Delete duplicate function.

* gn3/api/metadata.py (genotypes): Delete.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 0 insertions, 434 deletions

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index 79c0417..dfedd27 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -1033,437 +1033,3 @@ CONSTRUCT {
         })
     except (RemoteDisconnected, URLError):
         return jsonify({})
-
-
-@metadata.route("/genotypes/<name>", methods=["GET"])
-def genotypes(name):
-    """Fetch a genotype's metadata given it's name"""
-    try:
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-        ?genotype ?predicate ?object .
-        ?species rdfs:label ?speciesName .
-} WHERE {
-        ?genotype rdf:type gnc:Genotype ;
-                  rdfs:label "$name" ;
-                  ?predicate ?object .
-        OPTIONAL {
-            ?species ^xkos:classifiedUnder ?genotype ;
-                      rdfs:label ?speciesName .
-        }
-}
-""").substitute(prefix=RDF_PREFIXES, name=name))
-        results = json.loads(sparql.queryAndConvert().serialize(format="json-ld"))
-        if not results:
-            return jsonify({})
-        frame = {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "gnt": "http://genenetwork.org/term/",
-                "xkos": "http://rdf-vocabulary.ddialliance.org/xkos#",
-                "gnc": "http://genenetwork.org/category/",
-                "xsd": "http://www.w3.org/2001/XMLSchema#",
-                "name": "rdfs:label",
-                "chr": "gnt:chr",
-                "mb": "gnt:mb",
-                "mbMm8": "gnt:mbMm8",
-                "mb2016": "gnt:mb2016",
-                "sequence": "gnt:hasSequence",
-                "source": "gnt:hasSource",
-                "species": "xkos:classifiedUnder",
-                "alternateSource": "gnt:hasAltSourceName",
-                "comments": "rdfs:comments",
-                "chrNum": {
-                    "@id": "gnt:chrNum",
-                    "@type": "xsd:int",
-                }
-            },
-            "type": "gnc:Genotype",
-        }
-        return jsonld.compact(jsonld.frame(results, frame), frame)
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-
-@metadata.route("/genewikis/gn/<symbol>", methods=["GET"])
-def get_gn_genewiki_entries(symbol):
-    """Fetch the GN and NCBI GeneRIF entries"""
-    try:
-        args = request.args
-        page = args.get("page", 0)
-        page_size = args.get("per-page", 10)
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-         ?symbol ex:entries [
-              rdfs:comment ?comment ;
-              ex:species ?species_ ;
-              dct:created ?createTime ;
-              dct:references ?pmids ;
-              dct:creator ?creator ;
-              gnt:belongsToCategory ?categories ;
-         ] .
-         ?symbol rdf:type gnc:GNWikiEntry ;
-                 ex:totalCount ?totalCount ;
-                 ex:currentPage $offset .
-} WHERE {
-{
-    SELECT ?symbol ?comment (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_)
-        ?createTime ?creator
-        (GROUP_CONCAT(DISTINCT ?pubmed; SEPARATOR='; ') AS ?pmids)
-        (GROUP_CONCAT(DISTINCT ?category; SEPARATOR='; ') AS ?categories)
-        WHERE {
-        ?symbol rdfs:label ?label ;
-                rdfs:comment _:entry .
-        ?label bif:contains "'$symbol'" .
-        _:entry rdf:type gnc:GNWikiEntry ;
-                rdfs:comment ?comment .
-        OPTIONAL {
-        ?species ^xkos:classifiedUnder _:entry ;
-                 ^skos:member gnc:Species ;
-                 skos:prefLabel ?speciesName .
-        } .
-        OPTIONAL { _:entry dct:created ?createTime . } .
-        OPTIONAL { _:entry dct:references ?pubmed . } .
-        OPTIONAL {
-        ?investigator foaf:name ?creator ;
-                      ^dct:creator _:entry .
-        } .
-        OPTIONAL { _:entry gnt:belongsToCategory ?category . } .
-    } GROUP BY ?comment ?symbol ?createTime ?creator ORDER BY ?createTime LIMIT $limit OFFSET $offset
-}
-
-{
-        SELECT (COUNT(DISTINCT ?comment)/$limit+1 AS ?totalCount) WHERE {
-        ?symbol rdfs:comment _:entry ;
-                rdfs:label ?label .
-        _:entry rdfs:comment ?comment ;
-                rdf:type gnc:GNWikiEntry .
-        ?label bif:contains "'$symbol'" .
