Remove try ... except clauses around RDF endpoints.

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

1 files changed, 332 insertions, 370 deletions

diff --git a/gn3/api/metadata.py b/gn3/api/metadata.py
index eb42be4..fbdc8f5 100644
--- a/gn3/api/metadata.py
+++ b/gn3/api/metadata.py
@@ -1,11 +1,8 @@
 """API for fetching metadata using an API"""
 from string import Template
-from http.client import RemoteDisconnected
-from urllib.error import URLError
 from pathlib import Path
 
 from flask import Blueprint
-from flask import jsonify
 from flask import request
 from flask import current_app
 
@@ -143,12 +140,11 @@ metadata = Blueprint("metadata", __name__)
 @metadata.route("/datasets/<name>", methods=["GET"])
 def datasets(name):
     """Fetch a dataset's metadata given it's ACCESSION_ID or NAME"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
-	  ?dataset ?predicate ?term ;
+          ?dataset ?predicate ?term ;
                    gnt:usesNormalization ?normalization .
           ?inbredSet rdfs:label ?inbredSetName .
           ?platform ?platformPred  ?platformObject .
@@ -158,7 +154,7 @@ CONSTRUCT {
                         foaf:homepage ?homepage .
           ?type skos:prefLabel ?altName .
 } WHERE {
-	 ?dataset rdf:type dcat:Dataset ;
+        ?dataset rdf:type dcat:Dataset ;
                   ?predicate ?term ;
                   (rdfs:label|dct:identifier|skos:prefLabel) "$name" .
         FILTER (!regex(str(?predicate), '(usesNormalization)', 'i')) .
@@ -192,32 +188,29 @@ CONSTRUCT {
                   ?tissuePred ?tissueObj .
         } .
 }""").substitute(prefix=RDF_PREFIXES, name=name)
-        _context = {
-            "@context": BASE_CONTEXT | DATASET_CONTEXT,
-            "type": "dcat:Dataset",
-        }
-        __result = query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-        return __result | retrieve_dataset_metadata(
-            (Path(
-                current_app.config.get("DATA_DIR")
-            ) / "gn-docs/general/datasets" /
-             Path(__result.get("id", "")).stem).as_posix()
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | DATASET_CONTEXT,
+        "type": "dcat:Dataset",
+    }
+    __result = query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
+    return __result | retrieve_dataset_metadata(
+        (Path(
+            current_app.config.get("DATA_DIR")
+        ) / "gn-docs/general/datasets" /
+         Path(__result.get("id", "")).stem).as_posix()
+    )
 
 
 @metadata.route("/datasets/<group>/list", methods=["GET"])
 def list_datasets_by_group(group):
     """List datasets that belong to a given group"""
-    try:
-        args = request.args
-        page = args.get("page", 0)
-        page_size = args.get("per-page", 10)
-        _query = Template("""
+    args = request.args
+    page = args.get("page", 0)
+    page_size = args.get("per-page", 10)
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -233,7 +226,7 @@ CONSTRUCT {
 } WHERE {
 {
          SELECT ?datasetName ?accessionId ?createTime ?title WHERE {
-	 ?dataset rdf:type dcat:Dataset ;
+         ?dataset rdf:type dcat:Dataset ;
                   rdfs:label ?datasetName .
          ?inbredSet ^skos:member gnc:Set ;
                     ^xkos:classifiedUnder ?dataset ;
@@ -258,26 +251,23 @@ CONSTRUCT {
 }
 }
 """).substitute(prefix=RDF_PREFIXES, group=group, limit=page_size, offset=page)
-        _context = {
-            "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT,
-            "type": "resultItem",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT,
+        "type": "resultItem",
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/datasets/search/<term>", methods=["GET"])
 def search_datasets(term):
     """Search datasets"""
-    try:
-        args = request.args
-        page = args.get("page", 0)
-        page_size = args.get("per-page", 10)
-        _query = Template("""
+    args = request.args
+    page = args.get("page", 0)
+    page_size = args.get("per-page", 10)
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -293,7 +283,8 @@ CONSTRUCT {
           ]
 } WHERE {
 {
-        SELECT DISTINCT ?dataset ?label ?inbredSetName ?datasetType ?title WHERE {
+        SELECT DISTINCT ?dataset ?label ?inbredSetName ?datasetType ?title
+           WHERE {
         ?dataset rdf:type dcat:Dataset ;
                  rdfs:label ?label ;
                  ?datasetPredicate ?datasetObject ;
@@ -308,13 +299,14 @@ CONSTRUCT {
           ?classification ^xkos:classifiedUnder ?dataset ;
                           ^skos:member gnc:DatasetType ;
                           ?typePredicate ?typeName ;
-			  skos:prefLabel ?datasetType .
+                          skos:prefLabel ?datasetType .
         }
     } ORDER BY ?dataset LIMIT $limit OFFSET $offset
 }
 
