diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/metadata.py | 208 |
1 files changed, 95 insertions, 113 deletions
diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py index e1c4b10..ac6b4c3 100644 --- a/gn3/api/metadata.py +++ b/gn3/api/metadata.py @@ -7,11 +7,8 @@ from flask import jsonify from flask import request from flask import current_app -from pyld import jsonld # type: ignore - from gn3.db.rdf import RDF_PREFIXES -from gn3.db.rdf import (sparql_construct_query, - query_frame_and_compact, +from gn3.db.rdf import (query_frame_and_compact, query_and_compact, query_and_frame) @@ -125,8 +122,7 @@ metadata = Blueprint("metadata", __name__) def datasets(name): """Fetch a dataset's metadata given it's ACCESSION_ID or NAME""" try: - results = sparql_construct_query( - Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -180,15 +176,15 @@ CONSTRUCT { } . FILTER (!regex(str(?predicate), '(classifiedUnder|usesNormalization|contactPoint|hasPlatformInfo|tissueInfo)', 'i')) . FILTER (!regex(str(?platformPred), '(classifiedUnder|geoSeriesId|hasGoTreeValue)', 'i')) . -}""").substitute(prefix=RDF_PREFIXES, name=name), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - frame = { +}""").substitute(prefix=RDF_PREFIXES, name=name) + _context = { "@context": BASE_CONTEXT | DATASET_CONTEXT, "type": "dcat:Dataset", } - return jsonld.compact(jsonld.frame(results, frame), frame) - # The virtuoso server is misconfigured or it isn't running at all + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -200,8 +196,7 @@ def list_datasets_by_group(group): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -241,17 +236,15 @@ CONSTRUCT { } } } -""").substitute(prefix=RDF_PREFIXES, group=group, limit=page_size, offset=page), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - frame = { +""").substitute(prefix=RDF_PREFIXES, group=group, limit=page_size, offset=page) + _context = { "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT, "type": "resultItem", } - return jsonld.compact( - jsonld.frame(results, frame), - frame) - # The virtuoso server is misconfigured or it isn't running at all + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -263,8 +256,7 @@ def search_datasets(term): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -308,16 +300,15 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - return jsonld.frame( - results, { +""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page) + _context = { "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT, "type": "resultItem", - } + } + return query_and_frame( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") ) - # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @@ -330,8 +321,7 @@ def publications(name): name = f"gn:unpublished{name}" else: name = f"pubmed:{name}" - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -341,13 +331,11 @@ CONSTRUCT { ?predicate ?object . FILTER (!regex(str(?predicate), '(hasPubMedId)', 'i')) . } -""").substitute(name=name, prefix=RDF_PREFIXES), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - return jsonld.compact( - results, {"@context": BASE_CONTEXT | PUBLICATION_CONTEXT} +""").substitute(name=name, prefix=RDF_PREFIXES) + return query_and_compact( + _query, {"@context": BASE_CONTEXT | PUBLICATION_CONTEXT}, + current_app.config.get("SPARQL_ENDPOINT") ) - # The virtuoso server is misconfigured or it isn't running at all except (RemoteDisconnected, URLError): return jsonify({}) @@ -359,8 +347,7 @@ def search_publications(term): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -389,10 +376,8 @@ CONSTRUCT { } } } -""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - frame = { +""").substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page) + _context = { "@context": BASE_CONTEXT | SEARCH_CONTEXT | { "dct": "http://purl.org/dc/terms/", "ex": "http://example.org/stuff/1.0/", @@ -409,7 +394,10 @@ CONSTRUCT { "@container": "@index" } } - return jsonld.frame(results, frame) + return query_and_frame( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -420,8 +408,7 @@ def phenotypes(name): try: args = request.args dataset = args.get("dataset", "") - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -454,17 +441,15 @@ CONSTRUCT { FILTER(?type = gnc:Phenotype) . } } -""").substitute(prefix=RDF_PREFIXES, name=name, - dataset=dataset), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - if not results: - return jsonify({}) - frame = { +""").substitute(prefix=RDF_PREFIXES, name=name, dataset=dataset) + _context = { "@context": PHENOTYPE_CONTEXT, "type": "gnc:Phenotype", } - return jsonld.compact(jsonld.frame(results, frame), frame) + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -475,8 +460,7 @@ def fetch_phenotype_by_group(group, name): try: args = request.args