1])
@api.make()
def api_vault_depublish(ctx, coll):
"""Depublish data package.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to depublish
:returns: API status
"""
ret = vault_request_status_transitions(ctx, coll, constants.vault_package_state.PENDING_DEPUBLICATION)
if ret[0] == '':
log.write(ctx, 'api_vault_submit: iiAdminVaultActions')
ctx.iiAdminVaultActions()
return 'Success'
else:
return api.Error(ret[0], ret[1])
@api.make()
def api_vault_republish(ctx, coll):
"""Republish data package.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to republish
:returns: API status
"""
ret = vault_request_status_transitions(ctx, coll, constants.vault_package_state.PENDING_REPUBLICATION)
if ret[0] == '':
log.write(ctx, 'api_vault_submit: iiAdminVaultActions')
ctx.iiAdminVaultActions()
return 'Success'
else:
return api.Error(ret[0], ret[1])
@api.make()
def api_vault_copy_to_research(ctx, coll_origin, coll_target):
"""Copy data package from vault to research space.
:param ctx: Combined type of a callback and rei struct
:param coll_origin: Collection of data package to copy
:param coll_target: Collection to copy data package to
:returns: API status
"""
zone = user.zone(ctx)
# API error introduces post-error in requesting application.
if coll_target == "/" + zone + "/home":
return api.Error('HomeCollectionNotAllowed', 'Please select a specific research folder for your datapackage')
# Check if target is a research folder. I.e. none-vault folder.
parts = coll_target.split('/')
group_name = parts[3]
if group_name.startswith('vault-'):
return api.Error('RequiredIsResearchArea', 'Please select a specific research folder for your datapackage')
# Check whether datapackage folder already present in target folder.
# Get package name from origin path
parts = coll_origin.split('/')
new_package_collection = coll_target + '/' + parts[-1]
# Now check whether target collection already exist.
if collection.exists(ctx, new_package_collection):
return api.Error('PackageAlreadyPresentInTarget', 'This datapackage is already present at the specified place')
# Check if target path exists.
if not collection.exists(ctx, coll_target):
return api.Error('TargetPathNotExists', 'The target you specified does not exist')
# Check if user has READ ACCESS to specific vault packatge in collection coll_origin.
user_full_name = user.full_name(ctx)
category = groups.group_category(ctx, group_name)
is_datamanager = groups.user_is_datamanager(ctx, category, user.full_name(ctx))
if not is_datamanager:
# Check if research group has access by checking of research-group exists for this user.
research_group_access = collection.exists(ctx, coll_origin)
if not research_group_access:
return api.Error('NoPermissions', 'Insufficient rights to perform this action')
# Check for possible locks on target collection.
lock_count = meta_form.get_coll_lock_count(ctx, coll_target)
if lock_count:
return api.Error('TargetCollectionLocked', 'The folder you selected is locked.')
# Check if user has write access to research folder.
# Only normal user has write access.
if not groups.user_role(ctx, user_full_name, group_name) in ['normal', 'manager']:
return api.Error('NoWriteAccessTargetCollection', 'Not permitted to write in selected folder')
# Register to delayed rule queue.
delay = 10
ctx.delayExec(
"<PLUSET>%ds</PLUSET>" % delay,
"iiCopyFolderToResearch('%s', '%s')" % (coll_origin, coll_target),
"")
# TODO: response nog veranderen
return {"status": "ok",
"target": coll_target,
"origin": coll_origin}
@api.make()
def api_vault_preservable_formats_lists(ctx):
"""Retrieve lists of preservable file formats on the system.
:param ctx: Combined type of a callback and rei struct
:returns: dict -- Lists of preservable file formats {name => [ext...]}
"""
zone = user.zone(ctx)
# Retrieve all preservable file formats lists on the system.
files = [x for x in collection.data_objects(ctx, '/{}/yoda/file_formats'.format(zone))
if x.endswith('.json')]
# Return dict of list filename (without extension) -> JSON contents
return {os.path.splitext(pathutil.chop(x)[1])[0]:
jsonutil.read(ctx, x) for x in files}
@api.make()
def api_vault_unpreservable_files(ctx, coll, list_name):
"""Retrieve the set of unpreservable file formats in a collection.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of folder to check
:param list_name: Name of preservable file format list
:returns: Set of unpreservable file formats
"""
zone = pathutil.info(coll)[1]