 {
-        SELECT (COUNT(DISTINCT ?dataset)/$limit+1 AS ?pages) (COUNT(DISTINCT ?dataset) AS ?hits) WHERE {
+        SELECT (COUNT(DISTINCT ?dataset)/$limit+1 AS ?pages)
+            (COUNT(DISTINCT ?dataset) AS ?hits) WHERE {
         ?dataset rdf:type dcat:Dataset ;
                  ?p ?o .
         ?o bif:contains "'$term'" .
@@ -323,27 +315,24 @@ CONSTRUCT {
 
 }
 """).substitute(prefix=RDF_PREFIXES, term=term, limit=page_size, offset=page)
-        _context = {
-                "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT,
-                "type": "resultItem",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | DATASET_SEARCH_CONTEXT,
+        "type": "resultItem",
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/publications/<name>", methods=["GET"])
 def publications(name):
     """Fetch a publication's metadata given it's NAME"""
-    try:
-        if "unpublished" in name:
-            name = f"gn:unpublished{name}"
-        else:
-            name = f"pubmed:{name}"
-        _query = Template("""
+    if "unpublished" in name:
+        name = f"gn:unpublished{name}"
+    else:
+        name = f"pubmed:{name}"
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -354,22 +343,19 @@ CONSTRUCT {
     FILTER (!regex(str(?predicate), '(hasPubMedId)', 'i')) .
 }
 """).substitute(name=name, prefix=RDF_PREFIXES)
-        return query_and_compact(
-            _query, {"@context": BASE_CONTEXT | PUBLICATION_CONTEXT},
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    return query_and_compact(
+        _query, {"@context": BASE_CONTEXT | PUBLICATION_CONTEXT},
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/publications/search/<term>", methods=["GET"])
 def search_publications(term):
     """Search publications"""
-    try:
-        args = request.args
-        page = args.get("page", 0)
-        page_size = args.get("per-page", 10)
-        _query = Template("""
+    args = request.args
+    page = args.get("page", 0)
+    page_size = args.get("per-page", 10)
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -399,38 +385,36 @@ CONSTRUCT {
 }
 }
 """).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/",
-                "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
-                "fabio": "http://purl.org/spar/fabio/",
-                "title": "dct:title",
-                "pubmed": "fabio:hasPubMedId",
-                "currentPage": "ex:currentPage",
-                "url": "rdfs:label",
-            },
-            "type": "resultItem",
-            "paper": {
-                "@type": "fabio:ResearchPaper",
-                "@container": "@index"
-            }
+    _context = {
+        "@context": BASE_CONTEXT | SEARCH_CONTEXT | {
+            "dct": "http://purl.org/dc/terms/",
+            "ex": "http://example.org/stuff/1.0/",
+            "rdfs": "http://www.w3.org/2000/01/rdf-schema#",
+            "fabio": "http://purl.org/spar/fabio/",
+            "title": "dct:title",
+            "pubmed": "fabio:hasPubMedId",
+            "currentPage": "ex:currentPage",
+            "url": "rdfs:label",
+        },
+        "type": "resultItem",
+        "paper": {
+            "@type": "fabio:ResearchPaper",
+            "@container": "@index"
         }
-        return query_and_frame(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    }
+    return query_and_frame(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
+
 
