From 37bfb934e17cfe9fbc1ce197778cdd55fa37cb59 Mon Sep 17 00:00:00 2001 From: David Habgood Date: Mon, 13 Jan 2025 09:55:39 +1000 Subject: [PATCH] David/geojson for cql items (#320) * feat: ensure /cql and /object endpoints work with GeoJSON; include counts with /cql GeoJSON. * chore: black code * fix: revert incomplete/unnecessary change * fix: add accidentally deleted poetry.lock * fix: caching was not working correctly - key is now being set correctly --- poetry.lock | 1093 +++++++++-------- prez/dependencies.py | 6 +- prez/models/query_params.py | 23 +- .../profiles/prez_default_profiles.ttl | 8 +- prez/renderers/renderer.py | 279 ++++- prez/routers/base_router.py | 7 + prez/routers/custom_endpoints.py | 5 + prez/routers/ogc_features_router.py | 3 +- prez/services/listings.py | 282 +---- prez/services/objects.py | 49 +- prez/services/query_generation/cql.py | 17 +- tests/test_ogc.py | 12 +- 12 files changed, 977 insertions(+), 807 deletions(-) diff --git a/poetry.lock b/poetry.lock index c9ccae22..1bafa8a1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. +# This file is automatically @generated by Poetry 2.0.0 and should not be changed by hand. 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+groups = ["main"] +markers = "extra == \"server\"" files = [ {file = "uvicorn-0.32.1-py3-none-any.whl", hash = "sha256:82ad92fd58da0d12af7482ecdb5f2470a04c9c9a53ced65b9bbb4a205377602e"}, {file = "uvicorn-0.32.1.tar.gz", hash = "sha256:ee9519c246a72b1c084cea8d3b44ed6026e78a4a309cbedae9c37e4cb9fbb175"}, @@ -2138,13 +2222,14 @@ standard = ["colorama (>=0.4)", "httptools (>=0.6.3)", "python-dotenv (>=0.13)", [[package]] name = "virtualenv" -version = "20.28.0" +version = "20.28.1" description = "Virtual Python Environment builder" optional = false python-versions = ">=3.8" +groups = ["dev"] files = [ - {file = "virtualenv-20.28.0-py3-none-any.whl", hash = "sha256:23eae1b4516ecd610481eda647f3a7c09aea295055337331bb4e6892ecce47b0"}, - {file = "virtualenv-20.28.0.tar.gz", hash = "sha256:2c9c3262bb8e7b87ea801d715fae4495e6032450c71d2309be9550e7364049aa"}, + {file = "virtualenv-20.28.1-py3-none-any.whl", hash = "sha256:412773c85d4dab0409b83ec36f7a6499e72eaf08c80e81e9576bca61831c71cb"}, + {file = 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-2182,6 +2269,6 @@ files = [ server = ["uvicorn"] [metadata] -lock-version = "2.0" +lock-version = "2.1" python-versions = "^3.12" content-hash = "50cc8263f6ea2186ddfca948609a8a13a2de5f74d48f69d260d8f930b3e1a280" diff --git a/prez/dependencies.py b/prez/dependencies.py index b230f386..ed35a6bd 100755 --- a/prez/dependencies.py +++ b/prez/dependencies.py @@ -169,10 +169,10 @@ async def cql_get_parser_dependency( query_params: QueryParams = Depends(), queryable_props: list = Depends(get_queryable_props), ) -> CQLParser: - if query_params.filter: + if query_params._filter: try: crs = query_params.filter_crs - query = json.loads(query_params.filter) + query = json.loads(query_params._filter) cql_parser = CQLParser(cql=query, crs=crs, queryable_props=queryable_props) cql_parser.generate_jsonld() try: @@ -182,7 +182,7 @@ async def cql_get_parser_dependency( return cql_parser except json.JSONDecodeError: raise HTTPException(status_code=400, detail="Invalid JSON format.") - except Exception: + except Exception as e: raise HTTPException( status_code=400, detail="Invalid CQL format: Parsing failed." ) diff --git a/prez/models/query_params.py b/prez/models/query_params.py index a5657d1c..de5021f4 100755 --- a/prez/models/query_params.py +++ b/prez/models/query_params.py @@ -141,22 +141,23 @@ def __init__( ), datetime: Optional[tuple] = Depends(validate_datetime), bbox: List[float] = Depends(reformat_bbox), - filter_lang: FilterLangEnum = Query( + filter_lang: Optional[FilterLangEnum] = Query( default="cql2-json", description="Language of the filter expression", alias="filter-lang", ), - filter_crs: str = Query( + filter_crs: Optional[str] = Query( "http://www.opengis.net/def/crs/OGC/1.3/CRS84", description="CRS used for the filter expression", ), - q: str = Query(None, description="Search query", example="building"), - filter: str = Query( - default=None, - description="CQL JSON expression.", + q: Optional[str] = Query(None, description="Search query", example="building"), + _filter: Optional[str] = Query( + default=None, description="CQL JSON expression.", alias="filter" + ), + order_by: Optional[str] = Query( + default=None, description="Optional: Field to order by" ), - order_by: str = Query(default=None, description="Optional: Field to order by"), - order_by_direction: OrderByDirectionEnum = Query( + order_by_direction: Optional[OrderByDirectionEnum] = Query( default=None, description="Optional: Order direction, must be 'ASC' or 'DESC'", ), @@ -175,15 +176,15 @@ def __init__( self.datetime = datetime self.order_by = order_by self.order_by_direction = order_by_direction - self.filter = filter + self._filter = _filter self.mediatype = mediatype self.subscription_key = subscription_key self.validate_filter() def validate_filter(self): - if self.filter: + if self._filter: try: - json.loads(self.filter) + json.loads(self._filter) except json.JSONDecodeError: raise HTTPException( status_code=400, detail="Filter criteria must be valid JSON." diff --git a/prez/reference_data/profiles/prez_default_profiles.ttl b/prez/reference_data/profiles/prez_default_profiles.ttl index d9c05296..0f923a5b 100644 --- a/prez/reference_data/profiles/prez_default_profiles.ttl +++ b/prez/reference_data/profiles/prez_default_profiles.ttl @@ -63,23 +63,23 @@ PREFIX xsd: - a prof:Profile , prez:ListingProfile; + a prof:Profile , prez:ListingProfile ; dcterms:identifier "cqlgeo"^^xsd:token ; dcterms:description "A CQL profile targeted towards listing CQL results, including geospatial information." ; dcterms:title "CQL Geo profile" ; altr-ext:constrainsClass rdfs:Resource ; altr-ext:hasDefaultResourceFormat "text/anot+turtle" ; - altr-ext:hasResourceFormat "application/ld+json" , + altr-ext:hasResourceFormat "application/geo+json" , "application/ld+json" , "application/anot+ld+json" , "application/rdf+xml" , "text/anot+turtle" , "text/turtle" ; + shext:bnode-depth 2 ; sh:property [ - sh:minCount 0 ; sh:path ( sh:union ( - rdf:type + shext:allPredicateValues ( geo:hasGeometry geo:asWKT ) ) ) diff --git a/prez/renderers/renderer.py b/prez/renderers/renderer.py index c1e8cfae..81b148f9 100755 --- a/prez/renderers/renderer.py +++ b/prez/renderers/renderer.py @@ -2,20 +2,48 @@ import json import logging import time +from datetime import datetime +from typing import Dict, Optional +from urllib.parse import urlencode +from zoneinfo import ZoneInfo +from aiocache import cached +from fastapi import Depends from fastapi import status from fastapi.exceptions import HTTPException from fastapi.responses import StreamingResponse +from httpx import URL from rdf2geojson import convert -from rdflib import RDF, Graph, URIRef +from rdflib import Graph +from rdflib import URIRef +from rdflib.namespace import GEO, RDF +from sparql_grammar_pydantic import ( + IRI, + GraphPatternNotTriples, + GroupGraphPattern, + GroupGraphPatternSub, + OptionalGraphPattern, + TriplesBlock, + TriplesSameSubject, + TriplesSameSubjectPath, + Var, +) +from prez.cache import endpoints_graph_cache from prez.cache import prefix_graph +from prez.config import settings +from prez.dependencies import get_endpoint_uri, get_system_repo, get_url +from prez.models.ogc_features import Collection, Collections, Link, Links, Queryables +from prez.models.query_params import QueryParams +from prez.reference_data.prez_ns import OGCFEAT, ONT, PREZ from prez.renderers.csv_renderer import render_csv_dropdown from prez.renderers.json_renderer import NotFoundError, render_json_dropdown from prez.repositories import Repo from prez.services.annotations import get_annotation_properties -from prez.services.connegp_service import RDF_MEDIATYPES, RDF_SERIALIZER_TYPES_MAP +from prez.services.connegp_service import RDF_MEDIATYPES +from prez.services.connegp_service import RDF_SERIALIZER_TYPES_MAP from prez.services.curie_functions import get_curie_id_for_uri +from prez.services.query_generation.shacl import NodeShape log = logging.getLogger(__name__) @@ -28,6 +56,8 @@ async def return_from_graph( selected_class: URIRef, repo: Repo, system_repo: Repo, + query_params: Optional[QueryParams] = None, + url: str = None, ): profile_headers["Content-Disposition"] = "inline" @@ -66,6 +96,16 @@ async def return_from_graph( elif str(mediatype) == "application/geo+json": geojson = convert(g=graph, do_validate=False, iri2id=get_curie_id_for_uri) + count = None # for an object; no count query. + s_o = graph.subject_objects( + predicate=PREZ["count"] + ) # for a list; graph will contain a count. + for tup in s_o: + str_count = str(tup[1]) + count = get_geojson_int_count(str_count) + headers, geojson = await generate_geojson_extras( + count, geojson, query_params, "application/geo+json", url + ) content = io.BytesIO(json.dumps(geojson).encode("utf-8")) return StreamingResponse(content=content, media_type=mediatype) @@ -87,6 +127,16 @@ async def return_from_graph( ) +def get_geojson_int_count(count_str: str): + if count_str.startswith(">"): + count = int( + count_str[1:] + ) # TODO increment maximum counts based on current page. + else: + count = int(count_str) + return count + + async def return_rdf(graph: Graph, mediatype, profile_headers): RDF_SERIALIZER_TYPES_MAP["text/anot+turtle"] = "turtle" obj = io.BytesIO( @@ -112,3 +162,228 @@ async def return_annotated_rdf( log.debug(f"Time to get annotations: {time.time() - t_start}") # return graph.