# Retrieve JSON list of preservable file formats.
list_data = jsonutil.read(ctx, '/{}/yoda/file_formats/{}.json'.format(zone, list_name))
preservable_formats = set(list_data['formats'])
# Get basenames of all data objects within this collection.
data_names = itertools.imap(lambda x: pathutil.chop(x)[1],
collection.data_objects(ctx, coll, recursive=True))
# Exclude Yoda metadata files
data_names = itertools.ifilter(lambda
x: not re.match(r"yoda\-metadata(\[\d+\])?\.(xml|json)", x),
data_names)
# Data names -> lowercase extensions, without the dot.
exts = set(list(itertools.imap(lambda x: os.path.splitext(x)[1][1:].lower(), data_names)))
exts -= set([''])
# Return any ext that is not in the preservable list.
return list(exts - preservable_formats)
def rule_vault_copy_original_metadata_to_vault(rule_args, callback, rei):
"""Copy the original metadata JSON into the root of the package.
:param rule_args: [0] Path of a new package in the vault
:param callback: Callback to rule Language
:param rei: The rei struct
"""
vault_package = rule_args[0]
vault_copy_original_metadata_to_vault(callback, vault_package)
def vault_copy_original_metadata_to_vault(ctx, vault_package_path):
"""Copy original metadata to the vault package root.
:param ctx: Combined type of a callback and rei struct
:param vault_package_path: Path of a package in the vault
"""
original_metadata = vault_package_path + "/original/" + constants.IIJSONMETADATA
copied_metadata = vault_package_path + '/yoda-metadata[' + str(int(time.time())) + '].json'
# Copy original metadata JSON.
ctx.msiDataObjCopy(original_metadata, copied_metadata, 'destRescName={}++++verifyChksum='.format(config.resource_vault), 0)
# msi.data_obj_copy(ctx, original_metadata, copied_metadata, 'verifyChksum=', irods_types.BytesBuf())
def rule_vault_write_license(rule_args, callback, rei):
"""Write the license as a text file into the root of the vault package.
:param rule_args: [0] Path of a package in the vault
:param callback: Callback to rule Language
:param rei: The rei struct
"""
vault_pkg_coll = rule_args[0]
vault_write_license(callback, vault_pkg_coll)
def vault_write_license(ctx, vault_pkg_coll):
"""Write the license as a text file into the root of the vault package.
:param ctx: Combined type of a callback and rei struct
:param vault_pkg_coll: Path of a package in the vault
"""
zone = user.zone(ctx)
# Retrieve license.
license = ""
license_key = "License"
license_unit = "{}_%".format(constants.UUUSERMETADATAROOT)
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '{}' AND META_COLL_ATTR_NAME = '{}' AND META_COLL_ATTR_UNITS LIKE '{}'".format(vault_pkg_coll, license_key, license_unit),
genquery.AS_LIST, ctx)
for row in iter:
license = row[0]
if license == "":
# No license set in user metadata.
log.write(ctx, "rule_vault_write_license: No license found in user metadata <{}>".format(vault_pkg_coll))
elif license == "Custom":
# Custom license set in user metadata, no License.txt should exist in package.
license_file = vault_pkg_coll + "/License.txt"
if data_object.exists(ctx, license_file):
data_object.remove(ctx, license_file, force=True)
else:
# License set in user metadata, a License.txt should exist in package.
# Check if license text exists.
license_txt = "/{}{}/{}.txt".format(zone, constants.IILICENSECOLLECTION, license)
if data_object.exists(ctx, license_txt):
# Copy license file.
license_file = vault_pkg_coll + "/License.txt"
ctx.msiDataObjCopy(license_txt, license_file, 'destRescName={}++++forceFlag=++++verifyChksum='.format(config.resource_vault), 0)
# Fix ACLs.
try:
ctx.iiCopyACLsFromParent(license_file, 'default')
except Exception:
log.write(ctx, "rule_vault_write_license: Failed to set vault permissions on <{}>".format(license_file))
else:
log.write(ctx, "rule_vault_write_license: License text not available for <{}>".format(license))
