From a9a5678be6a572b9a33f08e1d4189e8e45a33017 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Tue, 10 Sep 2024 15:12:52 -0400
Subject: [PATCH 01/10] Issue #116 Option to show bnodes in 'graphic' mode

---
 README.md                                  |  2 +
 onto_tool/command_line.py                  |  3 ++
 onto_tool/onto_tool.py                     |  5 +-
 onto_tool/ontograph.py                     | 38 +++++++++-----
 tests/graphic/issue-116-bnode-subjects.ttl | 14 ++++++
 tests/graphic/issue-116-named-subjects.ttl | 14 ++++++
 tests/graphic/issue-116-ontology.ttl       | 16 ++++++
 tests/graphic/test_bnode_subject.py        | 58 ++++++++++++++++++++++
 8 files changed, 136 insertions(+), 14 deletions(-)
 create mode 100644 tests/graphic/issue-116-bnode-subjects.ttl
 create mode 100644 tests/graphic/issue-116-named-subjects.ttl
 create mode 100644 tests/graphic/issue-116-ontology.ttl
 create mode 100644 tests/graphic/test_bnode_subject.py

diff --git a/README.md b/README.md
index 5c6aece..6ab5f63 100644
--- a/README.md
+++ b/README.md
@@ -188,6 +188,8 @@ optional arguments:
                         Title to use for graph. If not supplied, the repo URI
                         will be used if graphing an endpoint, or 'Gist' if
                         graphing local files.
+  --show-bnode-subjects Use triples with blank nodes in the subject to generate
+                        the graphic.
 
 Sampling Limits:
   --instance-limit INSTANCE_LIMIT
diff --git a/onto_tool/command_line.py b/onto_tool/command_line.py
index e961494..a48aec8 100644
--- a/onto_tool/command_line.py
+++ b/onto_tool/command_line.py
@@ -198,6 +198,9 @@ def define_graphic_parser(subparsers):
         " graphing an endpoint, or 'Gist' if graphing local files.")
     graphic_parser.add_argument('ontology', nargs="*", default=[],
                                 help="Ontology file, directory or name pattern")
+    graphic_parser.add_argument("--show-bnode-subjects", action="store_true",
+                                help="Use triples with blank nodes in the subject to generate "
+                                "the graphic.")
 
 
 def define_export_parser(subparsers):
diff --git a/onto_tool/onto_tool.py b/onto_tool/onto_tool.py
index bfee329..069a51f 100644
--- a/onto_tool/onto_tool.py
+++ b/onto_tool/onto_tool.py
@@ -169,6 +169,8 @@ def generate_graphic(action, onto_files, endpoint, **kwargs):
         Read cached query results
     save_cache: TextIOWrapper
         Save query results as JSON to use with --cache
+    show_bnode_subjects: boolean
+        If true, triples with blank nodes in the subject will be used to generate the graphic
 
     Returns
     -------
@@ -308,7 +310,8 @@ def main(arguments):
                          exclude_pattern=args.exclude_pattern,
                          show_shacl=args.show_shacl,
                          cache=args.cache,
-                         save_cache=args.save_cache)
+                         save_cache=args.save_cache,
+                         show_bnode_subjects=args.show_bnode_subjects)
         return
 
     of = 'pretty-xml' if args.format == 'xml' else args.format
diff --git a/onto_tool/ontograph.py b/onto_tool/ontograph.py
index b7bc896..b4cdb49 100644
--- a/onto_tool/ontograph.py
+++ b/onto_tool/ontograph.py
@@ -84,6 +84,7 @@ def __init__(self, files, repo=None, **kwargs):
 
         self.show_shacl = kwargs.get('show_shacl')
         self.shapes = defaultdict(list)
+        self.show_bnode_subjects = kwargs.get('show_bnode_subjects')
 
     def __configure_data_source(self, repo, kwargs, title, version):
         """Determine graph title and output location from data source."""
@@ -172,7 +173,7 @@ def gather_schema_info_from_files(self):
             ontology = next(graph.subjects(RDF.type, OWL.Ontology))
             ontology_name = self.__strip_uri(ontology)
             classes = [self.__strip_uri(c) for c in graph.subjects(RDF.type, OWL.Class)
-                       if not isinstance(c, BNode)]
+                       if not isinstance(c, BNode) or self.show_bnode_subjects]
             obj_props = [self.__strip_uri(c)
                          for c in graph.subjects(RDF.type, OWL.ObjectProperty)]
             data_props = [self.__strip_uri(c)
@@ -182,8 +183,8 @@ def gather_schema_info_from_files(self):
             all_seen = set(classes + obj_props + data_props + annotation_props)
             gist_things = [
                 self.__strip_uri(s) for (s, o) in graph.subject_objects(RDF.type)
-                if not isinstance(s, BNode) and not s == ontology and not self.__strip_uri(s)
-                in all_seen]
+                if (not isinstance(s, BNode) or self.show_bnode_subjects) and
+                not s == ontology and not self.__strip_uri(s) in all_seen]
             imports = [self.__strip_uri(c)
                        for c in graph.objects(ontology, OWL.imports)]
 
@@ -202,6 +203,7 @@ def gather_schema_info_from_files(self):
     def gather_schema_info_from_repo(self):
         """Load schema data from SPARQL endpoint."""
         onto_data = defaultdict(lambda: defaultdict(list))
+        bnode_filter = "filter(!ISBLANK(?entity))" if not self.show_bnode_subjects else ""
         if self.single_graph:
             onto_query = """
             prefix owl: <http://www.w3.org/2002/07/owl#>
@@ -221,7 +223,7 @@ def gather_schema_info_from_repo(self):
                 {
                   ?entity a ?type .
                   FILTER(?type != owl:Ontology)
-                  filter(!ISBLANK(?entity))
+                  $bnode_filter
                 }
               }
             }
@@ -243,7 +245,7 @@ def gather_schema_info_from_repo(self):
               UNION
               {
                 ?entity rdfs:isDefinedBy ?ontology; a ?type .
-                filter(!ISBLANK(?entity))
+                ?bnode_filter
               }
             }
             """
@@ -254,7 +256,8 @@ def gather_schema_info_from_repo(self):
             str(OWL.AnnotationProperty): 'annotation_propertiesList',
             str(OWL.imports): 'imports'
         }
-        for entity in self.__remote_select_query(onto_query):
+        for entity in self.__remote_select_query(
+                Template(onto_query).substitute(bnode_filter=bnode_filter)):
             key = mapping.get(entity['type'], 'gist_thingsList')
             onto_data[entity['ontology']][key].append(
                 self.__strip_uri(entity['entity']))
@@ -481,6 +484,8 @@ def gather_instance_info(self):
             json.dump(self.cached_data, self.save_cache)
 
     def __build_class_hierarchy(self):
+        bnode_filter = "filter (!isblank(?class) && !isblank(?parent))\n" \
+            if not self.show_bnode_subjects else ""
         inheritance_query = Template("""
         prefix owl: <http://www.w3.org/2002/07/owl#>
         prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
@@ -498,7 +503,7 @@ def __build_class_hierarchy(self):
                     rdf:rest*/rdf:first ?parent .
             ?parent a owl:Class
           }
-          filter (!isblank(?class) && !isblank(?parent))
+          $bnode_filter
           OPTIONAL {
               ?class rdfs:label|skos:prefLabel ?c_label
               FILTER(lang(?c_label) = '$language' || lang(?c_label) = '')
@@ -508,7 +513,7 @@ def __build_class_hierarchy(self):
               FILTER(lang(?p_label) = '$language' || lang(?p_label) = '')
           }
         }
-        """).substitute(language=self.label_lang)
+        """).substitute(bnode_filter=bnode_filter, language=self.label_lang)
         parents = self.__select_query(inheritance_query, 'parents')
 
