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api.py
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# -*- coding: utf-8 -*-
#
# This file is part of CERN Analysis Preservation Framework.
# Copyright (C) 2016 CERN.
#
# CERN Analysis Preservation Framework 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.
#
# CERN Analysis Preservation Framework 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 CERN Analysis Preservation Framework; if not, write to the
# Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston,
# MA 02111-1307, USA.
#
# In applying this license, CERN does not
# waive the privileges and immunities granted to it by virtue of its status
# as an Intergovernmental Organization or submit itself to any jurisdiction.
"""Deposit API."""
import copy
import uuid
from functools import wraps
from flask import current_app, request
from flask_login import current_user
from invenio_access.models import ActionRoles, ActionUsers
from invenio_db import db
from invenio_deposit.api import Deposit, has_status, index, preserve
from invenio_deposit.utils import mark_as_action
from invenio_files_rest.errors import MultipartMissingParts
from invenio_files_rest.models import (
Bucket,
FileInstance,
ObjectVersion,
ObjectVersionTag,
)
from invenio_jsonschemas.errors import JSONSchemaNotFound
from invenio_jsonschemas.proxies import current_jsonschemas
from invenio_records.api import Record
from invenio_records.models import RecordMetadata
from invenio_records_files.models import RecordsBuckets
from invenio_records_rest.errors import InvalidDataRESTError
from invenio_rest.errors import FieldError
from jsonpatch import apply_patch
from jsonschema.exceptions import RefResolutionError, ValidationError
from sqlalchemy.exc import IntegrityError
from sqlalchemy.orm.exc import NoResultFound
from werkzeug.local import LocalProxy
from cap.modules.deposit.errors import DisconnectWebhookError, FileUploadError
from cap.modules.deposit.loaders import get_val_from_path
from cap.modules.deposit.utils import perform_copying_fields
from cap.modules.deposit.validators import NoRequiredValidator
from cap.modules.experiments.permissions import exp_need_factory
from cap.modules.records.api import CAPRecord
from cap.modules.records.errors import get_error_path
from cap.modules.repos.errors import GitError, GitHostNotSupported
from cap.modules.repos.integrator import (
attach_repo_to_deposit,
create_repo_as_user_and_attach,
create_schema_default_repo_and_attach,
)
from cap.modules.repos.utils import disconnect_subscriber
from cap.modules.schemas.resolvers import (
resolve_schema_by_url,
schema_name_to_url,
)
from cap.modules.user.errors import DoesNotExistInLDAP
from cap.modules.user.utils import (
get_existing_or_register_role,
get_existing_or_register_user,
)
from .errors import (
DepositValidationError,
ReviewError,
UniqueRequiredValidationError,
UpdateDepositPermissionsError,
)
from .fetchers import cap_deposit_fetcher
from .minters import cap_deposit_minter
from .permissions import (
AdminDepositPermission,
CloneDepositPermission,
DepositAdminActionNeed,
DepositReadActionNeed,
DepositUpdateActionNeed,
ReviewDepositPermission,
UpdateDepositPermission,
)
from .review import Reviewable
from .validators import get_custom_validator
_datastore = LocalProxy(lambda: current_app.extensions["security"].datastore)
PRESERVE_FIELDS = (
"_deposit",
"_buckets",
"_files",
"_review",
"_experiment",
"_access",
"_user_edited",
"_fetched_from",
"control_number",
"general_title",
"$schema",
)
DEPOSIT_ACTIONS = (
"deposit-read",
"deposit-update",
"deposit-admin",
)
def DEPOSIT_ACTIONS_NEEDS(id):
"""Method to construct action needs."""
return {
"deposit-read": DepositReadActionNeed(str(id)),
"deposit-update": DepositUpdateActionNeed(str(id)),
"deposit-admin": DepositAdminActionNeed(str(id)),
}
EMPTY_ACCESS_OBJECT = {
action: {"users": [], "roles": []} for action in DEPOSIT_ACTIONS
}
class CAPDeposit(Deposit, Reviewable):
"""Define API for changing deposit state."""