__iadd__(annotations_graph) return annotations_graph + + +async def generate_geojson_extras( + count, geojson, query_params, selected_mediatype, url +): + all_links = create_self_alt_links(selected_mediatype, url, query_params, count) + all_links_dict = Links(links=all_links).model_dump(exclude_none=True) + link_headers = generate_link_headers(all_links) + geojson["links"] = all_links_dict["links"] + geojson["timeStamp"] = get_brisbane_timestamp() + if count: # listing + geojson["numberMatched"] = count + geojson["numberReturned"] = len(geojson["features"]) + return link_headers, geojson + + +def _add_inbound_triple_pattern_match(construct_tss_list): + triple = (Var(value="inbound_s"), Var(value="inbound_p"), Var(value="focus_node")) + construct_tss_list.append(TriplesSameSubject.from_spo(*triple)) + inbound_tssp_list = [TriplesSameSubjectPath.from_spo(*triple)] + opt_inbound_gpnt = GraphPatternNotTriples( + content=OptionalGraphPattern( + group_graph_pattern=GroupGraphPattern( + content=GroupGraphPatternSub( + triples_block=TriplesBlock.from_tssp_list(inbound_tssp_list) + ) + ) + ) + ) + return opt_inbound_gpnt + + +def create_collections_json( + item_graph, annotations_graph, url, selected_mediatype, query_params, count: str +): + collections_list = [] + for s, p, o in item_graph.triples((None, RDF.type, GEO.FeatureCollection)): + curie_id = get_curie_id_for_uri(s) + collections_list.append( + Collection( + id=curie_id, + title=annotations_graph.value( + subject=s, predicate=PREZ.label, default=None + ), + description=annotations_graph.value( + subject=s, predicate=PREZ.description, default=None + ), + links=[ + Link( + href=URIRef( + f"{settings.system_uri}{url.path}/{curie_id}/items?{urlencode({'_mediatype': mt})}" + ), + rel="items", + type=mt, + ) + for mt in ["application/geo+json", *RDF_MEDIATYPES] + ], + ) + ) + self_alt_links = create_self_alt_links(selected_mediatype, url, query_params, count) + collections = Collections( + collections=collections_list, + links=self_alt_links, + ) + return collections + + +def create_self_alt_links(selected_mediatype, url, query_params=None, count=None): + self_alt_links = [] + for mt in [selected_mediatype, *RDF_MEDIATYPES]: + self_alt_links.append( + Link( + href=URIRef( + f"{settings.system_uri}{url.path}?{urlencode( dict(URL(str(url)).params) | {'_mediatype': mt} )}" + ), + rel="self" if mt == selected_mediatype else "alternate", + type=mt, + title="this document", + ) + ) + if count: # only for listings; add prev/next links + page = query_params.page + limit = query_params.limit + if page != 1: + prev_page = page - 1 + self_alt_links.append( + Link( + href=URIRef( + f"{settings.system_uri}{url.path}?{urlencode({'_mediatype': selected_mediatype, 'page': prev_page, 'limit': limit})}" + ), + rel="prev", + type=selected_mediatype, + title="previous page", + ) + ) + if count > page * limit: + next_page = page + 1 + self_alt_links.append( + Link( + href=URIRef( + f"{settings.system_uri}{url.path}?{urlencode({'_mediatype': selected_mediatype, 'page': next_page, 'limit': limit})}" + ), + rel="next", + type=selected_mediatype, + title="next page", + ) + ) + return self_alt_links + + +def generate_link_headers(links) -> Dict[str, str]: + link_header = ", ".join( + [f'<{link.href}>; rel="{link.rel}"; type="{link.type}"' for link in links] + ) + return {"Link": link_header} + + +async def handle_alt_profile(original_endpoint_type, pmts): + endpoint_nodeshape_map = { + ONT["ObjectEndpoint"]: URIRef("http://example.org/ns#AltProfilesForObject"), + ONT["ListingEndpoint"]: URIRef("http://example.org/ns#AltProfilesForListing"), + } + endpoint_uri = endpoint_nodeshape_map[original_endpoint_type] + endpoint_nodeshape = NodeShape( + uri=endpoint_uri, + graph=endpoints_graph_cache, + kind="endpoint", + focus_node=Var(value="focus_node"), + path_nodes={ + "path_node_1": IRI(value=pmts.selected["class"]) + }, # hack - not sure how (or if) the class can be + # 'dynamicaly' expressed in SHACL. The class is only known at runtime + ) + return endpoint_nodeshape + + +def get_brisbane_timestamp(): + # Get current time in Brisbane + brisbane_time = datetime.now(ZoneInfo("Australia/Brisbane")) + + # Format