         for inheritance_info in parents:
@@ -634,6 +639,7 @@ def __add_shacl_coloring(self):
             self.shapes[row['class']].append(row['property'])
 
     def __create_class_count_query(self, limit):
+        bnode_filter = "FILTER(!ISBLANK(?s))" if not self.show_bnode_subjects else ""
         class_query = """
             prefix owl: <http://www.w3.org/2002/07/owl#>
             prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
@@ -646,7 +652,7 @@ def __create_class_count_query(self, limit):
               {
                 select (group_concat(?o;separator=' ') as ?src) where {
                   $pattern
-                  FILTER(!ISBLANK(?s))
+                  $bnode_filter
                   FILTER (!STRSTARTS(STR(?o), 'http://www.w3.org/2002/07/owl#'))
                 } group by ?s LIMIT $limit
               }
@@ -654,10 +660,14 @@ def __create_class_count_query(self, limit):
             """
         query_text = Template(class_query).substitute(
             pattern=self.__filtered_graph_pattern(str(RDF.type)),
+            bnode_filter=bnode_filter,
             limit=limit)
         return query_text
 
     def __create_predicate_query(self, predicate, predicate_type, limit):
+        bnode_filter = "FILTER(!ISBLANK(?s))" if not self.show_bnode_subjects else ""
+        bnode_and_literal_filter = "FILTER(!ISBLANK(?s) && ISLITERAL(?o))" if not self.show_bnode_subjects \
+            else "FILTER(ISLITERAL(?o))"
         if predicate_type == str(OWL.ObjectProperty):
             type_query = """
                 prefix owl: <http://www.w3.org/2002/07/owl#>
@@ -674,7 +684,7 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                         (group_concat(?tgt_c;separator=' ') as ?tgt)
                     where {
                       $pattern
-                      FILTER(!ISBLANK(?s))
+                      $bnode_filter
                       ?s a ?src_c .
                       FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                       ?o a ?tgt_c .
@@ -695,7 +705,7 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                   {
                     select (group_concat(?src_c;separator=' ') as ?src) (SAMPLE(COALESCE(?dtype, xsd:string)) as ?dt) where {
                       $pattern
-                      FILTER(!ISBLANK(?s) && ISLITERAL(?o))
+                      $bnode_and_literal_filter
                       ?s a ?src_c .
                       FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                       BIND(DATATYPE(?o) as ?dtype) .
@@ -724,7 +734,7 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                             select (group_concat(?src_c;separator=' ') as ?src)
                                    (group_concat(?tgt_c;separator=' ') as ?tgt) where {
                               $pattern
-                              FILTER(!ISBLANK(?s))
+                              $bnode_filter
                               ?s a ?src_c .
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/ns/shacl#'))
@@ -742,7 +752,7 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                             select (group_concat(?src_c;separator=' ') as ?src)
                                    (SAMPLE(COALESCE(?dtype, xsd:string)) as ?dt) where {
                               $pattern
-                              FILTER(!ISBLANK(?s) && ISLITERAL(?o))
+                              $bnode_and_literal_filter
                               ?s a ?src_c .
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/ns/shacl#'))
@@ -756,6 +766,8 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                 """
         query_text = Template(type_query).substitute(
             pattern=self.__filtered_graph_pattern(predicate),
+            bnode_filter=bnode_filter,
+            bnode_and_literal_filter=bnode_and_literal_filter,
             limit=limit)
         return query_text
 
diff --git a/tests/graphic/issue-116-bnode-subjects.ttl b/tests/graphic/issue-116-bnode-subjects.ttl
new file mode 100644
index 0000000..c3bfc09
--- /dev/null
+++ b/tests/graphic/issue-116-bnode-subjects.ttl
@@ -0,0 +1,14 @@
+@prefix : <http://example.org/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+
+[] a :Person ;
+    :name "James" ;
+    :residesIn :_Virginia ;
+    .
+[] a :Person ;
+    :name "Betty" ;
+    :residesIn :_Maryland ;
+    .
+
+:_Virginia a :State .
+:_Maryland a :State .
diff --git a/tests/graphic/issue-116-named-subjects.ttl b/tests/graphic/issue-116-named-subjects.ttl
new file mode 100644
index 0000000..b5f18f0
--- /dev/null
+++ b/tests/graphic/issue-116-named-subjects.ttl
@@ -0,0 +1,14 @@
+@prefix : <http://example.org/> .
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+
+:_James a :Person ;
+    :name "James" ;
+    :residesIn :_Virginia ;
+    .
+:_Betty a :Person ;
+    :name "Betty" ;
+    :residesIn :_Maryland ;
+    .
+
+:_Virginia a :State .
+:_Maryland a :State .
diff --git a/tests/graphic/issue-116-ontology.ttl b/tests/graphic/issue-116-ontology.ttl
new file mode 100644
index 0000000..77aeac4
--- /dev/null
+++ b/tests/graphic/issue-116-ontology.ttl
@@ -0,0 +1,16 @@
+@prefix : <http://example.org/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:SmallOnt a owl:Ontology .
+
+:Person a rdfs:Class .
+:State a rdfs:Class .
+:residesIn a owl:ObjectProperty .
+:name a owl:DatatypeProperty .
+
+:Class1 a rdfs:Class .
+:Class2 a rdfs:Class .
+[] a rdfs:Class ;
+    rdfs:subClassOf  :Class1, :Class2 ;
+    rdfs:label "Unnamed Class" .
diff --git a/tests/graphic/test_bnode_subject.py b/tests/graphic/test_bnode_subject.py
new file mode 100644
index 0000000..5383f6b
--- /dev/null
+++ b/tests/graphic/test_bnode_subject.py
@@ -0,0 +1,58 @@
+import os
+from onto_tool import onto_tool
+import pydot
+import re
+
+
+def test_filter_bnode_subjects():
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--data',
+        '-t', 'Blank Node Subjects Filtered',
+        '--no-image',
+        '-o', 'tests-output/graphic/test_filter_bnode_subjects',
+        'tests/graphic/issue-116-bnode-subjects.ttl'
+    ])
+    assert not os.path.isfile('tests-output/graphic/test_filter_bnode_subjects.dot')
+
+
+def test_show_bnode_subjects():
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--data',
+        '--show-bnode-subjects',
+        '-t', 'Blank Node Subjects Shown',
+        '--no-image',
+        '-o', 'tests-output/graphic/test_show_bnode_subjects',
+        'tests/graphic/issue-116-bnode-subjects.ttl',
+        'tests/graphic/issue-116-ontology.ttl'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_show_bnode_subjects.dot')
+    edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
+    assert edges == [('"http://example.org/Person"', '"http://example.org/State"')]
+
+
+def test_show_named_subjects():
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--data',
+        '--show-bnode-subjects',
+        '-t', 'Named Node Subjects',
+        '--no-image',
+        '-o', 'tests-output/graphic/test_named_subjects',
+        'tests/graphic/issue-116-named-subjects.ttl',
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_named_subjects.dot')
+    edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
+    assert edges == [('"http://example.org/Person"', '"http://example.org/State"')]
+
+
+def test_show_ont_bnode_subjects():
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--schema',
+        '--show-bnode-subjects',
+        '-t', 'Ontology Named Node Subjects',
+        '--no-image',
+        '-o', 'tests-output/graphic/test_ont_bnode_subjects',
+        'tests/graphic/issue-116-ontology.ttl',
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_ont_bnode_subjects.dot')
+    label = instance_graph.get_nodes()[1].get("label")
+    assert re.sub(r"n[0-9a-fA-F]{34}", "BNODE_ID", label) == '"{issue-116-ontology.ttl\l\lSmallOnt||residesIn|name||Person\lState\lClass1\lClass2\lBNODE_ID}"'

