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schema_transformation.py
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schema_transformation.py
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# -*- coding: utf-8 -*-
"""Functions for handling schema updates within any yoda-metadata file."""
__copyright__ = 'Copyright (c) 2018-2023, Utrecht University'
__license__ = 'GPLv3, see LICENSE'
__all__ = ['rule_batch_transform_vault_metadata',
'rule_batch_vault_metadata_correct_orcid_format',
'rule_batch_vault_metadata_schema_report',
'rule_get_transformation_info',
'api_transform_metadata']
import json
import os
import re
import time
import genquery
import session_vars
import meta
import meta_form
import schema
import schema_transformations
from util import *
def execute_transformation(ctx, metadata_path, transform, keep_metadata_backup=True):
"""Transform a metadata file with the given transformation function."""
coll, data = os.path.split(metadata_path)
group_name = metadata_path.split('/')[3]
metadata = jsonutil.read(ctx, metadata_path)
metadata = transform(ctx, metadata)
# make_metadata_backup is only relevant for research
if group_name.startswith('research-'):
if keep_metadata_backup:
backup = '{}/transformation-backup[{}].json'.format(coll, str(int(time.time())))
data_object.copy(ctx, metadata_path, backup)
jsonutil.write(ctx, metadata_path, metadata)
elif group_name.startswith('vault-'):
new_path = '{}/yoda-metadata[{}].json'.format(coll, str(int(time.time())))
# print('TRANSFORMING in vault <{}> -> <{}>'.format(metadata_path, new_path))
jsonutil.write(ctx, new_path, metadata)
copy_acls_from_parent(ctx, new_path, "default")
ctx.rule_provenance_log_action("system", coll, "updated metadata schema")
log.write(ctx, "Transformed %s" % (new_path))
else:
raise AssertionError()
@api.make()
def api_transform_metadata(ctx, coll, keep_metadata_backup=True):
"""Transform a yoda-metadata file in the given collection to the active schema."""
metadata_path = meta.get_collection_metadata_path(ctx, coll)
if metadata_path.endswith('.json'):
# JSON metadata.
log.write(ctx, 'Transforming JSON metadata in the research space: <{}>'.format(metadata_path))
transform = get(ctx, metadata_path)
if transform is None:
return api.Error('undefined_transformation', 'No transformation found')
execute_transformation(ctx, metadata_path, transform, keep_metadata_backup)
else:
return api.Error('no_metadata', 'No metadata file found')
def get(ctx, metadata_path, metadata=None):
"""Find a transformation that can be executed on the given metadata JSON.
:param ctx: Combined type of a ctx and rei struct
:param metadata_path: Path to metadata JSON
:param metadata: Optional metadata object
:returns: Transformation function on success, or None if no transformation was found
"""
try:
src = schema.get_schema_id(ctx, metadata_path, metadata=metadata)
dst = schema.get_active_schema_id(ctx, metadata_path)
# Ideally, we would check that the metadata is valid in its current
# schema before claiming that we can transform it...
# print('{} -> {}'.format(src,dst))
return schema_transformations.get(src, dst)
except KeyError:
return None
except error.UUError:
# print('{} -> {} ERR {}'.format(src,dst, e))
return None
# TODO: @rule.make
def rule_get_transformation_info(rule_args, callback, rei):
"""Check if a yoda-metadata.json transformation is possible and if so, retrieve transformation description.
:param rule_args: [0] JSON path
[1] Transformation possible? true|false
[2] human-readable description of the transformation
:param callback: Callback to rule Language
:param rei: The rei struct
"""
json_path = rule_args[0]
rule_args[1:3] = 'false', ''
transform = get(callback, json_path)
if transform is not None:
rule_args[1:3] = 'true', transformation_html(transform)
def copy_acls_from_parent(ctx, path, recursive_flag):
"""
When inheritance is missing we need to copy ACLs when introducing new data in vault package.
