Merge pull request #51 from ternaustralia/edmond/entrypoint-update

Add v2 API. Add JSON resource rendering with pagination for properties and their values with JSON profile support

src/linkeddata_api/app.py

@@ -116,10 +116,11 @@ def create_app(config=None) -> Flask:
     app.register_blueprint(oidc_login, url_prefix="/api/oidc")
 
     # register api blueprints
-    from linkeddata_api.views import api_v1, home
+    from linkeddata_api.views import api_v1, api_v2, home
 
     app.register_blueprint(home.bp, url_prefix="/api")
     app.register_blueprint(api_v1.bp, url_prefix="/api/v1.0")
+    app.register_blueprint(api_v2.bp, url_prefix="/api/v2.0")
 
     # setup build_only route so that we can use url_for("root", _external=True) - "root" route required by oidc session login
     # app.add_url_rule("/", "root", build_only=True)

src/linkeddata_api/data/sparql.py

@@ -1,10 +1,8 @@
 import requests
 
 from . import exceptions
-from linkeddata_api.log_time import log_time
 
 
-@log_time
 def post(
     query: str, sparql_endpoint: str, accept: str = "application/sparql-results+json"
 ) -> requests.Response:

src/linkeddata_api/domain/label.py

@@ -3,10 +3,8 @@
 from jinja2 import Template
 
 from linkeddata_api import data
-from linkeddata_api.log_time import log_time
 
 
-@log_time
 def get(
     uri: str,
     sparql_endpoint: str,
@@ -152,7 +150,6 @@ def _get_from_list_query(uris: list[str]) -> str:
     return query
 
 
-@log_time
 def get_from_list(
     uris: list[str],
     sparql_endpoint: str,

src/linkeddata_api/domain/viewer/resource/__init__.py

@@ -9,7 +9,7 @@
 from . import json
 
 
-def _handle_json_response(uri: str, sparql_endpoint: str) -> str:
+def handle_json_response(uri: str, sparql_endpoint: str) -> str:
     try:
         result = json.get(uri, sparql_endpoint)
     except (RequestError, SPARQLNotFoundError, SPARQLResultJSONError) as err:
@@ -18,7 +18,7 @@ def _handle_json_response(uri: str, sparql_endpoint: str) -> str:
     return result.json()
 
 
-def _handle_rdf_response(
+def handle_rdf_response(
     uri: str, sparql_endpoint: str, format_: str, include_incoming_relationships: bool
 ) -> str:
     try:
@@ -56,9 +56,9 @@ def get(
     """
 
     if format_ == "application/json":
-        result = _handle_json_response(uri, sparql_endpoint)
+        result = handle_json_response(uri, sparql_endpoint)
     else:
-        result = _handle_rdf_response(
+        result = handle_rdf_response(
             uri, sparql_endpoint, format_, include_incoming_relationships
         )
     return result

src/linkeddata_api/domain/viewer/resource/json/__init__.py

@@ -11,12 +11,10 @@
 from linkeddata_api.domain.viewer.resource.json.sort_property_objects import (
     sort_property_objects,
 )
-from linkeddata_api.log_time import log_time
 
 logger = logging.getLogger(__name__)
 
 
-@log_time
 def _get_uris_from_rdf_list(uri: str, rows: list, sparql_endpoint: str) -> list[str]:
     new_uris = []
     for row in rows:
@@ -44,7 +42,6 @@ def _get_uris_from_rdf_list(uri: str, rows: list, sparql_endpoint: str) -> list[
     return new_uris
 
 
-@log_time
 def _get_uri_values_and_list_items(
     result: dict, sparql_endpoint: str, uri: Optional[str] = None
 ) -> tuple[list[str], list[str]]:
@@ -70,7 +67,6 @@ def _get_uri_values_and_list_items(
     return uri_values, list_items
 
 
-@log_time
 def _add_rows_for_rdf_list_items(result: dict, uri: str, sparql_endpoint: str) -> dict:
     """Add rdf:List items as new rows to the SPARQL result object
 
@@ -102,17 +98,15 @@ def _add_rows_for_rdf_list_items(result: dict, uri: str, sparql_endpoint: str) -
     return result
 