From 93daf38de74b6c5418c117e48ec63dabdcd05147 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Tue, 17 Sep 2024 14:52:43 -0400
Subject: [PATCH 02/10] Update documentation

---
 onto_tool/command_line.py | 3 +--
 onto_tool/onto_tool.py    | 2 +-
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/onto_tool/command_line.py b/onto_tool/command_line.py
index a48aec8..966e346 100644
--- a/onto_tool/command_line.py
+++ b/onto_tool/command_line.py
@@ -199,8 +199,7 @@ def define_graphic_parser(subparsers):
     graphic_parser.add_argument('ontology', nargs="*", default=[],
                                 help="Ontology file, directory or name pattern")
     graphic_parser.add_argument("--show-bnode-subjects", action="store_true",
-                                help="Use triples with blank nodes in the subject to generate "
-                                "the graphic.")
+                                help="Include blank node subjects when generating a graph.")
 
 
 def define_export_parser(subparsers):
diff --git a/onto_tool/onto_tool.py b/onto_tool/onto_tool.py
index 069a51f..1c0fccd 100644
--- a/onto_tool/onto_tool.py
+++ b/onto_tool/onto_tool.py
@@ -170,7 +170,7 @@ def generate_graphic(action, onto_files, endpoint, **kwargs):
     save_cache: TextIOWrapper
         Save query results as JSON to use with --cache
     show_bnode_subjects: boolean
-        If true, triples with blank nodes in the subject will be used to generate the graphic
+        If true, triples with blank nodes in the subject will not be used to filtered out.
 
     Returns
     -------

From 9b1db07efdd9b8f4db664056856585cc37e655d6 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Tue, 17 Sep 2024 14:57:36 -0400
Subject: [PATCH 03/10] Simplify bnode and literal filtering

---
 onto_tool/ontograph.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/onto_tool/ontograph.py b/onto_tool/ontograph.py
index b4cdb49..54c6c17 100644
--- a/onto_tool/ontograph.py
+++ b/onto_tool/ontograph.py
@@ -666,8 +666,6 @@ def __create_class_count_query(self, limit):
 
     def __create_predicate_query(self, predicate, predicate_type, limit):
         bnode_filter = "FILTER(!ISBLANK(?s))" if not self.show_bnode_subjects else ""
-        bnode_and_literal_filter = "FILTER(!ISBLANK(?s) && ISLITERAL(?o))" if not self.show_bnode_subjects \
-            else "FILTER(ISLITERAL(?o))"
         if predicate_type == str(OWL.ObjectProperty):
             type_query = """
                 prefix owl: <http://www.w3.org/2002/07/owl#>
@@ -705,7 +703,8 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                   {
                     select (group_concat(?src_c;separator=' ') as ?src) (SAMPLE(COALESCE(?dtype, xsd:string)) as ?dt) where {
                       $pattern
-                      $bnode_and_literal_filter
+                      FILTER(ISLITERAL(?o))
+                      $bnode_filter
                       ?s a ?src_c .
                       FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                       BIND(DATATYPE(?o) as ?dtype) .
@@ -752,7 +751,8 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
                             select (group_concat(?src_c;separator=' ') as ?src)
                                    (SAMPLE(COALESCE(?dtype, xsd:string)) as ?dt) where {
                               $pattern
-                              $bnode_and_literal_filter
+                              FILTER(ISLITERAL(?o))
+                              $bnode_filter
                               ?s a ?src_c .
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/2002/07/owl#'))
                               FILTER (!STRSTARTS(STR(?src_c), 'http://www.w3.org/ns/shacl#'))
@@ -767,7 +767,6 @@ def __create_predicate_query(self, predicate, predicate_type, limit):
         query_text = Template(type_query).substitute(
             pattern=self.__filtered_graph_pattern(predicate),
             bnode_filter=bnode_filter,
-            bnode_and_literal_filter=bnode_and_literal_filter,
             limit=limit)
         return query_text
 

From 7cbac385e321e39936c97d43fde9fe71af1b9dfa Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Tue, 17 Sep 2024 15:01:12 -0400
Subject: [PATCH 04/10] Typo in Template variable

---
 onto_tool/ontograph.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/onto_tool/ontograph.py b/onto_tool/ontograph.py
index 54c6c17..8bbb910 100644
--- a/onto_tool/ontograph.py
+++ b/onto_tool/ontograph.py
@@ -245,7 +245,7 @@ def gather_schema_info_from_repo(self):
               UNION
               {
                 ?entity rdfs:isDefinedBy ?ontology; a ?type .
-                ?bnode_filter
+                $bnode_filter
               }
             }
             """

From f072089be5f712c9956cac7d9cc561f03fa43bb2 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Thu, 19 Sep 2024 12:30:48 -0400
Subject: [PATCH 05/10] Issue #133 Migrate test outputs to temp directory

---
 tests/bundle/__init__.py            |  3 ---
 tests/bundle/test_markdown.py       | 16 +++++------
 tests/bundle/test_message.py        |  4 +--
 tests/bundle/test_sparql.py         | 30 ++++++++++-----------
 tests/bundle/test_syntax_error.py   |  4 +--
 tests/bundle/test_transform.py      | 16 +++++------
 tests/bundle/test_verify.py         | 38 +++++++++++++-------------
 tests/graphic/__init__.py           |  4 +--
 tests/graphic/test_bnode_subject.py | 24 ++++++++---------
 tests/graphic/test_instance.py      | 42 ++++++++++++++---------------
 tests/graphic/test_schema.py        |  7 ++---
 11 files changed, 92 insertions(+), 96 deletions(-)

diff --git a/tests/bundle/__init__.py b/tests/bundle/__init__.py
index a8dd25a..e69de29 100644
--- a/tests/bundle/__init__.py
+++ b/tests/bundle/__init__.py
@@ -1,3 +0,0 @@
-import os
-if not os.path.isdir('tests-output/bundle'):
-    os.makedirs('tests-output/bundle')
diff --git a/tests/bundle/test_markdown.py b/tests/bundle/test_markdown.py
index eac761c..ff05bae 100644
--- a/tests/bundle/test_markdown.py
+++ b/tests/bundle/test_markdown.py
@@ -3,28 +3,28 @@
 from os.path import basename
 
 
-def test_markdown_table():
+def test_markdown_table(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle',
+        'bundle', '-v', 'output', f'{tmp_path}',
         'tests/bundle/markdown.yaml'
     ])
 
-    html_text = open('tests-output/bundle/Table.html').read()
+    html_text = open(f'{tmp_path}/Table.html').read()
     assert '<table' in html_text.lower()
 
 
-def test_markdown_bulk():
+def test_markdown_bulk(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle',
+        'bundle', '-v', 'output', f'{tmp_path}',
         'tests/bundle/bulk_md.yaml'
     ])
 
-    inc_no_exc = [basename(f) for f in glob('tests-output/bundle/bulk_md/inc_no_exc/*')]
+    inc_no_exc = [basename(f) for f in glob(f'{tmp_path}/bulk_md/inc_no_exc/*')]
     assert sorted(inc_no_exc) == ['a1.html']
 