# Check if license URI exists.
license_uri_file = "/{}{}/{}.uri".format(zone, constants.IILICENSECOLLECTION, license)
if data_object.exists(ctx, license_uri_file):
# Retrieve license URI.
license_uri = data_object.read(ctx, license_uri_file)
license_uri = license_uri.strip()
license_uri = license_uri.strip('\"')
# Set license URI.
avu.set_on_coll(ctx, vault_pkg_coll, "{}{}".format(constants.UUORGMETADATAPREFIX, "license_uri"), license_uri)
else:
log.write(ctx, "rule_vault_write_license: License URI not available for <{}>".format(license))
@rule.make(inputs=[0], outputs=[1])
def rule_vault_enable_indexing(ctx, coll):
vault_enable_indexing(ctx, coll)
return "Success"
def vault_enable_indexing(ctx, coll):
if config.enable_open_search:
if not collection.exists(ctx, coll + "/index"):
# index collection does not exist yet
path = meta.get_latest_vault_metadata_path(ctx, coll)
ctx.msi_rmw_avu('-d', path, '%', '%', constants.UUFLATINDEX)
meta.ingest_metadata_vault(ctx, path)
# add indexing attribute and update opensearch
subprocess.call(["imeta", "add", "-C", coll + "/index", "irods::indexing::index", "yoda::metadata", "elasticsearch"])
@rule.make(inputs=[0], outputs=[1])
def rule_vault_disable_indexing(ctx, coll):
vault_disable_indexing(ctx, coll)
return "Success"
def vault_disable_indexing(ctx, coll):
if config.enable_open_search:
if collection.exists(ctx, coll + "/index"):
coll = coll + "/index"
# tricky: remove indexing attribute without updating opensearch
try:
msi.mod_avu_metadata(ctx, "-C", coll, "rm", "irods::indexing::index", "yoda::metadata", "elasticsearch")
except Exception:
pass
@api.make()
def api_vault_system_metadata(ctx, coll):
"""Return system metadata of a vault collection.
:param ctx: Combined type of a callback and rei struct
:param coll: Path to data package
:returns: Dict system metadata of a vault collection
"""
system_metadata = {}
# Package size.
data_count = collection.data_count(ctx, coll)
collection_count = collection.collection_count(ctx, coll)
size = collection.size(ctx, coll)
size_readable = misc.human_readable_size(size)
system_metadata["Data Package Size"] = "{} files, {} folders, total of {}".format(data_count, collection_count, size_readable)
# Modified date.
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '%s' AND META_COLL_ATTR_NAME = 'org_publication_lastModifiedDateTime'" % (coll),
genquery.AS_LIST, ctx
)
for row in iter:
# Python 3: https://docs.python.org/3/library/datetime.html#datetime.date.fromisoformat
# modified_date = date.fromisoformat(row[0])
modified_date = parser.parse(row[0])
modified_date = modified_date.strftime('%Y-%m-%d %H:%M:%S%z')
system_metadata["Modified date"] = "{}".format(modified_date)
# Landingpage URL.
landinpage_url = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '%s' AND META_COLL_ATTR_NAME = 'org_publication_landingPageUrl'" % (coll),
genquery.AS_LIST, ctx
)
for row in iter:
landinpage_url = row[0]
system_metadata["Landingpage"] = "<a href=\"{}\">{}</a>".format(landinpage_url, landinpage_url)
# Check for previous version.
previous_version = get_previous_version(ctx, coll)
if previous_version:
previous_version_doi = get_doi(ctx, previous_version)
system_metadata["Persistent Identifier DOI"] = persistent_identifier_doi = "previous version: <a href=\"https://doi.org/{}\">{}</a>".format(previous_version_doi, previous_version_doi)
# Persistent Identifier DOI.
package_doi = get_doi(ctx, coll)
if package_doi:
if previous_version:
persistent_identifier_doi = "<a href=\"https://doi.org/{}\">{}</a> (previous version: <a href=\"https://doi.org/{}\">{}</a>)".format(package_doi, package_doi, previous_version_doi, previous_version_doi)
else:
persistent_identifier_doi = "<a href=\"https://doi.org/{}\">{}</a>".format(package_doi, package_doi)