-@metadata.route("/phenotypes/<name>",methods=["GET"])
+@metadata.route("/phenotypes/<name>", methods=["GET"])
 @metadata.route("/phenotypes/<group>/<name>", methods=["GET"])
 def phenotypes(name, group=None):
     """Fetch a phenotype's metadata given it's name"""
-    try:
-        if group:
-            name = f"{group}_{name}"
-        _query = Template("""
+    if group:
+        name = f"{group}_{name}"
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -466,38 +450,35 @@ CONSTRUCT {
               gnt:chr ?chr ;
               gnt:mb ?mb .
         } .
-	OPTIONAL {
-	?dataset rdf:type dcat:Dataset ;
-                 gnt:belongsToGroup ?inbredSet ;
-                 xkos:classifiedUnder gnc:Phenotype ;
-                 rdfs:label ?datasetLabel ;
-		 skos:prefLabel ?datasetName .
-	?type ^skos:member gnc:DatasetType .
-	FILTER(?type = gnc:Phenotype) .
-	}
+         OPTIONAL {
+         ?dataset rdf:type dcat:Dataset ;
+                  gnt:belongsToGroup ?inbredSet ;
+                  xkos:classifiedUnder gnc:Phenotype ;
+                  rdfs:label ?datasetLabel ;
+                  skos:prefLabel ?datasetName .
+         ?type ^skos:member gnc:DatasetType .
+         FILTER(?type = gnc:Phenotype) .
+         }
 }
 """).substitute(prefix=RDF_PREFIXES, name=name)
-        _context = {
-            "@context": PHENOTYPE_CONTEXT,
-            "dataset": {
-                "type": "dcat:Dataset",
-            },
-            "type": "gnc:Phenotype",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": PHENOTYPE_CONTEXT,
+        "dataset": {
+            "type": "dcat:Dataset",
+        },
+        "type": "gnc:Phenotype",
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/genotypes/<name>", methods=["GET"])
 @metadata.route("/genotypes/<dataset>/<name>", methods=["GET"])
 def genotypes(name, dataset=""):
     """Fetch a genotype's metadata given it's name"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -526,52 +507,49 @@ CONSTRUCT {
 }
 """).substitute(prefix=RDF_PREFIXES,
                 name=name, dataset=dataset)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "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",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "prefLabel": "skos:prefLabel",
-                "dcat": "http://www.w3.org/ns/dcat#",
-                "dataset": "dcat:dataset",
-                "mb": "gnt:mb",
-                "mbMm8": "gnt:mbMm8",
-                "mb2016": "gnt:mb2016",
-                "sequence": "gnt:hasSequence",
-                "source": "gnt:hasSource",
-                "species": "gnt:belongsToSpecies",
-                "speciesName": "gnt:shortName",
-                "alternateSource": "gnt:hasAltSourceName",
-                "comments": "rdfs:comments",
-                "group": "gnt:belongsToGroup",
-                "chrNum": {
-                    "@id": "gnt:chrNum",
-                    "@type": "xsd:int",
-                }
-            },
-            "type": "gnc:Genotype",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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",
+            "skos": "http://www.w3.org/2004/02/skos/core#",
+            "prefLabel": "skos:prefLabel",
+            "dcat": "http://www.w3.org/ns/dcat#",
+            "dataset": "dcat:dataset",
+            "mb": "gnt:mb",
+            "mbMm8": "gnt:mbMm8",
+            "mb2016": "gnt:mb2016",
+            "sequence": "gnt:hasSequence",
+            "source": "gnt:hasSource",
+            "species": "gnt:belongsToSpecies",
+            "speciesName": "gnt:shortName",
+            "alternateSource": "gnt:hasAltSourceName",
+            "comments": "rdfs:comments",
+            "group": "gnt:belongsToGroup",
+            "chrNum": {
+                "@id": "gnt:chrNum",
+                "@type": "xsd:int",
+            }
+        },
+        "type": "gnc:Genotype",
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @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)
-        _query = Template("""
+    args = request.args
+    page = args.get("page", 0)
+    page_size = args.get("per-page", 10)
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -588,7 +566,8 @@ CONSTRUCT {
                  ex:currentPage $offset .
 } WHERE {
 {
-    SELECT ?symbol ?comment (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_)
+    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)
@@ -610,7 +589,8 @@ CONSTRUCT {
                       ^dct:creator _:entry .
         } .
         OPTIONAL { _:entry gnt:belongsToCategory ?category . } .
-    } GROUP BY ?comment ?symbol ?createTime ?creator ORDER BY ?createTime LIMIT $limit OFFSET $offset
+    } GROUP BY ?comment ?symbol ?createTime
+      ?creator ORDER BY ?createTime LIMIT $limit OFFSET $offset
 }
 