-    exc_no_inc = [basename(f) for f in glob('tests-output/bundle/bulk_md/exc_no_inc/*')]
+    exc_no_inc = [basename(f) for f in glob(f'{tmp_path}/bulk_md/exc_no_inc/*')]
     assert sorted(exc_no_inc) == ['a1.html', 'c3.html']
 
-    inc_and_exc = [basename(f) for f in glob('tests-output/bundle/bulk_md/inc_and_exc/*')]
+    inc_and_exc = [basename(f) for f in glob(f'{tmp_path}/bulk_md/inc_and_exc/*')]
     assert sorted(inc_and_exc) == ['b2.html', 'c3.html']
 
diff --git a/tests/bundle/test_message.py b/tests/bundle/test_message.py
index 9e8ee64..65fa23c 100644
--- a/tests/bundle/test_message.py
+++ b/tests/bundle/test_message.py
@@ -4,10 +4,10 @@
 from onto_tool import onto_tool
 
 
-def test_action_message(caplog):
+def test_action_message(caplog, tmp_path):
     caplog.set_level(logging.INFO)
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/message.yaml'
+        'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/message.yaml'
     ])
 
     logs = caplog.text
diff --git a/tests/bundle/test_sparql.py b/tests/bundle/test_sparql.py
index 6f07be3..3856486 100644
--- a/tests/bundle/test_sparql.py
+++ b/tests/bundle/test_sparql.py
@@ -8,11 +8,11 @@ def lists_equal(list_one, list_two):
     return len(list_one) == len(list_two) and sorted(list_one) == sorted(list_two)
 
 
-def test_sparql_queries():
+def test_sparql_queries(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/sparql.yaml'
+        'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/sparql.yaml'
     ])
-    with open('tests-output/bundle/sparql.csv') as csvfile:
+    with open(f'{tmp_path}/sparql.csv') as csvfile:
         actual = list(row for row in csv.DictReader(csvfile))
     expected = [
         {'s': 'https://data.clientX.com/d/topOntology',
@@ -25,12 +25,12 @@ def test_sparql_queries():
     assert actual == expected
 
 
-def test_sparql_updates():
+def test_sparql_updates(tmp_path):
     onto_tool.main([
-        '-k', 'bundle', '-v', 'output', 'tests-output/bundle/endpoint_sparql', 'tests/bundle/sparql_update.yaml'
+        '-k', 'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/sparql_update.yaml'
     ])
 
-    with open('tests-output/bundle/endpoint_sparql/sparql_update_select.csv') as csvfile:
+    with open(f'{tmp_path}/sparql_update_select.csv') as csvfile:
         actual = list(row for row in csv.DictReader(csvfile))
     expected = [
         {'person': 'http://example.com/John',
@@ -41,34 +41,34 @@ def test_sparql_updates():
     assert actual == expected
 
     constructed_graph = Graph()
-    constructed_graph.parse('tests-output/bundle/endpoint_sparql/sparql_update_construct.xml', format='xml')
+    constructed_graph.parse(f'{tmp_path}/sparql_update_construct.xml', format='xml')
     labels = list(constructed_graph.subject_objects(SKOS.prefLabel))
     assert lists_equal([(URIRef('http://example.com/John'), Literal('John Johnson')),
                         (URIRef('http://example.com/Jane'), Literal('Jane Johnson'))],
                        labels)
 
 
-def test_each_file():
+def test_each_file(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/sparql-each.yaml'
+        'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/sparql-each.yaml'
     ])
 
     # Verify CONSTRUCT
     constructed_graph = Graph()
-    constructed_graph.parse('tests-output/bundle/each/construct/upper_ontology.ttl', format='turtle')
+    constructed_graph.parse(f'{tmp_path}/each/construct/upper_ontology.ttl', format='turtle')
     labels = list(constructed_graph.subject_objects(SKOS.prefLabel))
     assert len(labels) == 5
     constructed_graph = Graph()
-    constructed_graph.parse('tests-output/bundle/each/construct/domain_ontology.ttl', format='turtle')
+    constructed_graph.parse(f'{tmp_path}/each/construct/domain_ontology.ttl', format='turtle')
     labels = list(constructed_graph.subject_objects(SKOS.prefLabel))
     assert len(labels) == 6
 
     # Verify SELECT
-    with open('tests-output/bundle/each/select/upper_ontology.csv') as csvfile:
+    with open(f'{tmp_path}/each/select/upper_ontology.csv') as csvfile:
         actual = list(row['label'] for row in csv.DictReader(csvfile))
     expected = ["Person", "Upper Ontology", "has phone number", "is friend of", "is private"]
     assert actual == expected
-    with open('tests-output/bundle/each/select/domain_ontology.csv') as csvfile:
+    with open(f'{tmp_path}/each/select/domain_ontology.csv') as csvfile:
         actual = list(row['label'] for row in csv.DictReader(csvfile))
     expected = ["Domain Ontology", "School", "Student", "Teacher", "teaches", "works for"]
     assert actual == expected
@@ -76,12 +76,12 @@ def test_each_file():
     # Verify UPDATE
     assert actual == expected
     constructed_graph = Graph()
-    constructed_graph.parse('tests-output/bundle/each/update/upper_ontology.ttl', format='turtle')
+    constructed_graph.parse(f'{tmp_path}/each/update/upper_ontology.ttl', format='turtle')
     labels = list(constructed_graph.subject_objects(SKOS.prefLabel))
     assert len(labels) == 5
     assert not list(constructed_graph.subject_objects(RDFS.label))
     constructed_graph = Graph()
-    constructed_graph.parse('tests-output/bundle/each/update/domain_ontology.ttl', format='turtle')
+    constructed_graph.parse(f'{tmp_path}/each/update/domain_ontology.ttl', format='turtle')
     labels = list(constructed_graph.subject_objects(SKOS.prefLabel))
     assert len(labels) == 6
     assert not list(constructed_graph.subject_objects(RDFS.label))
diff --git a/tests/bundle/test_syntax_error.py b/tests/bundle/test_syntax_error.py
index d443e10..64a884d 100644
--- a/tests/bundle/test_syntax_error.py
+++ b/tests/bundle/test_syntax_error.py
@@ -3,10 +3,10 @@
 import re
 
 
-def test_syntax_export(caplog):
+def test_syntax_export(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/syntax_error.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/syntax_error.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
diff --git a/tests/bundle/test_transform.py b/tests/bundle/test_transform.py
index e9bda3c..fae3b69 100644
--- a/tests/bundle/test_transform.py
+++ b/tests/bundle/test_transform.py
@@ -5,35 +5,35 @@
 from rdflib.namespace import SKOS, RDF
 
 
-def test_transform_sparql():
+def test_transform_sparql(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle',
+        'bundle', '-v', 'output', f'{tmp_path}',
         '-v', 'lang', 'en', 'tests/bundle/transform_sparql.yaml'
     ])
 
     updated_graph = Graph()
-    updated_graph.parse('tests-output/bundle/transform_sparql_data_en.ttl', format='turtle')
+    updated_graph.parse(f'{tmp_path}/transform_sparql_data_en.ttl', format='turtle')
     without_lang = [label for label in updated_graph.objects(None, SKOS.prefLabel)
                     if label.language != 'en']
     assert len(without_lang) == 0
 