system_metadata["Persistent Identifier DOI"] = persistent_identifier_doi
# Data Package Reference.
data_package_reference = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '{}' AND META_COLL_ATTR_NAME = '{}'".format(coll, constants.DATA_PACKAGE_REFERENCE),
genquery.AS_LIST, ctx
)
for row in iter:
data_package_reference = row[0]
system_metadata["Data Package Reference"] = "<a href=\"yoda/{}\">yoda/{}</a>".format(data_package_reference, data_package_reference)
# Persistent Identifier EPIC.
package_epic_pid = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '%s' AND META_COLL_ATTR_NAME = 'org_epic_pid'" % (coll),
genquery.AS_LIST, ctx
)
for row in iter:
package_epic_pid = row[0]
package_epic_url = ""
iter = genquery.row_iterator(
"META_COLL_ATTR_VALUE",
"COLL_NAME = '%s' AND META_COLL_ATTR_NAME = 'org_epic_url'" % (coll),
genquery.AS_LIST, ctx
)
for row in iter:
package_epic_url = row[0]
if package_epic_pid:
if package_epic_url:
persistent_identifier_epic = "<a href=\"{}\">{}</a>".format(package_epic_url, package_epic_pid)
else:
persistent_identifier_epic = "{}".format(package_epic_pid)
system_metadata["EPIC Persistent Identifier"] = persistent_identifier_epic
return system_metadata
def get_coll_vault_status(ctx, path, org_metadata=None):
"""Get the status of a vault folder."""
if org_metadata is None:
org_metadata = folder.get_org_metadata(ctx, path)
# Don't care about duplicate attr names here.
org_metadata = dict(org_metadata)
if constants.IIVAULTSTATUSATTRNAME in org_metadata:
x = org_metadata[constants.IIVAULTSTATUSATTRNAME]
try:
return constants.vault_package_state(x)
except Exception:
log.write(ctx, 'Invalid vault folder status <{}>'.format(x))
return constants.vault_package_state.EMPTY
@api.make()
def api_vault_collection_details(ctx, path):
"""Return details of a vault collection.
:param ctx: Combined type of a callback and rei struct
:param path: Path to data package
:returns: Dict with collection details
"""
if not collection.exists(ctx, path):
return api.Error('nonexistent', 'The given path does not exist')
# Check if collection is a research group.
space, _, group, subpath = pathutil.info(path)
if space != pathutil.Space.VAULT:
return {}
basename = pathutil.basename(path)
# Find group name to retrieve member type
group_parts = group.split('-')
if subpath.startswith("deposit-"):
research_group_name = 'deposit-' + '-'.join(group_parts[1:])
else:
research_group_name = 'research-' + '-'.join(group_parts[1:])
member_type = groups.user_role(ctx, user.full_name(ctx), research_group_name)
# Retrieve vault folder status.
status = get_coll_vault_status(ctx, path).value
# Check if collection has datamanager.
has_datamanager = True
# Check if user is datamanager.
category = groups.group_category(ctx, group)
is_datamanager = groups.user_is_datamanager(ctx, category, user.full_name(ctx))
# Check if collection is vault package.
metadata_path = meta.get_latest_vault_metadata_path(ctx, path)
if metadata_path is None:
return {'member_type': member_type, 'is_datamanager': is_datamanager}
else:
metadata = True
# Check if a vault action is pending.
vault_action_pending = False
coll_id = collection.id_from_name(ctx, path)
action_status = constants.UUORGMETADATAPREFIX + '"vault_status_action_' + coll_id
iter = genquery.row_iterator(
"COLL_ID",
"META_COLL_ATTR_NAME = '" + action_status + "' AND META_COLL_ATTR_VALUE = 'PENDING'",
genquery.AS_LIST, ctx
)
for _row in iter:
vault_action_pending = True
# Check if research group has access.
research_group_access = False
# Retrieve all access user IDs on collection.
iter = genquery.row_iterator(
"COLL_ACCESS_USER_ID",
"COLL_NAME = '{}'".format(path),
genquery.AS_LIST, ctx
)
for row in iter:
user_id = row[0]
# Retrieve all group names with this ID.
iter2 = genquery.row_iterator(
"USER_NAME",
"USER_ID = '{}'".format(user_id),
genquery.AS_LIST, ctx
)
for row2 in iter2:
user_name = row2[0]
