Merge pull request #84 from hsolbrig/WIndows_bug

Windows bug

.github/workflows/main.yaml

@@ -2,7 +2,6 @@ name: Build
 
 on:
   push:
-    branches: [ master ]
 
 jobs:
   update-requirements:

AUTHORS

@@ -1,4 +1,5 @@
 Alejandro González Hevia <alejandrgh11@gmail.com>
+Ben McAlister <benmcalister@users.noreply.github.com>
 Egon Willighagen <egon.willighagen@gmail.com>
 Harold Solbrig <hsolbri1@MacBook-Pro.local>
 Harold Solbrig <solbrig@earthlink.net>

ChangeLog

@@ -1,6 +1,15 @@
 CHANGES
 =======
 
+* Replace '/' with '\'
+
+v0.8.0
+------
+
+* Point at the correct slurper version
+* Add extra test files (may not be necessary)
+* Fix call to deprecated \`add\_bindings\` method
+* Update to remove dependency on protected method in v 6.0
 * Import the shim into the manifest tester
 * Add miscellaneous testing updates
 * Requirements match Pipenv

Pipfile

@@ -8,12 +8,11 @@ pbr = "*"
 
 [packages]
 chardet = "*"
-rdflib = ">=5.0.0"
 rdflib-shim = "*"
 requests = ">=2.22.0"
 urllib3 = "*"
-ShExJSG = ">=0.8.1"
+ShExJSG = ">=0.8.2"
 CFGraph = ">=0.2.1"
-PyShExC = "==0.9.0"
+PyShExC = "==0.9.1"
 sparqlslurper = ">=0.5.1"
 sparqlwrapper = ">=1.8.5"

pyshex/utils/url_utils.py

@@ -9,10 +9,10 @@ def generate_base(path: str) -> str:
     :param path: file location or url
     :return: file location or url sans actual name
     """
-    if ':' in path:
+    if '://' in path:
         parts = urlparse(path)
         parts_dict = parts._asdict()
         parts_dict['path'] = os.path.split(parts.path)[0] if '/' in parts.path else ''
         return urlunparse(ParseResult(**parts_dict)) + '/'
     else:
-        return (os.path.split(path)[0] if '/' in path else '') + '/'
+        return os.path.split(path)[0].replace('\\', '/') + '/'

requirements.txt

@@ -12,11 +12,10 @@
 
 cfgraph>=0.2.1
 chardet
-pyshexc==0.9.0
+pyshexc==0.9.1
 rdflib-shim
-rdflib>=5.0.0
 requests>=2.22.0
-shexjsg>=0.8.1
+shexjsg>=0.8.2
 sparqlslurper>=0.5.1
 sparqlwrapper>=1.8.5
 urllib3

tests/test_cli/test_evaluate.py

@@ -10,6 +10,7 @@
 from pyshex.user_agent import UserAgent
 from tests import datadir, SKIP_EXTERNAL_URLS, SKIP_EXTERNAL_URLS_MSG
 from tests.test_cli.clitests import CLITestCase, ArgParseExitException
+from tests.utils.web_server_utils import DRUGBANK_SPARQL_URL, is_up, is_down_reason
 
 update_test_files: bool = False
 
@@ -71,13 +72,12 @@ def test_start_predicate(self):
                      failexpected=True)
         self.assertFalse(update_test_files, "Updating test files")
 
-    @unittest.skipIf(SKIP_EXTERNAL_URLS, SKIP_EXTERNAL_URLS_MSG)
+    @unittest.skipIf(not is_up(DRUGBANK_SPARQL_URL), is_down_reason(DRUGBANK_SPARQL_URL))
     def test_sparql_query(self):
         """ Test a sample DrugBank sparql query """
         shex = os.path.join(datadir, 't1.shex')
         sparql = os.path.join(datadir, 't1.sparql')
-        rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
-        self.do_test([rdf, shex, '-sq', sparql], 't1', update_test_file=update_test_files)
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql], 't1', update_test_file=update_test_files)
 
 
 if __name__ == '__main__':

tests/test_cli/test_sparql_options.py

@@ -6,6 +6,8 @@
 from pyshex.shex_evaluator import evaluate_cli
 from tests import datadir, SKIP_EXTERNAL_URLS, SKIP_EXTERNAL_URLS_MSG
 from tests.test_cli.clitests import CLITestCase
+from tests.utils.web_server_utils import FHIRCAT_GRAPHDB_URL, is_up, is_down_reason, DRUGBANK_SPARQL_URL, \
+    DUMONTIER_GRAPHDB_URL
 
 
 def elapsed_filter(txt: str) -> str:
@@ -21,50 +23,51 @@ class SparqlQueryTestCase(CLITestCase):
     def prog_ep(self, argv: List[str]) -> bool:
         return bool(evaluate_cli(argv, prog=self.testprog))
 