:param ctx: Combined type of a ctx and rei struct
:param path: Path of object that needs the permissions of parent
:param recursive_flag: Either "default" for no recursion or "recursive"
"""
parent = os.path.dirname(path)
iter = genquery.row_iterator(
"COLL_ACCESS_NAME, COLL_ACCESS_USER_ID",
"COLL_NAME = '" + parent + "'",
genquery.AS_LIST, ctx
)
for row in iter:
access_name = row[0]
user_id = int(row[1])
user_name = user.name_from_id(ctx, user_id)
# iRODS keeps ACLs for deleted users in the iCAT database (https://github.com/irods/irods/issues/7778),
# so we need to skip ACLs referring to users that no longer exist.
if user_name == "":
continue
if access_name == "own":
log.write(ctx, "iiCopyACLsFromParent: granting own to <" + user_name + "> on <" + path + "> with recursiveFlag <" + recursive_flag + ">")
msi.set_acl(ctx, recursive_flag, "own", user_name, path)
elif access_name == "read object":
log.write(ctx, "iiCopyACLsFromParent: granting read to <" + user_name + "> on <" + path + "> with recursiveFlag <" + recursive_flag + ">")
msi.set_acl(ctx, recursive_flag, "read", user_name, path)
elif access_name == "modify object":
log.write(ctx, "iiCopyACLsFromParent: granting write to <" + user_name + "> on <" + path + "> with recursiveFlag <" + recursive_flag + ">")
msi.set_acl(ctx, recursive_flag, "write", user_name, path)
# TODO: @rule.make
def rule_batch_transform_vault_metadata(rule_args, callback, rei):
"""
Transform all metadata JSON files in the vault to the active schema.
:param rule_args: [0] First COLL_ID to check - initial = 0
[1] Batch size, <= 256
[2] Pause between checks (float)
[3] Delay between batches in seconds
:param callback: Callback to rule Language
:param rei: The rei struct
"""
coll_id = int(rule_args[0])
batch = int(rule_args[1])
pause = float(rule_args[2])
delay = int(rule_args[3])
rods_zone = session_vars.get_map(rei)["client_user"]["irods_zone"]
# Check one batch of metadata schemas.
# Find all research and vault collections, ordered by COLL_ID.
iter = genquery.row_iterator(
"ORDER(COLL_ID), COLL_NAME",
"COLL_NAME like '/%s/home/vault-%%' AND DATA_NAME like 'yoda-metadata%%json' AND COLL_ID >= '%d'" % (rods_zone, coll_id),
genquery.AS_LIST, callback)
# Check each collection in batch.
for row in iter:
coll_id = int(row[0])
coll_name = row[1]
path_parts = coll_name.split('/')
# Only process collections that are directly beneath the apex
# vault collection, e.g. /zoneName/home/vault-foo/data-package[123],
# since metadata in the original part of the data package should not
# be processed.
if not re.match(r"^\/[^\/]+\/home\/[^\/]+\/[^\/]+$", coll_name):
continue
try:
# Get vault package path.
vault_package = '/'.join(path_parts[:5])
metadata_path = meta.get_latest_vault_metadata_path(callback, vault_package)
log.write(callback, "[METADATA] Checking whether metadata needs to be transformed: " + metadata_path)
if metadata_path != '':
transform = get(callback, metadata_path)
if transform is not None:
log.write(callback, "[METADATA] Executing transformation for: " + metadata_path)
execute_transformation(callback, metadata_path, transform)
except Exception as e:
log.write(callback, "[METADATA] Exception occurred during schema transformation of %s: %s" % (coll_name, str(type(e)) + ":" + str(e)))
# Sleep briefly between checks.
time.sleep(pause)
# The next collection to check must have a higher COLL_ID.
coll_id += 1
else:
# All done.
coll_id = 0
log.write(callback, "[METADATA] Finished updating metadata.")
if coll_id != 0:
# Check the next batch after a delay.
callback.delayExec(
"<INST_NAME>irods_rule_engine_plugin-irods_rule_language-instance</INST_NAME><PLUSET>%ds</PLUSET>" % delay,
"rule_batch_transform_vault_metadata('%d', '%d', '%f', '%d')" % (coll_id, batch, pause, delay),
"")
# TODO: @rule.make
def rule_batch_vault_metadata_correct_orcid_format(rule_args, callback, rei):
"""
Correct ORCID person identifier with invalid format in metadata JSON files in the vault.