# Check if group is a research or intake group.
if user_name.startswith(("research-", "deposit-")):
research_group_access = True
result = {
"basename": basename,
"status": status,
"metadata": metadata,
"member_type": member_type,
"has_datamanager": has_datamanager,
"is_datamanager": is_datamanager,
"vault_action_pending": vault_action_pending,
"research_group_access": research_group_access
}
if config.enable_data_package_archive:
import vault_archive
result["archive"] = {
"archivable": vault_archive.vault_archivable(ctx, path),
"status": vault_archive.vault_archival_status(ctx, path)
}
if config.enable_data_package_download:
import vault_download
result["downloadable"] = vault_download.vault_downloadable(ctx, path)
return result
@api.make()
def api_vault_get_package_by_reference(ctx, reference):
"""Return path to data package with provided reference (UUID4).
:param ctx: Combined type of a callback and rei struct
:param reference: Data Package Reference (UUID4)
:returns: Path to data package
"""
data_package = ""
iter = genquery.row_iterator(
"COLL_NAME",
"META_COLL_ATTR_NAME = '{}' and META_COLL_ATTR_VALUE = '{}'".format(constants.DATA_PACKAGE_REFERENCE, reference),
genquery.AS_LIST, ctx)
for row in iter:
data_package = row[0]
if data_package == "":
return api.Error('not_found', 'Could not find data package with provided reference.')
_, _, path, subpath = pathutil.info(data_package)
return "/{}/{}".format(path, subpath)
@api.make()
def api_vault_get_landingpage_data(ctx, coll):
"""Retrieve landingpage data of data package.
Landinpage data consists of metadata and system metadata.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection to retrieve landingpage data from
:returns: API status
"""
meta_path = meta.get_latest_vault_metadata_path(ctx, coll)
# Try to load the metadata file.
try:
metadata = jsonutil.read(ctx, meta_path)
current_schema_id = meta.metadata_get_schema_id(metadata)
if current_schema_id is None:
return api.Error('no_schema_id', 'Please check the structure of this file.',
'schema id missing')
except jsonutil.ParseError:
return api.Error('bad_json', 'Please check the structure of this file.', 'JSON invalid')
except msi.Error as e:
return api.Error('internal', 'The metadata file could not be read.', e)
# Get deposit date and end preservation date based upon retention period
# "submitted for vault"
# deposit_date = '2016-02-29' # To be gotten from the action log
iter = genquery.row_iterator(
"order_desc(META_COLL_MODIFY_TIME), META_COLL_ATTR_VALUE",
"COLL_NAME = '" + coll + "' 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] == "submitted for vault":
deposit_timestamp = datetime.fromtimestamp(int(log_item_list[0]))
deposit_date = deposit_timestamp.strftime('%Y-%m-%d')
break
return {'metadata': metadata, 'deposit_date': deposit_date}
@api.make()
def api_vault_get_publication_terms(ctx):
"""Retrieve the publication terms."""
zone = user.zone(ctx)
terms_collection = "/{}{}".format(zone, constants.IITERMSCOLLECTION)
terms = ""
iter = genquery.row_iterator(
"DATA_NAME, order_asc(DATA_MODIFY_TIME)",
"COLL_NAME = '{}'".format(terms_collection),
genquery.AS_LIST, ctx)
for row in iter:
terms = row[0]
if terms == "":
return api.Error('TermsNotFound', 'No Terms and Agreements found.')
try:
terms_file = "/{}{}/{}".format(zone, constants.IITERMSCOLLECTION, terms)
return data_object.read(ctx, terms_file)
except Exception:
return api.Error('TermsReadFailed', 'Could not open Terms and Agreements.')