 
-@log_time
-def _get_uri_label_index(
+def get_uri_label_index(
     result: dict, sparql_endpoint: str, uri: Optional[str] = None
 ) -> dict[str, str]:
     uri_values, _ = _get_uri_values_and_list_items(result, sparql_endpoint, uri)
     uri_label_index = domain.label.get_from_list(uri_values, sparql_endpoint)
     return uri_label_index
 
 
-@log_time
-def _get_uri_internal_index(
+def get_uri_internal_index(
     result: dict, sparql_endpoint: str, uri: Optional[str] = None
 ) -> dict[str, str]:
     uri_values, _ = _get_uri_values_and_list_items(result, sparql_endpoint, uri)
@@ -122,7 +116,6 @@ def _get_uri_internal_index(
     return uri_internal_index
 
 
-@log_time
 def get(uri: str, sparql_endpoint: str) -> domain.schema.Resource:
     query = f"""
         SELECT ?p ?o ?listItem ?listItemNumber
@@ -139,7 +132,7 @@ def get(uri: str, sparql_endpoint: str) -> domain.schema.Resource:
 
     result = _add_rows_for_rdf_list_items(result, uri, sparql_endpoint)
     label = domain.label.get(uri, sparql_endpoint) or uri
-    types, properties = _get_types_and_properties(result, sparql_endpoint, uri)
+    types, properties = get_types_and_properties(result, sparql_endpoint, uri)
 
     profile_uri = ""
     ProfileClass = None
@@ -168,7 +161,6 @@ def get(uri: str, sparql_endpoint: str) -> domain.schema.Resource:
     )
 
 
-@log_time
 def _get_incoming_properties(uri: str, sparql_endpoint: str):
     query = f"""
         SELECT ?p ?o ?listItem ?listItemNumber
@@ -187,8 +179,8 @@ def _get_incoming_properties(uri: str, sparql_endpoint: str):
         sparql_endpoint,
     ).json()
 
-    uri_label_index = _get_uri_label_index(result, sparql_endpoint, uri)
-    uri_internal_index = _get_uri_internal_index(result, sparql_endpoint, uri)
+    uri_label_index = get_uri_label_index(result, sparql_endpoint, uri)
+    uri_internal_index = get_uri_internal_index(result, sparql_endpoint, uri)
 
     incoming_properties = []
 
@@ -231,8 +223,7 @@ def _get_incoming_properties(uri: str, sparql_endpoint: str):
     return incoming_properties
 
 
-@log_time
-def _get_types_and_properties(
+def get_types_and_properties(
     result: dict, sparql_endpoint: str, uri: Optional[str] = None
 ) -> tuple[list[domain.schema.URI], list[domain.schema.PredicateObjects]]:
 
@@ -242,10 +233,10 @@ def _get_types_and_properties(
     ] = defaultdict(set)
 
     # An index of URIs with label values.
-    uri_label_index = _get_uri_label_index(result, sparql_endpoint, uri)
+    uri_label_index = get_uri_label_index(result, sparql_endpoint, uri)
 
     # An index of all the URIs linked to and from this resource that are available internally.
-    uri_internal_index = _get_uri_internal_index(result, sparql_endpoint, uri)
+    uri_internal_index = get_uri_internal_index(result, sparql_endpoint, uri)
 
     if not uri_internal_index.get(uri) and uri is not None:
         raise data.exceptions.SPARQLNotFoundError(f"Resource with URI {uri} not found.")

src/linkeddata_api/domain/viewer/resource/json/profiles/custom_profiles.py

@@ -49,9 +49,9 @@ def _uri(self) -> str:
 
     @staticmethod
     def _process_sparql_values(results: dict) -> list[PredicateObjects]:
-        from linkeddata_api.domain.viewer.resource.json import _get_types_and_properties
+        from linkeddata_api.domain.viewer.resource.json import get_types_and_properties
 