-        }
-}
-}
-""").substitute(prefix=RDF_PREFIXES, symbol=symbol,
-                limit=page_size, offset=page))
-        results = sparql.queryAndConvert()
-        results = json.loads(results.serialize(format="json-ld"))
-        context = {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "ex": "http://example.org/stuff/1.0/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "gnt": "http://genenetwork.org/term/",
-                "gnc": "http://genenetwork.org/category/",
-                "dct": "http://purl.org/dc/terms/",
-                "xsd": "http://www.w3.org/2001/XMLSchema#",
-                "entries": "ex:entries",
-                "comment": "rdfs:comment",
-                "species": "ex:species",
-                "category": 'gnt:belongsToCategory',
-                "author": "dct:creator",
-                "pubmed": "dct:references",
-                "currentPage": "ex:currentPage",
-                "pages": "ex:totalCount",
-                "created": {
-                    "@id": "dct:created",
-                    "@type": "xsd:datetime"
-                },
-            },
-            "type": "gnc:GNWikiEntry"
-        }
-        return jsonld.compact(
-            jsonld.frame(results, context),
-            context)
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-@metadata.route("/genewikis/ncbi/<symbol>", methods=["GET"])
-def get_ncbi_genewiki_entries(symbol):
-    """Fetch the NCBI GeneRIF entries"""
-    try:
-        args = request.args
-        page = args.get("page", 0)
-        page_size = args.get("per-page", 10)
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-         ?symbol ex:entries [
-              rdfs:comment ?comment ;
-              gnt:hasGeneId ?geneId ;
-              ex:species ?species_ ;
-              dct:created ?createTime ;
-              dct:references ?pmids ;
-              dct:creator ?creator ;
-         ] .
-         ?symbol rdf:type gnc:GNWikiEntry ;
-                 ex:totalCount ?totalCount ;
-                 ex:currentPage $offset .
-} WHERE {
-{
-    SELECT ?symbol ?comment ?geneId (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_)
-        ?createTime ?creator
-        (GROUP_CONCAT(DISTINCT ?pubmed; SEPARATOR='; ') AS ?pmids)
-        WHERE {
-        ?symbol rdfs:label ?label ;
-                rdfs:comment _:entry .
-        ?label bif:contains "'$symbol'" .
-        _:entry rdf:type gnc:NCBIWikiEntry ;
-                rdfs:comment ?comment .
-        OPTIONAL {
-        ?species ^xkos:classifiedUnder _:entry ;
-                 ^skos:member gnc:Species ;
-                 skos:prefLabel ?speciesName .
-        } .
-        OPTIONAL { _:entry gnt:hasGeneId ?geneId . } .
-        OPTIONAL { _:entry dct:created ?createTime . } .
-        OPTIONAL { _:entry dct:references ?pubmed . } .
-        OPTIONAL {
-        ?investigator foaf:name ?creator ;
-                      ^dct:creator _:entry .
-        } .
-    } GROUP BY ?comment ?symbol ?createTime ?creator ?geneId ORDER BY ?createTime LIMIT $limit OFFSET $offset
-}
-
-{
-        SELECT (COUNT(DISTINCT ?comment)/$limit+1 AS ?totalCount) WHERE {
-        ?symbol rdfs:comment _:entry ;
-                rdfs:label ?label .
-        _:entry rdfs:comment ?comment ;
-                rdf:type gnc:NCBIWikiEntry .
-        ?label bif:contains "'$symbol'" .
-        }
-}
-}
-""").substitute(prefix=RDF_PREFIXES, symbol=symbol,
-                limit=page_size, offset=page))
-        results = sparql.queryAndConvert()
-        results = json.loads(results.serialize(format="json-ld"))
-        context = {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "ex": "http://example.org/stuff/1.0/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "gnt": "http://genenetwork.org/term/",
-                "gnc": "http://genenetwork.org/category/",
-                "dct": "http://purl.org/dc/terms/",
-                "xsd": "http://www.w3.org/2001/XMLSchema#",
-                "entries": "ex:entries",
-                "comment": "rdfs:comment",
-                "category": 'gnt:belongsToCategory',
-                "author": "dct:creator",
-                "species": "ex:species",
-                "geneId": "gnt:hasGeneId",
-                "pubmed": "dct:references",
-                "currentPage": "ex:currentPage",
-                "pages": "ex:totalCount",
-                "created": {
-                    "@id": "dct:created",
-                    "@type": "xsd:datetime"
-                },
-            },
-            "type": "gnc:GNWikiEntry"
-        }
-        return jsonld.compact(
-            jsonld.frame(results, context),
-            context)
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-
-@metadata.route("/species", methods=["GET"])
-def list_species():
-    """List all species"""
-    try:
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-        ?species ?predicate ?object .