 {
@@ -625,44 +605,41 @@ CONSTRUCT {
 }
 """).substitute(prefix=RDF_PREFIXES, symbol=symbol,
                 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#",
-                "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"
-                },
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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 query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+        },
+        "type": "gnc:GNWikiEntry"
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @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)
-        _query = Template("""
+    args = request.args
+    page, page_size = args.get("page", 0), args.get("per-page", 10)
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -679,7 +656,8 @@ CONSTRUCT {
                  ex:currentPage $offset .
 } WHERE {
 {
-    SELECT ?symbol ?comment ?geneId (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_)
+    SELECT ?symbol ?comment ?geneId
+         (GROUP_CONCAT(DISTINCT ?speciesName; SEPARATOR='; ') AS ?species_)
         ?createTime ?creator
         (GROUP_CONCAT(DISTINCT ?pubmed; SEPARATOR='; ') AS ?pmids)
         WHERE {
@@ -700,7 +678,8 @@ CONSTRUCT {
         ?investigator foaf:name ?creator ;
                       ^dct:creator _:entry .
         } .
-    } GROUP BY ?comment ?symbol ?createTime ?creator ?geneId ORDER BY ?createTime LIMIT $limit OFFSET $offset
+    } GROUP BY ?comment ?symbol ?createTime ?creator ?geneId
+      ORDER BY ?createTime LIMIT $limit OFFSET $offset
 }
 
 {
@@ -715,43 +694,40 @@ CONSTRUCT {
 }
 """).substitute(prefix=RDF_PREFIXES, symbol=symbol,
                 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#",
-                "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"
-                },
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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 query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+        },
+        "type": "gnc:GNWikiEntry"
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/species", methods=["GET"])
 def list_species():
     """List all species"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -767,32 +743,29 @@ CONSTRUCT {
 
 }
 """).substitute(prefix=RDF_PREFIXES)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "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",
-            },
-        }
-        return query_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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",
+        },
+    }
+    return query_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/species/<name>", methods=["GET"])
 def fetch_species(name):
     """Fetch a Single species information"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -809,32 +782,29 @@ CONSTRUCT {
 
 }
 """).substitute(prefix=RDF_PREFIXES, name=name)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "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",
-            },
-        }
-        return query_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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",
+        },
+    }
+    return query_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/groups", methods=["GET"])
 def groups():
     """Fetch the list of groups"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -850,33 +820,30 @@ CONSTRUCT {
 
 }
 """).substitute(prefix=RDF_PREFIXES)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "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",
-            },
-        }
-        return query_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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",
+        },
+    }
+    return query_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/groups/<name>", methods=["GET"])
 def fetch_group_by_species(name):
     """Fetch the list of groups (I.e. Inbredsets)"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -895,34 +862,31 @@ CONSTRUCT {
 
 }
 """).substitute(prefix=RDF_PREFIXES, name=name)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "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",
-            },
-        }
-        return query_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "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",
+        },
+    }
+    return query_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )
 
 
 @metadata.route("/probesets/<name>", methods=["GET"])
 @metadata.route("/probesets/<dataset>/<name>", methods=["GET"])
 def probesets(name, dataset=""):
     """Fetch a probeset's metadata given it's name"""
-    try:
-        _query = Template("""
+    _query = Template("""
 $prefix
 