dataset = args.get("dataset", "") - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -512,16 +496,15 @@ CONSTRUCT { """).substitute(prefix=RDF_PREFIXES, group=group, name=name, - dataset=dataset), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - if not results: - return jsonify({}) - frame = { + dataset=dataset) + _context = { "@context": PHENOTYPE_CONTEXT, "type": "gnc:Phenotype", } - return jsonld.compact(jsonld.frame(results, frame), frame) + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -530,8 +513,7 @@ CONSTRUCT { def genotypes(name): """Fetch a genotype's metadata given it's name""" try: - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -546,12 +528,8 @@ CONSTRUCT { rdfs:label ?speciesName . } } -""").substitute(prefix=RDF_PREFIXES, name=name), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - if not results: - return jsonify({}) - frame = { +""").substitute(prefix=RDF_PREFIXES, name=name) + _context = { "@context": BASE_CONTEXT | { "rdfs": "http://www.w3.org/2000/01/rdf-schema#", "gnt": "http://genenetwork.org/term/", @@ -575,7 +553,10 @@ CONSTRUCT { }, "type": "gnc:Genotype", } - return jsonld.compact(jsonld.frame(results, frame), frame) + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -587,8 +568,7 @@ def get_gn_genewiki_entries(symbol): args = request.args page = args.get("page", 0) page_size = args.get("per-page", 10) - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -641,10 +621,8 @@ CONSTRUCT { } } """).substitute(prefix=RDF_PREFIXES, symbol=symbol, - limit=page_size, offset=page), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - context = { + limit=page_size, offset=page) + _context = { "@context": BASE_CONTEXT | { "ex": "http://example.org/stuff/1.0/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -667,20 +645,21 @@ CONSTRUCT { }, "type": "gnc:GNWikiEntry" } - return jsonld.compact( - jsonld.frame(results, context), - context) + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) + @metadata.route("/genewikis/ncbi/<symbol>", methods=["GET"]) def get_ncbi_genewiki_entries(symbol): """Fetch the NCBI GeneRIF entries""" try: args = request.args page, page_size = args.get("page", 0), args.get("per-page", 10) - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -732,10 +711,8 @@ CONSTRUCT { } } """).substitute(prefix=RDF_PREFIXES, symbol=symbol, - limit=page_size, offset=page), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - context = { + limit=page_size, offset=page) + _context = { "@context": BASE_CONTEXT | { "ex": "http://example.org/stuff/1.0/", "rdfs": "http://www.w3.org/2000/01/rdf-schema#", @@ -759,9 +736,10 @@ CONSTRUCT { }, "type": "gnc:GNWikiEntry" } - return jsonld.compact( - jsonld.frame(results, context), - context) + return query_frame_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -770,8 +748,7 @@ CONSTRUCT { def list_species(): """List all species""" try: - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -786,10 +763,8 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - return jsonld.compact(results, { +""").substitute(prefix=RDF_PREFIXES) + _context = { "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", @@ -801,16 +776,20 @@ CONSTRUCT { "taxonomicId": "skos:notation", "fullName": "skos:prefLabel", }, - }) + } + return query_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) + @metadata.route("/species/<name>", methods=["GET"]) def fetch_species(name): """Fetch a Single species information""" try: - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -826,10 +805,8 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES, name=name), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - return jsonld.compact(results, { +""").substitute(prefix=RDF_PREFIXES, name=name) + _context = { "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", @@ -841,7 +818,11 @@ CONSTRUCT { "taxonomicId": "skos:notation", "fullName": "skos:prefLabel", }, - }) + } + return query_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) @@ -850,8 +831,7 @@ CONSTRUCT { def groups(): """Fetch the list of groups""" try: - results = sparql_construct_query( - query=Template(""" + _query = Template(""" $prefix CONSTRUCT { @@ -866,10 +846,8 @@ CONSTRUCT { } } -""").substitute(prefix=RDF_PREFIXES), - endpoint=current_app.config.get("SPARQL_ENDPOINT") - ) - return jsonld.compact(results, { +""").substitute(prefix=RDF_PREFIXES) + _context = { "@context": BASE_CONTEXT | { "skos": "http://www.w3.org/2004/02/skos/core#", "gnt": "http://genenetwork.org/term/", @@ -882,7 +860,11 @@ CONSTRUCT { "geneticType": "gnt:geneticType", "fullName": "skos:prefLabel", }, - }) + } + return query_and_compact( + _query, _context, + current_app.config.get("SPARQL_ENDPOINT") + ) except (RemoteDisconnected, URLError): return jsonify({}) |