the timestamp + timestamp = brisbane_time.strftime("%Y-%m-%dT%H:%M:%S%z") + + # Insert colon in timezone offset + return f"{timestamp[:-2]}:{timestamp[-2:]}" + + +# TODO cache this +async def generate_queryables_from_shacl_definition( + url: str = Depends(get_url), + endpoint_uri: URIRef = Depends(get_endpoint_uri), + system_repo: Repo = Depends(get_system_repo), +): + query = """ + PREFIX cql: + PREFIX dcterms: + PREFIX sh: + PREFIX rdf: + CONSTRUCT { + ?queryable cql:id ?id ; + cql:name ?title ; + cql:description ?description ; + cql:datatype ?type ; + cql:enum ?enums . + } + WHERE {?queryable a cql:Queryable ; + dcterms:identifier ?id ; + sh:name ?title ; + sh:description ?description ; + sh:datatype ?type . + OPTIONAL { ?queryable sh:in/rdf:rest*/rdf:first ?enums } + } + """ + g, _ = await system_repo.send_queries([query], []) + if ( + len(g) == 0 + ): # will auto generate queryables from data - less preferable approach + return None + jsonld_string = g.serialize(format="json-ld") + jsonld = json.loads(jsonld_string) + queryable_props = {} + for item in jsonld: + id_value = item["http://www.opengis.net/doc/IS/cql2/1.0/id"][0]["@value"] + queryable_props[id_value] = { + "title": item["http://www.opengis.net/doc/IS/cql2/1.0/name"][0]["@value"], + "type": item["http://www.opengis.net/doc/IS/cql2/1.0/datatype"][0][ + "@id" + ].split("#")[ + -1 + ], # hack + "description": item["http://www.opengis.net/doc/IS/cql2/1.0/description"][ + 0 + ]["@value"], + } + enum = item.get( + "http://www.opengis.net/doc/IS/cql2/1.0/enum" + ) # enums are optional. + if enum: + queryable_props[id_value]["enum"] = [enum_item["@id"] for enum_item in enum] + if endpoint_uri == OGCFEAT["queryables-global"]: + title = "Global Queryables" + description = ( + "Global queryable properties for all collections in the OGC Features API." + ) + else: + title = "Local Queryables" + description = ( + "Local queryable properties for the collection in the OGC Features API." + ) + queryable_params = { + "$id": f"{settings.system_uri}{url.path}", + "title": title, + "description": description, + "properties": queryable_props, + } + return Queryables(**queryable_params) + + +@cached(ttl=600, key_builder=lambda *args, **kwargs: args[1]) # first arg is function; subsequent are actual args. +async def _cached_feature_collection_query( + collection_uri, data_repo, feature_collection_query +): + """cache the feature collection information for 10 minutes as it is an expensive query at present""" + fc_item_graph, _ = await data_repo.send_queries([feature_collection_query], []) + return fc_item_graph \ No newline at end of file diff --git a/prez/routers/base_router.py b/prez/routers/base_router.py index cd8e0195..71515da7 100755 --- a/prez/routers/base_router.py +++ b/prez/routers/base_router.py @@ -12,6 +12,7 @@ get_negotiated_pmts, get_profile_nodeshape, get_system_repo, + get_url, ) from prez.models.query_params import QueryParams from prez.reference_data.prez_ns import EP, OGCE, ONT @@ -68,6 +69,7 @@ async def listings( ), data_repo: Repo = Depends(get_data_repo), system_repo: Repo = Depends(get_system_repo), + url: str = Depends(get_url), ): return await listing_function( data_repo=data_repo, @@ -81,6 +83,7 @@ async def listings( profile_nodeshape=profile_nodeshape, query_params=query_params, original_endpoint_type=ONT["ListingEndpoint"], + url=url, ) @@ -103,6 +106,7 @@ async def cql_post_listings( search_query: ConstructQuery = Depends(generate_search_query), data_repo: Repo = Depends(get_data_repo), system_repo: Repo = Depends(get_system_repo), + url: str = Depends(get_url), ): return await listing_function( data_repo=data_repo, @@ -116,6 +120,7 @@ async def cql_post_listings( profile_nodeshape=profile_nodeshape, query_params=query_params, original_endpoint_type=ONT["ListingEndpoint"], + url=url, ) @@ -143,6 +148,7 @@ async def objects( profile_nodeshape: NodeShape = Depends(get_profile_nodeshape), data_repo: Repo = Depends(get_data_repo), system_repo: Repo = Depends(get_system_repo), + url: str = Depends(get_url), ): return await object_function( data_repo=data_repo, @@ -150,4 +156,5 @@ async def objects( endpoint_structure=endpoint_structure, pmts=pmts, profile_nodeshape=profile_nodeshape, + url=url, ) diff --git a/prez/routers/custom_endpoints.py b/prez/routers/custom_endpoints.py index dac14910..457942e8 100644 --- a/prez/routers/custom_endpoints.py +++ b/prez/routers/custom_endpoints.py @@ -16,6 +16,7 @@ get_negotiated_pmts, get_profile_nodeshape, get_system_repo, + get_url, ) from prez.models.query_params import QueryParams from