deposit_fetcher = staticmethod(cap_deposit_fetcher)
deposit_minter = staticmethod(cap_deposit_minter)
published_record_class = CAPRecord
@property
def schema(self):
"""Schema property."""
return resolve_schema_by_url(self["$schema"])
@property
def record_schema(self):
"""Get corresponding schema path for record."""
return current_jsonschemas.path_to_url(self.schema.record_path)
def build_deposit_schema(self, record):
"""Get schema path for deposit."""
return current_jsonschemas.path_to_url(self.schema.deposit_path)
def pop_from_data(method, fields=None):
"""Remove fields from deposit data.
:param fields: List of fields to remove (default: ``('_deposit',)``).
"""
fields = fields or (
"_deposit",
"_access",
"_experiment",
"_fetched_from",
"_user_edited",
"general_title",
"$schema",
)
@wraps(method)
def wrapper(self, *args, **kwargs):
"""Check current deposit status."""
for field in fields:
if field in args[0]:
args[0].pop(field)
return method(self, *args, **kwargs)
return wrapper
def pop_from_data_patch(method, fields=None):
"""Remove fields from deposit data.
:param fields: List of fields to remove (default: ``('_deposit',)``).
"""
fields = fields or (
"/_deposit",
"/_access",
"/_files",
"/_experiment",
"/_fetched_from",
"/_user_edited",
"/$schema",
)
@wraps(method)
def wrapper(self, *args, **kwargs):
"""Check current deposit status."""
for field in fields:
for k, patch in enumerate(args[0]):
if field == patch.get("path", None):
del args[0][k]
return method(self, *args, **kwargs)
return wrapper
@mark_as_action
def permissions(self, pid=None):
"""Permissions action.
We expect an array of objects:
[{
"email": "",
"type": "user|egroup",
"op": "add|remove",
"action": "deposit-read|deposit-update|deposit-admin"
}]
"""
with AdminDepositPermission(self).require(403):
data = request.get_json()
if data is None:
raise InvalidDataRESTError()
return self.edit_permissions(data)
def _publish_edited(self):
record = super(CAPDeposit, self)._publish_edited()
record._add_deposit_permissions(record, record.id)
with db.session.begin_nested():
if self.files and record.files.bucket is not None:
# Unlock the record bucket
record.files.bucket.locked = False
# Lock the deposit's files bucket
self.files.bucket.locked = True
# Sync the record files with the deposit files
self.files.bucket.sync(record.files.bucket)
# lock the record bucket after update
record.files.bucket.locked = True
db.session.commit()
if record["_experiment"]:
record._add_experiment_permissions(record, record.id)
return record
@mark_as_action
def publish(self, *args, **kwargs):
"""Simple file check before publishing."""
with AdminDepositPermission(self).require(403):
# check if all deposit files has been uploaded
for file_ in self.files:
if file_.data["checksum"] is None:
raise MultipartMissingParts()
try:
return super(CAPDeposit, self).publish(*args, **kwargs)
except ValidationError as e:
raise DepositValidationError(e.message)
@has_status
@mark_as_action
def upload(self, pid, *args, **kwargs):
"""Upload action for repositories.
Can upload a repository or its single file and/or create a webhook.
Expects json with params:
* `url`: the git url, can point to repo or specific file
* `webhook`: the webhook type to be applied, can be null to just `attach` the repo # noqa
"""
with UpdateDepositPermission(self).require(403):
try:
_, rec = request.view_args.get("pid_value").data
data = request.get_json()
if data is None:
raise InvalidDataRESTError()
record_uuid = str(rec.id)
# For backward compatibility
# if no 'type' passed, pass 'repo_download_attach' as default
action_type = data.get("type", "repo_download_attach")
except Exception:
raise FileUploadError("Invalid arguments. Please try again.")
actions = {
"repo_create": create_repo_as_user_and_attach,
"repo_download_attach": attach_repo_to_deposit,
"repo_create_default": create_schema_default_repo_and_attach,
}
try:
actions[action_type](record_uuid, data)
except KeyError:
raise FileUploadError(
"Unsupported repository action. "
"Try create, attach or collab."