@api.make()
def api_grant_read_access_research_group(ctx, coll):
"""Grant read rights of research group for datapackage in vault.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to remove read rights from
:returns: API status
"""
if not collection.exists(ctx, coll):
return api.Error('nonexistent', 'The given path does not exist')
coll_parts = coll.split('/')
if len(coll_parts) != 5:
return api.Error('invalid_collection', 'The datamanager can only revoke permissions to vault packages')
space, zone, group, subpath = pathutil.info(coll)
if space != pathutil.Space.VAULT:
return api.Error('invalid_collection', 'The datamanager can only revoke permissions to vault packages')
# Find category
group_parts = group.split('-')
if subpath.startswith("deposit-"):
research_group_name = 'deposit-' + '-'.join(group_parts[1:])
else:
research_group_name = 'research-' + '-'.join(group_parts[1:])
category = groups.group_category(ctx, group)
# Is datamanager?
actor = user.full_name(ctx)
if groups.user_role(ctx, actor, 'datamanager-' + category) in ['normal', 'manager']:
# Grant research group read access to vault package.
try:
acl_kv = msi.kvpair(ctx, "actor", actor)
msi.sudo_obj_acl_set(ctx, "recursive", "read", research_group_name, coll, acl_kv)
except Exception:
policy_error = policies_datamanager.can_datamanager_acl_set(ctx, coll, actor, research_group_name, "1", "read")
if bool(policy_error):
return api.Error('ErrorACLs', 'Could not acquire datamanager access to {}.'.format(coll))
else:
return api.Error('ErrorACLs', str(policy_error))
else:
return api.Error('NoDatamanager', 'Actor must be a datamanager for granting access')
return {'status': 'Success', 'statusInfo': ''}
@api.make()
def api_revoke_read_access_research_group(ctx, coll):
"""Revoke read rights of research group for datapackage in vault.
:param ctx: Combined type of a callback and rei struct
:param coll: Collection of data package to remove read rights from
:returns: API status
"""
if not collection.exists(ctx, coll):
return api.Error('nonexistent', 'The given path does not exist')
coll_parts = coll.split('/')
if len(coll_parts) != 5:
return api.Error('invalid_collection', 'The datamanager can only revoke permissions to vault packages')
space, zone, group, subpath = pathutil.info(coll)
if space != pathutil.Space.VAULT:
return api.Error('invalid_collection', 'The datamanager can only revoke permissions to vault packages')
# Find category
group_parts = group.split('-')
if subpath.startswith("deposit-"):
research_group_name = 'deposit-' + '-'.join(group_parts[1:])
else:
research_group_name = 'research-' + '-'.join(group_parts[1:])
category = groups.group_category(ctx, group)
# Is datamanager?
actor = user.full_name(ctx)
if groups.user_role(ctx, actor, 'datamanager-' + category) in ['normal', 'manager']:
# Grant research group read access to vault package.
try:
acl_kv = msi.kvpair(ctx, "actor", actor)
msi.sudo_obj_acl_set(ctx, "recursive", "null", research_group_name, coll, acl_kv)
except Exception:
policy_error = policies_datamanager.can_datamanager_acl_set(ctx, coll, actor, research_group_name, "1", "read")
if bool(policy_error):
return api.Error('ErrorACLs', 'Could not acquire datamanager access to {}.'.format(coll))
else:
return api.Error('ErrorACLs', str(policy_error))
else:
return api.Error('NoDatamanager', 'Actor must be a datamanager for revoking access')
return {'status': 'Success', 'statusInfo': ''}
def copy_folder_to_vault(ctx, folder, target):
"""Copy folder and all its contents to target in vault.
The data will reside onder folder '/original' within the vault.
:param ctx: Combined type of a callback and rei struct
:param folder: Path of a folder in the research space
:param target: Path of a package in the vault space
:raises Exception: Raises exception when treewalk_and_ingest did not finish correctly
"""
destination = target + '/original'
origin = folder
# Origin is a never changing value to be able to designate a relative path within ingest_object
error = 0 # Initial error state. Should stay 0.
if treewalk_and_ingest(ctx, folder, destination, origin, error):
raise Exception('copy_folder_to_vault: Error copying folder to vault')
def treewalk_and_ingest(ctx, folder, target, origin, error):
"""Treewalk folder and ingest.