 
-def test_transform_java():
+def test_transform_java(tmp_path):
     onto_tool.main([
-        'bundle', '-v', 'output', 'tests-output/bundle',
+        'bundle', '-v', 'output', f'{tmp_path}',
         '-v', 'format', 'rdf-xml', 'tests/bundle/transform_java.yaml'
     ])
 
     updated_graph = Graph()
-    updated_graph.parse('tests-output/bundle/transform_sparql_data.xml', format='xml')
+    updated_graph.parse(f'{tmp_path}/transform_sparql_data.xml', format='xml')
     types = list(updated_graph.subject_objects(RDF.type))
     assert len(types) == 2
 
 
-def test_transform_shell(caplog):
+def test_transform_shell(caplog, tmp_path):
     with caplog.at_level(logging.DEBUG):
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle',
+            'bundle', '-v', 'output', f'{tmp_path}',
             'tests/bundle/transform_shell.yaml'
         ])
 
diff --git a/tests/bundle/test_verify.py b/tests/bundle/test_verify.py
index 384237c..9106fc3 100644
--- a/tests/bundle/test_verify.py
+++ b/tests/bundle/test_verify.py
@@ -7,10 +7,10 @@
 from rdflib.namespace import Namespace, RDF
 
 
-def test_verify_select(caplog):
+def test_verify_select(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_select.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_select.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -19,16 +19,16 @@ def test_verify_select(caplog):
     assert 'Verification query inline' in logs
     assert 'http://example.com/unlabeled' in logs
 
-    with open('tests-output/bundle/verify_select_errors.csv') as errors:
+    with open(f'{tmp_path}/verify_select_errors.csv') as errors:
         actual = list(row for row in csv.DictReader(errors))
     expected = [{'unlabeled': 'http://example.com/unlabeled'}]
     assert actual == expected
 
 
-def test_verify_ask(caplog):
+def test_verify_ask(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_ask.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_ask.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -36,10 +36,10 @@ def test_verify_ask(caplog):
     assert re.search(r'Verification ASK .*verify_domain.* False', caplog.text)
 
 
-def test_verify_select_multiple(caplog):
+def test_verify_select_multiple(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_select_multiple.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_select_multiple.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -50,21 +50,21 @@ def test_verify_select_multiple(caplog):
     assert re.search(r'Verification query .*verify_domain_select', logs)
     assert 'http://example.com/nonexistent' in logs
 
-    with open('tests-output/bundle/verify_select_results/verify_label_select_query.csv') as errors:
+    with open(f'{tmp_path}/verify_select_results/verify_label_select_query.csv') as errors:
         actual = list(row for row in csv.DictReader(errors))
     expected = [{'unlabeled': 'http://example.com/unlabeled'}]
     assert actual == expected
 
-    with open('tests-output/bundle/verify_select_results/verify_domain_select_query.csv') as errors:
+    with open(f'{tmp_path}/verify_select_results/verify_domain_select_query.csv') as errors:
         actual = list(row for row in csv.DictReader(errors))
     expected = [{'domain': 'http://example.com/nonexistent'}]
     assert actual == expected
 
 
-def test_verify_construct(caplog):
+def test_verify_construct(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_construct.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_construct.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -77,7 +77,7 @@ def test_verify_construct(caplog):
 
     validation_graph = Graph()
     validation_graph.parse(
-        'tests-output/bundle/verify_construct_results/verify_label_construct_query.ttl',
+        f'{tmp_path}/verify_construct_results/verify_label_construct_query.ttl',
         format='turtle')
     sh = Namespace('http://www.w3.org/ns/shacl#')
     errors = [validation_graph.subjects(RDF.type, sh.ValidationResult)]
@@ -85,7 +85,7 @@ def test_verify_construct(caplog):
 
     validation_graph = Graph()
     validation_graph.parse(
-        'tests-output/bundle/verify_construct_results/verify_domain_construct_query.ttl',
+        f'{tmp_path}/verify_construct_results/verify_domain_construct_query.ttl',
         format='turtle')
     sh = Namespace('http://www.w3.org/ns/shacl#')
     errors = [validation_graph.subjects(RDF.type, sh.ValidationResult)]
@@ -95,10 +95,10 @@ def test_verify_construct(caplog):
     assert not isfile('test/bundle/verify_construct_results/verify_no_errors_construct_query.ttl')
 
 
-def test_verify_construct_endpoint(caplog):
+def test_verify_construct_endpoint(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_construct_endpoint.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_construct_endpoint.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -109,17 +109,17 @@ def test_verify_construct_endpoint(caplog):
 
     validation_graph = Graph()
     validation_graph.parse(
-        'tests-output/bundle/verify_construct_results/verify_fixed_error.ttl',
+        f'{tmp_path}/verify_construct_results/verify_fixed_error.ttl',
         format='turtle')
     sh = Namespace('http://www.w3.org/ns/shacl#')
     errors = [validation_graph.subjects(RDF.type, sh.ValidationResult)]
     assert len(errors) == 1
 
 
-def test_verify_shacl(caplog):
+def test_verify_shacl(caplog, tmp_path):
     with raises(SystemExit) as wrapped_exit:
         onto_tool.main([
-            'bundle', '-v', 'output', 'tests-output/bundle', 'tests/bundle/verify_shacl.yaml'
+            'bundle', '-v', 'output', f'{tmp_path}', 'tests/bundle/verify_shacl.yaml'
         ])
     assert wrapped_exit.type == SystemExit
     assert wrapped_exit.value.code == 1
@@ -129,7 +129,7 @@ def test_verify_shacl(caplog):
     assert 'skos:prefLabel' in logs
 
     validation_graph = Graph()
-    validation_graph.parse('tests-output/bundle/verify_shacl_errors.ttl', format='turtle')
+    validation_graph.parse(f'{tmp_path}/verify_shacl_errors.ttl', format='turtle')
     sh = Namespace('http://www.w3.org/ns/shacl#')
     errors = [validation_graph.subjects(RDF.type, sh.ValidationResult)]
     assert len(errors) == 1
diff --git a/tests/graphic/__init__.py b/tests/graphic/__init__.py
index 32b67ce..8b13789 100644
--- a/tests/graphic/__init__.py
+++ b/tests/graphic/__init__.py
@@ -1,3 +1 @@
-import os
-if not os.path.isdir('tests-output/graphic'):
-    os.makedirs('tests-output/graphic')
+
diff --git a/tests/graphic/test_bnode_subject.py b/tests/graphic/test_bnode_subject.py
index 5383f6b..7cc4ac1 100644
--- a/tests/graphic/test_bnode_subject.py
+++ b/tests/graphic/test_bnode_subject.py
@@ -4,55 +4,55 @@
 import re
 
 
-def test_filter_bnode_subjects():
+def test_filter_bnode_subjects(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '-t', 'Blank Node Subjects Filtered',
         '--no-image',
-        '-o', 'tests-output/graphic/test_filter_bnode_subjects',
+        '-o', f'{tmp_path}/test_filter_bnode_subjects',
         'tests/graphic/issue-116-bnode-subjects.ttl'
     ])
-    assert not os.path.isfile('tests-output/graphic/test_filter_bnode_subjects.dot')
+    assert not os.path.isfile(f'{tmp_path}/test_filter_bnode_subjects.dot')
 
 
-def test_show_bnode_subjects():
+def test_show_bnode_subjects(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '--show-bnode-subjects',
         '-t', 'Blank Node Subjects Shown',
         '--no-image',
-        '-o', 'tests-output/graphic/test_show_bnode_subjects',
+        '-o', f'{tmp_path}/test_show_bnode_subjects',
         'tests/graphic/issue-116-bnode-subjects.ttl',
         'tests/graphic/issue-116-ontology.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_show_bnode_subjects.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_show_bnode_subjects.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [('"http://example.org/Person"', '"http://example.org/State"')]
 