)
except GitHostNotSupported:
raise FileUploadError("Host isn't provided or not supported")
except GitError as err:
raise FileUploadError(err.message)
return self
@has_status
@mark_as_action
def disconnect_webhook(self, pid, *args, **kwargs):
"""Disconnect webhook for repostiories.
Expects json with subscriber id as a param:
"""
with UpdateDepositPermission(self).require(403):
data = request.get_json()
sub_id = data.get("subscriber_id")
if sub_id is None:
raise DisconnectWebhookError("Missing subscriber_id parameter")
try:
disconnect_subscriber(sub_id)
except NoResultFound:
raise DisconnectWebhookError(
"This webhook was not registered with analysis."
)
return self
@index
@mark_as_action
def clone(self, pid=None, id_=None):
"""Clone a deposit.
Adds snapshot of the files when deposit is cloned.
"""
with CloneDepositPermission(self).require(403):
data = copy.deepcopy(self.dumps())
# control number exist only in case of a published draft(record)
if data:
data.pop("_deposit", None)
data.pop("control_number", None)
deposit = super(CAPDeposit, self).create(data, id_=id_)
deposit["_deposit"]["cloned_from"] = {
"type": pid.pid_type,
"value": pid.pid_value,
"revision_id": self.revision_id,
}
bucket = self.files.bucket.snapshot()
RecordsBuckets.create(record=deposit.model, bucket=bucket)
# optionally we might need to do: deposit.files.flush()
deposit.commit()
return deposit
@index
@mark_as_action
def review(self, pid, *args, **kwargs):
"""Review actions for a deposit.
Adds review and comments for a deposit.
"""
with ReviewDepositPermission(self).require(403):
if self.schema_is_reviewable():
data = request.get_json()
if data is None:
raise InvalidDataRESTError()
if data.get("id"):
self.update_review(data)
else:
self.create_review(data)
else:
raise ReviewError(None)
self.commit()
return self
def _prepare_edit(self, record):
"""Update selected keys for edit method.
Override method from `invenio_deposit.api:Deposit` class.
Copy deposit metadata instead of record metadata.
:param record: The published record.
"""
data = self.dumps()
# Keep current record revision for merging.
data["_deposit"]["pid"]["revision_id"] = record.revision_id
data["_deposit"]["status"] = "draft"
return data
@mark_as_action
def edit(self, *args, **kwargs):
"""Edit deposit."""
with UpdateDepositPermission(self).require(403):
self = super(CAPDeposit, self).edit(*args, **kwargs)
# unlock the bucket, so files can be added/updated/deleted
# when user tries to edit file required by published record
# new version will be created
self.files.bucket.locked = False
db.session.commit()
return self
@pop_from_data
def update(self, data, *args, **kwargs):
"""Update deposit."""
with UpdateDepositPermission(self).require(403):
schema = {"$ref": self["$schema"]}
validated_data = None
# 1. Maybe check if should continue with action
# 2. Maybe merge for more customized
validated_data = self.validation(schema, data)
data = validated_data if validated_data else data
super(CAPDeposit, self).update(data, *args, **kwargs)
@pop_from_data_patch
def patch(self, *args, **kwargs):
"""Patch deposit."""
with UpdateDepositPermission(self).require(403):
schema = {"$ref": self["$schema"]}
patch = copy.deepcopy(request.get_json(force=True))
patched_data = apply_patch(self.model.json, patch)
self.validation(schema, patched_data)
return super(CAPDeposit, self).patch(*args, **kwargs)
def validation(self_or_cls, schema, data_to_validate, **kwargs):
"""Validation function to validate the data.
Validates the data in order provided in schema configuration.