+    @unittest.skipIf(not is_up(DRUGBANK_SPARQL_URL), is_down_reason(DRUGBANK_SPARQL_URL))
     def test_sparql_query(self):
         """ Test a sample DrugBank sparql query """
         shex = os.path.join(datadir, 't1.shex')
         sparql = os.path.join(datadir, 't1.sparql')
-        rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
-        self.do_test([rdf, shex, '-sq', sparql], 'dbsparql1')
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql], 'dbsparql1')
 
+    @unittest.skipIf(not is_up(DRUGBANK_SPARQL_URL), is_down_reason(DRUGBANK_SPARQL_URL))
     def test_print_queries(self):
         """ Test a sample DrugBank sparql query printing queries"""
         shex = os.path.join(datadir, 't1.shex')
         sparql = os.path.join(datadir, 't1.sparql')
-        rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
-        self.do_test([rdf, shex, '-sq', sparql, '-ps'], 'dbsparql2', text_filter=elapsed_filter)
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql, '-ps'], 'dbsparql2', text_filter=elapsed_filter)
 
+    @unittest.skipIf(not is_up(DRUGBANK_SPARQL_URL), is_down_reason(DRUGBANK_SPARQL_URL))
     def test_print_results(self):
         """ Test a sample DrugBank sparql query printing results"""
         shex = os.path.join(datadir, 't1.shex')
         sparql = os.path.join(datadir, 't1.sparql')
-        rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
-        self.do_test([rdf, shex, '-sq', sparql, '-pr', "--stopafter", "1"], 'dbsparql3', text_filter=elapsed_filter)
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql, '-pr', "--stopafter", "1"], 'dbsparql3', text_filter=elapsed_filter)
 
+    @unittest.skipIf(not is_up(DRUGBANK_SPARQL_URL), is_down_reason(DRUGBANK_SPARQL_URL))
     def test_named_graph(self):
         """ Test a sample DrugBank using any named graph """
 
         shex = os.path.join(datadir, 't1.shex')
         sparql = os.path.join(datadir, 't1.sparql')
-        rdf = 'http://wifo5-04.informatik.uni-mannheim.de/drugbank/sparql'
         self.maxDiff = None
-        self.do_test([rdf, shex, '-sq', sparql, '-ps', '-gn', "", "-pr"], 'dbsparql4', failexpected=True,
-                     text_filter=elapsed_filter)
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql, '-ps', '-gn', "", "-pr"], 'dbsparql4',
+                     failexpected=True, text_filter=elapsed_filter)
 
         graphid = "<http://identifiers.org/drugbank:>"
-        self.do_test([rdf, shex, '-sq', sparql, '-ps', '-gn', graphid, "-pr"], 'dbsparql5', failexpected=True,
-                     text_filter=elapsed_filter)
+        self.do_test([DRUGBANK_SPARQL_URL, shex, '-sq', sparql, '-ps', '-gn', graphid, "-pr"], 'dbsparql5',
+                     failexpected=True, text_filter=elapsed_filter)
 
+    @unittest.skipIf(not is_up(DUMONTIER_GRAPHDB_URL), is_down_reason(DUMONTIER_GRAPHDB_URL))
     def test_named_graph_types(self):
         """ Test a Drugbank query with named graph in the query """
         shex = os.path.join(datadir, 'schemas', 'biolink-modelnc.shex')
-        rdf = 'http://graphdb.dumontierlab.com/repositories/ncats-red-kg'
         self.maxDiff = None
-        self.do_test([rdf, shex, '-ss', '-gn', '', '-ps', '-pr', '-ut', '-sq',
+        self.do_test([DUMONTIER_GRAPHDB_URL, shex, '-ss', '-gn', '', '-ps', '-pr', '-ut', '-sq',
                       'select ?item where{?item a <http://w3id.org/biolink/vocab/Protein>} LIMIT 20'],
                      'dbsparql6', failexpected=True, text_filter=elapsed_filter)
 
