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Remove openMINDS v3 /v4 adapters now that the KG is on v4 #112

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2 changes: 1 addition & 1 deletion doc/modules.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ openMINDS
modules/openminds_stimulation
modules/openminds_publications

**fairgraph** currently provides the following modules for working with KG v3:
**fairgraph** currently provides the following modules:

:doc:`modules/openminds_core`
covers general origin, location and content of research products.
Expand Down
73 changes: 5 additions & 68 deletions fairgraph/client.py
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Expand Up @@ -19,7 +19,6 @@
# limitations under the License.

from __future__ import annotations
from copy import deepcopy
import os
import logging
from typing import Any, Dict, Iterable, List, Optional, Union, TYPE_CHECKING
Expand All @@ -37,13 +36,7 @@
from openminds.registry import lookup_type

from .errors import AuthenticationError, AuthorizationError, ResourceExistsError
from .utility import (
adapt_namespaces_for_query,
adapt_namespaces_3to4,
adapt_namespaces_4to3,
adapt_type_4to3,
handle_scope_keyword,
)
from .utility import handle_scope_keyword
from .base import OPENMINDS_VERSION

if TYPE_CHECKING:
Expand Down Expand Up @@ -144,7 +137,6 @@ def __init__(
self.cache: Dict[str, JsonLdDocument] = {}
self._query_cache: Dict[str, str] = {}
self.accepted_terms_of_use = False
self._migrated = None
if allow_interactive:
self.user_info()

Expand Down Expand Up @@ -214,30 +206,8 @@ def _check_response(
else:
raise Exception(f"Error: {response.error} {error_context}")
else:
if self.migrated is False:
adapt_namespaces_3to4(response.data)
return response

@property
def migrated(self):
# This is a temporary work-around for use during the transitional period
# from openMINDS v3 to v4 (change of namespace)
if self._migrated is None:
self._migrated = True # to stop the call to _check_response() in instance_from_full_uri from recurring

# This is the released controlled term for "left handedness", which should be accessible to everyone
result = self.instance_from_full_uri(
"https://kg.ebrains.eu/api/instances/92631f2e-fc6e-4122-8015-a0731c67f66c", release_status="released"
)
_type = result["@type"]
if isinstance(_type, list):
_type = _type[0]
if "om-i.org" in _type:
self._migrated = True
else:
self._migrated = False
return self._migrated

def query(
self,
query: Dict[str, Any],
Expand Down Expand Up @@ -289,8 +259,6 @@ def _query(release_status, from_index, size):
)

else:
if self.migrated is False:
query = adapt_namespaces_for_query(query)

def _query(release_status, from_index, size):
response = self._kg_client.queries.test_query(
Expand Down Expand Up @@ -356,9 +324,6 @@ def list(
"""
release_status = handle_scope_keyword(scope, release_status)

if self.migrated is False:
target_type = adapt_type_4to3(target_type)