-} WHERE {
-        ?species ^skos:member gnc:Species ;
-                 ?predicate ?object .
-        VALUES ?predicate {
-               rdfs:label skos:prefLabel
-               skos:altLabel gnt:shortName
-               gnt:family skos:notation
-        }
-
-}
-""").substitute(prefix=RDF_PREFIXES))
-        results = sparql.queryAndConvert()
-        results = json.loads(
-            results.serialize(format="json-ld")
-        )
-        return jsonld.compact(results, {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "gnt": "http://genenetwork.org/term/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "name": "rdfs:label",
-                "family": "gnt:family",
-                "shortName": "gnt:shortName",
-                "alternateName": "skos:altLabel",
-                "taxonomicId": "skos:notation",
-                "fullName": "skos:prefLabel",
-            },
-        })
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-@metadata.route("/species/<name>", methods=["GET"])
-def fetch_species(name):
-    """Fetch a Single species information"""
-    try:
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-        ?species ?predicate ?object .
-} WHERE {
-        ?species ^skos:member gnc:Species ;
-                 gnt:shortName "$name" ;
-                 ?predicate ?object .
-        VALUES ?predicate {
-               rdfs:label skos:prefLabel
-               skos:altLabel gnt:shortName
-               gnt:family skos:notation
-        }
-
-}
-""").substitute(prefix=RDF_PREFIXES, name=name))
-        results = sparql.queryAndConvert()
-        results = json.loads(
-            results.serialize(format="json-ld")
-        )
-        return jsonld.compact(results, {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "gnt": "http://genenetwork.org/term/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "name": "rdfs:label",
-                "family": "gnt:family",
-                "shortName": "gnt:shortName",
-                "alternateName": "skos:altLabel",
-                "taxonomicId": "skos:notation",
-                "fullName": "skos:prefLabel",
-            },
-        })
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-
-@metadata.route("/groups", methods=["GET"])
-def groups():
-    """Fetch the list of groups"""
-    try:
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-        ?group ?predicate ?object .
-} WHERE {
-        ?group ^skos:member gnc:Set ;
-                 ?predicate ?object .
-        VALUES ?predicate {
-               rdfs:label skos:prefLabel
-               gnt:geneticType gnt:mappingMethod
-               gnt:code gnt:family
-        }
-
-}
-""").substitute(prefix=RDF_PREFIXES))
-        results = sparql.queryAndConvert()
-        results = json.loads(
-            results.serialize(format="json-ld")
-        )
-        return jsonld.compact(results, {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "gnt": "http://genenetwork.org/term/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "name": "rdfs:label",
-                "family": "gnt:family",
-                "shortName": "gnt:shortName",
-                "code": "gnt:code",
-                "mappingMethod": "gnt:mappingMethod",
-                "geneticType": "gnt:geneticType",
-                "fullName": "skos:prefLabel",
-            },
-        })
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
-
-
-@metadata.route("/groups/<name>", methods=["GET"])
-def fetch_group_by_species(name):
-    """Fetch the list of groups"""
-    try:
-        sparql = SPARQLWrapper(current_app.config.get("SPARQL_ENDPOINT"))
-        sparql.setQuery(Template("""
-$prefix
-
-CONSTRUCT {
-        ?group ?predicate ?object .
-} WHERE {
-        ?species gnt:shortName "$name" ;
-                 ^skos:member gnc:Species .
-        ?group ^skos:member gnc:Set ;
-               xkos:generalizes ?species ;
-               ?predicate ?object .
-        VALUES ?predicate {
-               rdfs:label skos:prefLabel
-               gnt:geneticType gnt:mappingMethod
-               gnt:code gnt:family
-        }
-
-}
-""").substitute(prefix=RDF_PREFIXES, name=name))
-        results = sparql.queryAndConvert()
-        results = json.loads(
-            results.serialize(format="json-ld")
-        )
-        return jsonld.compact(results, {
-            "@context": {
-                "data": "@graph",
-                "type": "@type",
-                "id": "@id",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "gnt": "http://genenetwork.org/term/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "name": "rdfs:label",
-                "family": "gnt:family",
-                "shortName": "gnt:shortName",
-                "code": "gnt:code",
-                "mappingMethod": "gnt:mappingMethod",
-                "geneticType": "gnt:geneticType",
-                "fullName": "skos:prefLabel",
-            },
-        })
-    except (RemoteDisconnected, URLError):
-        return jsonify({})