:param ctx: Combined type of a callback and rei struct
:param folder: Will change every time as it represents every folder that has to be copied to vault
:param target: Target of ingest
:param origin: Origin of treewalk
:param error: 0/1 indicating if treewalk or ingest failed
:returns: Error status (which should remain 0 for further processing in iterative manner)
"""
parent_coll, coll = pathutil.chop(folder)
# 1. Process this collection itself as a collection.
# INGEST
if error == 0:
# INGEST COLLECTION
error = ingest_object(ctx, parent_coll, coll, True, target, origin)
# 2. Process dataobjects located directly within the collection
if error == 0:
iter = genquery.row_iterator(
"DATA_NAME",
"COLL_NAME = '" + folder + "'",
genquery.AS_LIST, ctx
)
for row in iter:
# INGEST OBJECT
error = ingest_object(ctx, folder, row[0], False, target, origin)
if error:
break
if error == 0:
# 3. Process the subfolders
# Loop through subfolders which have folder as parent folder
iter = genquery.row_iterator(
"COLL_NAME",
"COLL_PARENT_NAME = '" + folder + "'",
genquery.AS_LIST, ctx
)
for row in iter:
error = treewalk_and_ingest(ctx, row[0], target, origin, error)
if error:
break
return error
def ingest_object(ctx, parent, item, item_is_collection, destination, origin):
source_path = parent + "/" + item
read_access = msi.check_access(ctx, source_path, 'read object', irods_types.BytesBuf())['arguments'][2]
if read_access != b'\x01':
try:
msi.set_acl(ctx, "default", "admin:read", user.full_name(ctx), source_path)
except msi.Error:
return 1
dest_path = destination
if source_path != origin:
markIncomplete = False
# rewrite path to copy objects that are located underneath the toplevel collection
source_length = len(source_path)
relative_path = source_path[len(origin) + 1: source_length]
dest_path = destination + '/' + relative_path
else:
markIncomplete = True
if item_is_collection:
# CREATE COLLECTION
try:
msi.coll_create(ctx, dest_path, '', irods_types.BytesBuf())
except msi.Error:
return 1
if markIncomplete:
avu.set_on_coll(ctx, dest_path, constants.IIVAULTSTATUSATTRNAME, constants.vault_package_state.INCOMPLETE)
else:
# CREATE COPY OF DATA OBJECT
try:
# msi.data_obj_copy(ctx, source_path, dest_path, '', irods_types.BytesBuf())
ctx.msiDataObjCopy(source_path, dest_path, 'verifyChksum=', 0)
except msi.Error:
return 1
if read_access != b'\x01':
try:
msi.set_acl(ctx, "default", "admin:null", user.full_name(ctx), source_path)
except msi.Error:
return 1
return 0
def set_vault_permissions(ctx, group_name, folder, target):
"""Set permissions in the vault as such that data can be copied to the vault."""
parts = group_name.split('-')
base_name = '-'.join(parts[1:])
parts = folder.split('/')
vault_group_name = constants.IIVAULTPREFIX + base_name
# Check if noinherit is set
zone = user.zone(ctx)
vault_path = "/" + zone + "/home/" + vault_group_name
inherit = "0"
iter = genquery.row_iterator(
"COLL_INHERITANCE",
"COLL_NAME = '" + vault_path + "'",
genquery.AS_LIST, ctx
)
for row in iter:
# COLL_INHERITANCE can be empty which is interpreted as noinherit
inherit = row[0]
if inherit == "1":
msi.set_acl(ctx, "recursive", "admin:noinherit", "", vault_path)
# Check if research group has read-only access
iter = genquery.row_iterator(
"USER_ID",
"USER_NAME = '" + group_name + "'",
genquery.AS_LIST, ctx
)
for row in iter:
group_id = row[0]
access_name = "null"
iter = genquery.row_iterator(
"COLL_ACCESS_NAME",
"COLL_ACCESS_USER_ID = '" + group_id + "'",
genquery.AS_LIST, ctx
)
for row in iter:
access_name = row[0]
if access_name != "read object":
# Grant the research group read-only access to the collection to enable browsing through the vault.
try:
msi.set_acl(ctx, "default", "admin:read", group_name, vault_path)
log.write(ctx, "Granted " + group_name + " read access to " + vault_path)
except msi.Error:
log.write(ctx, "Failed to grant " + group_name + " read access to " + vault_path)
# Check if vault group has ownership
iter = genquery.row_iterator(
"USER_ID",
"USER_NAME = '" + vault_group_name + "'",
genquery.AS_LIST, ctx
)
for row in iter:
vault_group_id = row[0]
vault_group_access_name = "null"