 CONSTRUCT {
@@ -975,60 +939,58 @@ CONSTRUCT {
         OPTIONAL {
                 ?inbredSet ^skos:member gnc:Set ;
                            ^gnt:belongsToGroup ?dataset ;
-                	   rdfs:label ?groupName ;
+                           rdfs:label ?groupName ;
                            xkos:generalizes ?species .
                 ?species gnt:shortName ?speciesShortName .
         } .
 }
 """).substitute(prefix=RDF_PREFIXES, name=name, dataset=dataset)
-        _context = {
-            "@context": BASE_CONTEXT | {
-                "alias": "skos:altLabel",
-                "alignID": "gnt:hasAlignID",
-                "blatMbEnd": "gnt:hasBlatMbEnd",
-                "blatMbStart": "gnt:hasBlatMbStart",
-                "blatScore": "gnt:hasBlatScore",
-                "blatSeq": "gnt:hasBlatSeq",
-                "chip": "gnt:hasChip",
-                "chr": "gnt:chr",
-                "chromosome": "gnt:chromosome",
-                "comments": "rdfs:comments",
-                "dct": "http://purl.org/dc/terms/",
-                "description": "dct:description",
-                "geneID": "gnt:hasGeneId",
-                "group": "gnt:belongsToGroup",
-                "dataset": "gnt:belongsToDataset",
-                "tissue": "gnt:hasTissue",
-                "kgID": "gnt:hasKgID",
-                "location": "gnt:location",
-                "mb": "gnt:mb",
-                "name": "rdfs:label",
-                "proteinID": "gnt:hasProteinID",
-                "references": "dct:references",
-                "rgdID": "gnt:hasRgdID",
-                "skos": "http://www.w3.org/2004/02/skos/core#",
-                "species": "gnt:belongsToSpecies",
-                "specificity": "gnt:hasSpecificity",
-                "strand": "gnt:Strand",
-                "strandProbe": "gnt:strandProbe",
-                "symbol": "gnt:geneSymbol",
-                "targetID": "gnt:hasTargetId",
-                "targetRegion": "gnt:targetsRegion",
-                "targetSequence": "gnt:hasTargetSeq",
-                "transcript": "gnt:transcript",
-                "txEnd": "gnt:TxEnd",
-                "txStart": "gnt:TxStart",
-                "unigenID": "gnt:hasUnigenID",
-                "uniprot": "gnt:uniprot",
-            },
-            "probeset": {
-                "type": "gnc:Probeset",
-            },
+    _context = {
+        "@context": BASE_CONTEXT | {
+            "alias": "skos:altLabel",
+            "alignID": "gnt:hasAlignID",
+            "blatMbEnd": "gnt:hasBlatMbEnd",
+            "blatMbStart": "gnt:hasBlatMbStart",
+            "blatScore": "gnt:hasBlatScore",
+            "blatSeq": "gnt:hasBlatSeq",
+            "chip": "gnt:hasChip",
+            "chr": "gnt:chr",
+            "chromosome": "gnt:chromosome",
+            "comments": "rdfs:comments",
+            "dct": "http://purl.org/dc/terms/",
+            "description": "dct:description",
+            "geneID": "gnt:hasGeneId",
+            "group": "gnt:belongsToGroup",
+            "dataset": "gnt:belongsToDataset",
+            "tissue": "gnt:hasTissue",
+            "kgID": "gnt:hasKgID",
+            "location": "gnt:location",
+            "mb": "gnt:mb",
+            "name": "rdfs:label",
+            "proteinID": "gnt:hasProteinID",
+            "references": "dct:references",
+            "rgdID": "gnt:hasRgdID",
+            "skos": "http://www.w3.org/2004/02/skos/core#",
+            "species": "gnt:belongsToSpecies",
+            "specificity": "gnt:hasSpecificity",
+            "strand": "gnt:Strand",
+            "strandProbe": "gnt:strandProbe",
+            "symbol": "gnt:geneSymbol",
+            "targetID": "gnt:hasTargetId",
+            "targetRegion": "gnt:targetsRegion",
+            "targetSequence": "gnt:hasTargetSeq",
+            "transcript": "gnt:transcript",
+            "txEnd": "gnt:TxEnd",
+            "txStart": "gnt:TxStart",
+            "unigenID": "gnt:hasUnigenID",
+            "uniprot": "gnt:uniprot",
+        },
+        "probeset": {
             "type": "gnc:Probeset",
-        }
-        return query_frame_and_compact(
-            _query, _context,
-            current_app.config.get("SPARQL_ENDPOINT")
-        )
-    except (RemoteDisconnected, URLError):
-        return jsonify({})
+        },
+        "type": "gnc:Probeset",
+    }
+    return query_frame_and_compact(
+        _query, _context,
+        current_app.config.get("SPARQL_ENDPOINT")
+    )