:param rule_args: [0] First COLL_ID to check - initial = 0
[1] Batch size, <= 256
[2] Pause between checks (float)
[3] Delay between batches in seconds
[4] Dry-run mode ('true' or 'false'; everything else is considered 'false')
:param callback: Callback to rule Language
:param rei: The rei struct
"""
coll_id = int(rule_args[0])
batch = int(rule_args[1])
pause = float(rule_args[2])
delay = int(rule_args[3])
dryrun_mode = rule_args[4] == "true"
rods_zone = session_vars.get_map(rei)["client_user"]["irods_zone"]
# Check one batch of metadata schemas.
# Find all vault collections, ordered by COLL_ID.
iter = genquery.row_iterator(
"ORDER(COLL_ID), COLL_NAME",
"COLL_NAME like '/%s/home/vault-%%' AND COLL_NAME not like '%%/original' AND DATA_NAME like 'yoda-metadata%%json' AND COLL_ID >= '%d'" % (rods_zone, coll_id),
genquery.AS_LIST, callback)
# Check each collection in batch.
for row in iter:
coll_id = int(row[0])
coll_name = row[1]
path_parts = coll_name.split('/')
try:
# Get vault package path.
vault_package = '/'.join(path_parts[:5])
metadata_path = meta.get_latest_vault_metadata_path(callback, vault_package)
if metadata_path != '':
metadata = jsonutil.read(callback, metadata_path)
# We only need to transform metadata with schemas that do not constrain ORCID format
license_url = metadata.get("links", {})[0].get("href", "")
license = license_url.replace("https://yoda.uu.nl/schemas/", "").replace("/metadata.json", "")
if license not in ['core-1', 'core-2', 'default-1', 'default-2', 'default-3', 'hptlab-1', 'teclab-1', 'dag-0', 'vollmer-0']:
log.write(callback, "Skipping data package '%s' for ORCID transformation because license '%s' is excluded."
% (vault_package, license))
continue
# Correct the incorrect orcid(s) if possible
# result is a dict containing 'data_changed' 'metadata'
result = transform_orcid(callback, metadata)
# In order to minimize changes within the vault only save a new metadata.json if there actually has been at least one orcid correction.
if result['data_changed'] and not dryrun_mode:
# orcid('s) has/have been adjusted. Save the changes in the same manner as execute_transformation for vault packages.
coll, data = os.path.split(metadata_path)
new_path = '{}/yoda-metadata[{}].json'.format(coll, str(int(time.time())))
log.write(callback, 'TRANSFORMING in vault <{}> -> <{}>'.format(metadata_path, new_path))
jsonutil.write(callback, new_path, result['metadata'])
copy_acls_from_parent(callback, new_path, "default")
callback.rule_provenance_log_action("system", coll, "updated person identifier metadata")
log.write(callback, "Transformed ORCIDs for: %s" % (new_path))
elif result['data_changed']:
log.write(callback, "Would have transformed ORCIDs for: %s if dry run mode was disabled." % (metadata_path))
except Exception as e:
log.write(callback, "Exception occurred during ORCID transformation of %s: %s" % (coll_name, str(type(e)) + ":" + str(e)))
# Sleep briefly between checks.
time.sleep(pause)
# The next collection to check must have a higher COLL_ID.
coll_id += 1
else:
# All done.
coll_id = 0
log.write(callback, "[METADATA] Finished correcting ORCID's within vault metadata.")
if coll_id != 0:
# Check the next batch after a delay.
callback.delayExec(
"<INST_NAME>irods_rule_engine_plugin-irods_rule_language-instance</INST_NAME><PLUSET>%ds</PLUSET>" % delay,
"rule_batch_vault_metadata_correct_orcid_format('%d', '%d', '%f', '%d')" % (coll_id, batch, pause, delay),
"")
def transform_orcid(ctx, m):
"""
Transform all present orcid's into the correct format. If possible!