"""
current_data = None
if hasattr(self_or_cls, 'model'):
current_data = self_or_cls.model.json
data_to_validate = self_or_cls.check_data(
schema=schema,
current_data=current_data,
submitted_data=data_to_validate,
)
return data_to_validate
def edit_permissions(self, data):
"""Edit deposit permissions.
We expect an array of objects:
[{
"email": "",
"type": "user|egroup",
"op": "add|remove",
"action": "deposit-read|deposit-update|deposit-admin"
}]
"""
with db.session.begin_nested():
for obj in data:
if obj["type"] == "user":
try:
user = get_existing_or_register_user(obj["email"])
except DoesNotExistInLDAP:
raise UpdateDepositPermissionsError(
"User with this mail does not exist in LDAP."
)
if obj["op"] == "add":
try:
self._add_user_permissions(
user, [obj["action"]], db.session
)
except IntegrityError:
raise UpdateDepositPermissionsError(
"Permission already exist."
)
elif obj["op"] == "remove":
try:
self._remove_user_permissions(
user, [obj["action"]], db.session
)
except NoResultFound:
raise UpdateDepositPermissionsError(
"Permission does not exist."
)
elif obj["type"] == "egroup":
try:
role = get_existing_or_register_role(obj["email"])
except DoesNotExistInLDAP:
raise UpdateDepositPermissionsError(
"Egroup with this mail does not exist in LDAP."
)
if obj["op"] == "add":
try:
self._add_egroup_permissions(
role, [obj["action"]], db.session
)
except IntegrityError:
raise UpdateDepositPermissionsError(
"Permission already exist."
)
elif obj["op"] == "remove":
try:
self._remove_egroup_permissions(
role, [obj["action"]], db.session
)
except NoResultFound:
raise UpdateDepositPermissionsError(
"Permission does not exist."
)
self.commit()
return self
@preserve(result=False, fields=PRESERVE_FIELDS)
def clear(self, *args, **kwargs):
"""Clear only drafts."""
super(CAPDeposit, self).clear(*args, **kwargs)
def is_published(self):
"""Check if deposit is published."""
return self["_deposit"].get("pid") is not None
def get_record_metadata(self):
"""Get Record Metadata instance for deposit."""
return RecordMetadata.query.filter_by(id=self.id).one_or_none()
def commit(self, *args, **kwargs):
"""Synchronize files before commit."""
self.files.flush()
# mark as manually edited
if current_user:
self["_user_edited"] = True
return super(CAPDeposit, self).commit(*args, **kwargs)
def _add_user_permissions(self, user, permissions, session):
"""Adds permissions for user for this deposit."""
for permission in permissions:
session.add(
ActionUsers.allow(
DEPOSIT_ACTIONS_NEEDS(self.id)[permission], user=user
)
)
session.flush()
self["_access"][permission]["users"].append(user.id)
def _remove_user_permissions(self, user, permissions, session):
"""Remove permissions for user for this deposit."""
for permission in permissions:
session.delete(
ActionUsers.query.filter(
ActionUsers.action == permission,
ActionUsers.argument == str(self.id),
ActionUsers.user_id == user.id,
).one()
)
session.flush()
self["_access"][permission]["users"].remove(user.id)
def _add_egroup_permissions(self, egroup, permissions, session):
for permission in permissions:
session.add(
ActionRoles.allow(
DEPOSIT_ACTIONS_NEEDS(self.id)[permission], role=egroup
)
)
session.flush()
if egroup.id not in self["_access"][permission]["roles"]:
self["_access"][permission]["roles"].append(egroup.id)
def _remove_egroup_permissions(self, egroup, permissions, session):
for permission in permissions:
session.delete(
ActionRoles.query.filter(
ActionRoles.action == permission,
ActionRoles.argument == str(self.id),
ActionRoles.role_id == egroup.id,
).one()
)
session.flush()
self["_access"][permission]["roles"].remove(egroup.id)
def _add_experiment_permissions(self, experiment, permissions):
"""Add read permissions to everybody assigned to experiment."""
