Merge pull request #84 from hsolbrig/WIndows_bug

Windows bug

Author: hsolbrig

.github/workflows/main.yaml

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

.github/workflows/pr-test.yaml

@@ -1,4 +1,5 @@
 Alejandro González Hevia <[email protected]>
+Ben McAlister <[email protected]>
 Egon Willighagen <[email protected]>
 Harold Solbrig <[email protected]>
 Harold Solbrig <[email protected]>

AUTHORS

@@ -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

ChangeLog

@@ -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"

Pipfile

@@ -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('\\', '/') + '/'

pyshex/utils/url_utils.py

@@ -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

requirements.txt

@@ -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/data/earl_report.ttl

@@ -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 """