prez.reference_data.prez_ns import ONT @@ -51,6 +52,7 @@ async def dynamic_list_handler( ), data_repo: Repo = Depends(get_data_repo), system_repo: Repo = Depends(get_system_repo), + url: str = Depends(get_url), ): return await listing_function( data_repo=data_repo, @@ -64,6 +66,7 @@ async def dynamic_list_handler( profile_nodeshape=profile_nodeshape, query_params=query_params, original_endpoint_type=ONT["ListingEndpoint"], + url=url, ) return dynamic_list_handler @@ -75,6 +78,7 @@ async def dynamic_object_handler( profile_nodeshape: NodeShape = Depends(get_profile_nodeshape), data_repo: Repo = Depends(get_data_repo), system_repo: Repo = Depends(get_system_repo), + url: str = Depends(get_url), ): return await object_function( data_repo=data_repo, @@ -82,6 +86,7 @@ async def dynamic_object_handler( endpoint_structure=endpoint_structure, pmts=pmts, profile_nodeshape=profile_nodeshape, + url=url, ) return dynamic_object_handler diff --git a/prez/routers/ogc_features_router.py b/prez/routers/ogc_features_router.py index 9e0a3529..1bc6e912 100755 --- a/prez/routers/ogc_features_router.py +++ b/prez/routers/ogc_features_router.py @@ -31,6 +31,7 @@ from prez.models.ogc_features import OGCFeaturesLandingPage, generate_landing_page_links from prez.models.query_params import QueryParams from prez.reference_data.prez_ns import OGCFEAT +from prez.renderers.renderer import generate_link_headers from prez.repositories import Repo from prez.routers.api_extras_examples import ogc_features_openapi_extras from prez.routers.conformance import router as conformance_router @@ -45,7 +46,7 @@ catch_prefix_not_found_exception, catch_uri_not_found_exception, ) -from prez.services.listings import generate_link_headers, ogc_features_listing_function +from prez.services.listings import ogc_features_listing_function from prez.services.objects import ogc_features_object_function from prez.services.query_generation.cql import CQLParser from prez.services.query_generation.shacl import NodeShape diff --git a/prez/services/listings.py b/prez/services/listings.py index 5d1f2c5b..f22ed564 100755 --- a/prez/services/listings.py +++ b/prez/services/listings.py @@ -2,47 +2,41 @@ import io import json import logging -from datetime import datetime -from typing import Dict -from urllib.parse import urlencode -from zoneinfo import ZoneInfo -from aiocache import cached -from fastapi import Depends from fastapi.responses import PlainTextResponse from rdf2geojson import convert -from rdflib import Literal, URIRef +from rdflib import Literal from rdflib.namespace import GEO, RDF, Namespace from sparql_grammar_pydantic import ( IRI, Bind, Expression, GraphPatternNotTriples, - GroupGraphPattern, - GroupGraphPatternSub, IRIOrFunction, - OptionalGraphPattern, PrimaryExpression, - TriplesBlock, TriplesSameSubject, TriplesSameSubjectPath, Var, ) -from prez.cache import endpoints_graph_cache -from prez.config import settings -from prez.dependencies import get_endpoint_uri, get_system_repo, get_url from prez.enums import NonAnnotatedRDFMediaType -from prez.models.ogc_features import Collection, Collections, Link, Links, Queryables -from prez.reference_data.prez_ns import ALTREXT, OGCFEAT, ONT, PREZ -from prez.renderers.renderer import return_annotated_rdf, return_from_graph -from prez.repositories import Repo -from prez.services.connegp_service import RDF_MEDIATYPES +from prez.reference_data.prez_ns import ALTREXT, OGCFEAT, PREZ +from prez.renderers.renderer import ( + return_annotated_rdf, + return_from_graph, + generate_geojson_extras, + handle_alt_profile, + generate_queryables_from_shacl_definition, + _add_inbound_triple_pattern_match, + _cached_feature_collection_query, + create_collections_json, + generate_link_headers, + get_geojson_int_count, +) from prez.services.curie_functions import get_curie_id_for_uri from prez.services.generate_queryables import generate_queryables_json from prez.services.link_generation import add_prez_links from prez.services.query_generation.count import CountQuery -from prez.services.query_generation.shacl import NodeShape from prez.services.query_generation.umbrella import ( PrezQueryConstructor, merge_listing_query_grammar_inputs, @@ -53,6 +47,14 @@ DWC = Namespace("http://rs.tdwg.org/dwc/terms/") +def _add_geom_triple_pattern_match(tssp_list: list[TriplesSameSubjectPath]): + triples = [ + (Var(value="focus_node"), IRI(value=GEO.hasGeometry), Var(value="bn")), + (Var(value="bn"), IRI(value=GEO.asWKT), Var(value="wkt")), + ] + tssp_list.extend([TriplesSameSubjectPath.from_spo(*triple) for triple in triples]) + + async def listing_function( data_repo, system_repo, @@ -65,6 +67,7 @@ async def listing_function( profile_nodeshape, query_params, original_endpoint_type, + url, ): if ( pmts.selected["profile"] == ALTREXT["alt-profile"] @@ -78,6 +81,11 @@ async def listing_function( concept_hierarchy_query=concept_hierarchy_query, query_params=query_params, ) + if ( + pmts.selected["mediatype"] == "application/geo+json" + ): # Ensure the focus nodes have a geometry in the SPARQL + # subselect. If they are missing, the subsequent GeoJSON conversion will drop any Features without geometries. + _add_geom_triple_pattern_match(subselect_kwargs["inner_select_tssp_list"]) # merge subselect and profile triples same subject (for construct triples) construct_tss_list = [] @@ -113,7 +121,9 @@ async def listing_function( return PlainTextResponse(queries[0], media_type="application/sparql-query") # add a count query if it's an annotated mediatype - if "anot+" in pmts.selected["mediatype"] and not search_query: + if ("anot+" in pmts.selected["mediatype"] and not search_query) or ( + pmts.selected["mediatype"] == "application/geo+json" + ): subselect = copy.deepcopy(main_query.inner_select) count_query = CountQuery(original_subselect=subselect).to_string() queries.append(count_query) @@ -144,6 +154,8 @@ async def listing_function( pmts.selected["class"], data_repo, system_repo, + query_params, + url, ) @@ -285,12 +297,7 @@ async def ogc_features_listing_function( count_g, _ = await data_repo.send_queries([count_query], []) if count_g: count = str(next(iter(count_g.objects()))) - if count.startswith(">"): - count = int( - count[1:] - ) # TODO increment maximum counts based on current page. - else: - count = int(count) + count = get_geojson_int_count(count) if selected_mediatype == "application/json": if endpoint_uri_type[0] in [ @@ -327,227 +334,12 @@ async def ogc_features_listing_function( elif selected_mediatype == "application/geo+json": geojson = convert(g=item_graph, do_validate=False, iri2id=get_curie_id_for_uri) - all_links = create_self_alt_links(selected_mediatype, url, query_params, count) - all_links_dict = Links(links=all_links).model_dump(exclude_none=True) - link_headers = generate_link_headers(all_links) - geojson["links"] = all_links_dict["links"] - geojson["timeStamp"] = get_brisbane_timestamp() - geojson["numberMatched"] = count - geojson["numberReturned"] = len(geojson["features"]) + link_headers, geojson = await generate_geojson_extras( + count, geojson, query_params, selected_mediatype, url + ) content = io.BytesIO(json.dumps(geojson).encode("utf-8")) elif selected_mediatype in NonAnnotatedRDFMediaType: content = io.BytesIO( item_graph.serialize(format=selected_mediatype, encoding="utf-8") ) return content, link_headers - - -def _add_inbound_triple_pattern_match(construct_tss_list): - triple = (Var(value="inbound_s"), Var(value="inbound_p"), Var(value="focus_node")) - construct_tss_list.append(TriplesSameSubject.from_spo(*triple)) - inbound_tssp_list = [TriplesSameSubjectPath.from_spo(*triple)] - opt_inbound_gpnt = GraphPatternNotTriples( - content=OptionalGraphPattern( - group_graph_pattern=GroupGraphPattern( - content=GroupGraphPatternSub( - triples_block=TriplesBlock.from_tssp_list(inbound_tssp_list) - ) - ) - ) - ) - return opt_inbound_gpnt - - -def create_collections_json( - item_graph, annotations_graph, url, selected_mediatype, query_params, count: str -): - collections_list = [] - for s, p, o in item_graph.triples((None, RDF.type, GEO.FeatureCollection)): - curie_id = get_curie_id_for_uri(s) - collections_list.append( - Collection( - id=curie_id, - title=annotations_graph.value( - subject=s, predicate=PREZ.label, default=None - ), - description=annotations_graph.value( - subject=s, predicate=PREZ.description, default=None - ), - links=[ - Link( - href=URIRef( - f"{settings.system_uri}{url.path}/{curie_id}/items?{urlencode({'_mediatype': mt})}" - ), - rel="items", - type=mt, - ) - for mt in ["application/geo+json", *RDF_MEDIATYPES] - ], - ) - ) - self_alt_links = create_self_alt_links(selected_mediatype, url, query_params, count) - collections = Collections( - collections=collections_list, - links=self_alt_links, - ) - return collections - - -def create_self_alt_links(selected_mediatype, url, query_params=None, count=None): - self_alt_links = [] - for mt in [selected_mediatype, *RDF_MEDIATYPES]: - self_alt_links.append( - Link( - href=URIRef( - f"{settings.system_uri}{url.path}?