def _list(release_status, from_index, size):
response = self._kg_client.instances.list(
stage=STAGE_MAP[release_status],
Expand Down Expand Up @@ -419,8 +384,7 @@ def _get_instance(release_status):
error_context = f"_get_instance(release_status={release_status} uri={uri})"
# Normal KG URIs start with https://kg.ebrains.eu/api/instances/ with a UUID
# but for openMINDS controlled terms we may have the openMINDS URI
# of the form https://openminds.ebrains.eu/instances/ageCategory/juvenile (v3)
# or https://openminds.om-i.org/instances/ageCategory/juvenile (v4)
# of the form https://openminds.om-i.org/instances/ageCategory/juvenile
# We use different query methods for these different cases.
kg_namespace = self._kg_client.instances._kg_config.id_namespace
if uri.startswith(kg_namespace):
Expand All @@ -435,16 +399,8 @@ def _get_instance(release_status):
data = None
else:
data = response.data
elif uri.startswith("https://openminds.om-i.org/instances") or uri.startswith(
"https://openminds.ebrains.eu/instances"
):
elif uri.startswith("https://openminds.om-i.org/instances"):
payload = [uri]
if self.migrated:
if uri.startswith("https://openminds.ebrains.eu"):
payload = [uri.replace("ebrains.eu", "om-i.org")]
else:
if uri.startswith("https://openminds.om-i.org"):
payload = [uri.replace("om-i.org", "ebrains.eu")]
response = self._kg_client.instances.get_by_identifiers(
stage=STAGE_MAP[release_status],
payload=payload,
Expand Down Expand Up @@ -491,9 +447,6 @@ def create_new_instance(
raise ValueError("payload contains undefined ids")
if instance_id:
UUID(instance_id)
if self.migrated is False:
data = deepcopy(data)
adapt_namespaces_4to3(data)
if instance_id:
response = self._kg_client.instances.create_new_with_id(
space=space,
Expand All @@ -519,9 +472,6 @@ def update_instance(self, instance_id: str, data: JsonLdDocument) -> JsonLdDocum
data (dict): a JSON-LD document that modifies some or all of the data of the existing instance.
"""
UUID(instance_id)
if self.migrated is False:
data = deepcopy(data)
adapt_namespaces_4to3(data)
response = self._kg_client.instances.contribute_to_partial_replacement(
instance_id=instance_id,
payload=data,
Expand All @@ -546,9 +496,6 @@ def replace_instance(self, instance_id: str, data: JsonLdDocument) -> JsonLdDocu
data (dict): a JSON-LD document that will replace the existing instance.
"""
UUID(instance_id)
if self.migrated is False:
data = deepcopy(data)
adapt_namespaces_4to3(data)
response = self._kg_client.instances.contribute_to_full_replacement(
instance_id=instance_id,
payload=data,
Expand Down Expand Up @@ -746,10 +693,7 @@ def configure_space(self, space_name: Optional[str] = None, types: Optional[List
)
raise Exception(err_msg)
for cls in types:
if self.migrated:
target_type = cls.type_
else:
target_type = adapt_type_4to3(cls.type_)
target_type = cls.type_
result = self._kg_admin_client.assign_type_to_space(space=space_name, target_type=target_type)
if result: # error
raise Exception(f"Unable to assign {cls.__name__} to space {space_name}: {result}")
Expand Down Expand Up @@ -780,26 +724,19 @@ def space_info(
number of instances of each class in the given spaces.
"""
release_status = handle_scope_keyword(scope, release_status)
# todo: if not self.migrated, adapt type before lookup
result = self._kg_client.types.list(space=space_name, stage=STAGE_MAP[release_status])
if result.error:
raise Exception(result.error)
response = {}
for item in result.data:
if self.migrated:
type_iri = item.identifier
else:
type_ = {"@type": item.identifier}
adapt_namespaces_3to4(type_)
type_iri = type_["@type"]
type_iri = item.identifier
try:
cls = lookup_type(type_iri, OPENMINDS_VERSION)
except (KeyError, ValueError) as err:
ignore_list = [
"https://core.kg.ebrains.eu/vocab/type/Bookmark",
"https://core.kg.ebrains.eu/vocab/meta/type/Query",
"https://openminds.om-i.org/types/Query",
"https://openminds.ebrains.eu/core/URL",
"https://openminds.om-i.org/types/URL"
]
if ignore_errors or any(ignore in str(err) for ignore in ignore_list):
Expand Down
3 changes: 1 addition & 2 deletions fairgraph/node.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,6 @@
as_list, # temporary for backwards compatibility (a lot of code imports it from here)
expand_uri,
normalize_data,
types_match,
)

if TYPE_CHECKING:
Expand Down Expand Up @@ -308,7 +307,7 @@ def _normalize_type(data_item):

type_from_data = _get_type_from_data(data)
# check types match
if not types_match(cls.type_, type_from_data):
if cls.type_ != type_from_data:
raise TypeError("type mismatch {} - {}".format(cls.type_, type_from_data))

# normalize data by expanding keys
Expand Down
10 changes: 5 additions & 5 deletions fairgraph/queries.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ class QueryProperty:

Example:
>>> p = QueryProperty(
... "https://openminds.ebrains.eu/vocab/fullName",
... "https://openminds.om-i.org/props/fullName",
... name="full_name",
... filter=Filter("CONTAINS", parameter="name"),
... sorted=True,
Expand Down Expand Up @@ -229,26 +229,26 @@ class Query:

Example:
>>> q = Query(
... node_type="https://openminds.ebrains.eu/core/ModelVersion",
... node_type="https://openminds.om-i.org/types/ModelVersion",
... label="fg-testing-modelversion",
... space="model",
... properties=[
... QueryProperty("@type"),
... QueryProperty(
... "https://openminds.ebrains.eu/vocab/fullName",
... "https://openminds.om-i.org/props/fullName",
... name="vocab:fullName",
... filter=Filter("CONTAINS", parameter="name"),
... sorted=True,
... required=True,
... ),
... QueryProperty(
... "https://openminds.ebrains.eu/vocab/versionIdentifier",
... "https://openminds.om-i.org/props/versionIdentifier",
... name="vocab:versionIdentifier",
... filter=Filter("EQUALS", parameter="version"),
... required=True,
... ),
... QueryProperty(
... "https://openminds.ebrains.eu/vocab/format",
... "https://openminds.om-i.org/props/format",
... name="vocab:format",
... ensure_order=True,
... properties=[
Expand Down
133 changes: 0 additions & 133 deletions fairgraph/utility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,16 +18,11 @@
# limitations under the License.