:param ctx: Combined type of a callback and rei struct
:param m: Metadata to transform
:returns: Dict with indication whether data has changed and transformed JSON object with regard to ORCID
"""
data_changed = False
# Only Creators and Contributors hold Person identifiers that can hold ORCIDs.
for pi_holder in ['Creator', 'Contributor']:
if m.get(pi_holder, False):
for holder in m[pi_holder]:
for pi in holder.get('Person_Identifier', dict()):
if pi.get('Name_Identifier_Scheme', None) == 'ORCID':
# If incorrect ORCID format => try to correct.
if not re.search("^(https://orcid.org/)[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$", pi.get('Name_Identifier', None)):
original_orcid = pi['Name_Identifier']
corrected_orcid = correctify_orcid(original_orcid)
# Only it an actual correction took place change the value and mark this data as 'changed'.
if corrected_orcid is None:
log.write(ctx, "Warning: unable to automatically fix ORCID '%s'" % (original_orcid))
elif corrected_orcid != original_orcid:
log.write(ctx, "Updating ORCID '%s' to '%s'" % (original_orcid, corrected_orcid))
pi['Name_Identifier'] = corrected_orcid
data_changed = True
return {'metadata': m, 'data_changed': data_changed}
def correctify_orcid(org_orcid):
"""Function to correct illformatted ORCIDs. Returns None if value cannot be fixed."""
# Get rid of all spaces.
orcid = org_orcid.replace(' ', '')
# Upper-case X.
orcid = org_orcid.replace('x', 'X')
# The last part should hold a valid id like eg: 1234-1234-1234-123X.
# If not, it is impossible to correct it to the valid orcid format
orcs = orcid.split('/')
if not re.search("^[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]$", orcs[-1]):
return None
return "https://orcid.org/{}".format(orcs[-1])
def html(f):
"""Get a human-readable HTML description of a transformation function.
The text is derived from the function's docstring.
:param f: Transformation function
:returns: Human-readable HTML description of a transformation function
"""
description = '\n'.join(map(lambda paragraph:
'<p>{}</p>'.format( # Trim whitespace.
re.sub('\s+', ' ', paragraph).strip()),
# Docstring paragraphs are separated by blank lines.
re.split('\n{2,}', f.__doc__)))
# Remove docstring.
description = re.sub('((:param).*)|((:returns:).*)', ' ', description)
return description
@rule.make(inputs=[], outputs=[0])
def rule_batch_vault_metadata_schema_report(ctx):
"""Show vault metadata schema about each data package in vault
:param ctx: Combined type of a callback and rei struct
:returns: JSON-encoded dictionary, where each key is a vault data package path.
Values are dictionaries with keys "schema" (contains the short name of the schema
(e.g. 'default-3', as per the information in the metadata file, or empty if no metadata
schema could be found), and match_schema (contains a boolean value that indicates whether
the metadata matches the JSON schema). match_schema only has a meaning if a metadata schema
could be found.
"""
results = dict()
schema_cache = dict()
# Find all vault collections
iter = genquery.row_iterator(
"COLL_NAME",
"COLL_NAME like '/%s/home/vault-%%' AND COLL_NAME not like '%%/original' AND COLL_NAME NOT LIKE '%%/original/%%' AND DATA_NAME like 'yoda-metadata%%json'" %
(user.zone(ctx)),
genquery.AS_LIST, ctx)
for row in iter:
coll_name = row[0]
metadata_path = meta.get_latest_vault_metadata_path(ctx, coll_name)
if metadata_path == '' or metadata_path is None:
log.write(ctx, "Vault metadata schema report skips %s, because metadata could not be found."
% (coll_name))
continue
try:
metadata = jsonutil.read(ctx, metadata_path)
except Exception as exc:
log.write(ctx, "Vault metadata report skips %s, because of exception while reading metadata file %s: %s."
% (coll_name, metadata_path, str(exc)))
continue
# Determine schema
schema_id = schema.get_schema_id(ctx, metadata_path)
schema_shortname = schema_id.split("/")[-2]
# Retrieve schema and cache it for future use
schema_path = schema.get_schema_path_by_id(ctx, metadata_path, schema_id)
if schema_shortname in schema_cache:
schema_contents = schema_cache[schema_shortname]
else:
schema_contents = jsonutil.read(ctx, schema_path)
schema_cache[schema_shortname] = schema_contents
# Check whether metadata matches schema and log any errors
error_list = meta.get_json_metadata_errors(ctx, metadata_path, metadata=metadata, schema=schema_contents)
match_schema = len(error_list) == 0
if not match_schema:
log.write(ctx, "Vault metadata schema report: metadata %s did not match schema %s: %s" %
(metadata_path, schema_shortname, str([meta_form.humanize_validation_error(e).encode('utf-8') for e in error_list])))
# Update results
results[coll_name] = {"schema": schema_shortname, "match_schema": match_schema}
return json.dumps(results)