+    @unittest.skipIf(not is_up(FHIRCAT_GRAPHDB_URL), is_down_reason(FHIRCAT_GRAPHDB_URL))
     def test_infer_setting(self):
         """ Test setting infer to False """
 

tests/test_issues/data/wikidata/disease/Q12135.ttl

@@ -1,7 +1,7 @@
 @prefix do: <http://purl.obolibrary.org/obo/DOID_> .
 @prefix doio: <http://identifiers.org/doid/> .
-@prefix ns1: <http://www.wikidata.org/prop/direct-normalized/> .
-@prefix ns2: <http://wikiba.se/ontology#> .
+@prefix ns1: <http://wikiba.se/ontology#> .
+@prefix ns2: <http://www.wikidata.org/prop/direct-normalized/> .
 @prefix p: <http://www.wikidata.org/prop/> .
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <http://schema.org/> .
@@ -52,7 +52,7 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "mentális zavar",
         "penyakit mental",
         "perturbação mental",
-        "psihiski traucējumi",
+        "psihiskie traucējumi",
         "psika malsano",
         "psychische Störung",
         "psychische aandoening",
@@ -109,7 +109,7 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "精神障害",
         "精神障礙",
         "정신 질환" ;
-    schema:dateModified "2021-12-15T09:38:30+00:00"^^xsd:dateTime ;
+    schema:dateModified "2022-01-12T13:37:45+00:00"^^xsd:dateTime ;
     schema:description "Loại bệnh về tinh thần con người",
         "affezione che colpisce il pensiero, i sentimenti o il comportamento di una persona",
         "alteración de los procesos cognitivos y afectivos del desarrollo",
@@ -141,10 +141,10 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "同心理、神經有關嘅疾病",
         "疾病",
         "精神疾患の総称" ;
-    schema:version 1544198221 ;
-    ns2:identifiers 45 ;
-    ns2:sitelinks 108 ;
-    ns2:statements 89 ;
+    schema:version 1561097645 ;
+    ns1:identifiers 47 ;
+    ns1:sitelinks 109 ;
+    ns1:statements 91 ;
     skos:altLabel "Gemütskrankheit",
         "Rối loạn tinh thần",
         "Rối loạn tâm thần",
@@ -169,7 +169,7 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "gangguan jiwa",
         "gangguan mental",
         "gangguan minda",
-        "garīga slimība",
+        "garīgā slimības",
         "maladie mentale",
         "maladie psychiatrique",
         "malaltia mental",
@@ -186,23 +186,26 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "mental hastalık",
         "mental health morbidity",
         "mental illness",
+        "mental illnesses",
         "mental liding",
         "mental morbidity",
         "mental or behavioural disorder",
         "mental ya da davranış bozukluğu",
-        "mentāla slimība",
+        "mentālā slimības",
         "mielenterveyden häiriö",
         "mielenterveyden häiriöt",
         "obsolete mental disorder",
         "penyakit minda",
-        "psihiskie traucējumi",
+        "psihiskā slimības",
         "psihička bolest",
         "psika perturbo",
         "psikiyatrik bozukluk",
         "psikiyatrik hastalık",
         "psychiatric condition",
         "psychiatric disease",
         "psychiatric disorder",
+        "psychiatric disorders",
+        "psychiatric illness",
         "psychiatric morbidity",
         "psychická choroba",
         "psychická nemoc",
@@ -271,12 +274,14 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
         "精神錯亂",
         "精神障礙症" ;
     p:P1014 <http://www.wikidata.org/entity/statement/Q12135-820B9A9C-13D9-44A5-A802-1A6A372F4F42> ;
+    p:P10192 <http://www.wikidata.org/entity/statement/Q12135-aa842932-49be-41c5-c977-7f4900d65751> ;