from __future__ import annotations
from copy import deepcopy
import hashlib
import logging
from typing import Any, Dict, Iterable, List, Optional, Tuple, Union, TYPE_CHECKING
import warnings

from openminds.registry import lookup_type

from .base import OPENMINDS_VERSION

if TYPE_CHECKING:
from .client import KGClient
from .kgobject import KGObject
Expand Down Expand Up @@ -446,134 +441,6 @@ def accepted_terms_of_use(client: KGClient, accept_terms_of_use: bool = False) -
return False


def types_match(a, b):
# temporarily, during the openMINDS transition v3-v4, we allow different namespaces for the types
assert isinstance(a, str), a
assert isinstance(b, str), b
if a == b:
return True
elif a.split("/")[-1] == b.split("/")[-1]:
logger.warning(f"Assuming {a} matches {b} in types_match()")
return True
else:
return False


def _adapt_namespaces(data, adapt_keys, adapt_type, adapt_instance_uri):
if isinstance(data, list):
for item in data:
_adapt_namespaces(item, adapt_keys, adapt_type, adapt_instance_uri)
elif isinstance(data, dict):
# adapt property URIs
old_keys = tuple(data.keys())
new_keys = adapt_keys(old_keys)
for old_key, new_key in zip(old_keys, new_keys):
data[new_key] = data.pop(old_key)
for key, value in data.items():
if key == "@id":
data[key] = adapt_instance_uri(value)
elif isinstance(value, (list, dict)):
_adapt_namespaces(value, adapt_keys, adapt_type, adapt_instance_uri)
# adapt @type URIs
if "@type" in data:
data["@type"] = adapt_type(data["@type"])
else:
pass


def adapt_namespaces_3to4(data):

def adapt_keys_3to4(uri_list):
replacement = ("openminds.ebrains.eu/vocab", "openminds.om-i.org/props")
return (uri.replace(*replacement) for uri in uri_list)

def adapt_type_3to4(uri):
if isinstance(uri, list):
assert len(uri) == 1
uri = uri[0]
return f"https://openminds.om-i.org/types/{uri.split('/')[-1]}"

def adapt_instance_uri_3to4(uri):
if uri.startswith("https://openminds"):
return uri.replace("ebrains.eu", "om-i.org")
else:
return uri

return _adapt_namespaces(data, adapt_keys_3to4, adapt_type_3to4, adapt_instance_uri_3to4)


def adapt_type_4to3(uri):
if isinstance(uri, list):
assert len(uri) == 1
uri = uri[0]
cls = lookup_type(uri, OPENMINDS_VERSION)

if cls.__module__ == "test.test_client":
return cls.type_

module_name = cls.__module__.split(".")[2] # e.g., 'fairgraph.openminds.core.actors.person' -> "core"
module_name = {"controlled_terms": "controlledTerms", "specimen_prep": "specimenPrep"}.get(
module_name, module_name
)
return f"https://openminds.ebrains.eu/{module_name}/{cls.__name__}"


def adapt_namespaces_4to3(data):

def adapt_keys_4to3(uri_list):
replacement = ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab")
return (uri.replace(*replacement) for uri in uri_list)

def adapt_instance_uri_4to3(uri):
if uri.startswith("https://openminds"):
return uri.replace("om-i.org", "ebrains.eu")
else:
return uri

return _adapt_namespaces(data, adapt_keys_4to3, adapt_type_4to3, adapt_instance_uri_4to3)


def adapt_namespaces_for_query(query):
"""Map from v4+ to v3 openMINDS namespace"""

def adapt_path(item_path, replacement):
if isinstance(item_path, str):
return item_path.replace(*replacement)
elif isinstance(item_path, list):
return [adapt_path(part, replacement) for part in item_path]
else:
assert isinstance(item_path, dict)
new_item_path = item_path.copy()
new_item_path["@id"] = item_path["@id"].replace(*replacement)
if "typeFilter" in item_path:
if isinstance(item_path["typeFilter"], list):
new_item_path["typeFilter"] = [
{"@id": adapt_type_4to3(subitem["@id"])} for subitem in item_path["typeFilter"]
]
else:
new_item_path["typeFilter"]["@id"] = adapt_type_4to3(item_path["typeFilter"]["@id"])
return new_item_path

def adapt_structure(structure, replacement):
for item in structure:
item["path"] = adapt_path(item["path"], replacement)
if "structure" in item:
adapt_structure(item["structure"], replacement)

def adapt_filters(structure, replacement):
for item in structure:
if "filter" in item and "value" in item["filter"]:
item["filter"]["value"] = item["filter"]["value"].replace(*replacement)
if "structure" in item:
adapt_filters(item["structure"], replacement)

migrated_query = deepcopy(query)
migrated_query["meta"]["type"] = adapt_type_4to3(migrated_query["meta"]["type"])
adapt_structure(migrated_query["structure"], ("openminds.om-i.org/props", "openminds.ebrains.eu/vocab"))
adapt_filters(migrated_query["structure"], ("openminds.om-i.org/instances", "openminds.ebrains.eu/instances"))
return migrated_query


def initialise_instances(class_list):
"""Cast openMINDS instances to their fairgraph subclass"""
for cls in class_list:
Expand Down
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