exp_need = exp_need_factory(experiment)
# give read access to members of collaboration
with db.session.begin_nested():
for au in ActionUsers.query_by_action(exp_need).all():
self._add_user_permissions(au.user, permissions, db.session)
for ar in ActionRoles.query_by_action(exp_need).all():
self._add_egroup_permissions(ar.role, permissions, db.session)
def _set_experiment(self):
schema = resolve_schema_by_url(self["$schema"])
self["_experiment"] = schema.experiment
def _create_buckets(self):
bucket = Bucket.create()
RecordsBuckets.create(record=self.model, bucket=bucket)
def validate(self, **kwargs):
"""Validate data using schema with ``JSONResolver``."""
if "$schema" in self and self["$schema"]:
try:
schema = self["$schema"]
if not isinstance(schema, dict):
schema = {"$ref": schema}
resolver = current_app.extensions[
"invenio-records"
].ref_resolver_cls.from_schema(schema)
validator = NoRequiredValidator(schema, resolver=resolver)
errors = []
for err in validator.iter_errors(self):
if (
err.__class__ is UniqueRequiredValidationError
and self["_deposit"]["id"] in err.uuids
):
pass
else:
errors.append(
FieldError(get_error_path(err), str(err.message))
)
if errors:
raise DepositValidationError(None, errors=errors)
except RefResolutionError:
raise DepositValidationError(
"Schema {} not found.".format(self["$schema"])
)
else:
raise DepositValidationError("You need to provide a valid schema.")
def save_file(self, content, filename, size, failed=False):
"""Save file with given content in deposit bucket.
If downloading a content failed, file will be still created,
with tag `failed`.
:param content: stream
:param filename: name that file will be saved with
:param size: size of content
:param failed: if failed during downloading the content
"""
obj = ObjectVersion.create(bucket=self.files.bucket, key=filename)
obj.file = FileInstance.create()
self.files.flush()
if not failed:
self.files[filename].file.set_contents(
content,
default_location=self.files.bucket.location.uri,
size=size,
)
print("File {} saved ({}b).\n".format(filename, size))
else:
ObjectVersionTag.create(
object_version=obj, key="status", value="failed"
)
print("File {} not saved.\n".format(filename))
self.files.flush()
db.session.commit()
return obj
@classmethod
def get_record(cls, id_, with_deleted=False):
"""Get record instance."""
deposit = super(CAPDeposit, cls).get_record(
id_=id_, with_deleted=with_deleted
)
deposit["_files"] = deposit.files.dumps()
return deposit
@classmethod
@index
def create(cls, data, id_=None, owner=current_user):
"""Create a new deposit.
:param data: metadata, need to contain $schema|$ana_type field
:type data: dict
:param id_: specify a UUID to use for the new record, instead of
automatically generated
:type id_: `uuid.UUID`
:param owner: owner of a new deposit (will get all permissions)
:type owner: `invenio_accounts.models.User`
:warn: if user session owner will be automatically current_user
:return: newly created deposit
:rtype: `CAPDeposit`
Process:
* fill deposit metadata based on given data
* initialize the follow internal fields (underscore prefixed):
_experiment: 'experiment_of_given_schema'
_deposit: {
'id': pid_value,
'status': 'draft',
'owners': [owner_id],
'created_by': owner_id
}
_access: {
'deposit-admin': {
'roles': [],
'users': [owner.id]
},
'deposit-update': {
'roles': [],
'users': [owner.id]
},
'deposit-read': {
'roles': [],
'users': [owner.id]
}
}
* validate metadata against given schema (defined by $schema|$ana_type)
* create RecordMetadata instance
* create bucket for storing deposit files
* set owner permissions in the db
* index deposit in elasticsearch
"""
if current_user and current_user.is_authenticated:
owner = current_user
with db.session.begin_nested():
uuid_ = id_ or uuid.uuid4()
data = cls._preprocess_create_data(data, uuid_, owner)
# create RecordMetadata instance
deposit = Record.create(
data, id_=uuid_, validator=NoRequiredValidator
)
deposit.__class__ = cls
# create files bucket
bucket = Bucket.create()
RecordsBuckets.create(record=deposit.model, bucket=bucket)
# give owner permissions to the deposit
if owner:
for permission in DEPOSIT_ACTIONS:
db.session.add(
ActionUsers.allow(
DEPOSIT_ACTIONS_NEEDS(deposit.id)[permission],
user=owner,
)
)
db.session.flush()
return deposit
@classmethod
def _preprocess_create_data(cls, data, uuid_, owner):
"""Preprocess metadata for new deposit.