     p:P1036 <http://www.wikidata.org/entity/statement/Q12135-12129e3d-43ea-4bf9-6345-0577e61808f6> ;
     p:P1051 <http://www.wikidata.org/entity/statement/Q12135-90EF8470-2B5A-47D4-B9C5-C14D32F005A8> ;
     p:P1296 <http://www.wikidata.org/entity/statement/Q12135-193D4239-E18C-481C-A1C1-9D12FDC61055> ;
     p:P1343 <http://www.wikidata.org/entity/statement/Q12135-83f28510-3b3e-4f47-925b-60be5f7b522c>,
         <http://www.wikidata.org/entity/statement/Q12135-84EDF737-087C-49ED-93E9-A927A63F2FEF>,
         <http://www.wikidata.org/entity/statement/Q12135-e169a132-f9b8-400b-9e63-f013bd1502f6> ;
+    p:P1368 <http://www.wikidata.org/entity/statement/Q12135-270c4ab4-46fe-5e37-906a-89665ac85cd6> ;
     p:P1417 <http://www.wikidata.org/entity/statement/Q12135-B8F67DCC-83BD-4DFD-876B-31AA65EF06C6> ;
     p:P1542 <http://www.wikidata.org/entity/statement/Q12135-cbe8d6b4-487a-340f-b52e-620be0722b7e> ;
     p:P1692 <http://www.wikidata.org/entity/statement/Q12135-5EA6E026-77BB-4557-A311-D9E9282BE866>,
@@ -359,27 +364,29 @@ wd:Q12135 rdfs:label "Afiechyd meddwl",
     p:P950 <http://www.wikidata.org/entity/statement/Q12135-dfe86976-9fab-4163-90cc-390e0ffdcfd9> ;
     p:P973 <http://www.wikidata.org/entity/statement/Q12135-0f1d7aab-41b4-fc6a-7b08-f4dd35fcb946> ;
     p:P989 <http://www.wikidata.org/entity/statement/Q12135-71990294-F9D9-4BE8-B123-65C1372DA9CD> ;
-    ns1:P1014 <http://vocab.getty.edu/aat/300055131> ;
-    ns1:P227 <https://d-nb.info/gnd/4047686-8> ;
-    ns1:P2347 <http://www.yso.fi/onto/yso/p990> ;
-    ns1:P244 <https://id.loc.gov/authorities/names/sh85083643> ;
-    ns1:P2581 <http://babelnet.org/rdf/s00027818n> ;
-    ns1:P268 <http://data.bnf.fr/ark:/12148/cb11942041r#about> ;
-    ns1:P3916 <http://vocabularies.unesco.org/thesaurus/concept5463> ;
-    ns1:P486 <http://id.nlm.nih.gov/mesh/D001523> ;
-    ns1:P508 <http://purl.org/bncf/tid/6114> ;
-    ns1:P6366 <http://ma-graph.org/entity/2780875785> ;
-    ns1:P646 <http://g.co/kg/m/04x4r> ;
-    ns1:P672 <http://id.nlm.nih.gov/mesh/F03> ;
-    ns1:P7033 <http://vocabulary.curriculum.edu.au/scot/4979.rdf> ;
-    ns1:P8408 <http://kbpedia.org/kko/rc/PsychologicalAilment> ;
-    ns1:P950 <http://datos.bne.es/resource/XX525721> ;
+    ns2:P1014 <http://vocab.getty.edu/aat/300055131> ;
+    ns2:P227 <https://d-nb.info/gnd/4047686-8> ;
+    ns2:P2347 <http://www.yso.fi/onto/yso/p990> ;
+    ns2:P244 <https://id.loc.gov/authorities/names/sh85083643> ;
+    ns2:P2581 <http://babelnet.org/rdf/s00027818n> ;
+    ns2:P268 <http://data.bnf.fr/ark:/12148/cb11942041r#about> ;
+    ns2:P3916 <http://vocabularies.unesco.org/thesaurus/concept5463> ;
+    ns2:P486 <http://id.nlm.nih.gov/mesh/D001523> ;
+    ns2:P508 <http://purl.org/bncf/tid/6114> ;
+    ns2:P6366 <http://ma-graph.org/entity/2780875785> ;
+    ns2:P646 <http://g.co/kg/m/04x4r> ;
+    ns2:P672 <http://id.nlm.nih.gov/mesh/F03> ;
+    ns2:P7033 <http://vocabulary.curriculum.edu.au/scot/4979.rdf> ;
+    ns2:P8408 <http://kbpedia.org/kko/rc/PsychologicalAilment> ;
+    ns2:P950 <http://datos.bne.es/resource/XX525721> ;
     wdt:P1014 "300055131" ;
+    wdt:P10192 "homoit0001011" ;
     wdt:P1036 "616.89" ;
     wdt:P1051 "12879" ;
     wdt:P1296 "0193785" ;
     wdt:P1343 wd:Q2657718,
         wd:Q602358 ;
+    wdt:P1368 "000075073" ;
     wdt:P1417 "science/mental-disorder" ;
     wdt:P1542 wd:Q944142 ;
     wdt:P1692 "290-299.99",