{urlencode({'_mediatype': mt})}" - ), - rel="self" if mt == selected_mediatype else "alternate", - type=mt, - title="this document", - ) - ) - if count: # only for listings; add prev/next links - page = query_params.page - limit = query_params.limit - if page != 1: - prev_page = page - 1 - self_alt_links.append( - Link( - href=URIRef( - f"{settings.system_uri}{url.path}?{urlencode({'_mediatype': selected_mediatype, 'page': prev_page, 'limit': limit})}" - ), - rel="prev", - type=selected_mediatype, - title="previous page", - ) - ) - if count > page * limit: - next_page = page + 1 - self_alt_links.append( - Link( - href=URIRef( - f"{settings.system_uri}{url.path}?{urlencode({'_mediatype': selected_mediatype, 'page': next_page, 'limit': limit})}" - ), - rel="next", - type=selected_mediatype, - title="next page", - ) - ) - return self_alt_links - - -def generate_link_headers(links) -> Dict[str, str]: - link_header = ", ".join( - [f'<{link.href}>; rel="{link.rel}"; type="{link.type}"' for link in links] - ) - return {"Link": link_header} - - -async def handle_alt_profile(original_endpoint_type, pmts): - endpoint_nodeshape_map = { - ONT["ObjectEndpoint"]: URIRef("http://example.org/ns#AltProfilesForObject"), - ONT["ListingEndpoint"]: URIRef("http://example.org/ns#AltProfilesForListing"), - } - endpoint_uri = endpoint_nodeshape_map[original_endpoint_type] - endpoint_nodeshape = NodeShape( - uri=endpoint_uri, - graph=endpoints_graph_cache, - kind="endpoint", - focus_node=Var(value="focus_node"), - path_nodes={ - "path_node_1": IRI(value=pmts.selected["class"]) - }, # hack - not sure how (or if) the class can be - # 'dynamicaly' expressed in SHACL. The class is only known at runtime - ) - return endpoint_nodeshape - - -def get_brisbane_timestamp(): - # Get current time in Brisbane - brisbane_time = datetime.now(ZoneInfo("Australia/Brisbane")) - - # Format the timestamp - timestamp = brisbane_time.strftime("%Y-%m-%dT%H:%M:%S%z") - - # Insert colon in timezone offset - return f"{timestamp[:-2]}:{timestamp[-2:]}" - - -# TODO cache this -async def generate_queryables_from_shacl_definition( - url: str = Depends(get_url), - endpoint_uri: URIRef = Depends(get_endpoint_uri), - system_repo: Repo = Depends(get_system_repo), -): - query = """ - PREFIX cql: - PREFIX dcterms: - PREFIX sh: - PREFIX rdf: - CONSTRUCT { - ?queryable cql:id ?id ; - cql:name ?title ; - cql:description ?description ; - cql:datatype ?type ; - cql:enum ?enums . - } - WHERE {?queryable a cql:Queryable ; - dcterms:identifier ?id ; - sh:name ?title ; - sh:description ?description ; - sh:datatype ?type . - OPTIONAL { ?queryable sh:in/rdf:rest*/rdf:first ?enums } - } - """ - g, _ = await system_repo.send_queries([query], []) - if ( - len(g) == 0 - ): # will auto generate queryables from data - less preferable approach - return None - jsonld_string = g.serialize(format="json-ld") - jsonld = json.loads(jsonld_string) - queryable_props = {} - for item in jsonld: - id_value = item["http://www.opengis.net/doc/IS/cql2/1.0/id"][0]["@value"] - queryable_props[id_value] = { - "title": item["http://www.opengis.net/doc/IS/cql2/1.0/name"][0]["@value"], - "type": item["http://www.opengis.net/doc/IS/cql2/1.0/datatype"][0][ - "@id" - ].split("#")[ - -1 - ], # hack - "description": item["http://www.opengis.net/doc/IS/cql2/1.0/description"][ - 0 - ]["@value"], - } - enum = item.get( - "http://www.opengis.net/doc/IS/cql2/1.0/enum" - ) # enums are optional. - if enum: - queryable_props[id_value]["enum"] = [enum_item["@id"] for enum_item in enum] - if endpoint_uri == OGCFEAT["queryables-global"]: - title = "Global Queryables" - description = ( - "Global queryable properties for all collections in the OGC Features API." - ) - else: - title = "Local Queryables" - description = ( - "Local queryable properties for the collection in the OGC Features API." - ) - queryable_params = { - "$id": f"{settings.system_uri}{url.path}", - "title": title, - "description": description, - "properties": queryable_props, - } - return Queryables(**queryable_params) - - -@cached(ttl=600, key=lambda collection_uri: collection_uri) -async def _cached_feature_collection_query( - collection_uri, data_repo, feature_collection_query -): - """cache the feature collection information for 10 minutes as it is an expensive query at present""" - fc_item_graph, _ = await data_repo.send_queries([feature_collection_query], []) - return fc_item_graph diff --git a/prez/services/objects.py b/prez/services/objects.py index 00248a15..5456ae2b 100755 --- a/prez/services/objects.py +++ b/prez/services/objects.py @@ -21,35 +21,24 @@ from prez.services.connegp_service import RDF_MEDIATYPES from prez.services.curie_functions import get_curie_id_for_uri from prez.services.link_generation import add_prez_links -from