-        _, properties = _get_types_and_properties(
+        _, properties = get_types_and_properties(
             results,
             "https://graphdb.tern.org.au/repositories/dawe_vocabs_core",
         )

src/linkeddata_api/views/api_v2/__init__.py

@@ -0,0 +1,7 @@
+from .blueprint import bp
+
+# import all sub modules with views registered with blueprint
+from . import ontology_viewer
+from . import version_info
+from . import rdf_tools
+from . import viewer

src/linkeddata_api/views/api_v2/blueprint.py

@@ -0,0 +1,3 @@
+from flask_tern.openapi import OpenApiBlueprint
+
+bp = OpenApiBlueprint("api_v2", __name__)

src/linkeddata_api/views/api_v2/ontology_viewer/__init__.py

@@ -0,0 +1 @@
+from . import classes

src/linkeddata_api/views/api_v2/ontology_viewer/classes/__init__.py

@@ -0,0 +1 @@
+from . import flat

src/linkeddata_api/views/api_v2/ontology_viewer/classes/flat/__init__.py

@@ -0,0 +1,18 @@
+from flask import request
+from flask_tern import openapi
+from flask_tern.logging import create_audit_event, log_audit
+
+from linkeddata_api.domain.pydantic_jsonify import jsonify
+from linkeddata_api.views.api_v2.blueprint import bp
+from . import crud
+
+
+@bp.route("/ontology_viewer/classes/flat")
+@openapi.validate(validate_response=False)
+def classes_flat_get():
+    # TODO: add log audit.
+
+    ontology_id = request.args.get("ontology_id")
+    classes = crud.get(ontology_id)
+
+    return jsonify(classes)

src/linkeddata_api/views/api_v2/ontology_viewer/classes/flat/crud.py

@@ -0,0 +1,89 @@
+from typing import List
+
+import requests
+from jinja2 import Template
+from werkzeug.exceptions import HTTPException
+from werkzeug.wrappers import Response
+from flask_tern.cache import cache
+
+from . import schema
+
+
+ontology_id_mapping = {
+    "tern-ontology": {
+        "sparql_endpoint": "https://graphdb.tern.org.au/repositories/knowledge_graph_core",
+        "named_graph": "https://w3id.org/tern/ontologies/tern/",
+    }
+}
+
+
+query_template = Template(
+    """
+# Get a list of classes ordered by label.
+#   Only one string or langString of type "en" is retrieved as label.
+
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX sh: <http://www.w3.org/ns/shacl#>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+
+SELECT distinct ?id (SAMPLE(?_label) as ?label)
+FROM <http://www.ontotext.com/explicit>
+FROM <{{ named_graph }}>
+WHERE {
+    {
+        ?_class a sh:NodeShape .
+        ?_class sh:targetClass ?id .
+
+        FILTER(!isBlank(?id))
+
+        {
+            ?id rdfs:label ?_label .
+        }
+        UNION {
+            ?id skos:prefLabel ?_label .
+        }
+    }
+}
+GROUP BY ?id
+ORDER BY ?label
+"""
+)
+
+
+@cache.memoize()
+def get(ontology_id: str) -> List[schema.ClassItem]:
+    try:
+        mapping = ontology_id_mapping[ontology_id]
+    except KeyError as err:
+        description = f"Unknown ontology ID '{ontology_id}'. Valid ontology IDs: {list(ontology_id_mapping.keys())}"
+        raise HTTPException(
+            description=description, response=Response(description, status=404)
+        ) from err
+
+    query = query_template.render(named_graph=mapping["named_graph"])
+    headers = {
+        "accept": "application/sparql-results+json",
+        "content-type": "application/sparql-query",
+    }
+
+    r = requests.post(
+        url=mapping["sparql_endpoint"], headers=headers, data=query, timeout=60
+    )
+
+    try:
+        r.raise_for_status()
+    except requests.exceptions.HTTPError as err:
+        raise HTTPException(
+            description=err.response.text,
+            response=Response(err.response.text, status=502),
+        ) from err
+
+    resultset = r.json()
+    classes = []
+    for row in resultset["results"]["bindings"]:
+        classes.append(
+            schema.ClassItem(id=row["id"]["value"], label=row["label"]["value"])
+        )
+
+    return classes

src/linkeddata_api/views/api_v2/ontology_viewer/classes/flat/schema.py

@@ -0,0 +1,6 @@
+from pydantic import BaseModel
+
+
+class ClassItem(BaseModel):
+    id: str
+    label: str