 
-def test_show_named_subjects():
+def test_show_named_subjects(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '--show-bnode-subjects',
         '-t', 'Named Node Subjects',
         '--no-image',
-        '-o', 'tests-output/graphic/test_named_subjects',
+        '-o', f'{tmp_path}/test_named_subjects',
         'tests/graphic/issue-116-named-subjects.ttl',
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_named_subjects.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_named_subjects.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [('"http://example.org/Person"', '"http://example.org/State"')]
 
 
-def test_show_ont_bnode_subjects():
+def test_show_ont_bnode_subjects(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--schema',
         '--show-bnode-subjects',
         '-t', 'Ontology Named Node Subjects',
         '--no-image',
-        '-o', 'tests-output/graphic/test_ont_bnode_subjects',
+        '-o', f'{tmp_path}/test_ont_bnode_subjects',
         'tests/graphic/issue-116-ontology.ttl',
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_ont_bnode_subjects.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_ont_bnode_subjects.dot')
     label = instance_graph.get_nodes()[1].get("label")
     assert re.sub(r"n[0-9a-fA-F]{34}", "BNODE_ID", label) == '"{issue-116-ontology.ttl\l\lSmallOnt||residesIn|name||Person\lState\lClass1\lClass2\lBNODE_ID}"'
diff --git a/tests/graphic/test_instance.py b/tests/graphic/test_instance.py
index e8a9405..1a1c497 100644
--- a/tests/graphic/test_instance.py
+++ b/tests/graphic/test_instance.py
@@ -3,17 +3,17 @@
 import pydot
 
 
-def test_local_instance():
+def test_local_instance(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '-t', 'Local Instance Data',
         '--no-image',
-        '-o', 'tests-output/graphic/test_instance',
+        '-o', f'{tmp_path}/test_instance',
         'tests/graphic/domain_ontology.ttl',
         'tests/graphic/upper_ontology.ttl',
         'tests/graphic/instance_data.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_instance.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_instance.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('"http://example.com/Student"', '"http://example.com/Person"'),
@@ -22,15 +22,15 @@ def test_local_instance():
     ]
 
 
-def test_multi_language():
+def test_multi_language(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '-t', 'Multi Language Labels',
         '--no-image',
-        '-o', 'tests-output/graphic/test_multi_lingual_en',
+        '-o', f'{tmp_path}/test_multi_lingual_en',
         'tests/graphic/multi_language.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_multi_lingual_en.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_multi_lingual_en.dot')
     edges = list(sorted((e.get_source(), e.get_label(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('"http://example.com/Person"', 'likes', '"http://example.com/Dessert"')
@@ -40,25 +40,25 @@ def test_multi_language():
         'graphic', '--predicate-threshold', '0', '--data',
         '-t', 'Multi Language Labels',
         '--no-image', '--label-language', 'fr',
-        '-o', 'tests-output/graphic/test_multi_lingual_fr',
+        '-o', f'{tmp_path}/test_multi_lingual_fr',
         'tests/graphic/multi_language.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_multi_lingual_fr.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_multi_lingual_fr.dot')
     edges = list(sorted((e.get_source(), e.get_label(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('"http://example.com/Person"', 'aime', '"http://example.com/Dessert"')
     ]
 
 
-def test_inheritance():
+def test_inheritance(tmp_path):
     onto_tool.main([
                        'graphic', '--predicate-threshold', '0', '--data',
                        '-t', 'Inheritance is Difficult',
                        '--no-image',
-                       '-o', 'tests-output/graphic/test_inheritance',
+                       '-o', f'{tmp_path}/test_inheritance',
                        'tests/graphic/inheritance_hierarchy.ttl'
                    ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_inheritance.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_inheritance.dot')
     edges = list(sorted((e.get_source(), e.get_label() or '', e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('"http://example.org/Person"', 'memberOf', '"http://example.org/Organization"'),
@@ -73,28 +73,28 @@ def test_inheritance():
     assert 'age' not in instance_graph.get_node('"http://example.org/Student"')[0].get_label()
 
 
-def test_verify_construct(caplog):
+def test_verify_construct(caplog, tmp_path):
     onto_tool.main([
                        'graphic', '--data',
                        '-t', 'Local Instance Data',
                        '--no-image',
-                       '-o', 'tests-output/graphic/test_instance'
+                       '-o', f'{tmp_path}/test_instance'
                    ] + glob.glob('tests/graphic/*_ontology.ttl'))
     logs = caplog.text
     assert 'No data found' in logs
 
 
-def test_concentration():
+def test_concentration(tmp_path):
     # First, with concentration
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '--debug',
         '-t', 'Looney Tunes',
         '--no-image',
-        '-o', 'tests-output/graphic/concentration',
+        '-o', f'{tmp_path}/concentration',
         'tests/graphic/concentration.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/concentration.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/concentration.dot')
     assert 1 == sum(1 for e in instance_graph.get_edges() if e.get_label() == 'playsWith')
 
     # Then, without
@@ -103,24 +103,24 @@ def test_concentration():
         '-t', 'Looney Tunes',
         '--no-image',
         '--link-concentrator-threshold', '0',
-        '-o', 'tests-output/graphic/concentration',
+        '-o', f'{tmp_path}/concentration',
         'tests/graphic/concentration.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/concentration.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/concentration.dot')
     assert 4 == sum(1 for e in instance_graph.get_edges() if e.get_label() == 'playsWith')
 
 
-def test_shacl_instances():
+def test_shacl_instances(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
         '-t', 'Local Instance Data',
         '--no-image',
-        '-o', 'tests-output/graphic/test_instance',
+        '-o', f'{tmp_path}/test_instance',
         'tests/graphic/domain_ontology.ttl',
         'tests/graphic/upper_ontology.ttl',
         'tests/graphic/instance_data.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_instance.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_instance.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     shacl_namespace = "http://www.w3.org/ns/shacl#"
     shacl_edges = [edge for edge in edges if any(shacl_namespace in part for part in edge)]
diff --git a/tests/graphic/test_schema.py b/tests/graphic/test_schema.py
index 9f50428..efc1272 100644
--- a/tests/graphic/test_schema.py
+++ b/tests/graphic/test_schema.py
@@ -2,17 +2,18 @@
 import pydot
 
 
-def test_local_instance():
+def test_local_instance(tmp_path):
+    out_file = tmp_path / 'test_schema'
     onto_tool.main([
         'graphic',
         '-t', 'Local Ontology',
         '--no-image',
-        '-o', 'tests-output/graphic/test_schema',
+        '-o', f'{out_file}',
         'tests/graphic/domain_ontology.ttl',
         'tests/graphic/upper_ontology.ttl',
         'tests/graphic/instance_data.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file('tests-output/graphic/test_schema.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{out_file}.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('Domain', 'Upper'),

From f7c96dcec4a5c0c0aedc2c8cdc483d8c812c50e4 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Thu, 19 Sep 2024 15:38:42 -0400
Subject: [PATCH 06/10] test_schema outdir pattern follows other tests

---
 tests/graphic/test_schema.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/graphic/test_schema.py b/tests/graphic/test_schema.py
index efc1272..1213003 100644
--- a/tests/graphic/test_schema.py
+++ b/tests/graphic/test_schema.py
@@ -3,17 +3,16 @@
 
 
 def test_local_instance(tmp_path):
-    out_file = tmp_path / 'test_schema'
     onto_tool.main([
         'graphic',
         '-t', 'Local Ontology',
         '--no-image',
-        '-o', f'{out_file}',
+        '-o', f'{tmp_path}/test_schema',
         'tests/graphic/domain_ontology.ttl',
         'tests/graphic/upper_ontology.ttl',
         'tests/graphic/instance_data.ttl'
     ])
-    (instance_graph,) = pydot.graph_from_dot_file(f'{out_file}.dot')
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_schema.dot')
     edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
     assert edges == [
         ('Domain', 'Upper'),