prez.services.listings import ( +from prez.renderers.renderer import ( create_self_alt_links, generate_link_headers, get_brisbane_timestamp, - listing_function, ) +from prez.services.listings import listing_function from prez.services.query_generation.umbrella import PrezQueryConstructor log = logging.getLogger(__name__) async def object_function( - data_repo, - system_repo, - endpoint_structure, - pmts, - profile_nodeshape, + data_repo, system_repo, endpoint_structure, pmts, profile_nodeshape, url ): if pmts.selected["profile"] == ALTREXT["alt-profile"]: - none_keys = [ - "endpoint_nodeshape", - "concept_hierarchy_query", - "cql_parser", - "search_query", - ] - none_kwargs = {key: None for key in none_keys} query_params = QueryParams( mediatype=pmts.selected["mediatype"], - filter=None, + _filter=None, q=None, page=1, limit=100, @@ -68,7 +57,11 @@ async def object_function( profile_nodeshape=profile_nodeshape, query_params=query_params, original_endpoint_type=ONT["ObjectEndpoint"], - **none_kwargs, + url=url, + endpoint_nodeshape=None, + concept_hierarchy_query=None, + cql_parser=None, + search_query=None, ) if "anot+" in pmts.selected["mediatype"]: profile_nodeshape.tss_list.append( @@ -84,14 +77,18 @@ async def object_function( construct_tss_list=profile_nodeshape.tss_list, ).to_string() - if pmts.requested_mediatypes and (pmts.requested_mediatypes[0][0] == "application/sparql-query"): + if pmts.requested_mediatypes and ( + pmts.requested_mediatypes[0][0] == "application/sparql-query" + ): return PlainTextResponse(query, media_type="application/sparql-query") query_start_time = time.time() item_graph, _ = await data_repo.send_queries([query], []) log.debug(f"Query time: {time.time() - query_start_time}") if settings.prez_ui_url: # If HTML or no specific media type requested - if pmts.requested_mediatypes and (pmts.requested_mediatypes[0][0] in ("text/html", "*/*")): + if pmts.requested_mediatypes and ( + pmts.requested_mediatypes[0][0] in ("text/html", "*/*") + ): item_uri = URIRef(profile_nodeshape.focus_node.value) await add_prez_links(item_graph, data_repo, endpoint_structure, [item_uri]) prez_link = item_graph.value( @@ -114,6 +111,7 @@ async def object_function( pmts.selected["class"], data_repo, system_repo, + url=url, ) @@ -126,12 +124,12 @@ def create_parent_link(url): async def ogc_features_object_function( - template_queries, - selected_mediatype, - url, - data_repo, - system_repo, - path_params, + template_queries, + selected_mediatype, + url, + data_repo, + system_repo, + path_params, ): collection_uri = path_params.get("collection_uri") feature_uri = path_params.get("feature_uri") @@ -144,7 +142,8 @@ async def ogc_features_object_function( for query in template_queries: queries.append( query.replace( - "VALUES ?focusNode { UNDEF }", f"VALUES ?focusNode {{ {focus_uri.n3()} }}" + "VALUES ?focusNode { UNDEF }", + f"VALUES ?focusNode {{ {focus_uri.n3()} }}", ) ) else: diff --git a/prez/services/query_generation/cql.py b/prez/services/query_generation/cql.py index 62ab7a17..3b39e550 100755 --- a/prez/services/query_generation/cql.py +++ b/prez/services/query_generation/cql.py @@ -92,7 +92,7 @@ def __init__( queryable_props=None, ): self.ggps_inner_select = None - self.inner_select_gpnt_list = None + self.inner_select_gpnt_list: list[GraphPatternNotTriples] = [] self.inner_select_vars: list[Var] = [] self.cql: dict = cql self.cql_json = cql_json @@ -127,12 +127,15 @@ def parse(self): ) self.query_str = self.query_object.to_string() gpotb = self.query_object.where_clause.group_graph_pattern.content - gpnt_list = [ - i - for i in gpotb.graph_patterns_or_triples_blocks - if isinstance(i, GraphPatternNotTriples) - ] - self.inner_select_gpnt_list = gpnt_list + gpnt_list = [] + if gpotb.graph_patterns_or_triples_blocks: + gpnt_list = [ + i + for i in gpotb.graph_patterns_or_triples_blocks + if isinstance(i, GraphPatternNotTriples) + ] + if gpnt_list: + self.inner_select_gpnt_list = gpnt_list def parse_logical_operators( self, element, existing_ggps=None diff --git a/tests/test_ogc.py b/tests/test_ogc.py index a9866195..fd446aa1 100644 --- a/tests/test_ogc.py +++ b/tests/test_ogc.py @@ -66,12 +66,12 @@ def override_get_data_repo(): ), "errorconditions", "feature", - # pytest.param( - # "features", - # marks=pytest.mark.xfail( - # reason="endpoint that causes an error in pytest works manually with the same data in Fuseki" - # ), - # ), + pytest.param( + "features", + marks=pytest.mark.xfail( + reason="endpoint that causes an error in pytest works manually with the same data in Fuseki" + ), + ), "general", "landingpage", ],