:param data: metadata, need to contain $schema|$ana_type field
:type data: dict
:param id_: specify a UUID to use for the new record, instead of
automatically generated
:type id_: `uuid.UUID`
:param owner: owner of a new deposit (will get all permissions)
:type owner: `invenio_accounts.models.User`
:returns: processed metadata dictionary
:rtype: dict
"""
if not isinstance(data, dict) or data == {}:
raise DepositValidationError("Empty deposit data.")
if "$ana_type" in data:
try:
ana_type = data.pop("$ana_type")
data["$schema"] = schema_name_to_url(ana_type)
except JSONSchemaNotFound:
raise DepositValidationError(
f"Schema {ana_type} is not a valid deposit schema."
)
elif "$schema" not in data:
raise DepositValidationError("Schema not specified.")
try:
schema = resolve_schema_by_url(data["$schema"])
data["_experiment"] = schema.experiment
except JSONSchemaNotFound:
raise DepositValidationError(
f'Schema {data["$schema"]} is not a valid deposit schema.'
)
_schema = {"$ref": data["$schema"]}
cls.validation(cls, _schema, data)
# minting is done by invenio on POST action preprocessing,
# if method called programatically mint PID here
if "_deposit" not in data:
cls.deposit_minter(uuid_, data, schema=schema)
if owner:
data["_deposit"]["owners"] = [owner.id]
data["_deposit"]["created_by"] = owner.id
data["_access"] = {
permission: {"users": [owner.id], "roles": []}
for permission in DEPOSIT_ACTIONS
}
else:
data["_deposit"]["owners"] = []
data["_access"] = copy.deepcopy(EMPTY_ACCESS_OBJECT)
return data
@classmethod
def check_data(
cls, schema=None, current_data=None, submitted_data=None, **kwargs
):
if not any([schema, submitted_data]):
return
validator = get_custom_validator(schema, **kwargs)
errors = []
data = submitted_data
ordered_list = []
error_list = [e for e in validator.iter_errors(submitted_data)]
for err in error_list:
_validator = err.validator
if _validator in CUSTOM_POST_VALIDATORS:
_validator_value = err.validator_value
_order = (
_validator_value["x-cap-order"]
if "x-cap-order" in _validator_value
else 9999
)
ordered_list.append((_order, err))
ordered_list.sort(key=lambda x: x[0])
for field in ordered_list:
err = field[1]
_method = CUSTOM_POST_VALIDATORS[err.validator]
_error, data = _method(err, current_data, data)
if _error:
errors.append(FieldError(get_error_path(err), str(err.message)))
if errors:
raise DepositValidationError(
"You cannot edit this field.", errors=errors
)
return data
def has_changed(error, current, new):
error_path = get_error_path(error)
current_version = get_val_from_path(current, error_path) or None
new_version = get_val_from_path(new, error_path)
if not new_version:
new_version = current_version
if current_version != new_version:
return True, current
else:
return False, new
def copy_to_fields(error, current, new):
data = error.instance
paths = error.validator_value.get("path")
perform_copying_fields(new, data, paths)
return False, new
CUSTOM_POST_VALIDATORS = {
"x-cap-copy": copy_to_fields,
"x-cap-copyto": copy_to_fields,
"x-cap-permission": has_changed,
}