tests/test_issues/data/wikidata/disease/Q36956.ttl

@@ -113,13 +113,13 @@ wd:Q36956 rdfs:label "Abïl",
         "麻瘋",
         "麻风",
         "한센병" ;
-    schema:dateModified "2021-12-15T09:19:56+00:00"^^xsd:dateTime ;
+    schema:dateModified "2022-01-13T12:44:54+00:00"^^xsd:dateTime ;
     schema:description "Aansteeklike siekte",
-        "Chronic infection caused by bacteria Mycobacteria lepræ and lepromatosis",
         "Enfermidade causadora de feridas e erosões na pele.",
         "Một loại bệnh do vi khuẩn Mycobacterium leprae gây ra.",
         "Zarazna bolest",
         "bakterielle, schwach infektiöse Hautkrankheit mit Nerven- und Knochendegeneration",
+        "chronic infection caused by bacteria Mycobacteria lepræ and lepromatosis",
         "enfermedad bacteriana crónica de la piel y de los nervios de las manos y pies y a veces, del revestimiento de la nariz.",
         "fertőző betegség",
         "infeksjonssykdom forårsaket av lepra-basillen",
@@ -145,10 +145,10 @@ wd:Q36956 rdfs:label "Abïl",
         "ᅟinfekta malsano kaŭzata de bakterio",
         "らい菌の感染によって生じる慢性の疾患",
         "一种慢性传染病" ;
-    schema:version 1544188941 ;
-    ns2:identifiers 54 ;
-    ns2:sitelinks 133 ;
-    ns2:statements 141 ;
+    schema:version 1561621579 ;
+    ns2:identifiers 55 ;
+    ns2:sitelinks 134 ;
+    ns2:statements 142 ;
     skos:altLabel "Aussatz",
         "Aussätzige",
         "Bélpoklosság",
@@ -163,7 +163,6 @@ wd:Q36956 rdfs:label "Abïl",
         "HANSEN DISEASE",
         "Hansen Pēⁿ",
         "Hansen's disease",
-        "Hansen's disease, Leprosy",
         "Hansen-Krankheit",
         "Hansen-kór",
         "Hansenin tauti",
@@ -437,6 +436,7 @@ wd:Q36956 rdfs:label "Abïl",
     p:P8189 <http://www.wikidata.org/entity/statement/Q36956-8AFBCCFF-5A14-4E75-995E-7A029E22E43A> ;
     p:P828 <http://www.wikidata.org/entity/statement/Q36956-c39c29c6-4e60-fbe5-7034-aebf7f53de0d>,
         <http://www.wikidata.org/entity/statement/Q36956-f6d0adcc-4bf5-82ae-45c7-1381069796b8> ;
+    p:P8401 <http://www.wikidata.org/entity/statement/Q36956-f054ca8d-4a8c-4463-deb9-3f0acc514383> ;
     p:P8408 <http://www.wikidata.org/entity/statement/Q36956-80DF6758-66D5-4039-8B01-6FF77A35BBB9> ;
     p:P902 <http://www.wikidata.org/entity/statement/Q36956-D6C93CDA-983A-46B4-AC54-1E69CC8DE99D> ;
     p:P910 <http://www.wikidata.org/entity/statement/Q36956-3CA8A7C7-D284-43C0-BF0F-FE7F4C5D4D1D> ;
@@ -567,6 +567,7 @@ wd:Q36956 rdfs:label "Abïl",
     wdt:P8189 "987007563027805171" ;
     wdt:P828 wd:Q10748967,
         wd:Q155891 ;
+    wdt:P8401 "leprosy" ;
     wdt:P8408 "Leprosy" ;
     wdt:P902 "007983" ;
     wdt:P910 wd:Q7214744 ;