From 24e68b23cd220a35cd2499af3cd10ad39771657c Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Fri, 20 Sep 2024 09:24:44 -0400
Subject: [PATCH 07/10] Remove extra newline

---
 tests/graphic/__init__.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/graphic/__init__.py b/tests/graphic/__init__.py
index 8b13789..e69de29 100644
--- a/tests/graphic/__init__.py
+++ b/tests/graphic/__init__.py
@@ -1 +0,0 @@
-

From 8f622199ed1e5db78358354cf0d6d1bff4533de5 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Fri, 20 Sep 2024 09:17:24 -0400
Subject: [PATCH 08/10] Issue #100 Add sparql-endpoint-fixture to test remote
 ontology

---
 tests/__init__.py                     |  3 ++
 tests/graphic/domain_ontology.trig    | 32 +++++++++++++++++++
 tests/graphic/instance_data.trig      | 16 ++++++++++
 tests/graphic/issue-116-ontology.trig | 18 +++++++++++
 tests/graphic/issue-116-ontology.ttl  | 19 ++++++++----
 tests/graphic/test_bnode_subject.py   | 39 ++++++++++++++++++++++++
 tests/graphic/test_instance.py        | 23 ++++++++++++++
 tests/graphic/test_schema.py          | 44 +++++++++++++++++++++++++++
 tests/graphic/upper_ontology.trig     | 29 ++++++++++++++++++
 9 files changed, 217 insertions(+), 6 deletions(-)
 create mode 100644 tests/graphic/domain_ontology.trig
 create mode 100644 tests/graphic/instance_data.trig
 create mode 100644 tests/graphic/issue-116-ontology.trig
 create mode 100644 tests/graphic/upper_ontology.trig

diff --git a/tests/__init__.py b/tests/__init__.py
index e69de29..7477c34 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -0,0 +1,3 @@
+pytest_plugins = [
+    "sparql_endpoint_fixture.endpoint"
+]
diff --git a/tests/graphic/domain_ontology.trig b/tests/graphic/domain_ontology.trig
new file mode 100644
index 0000000..102f54c
--- /dev/null
+++ b/tests/graphic/domain_ontology.trig
@@ -0,0 +1,32 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix : <http://example.com/> .
+
+:DomainOntGraph {
+    :Domain a owl:Ontology; owl:imports :Upper; rdfs:label "Domain Ontology" .
+
+    :Student a owl:Class ;
+             rdfs:subClassOf :Person ;
+             rdfs:isDefinedBy :Domain ;
+            rdfs:label "Student" .
+
+    :Teacher a owl:Class ;
+             rdfs:subClassOf :Person ;
+             rdfs:isDefinedBy :Domain ;
+            rdfs:label "Teacher" .
+
+    :School a owl:Class ;
+             rdfs:isDefinedBy :Domain ;
+            rdfs:label "School" .
+
+    :worksFor a owl:ObjectProperty ;
+             rdfs:isDefinedBy :Domain ;
+                rdfs:domain :Teacher ;
+                rdfs:range :School ;
+                rdfs:label "works for" .
+
+    :teaches a owl:ObjectProperty ;
+                rdfs:label "teaches" .
+}
diff --git a/tests/graphic/instance_data.trig b/tests/graphic/instance_data.trig
new file mode 100644
index 0000000..8fb45c6
--- /dev/null
+++ b/tests/graphic/instance_data.trig
@@ -0,0 +1,16 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix : <http://example.com/> .
+
+:InstanceDataGraph {
+    :Instances a owl:Ontology; owl:imports :Domain; rdfs:label "Instance Data" .
+
+    :_t1 a :Teacher; :worksFor :_u1; :teaches :_s1; rdfs:isDefinedBy :Instances .
+    :_u1 a :School; rdfs:isDefinedBy :Instances .
+    :_s1 a :Student; :isFriendOf :_p1; rdfs:isDefinedBy :Instances .
+    :_p1 a :Person; :hasPhoneNumber "123-456-7890"; rdfs:isDefinedBy :Instances .
+    :_h1 a sh:NodeShape ; sh:targetClass :School ; rdfs:isDefinedBy :Instances .
+}
diff --git a/tests/graphic/issue-116-ontology.trig b/tests/graphic/issue-116-ontology.trig
new file mode 100644
index 0000000..3f244b8
--- /dev/null
+++ b/tests/graphic/issue-116-ontology.trig
@@ -0,0 +1,18 @@
+@prefix : <http://example.org/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:OntGraph {
+    :SmallOnt a owl:Ontology .
+
+    :Person a rdfs:Class .
+    :State a rdfs:Class .
+    :residesIn a owl:ObjectProperty .
+    :name a owl:DatatypeProperty .
+
+    :Class1 a rdfs:Class .
+    :Class2 a rdfs:Class .
+    [] a rdfs:Class ;
+        rdfs:subClassOf  :Class1, :Class2 ;
+        rdfs:label "Unnamed Class" .
+}
diff --git a/tests/graphic/issue-116-ontology.ttl b/tests/graphic/issue-116-ontology.ttl
index 77aeac4..53ac746 100644
--- a/tests/graphic/issue-116-ontology.ttl
+++ b/tests/graphic/issue-116-ontology.ttl
@@ -4,13 +4,20 @@
 
 :SmallOnt a owl:Ontology .
 
-:Person a rdfs:Class .
-:State a rdfs:Class .
-:residesIn a owl:ObjectProperty .
-:name a owl:DatatypeProperty .
+:Person a rdfs:Class ;
+    rdfs:isDefinedBy :SmallOnt .
+:State a rdfs:Class ;
+    rdfs:isDefinedBy :SmallOnt .
+:residesIn a owl:ObjectProperty ;
+    rdfs:isDefinedBy :SmallOnt .
+:name a owl:DatatypeProperty ;
+    rdfs:isDefinedBy :SmallOnt .
 
-:Class1 a rdfs:Class .
-:Class2 a rdfs:Class .
+:Class1 a rdfs:Class ;
+    rdfs:isDefinedBy :SmallOnt .
+:Class2 a rdfs:Class ;
+    rdfs:isDefinedBy :SmallOnt .
 [] a rdfs:Class ;
+    rdfs:isDefinedBy :SmallOnt ;
     rdfs:subClassOf  :Class1, :Class2 ;
     rdfs:label "Unnamed Class" .
diff --git a/tests/graphic/test_bnode_subject.py b/tests/graphic/test_bnode_subject.py
index 7cc4ac1..ee17e0f 100644
--- a/tests/graphic/test_bnode_subject.py
+++ b/tests/graphic/test_bnode_subject.py
@@ -56,3 +56,42 @@ def test_show_ont_bnode_subjects(tmp_path):
     (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_ont_bnode_subjects.dot')
     label = instance_graph.get_nodes()[1].get("label")
     assert re.sub(r"n[0-9a-fA-F]{34}", "BNODE_ID", label) == '"{issue-116-ontology.ttl\l\lSmallOnt||residesIn|name||Person\lState\lClass1\lClass2\lBNODE_ID}"'
+
+
+def test_remote_show_ont_bnode_subjects(tmp_path, sparql_endpoint):
+    repo_uri = 'https://my.rdfdb.com/repo/sparql'
+    rdf_files = ['tests/graphic/issue-116-ontology.ttl']
+    sparql_endpoint(repo_uri, rdf_files)
+
+    print(tmp_path)
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--schema',
+        '--endpoint', f'{repo_uri}',
+        '--show-bnode-subjects',
+        '-t', 'Ontology Named Node Subjects',
+        '--no-image',
+        '-o', f'{tmp_path}/test_ont_bnode_subjects'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_ont_bnode_subjects.dot')
+    label = instance_graph.get_nodes()[1].get("label")
+    assert re.sub(r"n[0-9a-fA-F]{34}", "BNODE_ID", label) == '"{http://example.org/SmallOnt\l\lSmallOnt||residesIn|name||Class1\lClass2\lPerson\lState\lBNODE_ID}"'
+
+
+def test_remote_show_ont_trig(tmp_path, sparql_endpoint):
+    repo_uri = 'https://my.rdfdb.com/repo/sparql'
+    rdf_files = ['tests/graphic/issue-116-ontology.trig']
+    sparql_endpoint(repo_uri, rdf_files)
+
+    print(tmp_path)
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--schema',
+        '--single-ontology-graphs',
+        '--endpoint', f'{repo_uri}',
+        '--show-bnode-subjects',
+        '-t', 'Ontology Named Node Subjects',
+        '--no-image',
+        '-o', f'{tmp_path}/test_ont_bnode_subjects'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_ont_bnode_subjects.dot')
+    label = instance_graph.get_nodes()[1].get("label")
+    assert re.sub(r"n[0-9a-fA-F]{34}", "BNODE_ID", label) == '"{http://example.org/SmallOnt\l\lSmallOnt||residesIn|name||Class1\lClass2\lPerson\lState\lBNODE_ID}"'
diff --git a/tests/graphic/test_instance.py b/tests/graphic/test_instance.py
index 1a1c497..f4c7551 100644
--- a/tests/graphic/test_instance.py
+++ b/tests/graphic/test_instance.py
@@ -22,6 +22,29 @@ def test_local_instance(tmp_path):
     ]
 
 
+def test_remote_instance(tmp_path, sparql_endpoint):
+    repo_uri = 'https://my.rdfdb.com/repo/sparql'
+    rdf_files = ['tests/graphic/domain_ontology.ttl',
+                 'tests/graphic/upper_ontology.ttl',
+                 'tests/graphic/instance_data.ttl']
+    sparql_endpoint(repo_uri, rdf_files)
+
+    onto_tool.main([
+        'graphic', '--predicate-threshold', '0', '--data',
+        '--endpoint', f'{repo_uri}',
+        '-t', 'Remote Instance Data',
+        '--no-image',
+        '-o', f'{tmp_path}/test_instance'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_instance.dot')
+    edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
+    assert edges == [
+        ('"http://example.com/Student"', '"http://example.com/Person"'),
+        ('"http://example.com/Teacher"', '"http://example.com/School"'),
+        ('"http://example.com/Teacher"', '"http://example.com/Student"')
+    ]
+
+
 def test_multi_language(tmp_path):
     onto_tool.main([
         'graphic', '--predicate-threshold', '0', '--data',
diff --git a/tests/graphic/test_schema.py b/tests/graphic/test_schema.py
index 1213003..068b4f3 100644
--- a/tests/graphic/test_schema.py
+++ b/tests/graphic/test_schema.py
@@ -18,3 +18,47 @@ def test_local_instance(tmp_path):
         ('Domain', 'Upper'),
         ('Instances', 'Domain')
     ]
+
+
+def test_remote_instance(tmp_path, sparql_endpoint):
+    repo_uri = 'https://my.rdfdb.com/repo/sparql'
+    rdf_files = ['tests/graphic/domain_ontology.ttl',
+                 'tests/graphic/upper_ontology.ttl',
+                 'tests/graphic/instance_data.ttl']
+    sparql_endpoint(repo_uri, rdf_files)
+
+    onto_tool.main([
+        'graphic',
+        '--endpoint', f'{repo_uri}',
+        '-t', 'Remote Ontology',
+        '--no-image',
+        '-o', f'{tmp_path}/test_schema'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_schema.dot')
+    edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
+    assert edges == [
+        ('Domain', 'Upper'),
+        ('Instances', 'Domain')
+    ]
+
+
+def test_remote_graphs(tmp_path, sparql_endpoint):
+    repo_uri = 'https://my.rdfdb.com/repo/sparql'
+    rdf_files = ['tests/graphic/domain_ontology.trig',
+                 'tests/graphic/upper_ontology.trig',
+                 'tests/graphic/instance_data.trig']
+    sparql_endpoint(repo_uri, rdf_files)
+
+    onto_tool.main([
+        'graphic', '--single-ontology-graphs',
+        '--endpoint', f'{repo_uri}',
+        '-t', 'Remote Ontology',
+        '--no-image',
+        '-o', f'{tmp_path}/test_schema'
+    ])
+    (instance_graph,) = pydot.graph_from_dot_file(f'{tmp_path}/test_schema.dot')
+    edges = list(sorted((e.get_source(), e.get_destination()) for e in instance_graph.get_edges()))
+    assert edges == [
+        ('Domain', 'Upper'),
+        ('Instances', 'Domain')
+    ]
diff --git a/tests/graphic/upper_ontology.trig b/tests/graphic/upper_ontology.trig
new file mode 100644
index 0000000..f9d4d96
--- /dev/null
+++ b/tests/graphic/upper_ontology.trig
@@ -0,0 +1,29 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix : <http://example.com/> .
+
+:UpperOntGraph {
+    :Upper a owl:Ontology; rdfs:label "Upper Ontology" .
+
+    :Person a owl:Class ;
+             rdfs:isDefinedBy :Upper ;
+            rdfs:label "Person" .
+
+    :isPrivate a owl:AnnotationProperty ;
+             rdfs:isDefinedBy :Upper ;
+                    rdfs:range xsd:boolean ;
+                    rdfs:label "is private" .
+
+    :hasPhoneNumber a owl:DatatypeProperty ;
+             rdfs:isDefinedBy :Upper ;
+                    rdfs:range xsd:string ;
+                    rdfs:label "has phone number" .
+
+    :isFriendOf a owl:ObjectProperty ;
+             rdfs:isDefinedBy :Upper ;
+                rdfs:domain :Person ;
+                rdfs:range :Person ;
+                rdfs:label "is friend of" .
+}

From b8fcae138a13a9c55452cb9e4b72ccf2e8fcc293 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Fri, 20 Sep 2024 13:37:12 -0400
Subject: [PATCH 09/10] Add sparql endpoin fixture to requirements.txt

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 26570dd..f19d736 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,3 +18,4 @@ namedentities>=1.5.2
 zipp>=3.1.0
 pytest~=6.1.2
 SPARQLWrapper~=1.8.5
+sparql-endpoint-fixture>=0.5.0

From 312ab8ca4974324ca1c4421fd7fce3461b771562 Mon Sep 17 00:00:00 2001
From: Kate Studzinski <kate.studzinski@semanticarts.com>
Date: Wed, 23 Oct 2024 18:18:42 -0400
Subject: [PATCH 10/10] Update setuptools version requirement

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index f19d736..af9b8e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -13,7 +13,7 @@ isodate>=0.6.0
 jsonschema>=3.2.0
 attrs>=19.3.0
 pyrsistent>=0.16.0
-setuptools>=40.8.0
+setuptools<58.0.0
 namedentities>=1.5.2
 zipp>=3.1.0
 pytest~=6.1.2