CHANGELOG.md

@@ -3,3 +3,6 @@
 ## v0.0.1
  * Initial release.
 
+## v0.1.0
+ * Allow single RDF ontoly submission (JSON ontology file is now optional)
+ * Enable logging to STDOUT by default

pytest.ini

@@ -7,6 +7,7 @@ addopts =
     --verbose
     --tb=short
     --cov=src/cleverswarm_python_client
+    --cov-config=.coveragerc
     --cov-report=html
     --cov-report=term-missing
     --cov-fail-under=85

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = cleverswarm_python_client
-version = 0.0.1
+version = 0.1.0
 description = A set of Python client utilities and SDK for interacting with CleverSwarm micro-services
 long_description = file: README.md
 long_description_content_type = text/markdown

src/cleverswarm_python_client/cswarm_benchmark_client.py

@@ -19,6 +19,7 @@ CleverSwarm - text to knowledge graph extraction benchmark client.
 
 import argparse
 import logging
+import os
 import sys
 from pathlib import Path
 from typing import Dict, List, Set
@@ -282,13 +283,12 @@ class BenchmarkCLI(object):
 def main():
     """Main entry point for the benchmark client console script."""
 
-    handler = logging.StreamHandler(sys.stdout)
-    handler.setLevel(logging.DEBUG)
-    formatter = logging.Formatter(
-        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    logging.basicConfig(
+        level=os.environ.get("PYTHON_LOGGING_LEVEL", logging.INFO),
+        stream=sys.stderr,
+        datefmt="%Y-%m-%dT%H:%M:%S",
+        format=("%(asctime)s - %(name)s - %(levelname)s - %(message)s"),
     )
-    handler.setFormatter(formatter)
-    logger.addHandler(handler)
 
     parser = argparse.ArgumentParser(
         description="CleverSwarm benchmark client for REST API."

src/cleverswarm_python_client/cswarm_text_to_kg_client.py

@@ -19,6 +19,7 @@ CleverSwarm - unstructured text to knowledge graph triplets extractor client.
 
 import argparse
 import logging
+import os
 import sys
 from pathlib import Path
 from typing import Any, Dict
@@ -76,7 +77,10 @@ class TextoToKGCLI(object):
         force_filetype: FileTypeAPI = FileTypeAPI.AutoDetect,
     ):
         input_text_path: Path = self._input_prefix / input_text
-        ontology_json_path: Path = self._input_prefix / ontology_json
+        # Ontology JSON file is optional - only create path if it was provided
+        ontology_json_path: Path | None = (
+            self._input_prefix / ontology_json if ontology_json else None
+        )
         ontology_owl_path: Path = self._input_prefix / ontology_owl
         wildcards_path: Path = Path(wildcards) if wildcards else None
 
@@ -85,11 +89,19 @@ class TextoToKGCLI(object):
                 f"Unstructured input text does not exist or is not a file: {str(input_text_path)}"
             )
 
-        if not ontology_json_path.exists() or not ontology_json_path.is_file():
+        # If ontology_json was provided, validate that the file exists
+        if (
+            ontology_json
+            and ontology_json_path
+            and (not ontology_json_path.exists() or not ontology_json_path.is_file())
+        ):
             raise ClientException(
-                f"Input ontology JSON file does not exist or is not a file: {str(ontology_json_path)}"
+                f"Specified optional Ontology JSON file does not exist or is not a file: {str(ontology_json_path)}"
             )
 
+        # Ontology JSON file is optional - use the path if it was provided and exists
+        ontology_json_path_final: Path | None = ontology_json_path
+
         if not ontology_owl_path.exists() or not ontology_owl_path.is_file():
             raise ClientException(
                 f"Input ontology OWL file does not exist or is not a file: {str(ontology_owl_path)}"
@@ -106,7 +118,7 @@ class TextoToKGCLI(object):
         if wildcards_job:
             job_id: str = self._client.create_unstructured_to_kg_wildcards_job(
                 input_text_path,
-                ontology_json_path,
+                ontology_json_path_final,
                 ontology_owl_path,
                 wildcards_path,
                 force_filetype=force_filetype,
@@ -114,7 +126,7 @@ class TextoToKGCLI(object):
         else:
             job_id: str = self._client.create_unstructured_to_kg_job(
                 input_text_path,
-                ontology_json_path,
+                ontology_json_path_final,
                 ontology_owl_path,
                 force_filetype=force_filetype,
             )
@@ -211,13 +223,12 @@ class TextoToKGCLI(object):
 def main():
     """Main entry point for the text-to-KG client console script."""
 
-    handler = logging.StreamHandler(sys.stdout)
-    handler.setLevel(logging.DEBUG)
-    formatter = logging.Formatter(
-        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    logging.basicConfig(
+        level=os.environ.get("PYTHON_LOGGING_LEVEL", logging.INFO),
+        stream=sys.stderr,
+        datefmt="%Y-%m-%dT%H:%M:%S",
+        format=("%(asctime)s - %(name)s - %(levelname)s - %(message)s"),
     )
-    handler.setFormatter(formatter)
-    logger.addHandler(handler)
 
     parser = argparse.ArgumentParser(
         description="CleverSwarm unstructured text to Knowledge Graph triplets client for REST API."
@@ -272,7 +283,7 @@ def main():
     parser.add_argument(
         "--ontology_json",
         type=str,
-        help="Enriched ontology file with descriptions in JSON format",
+        help="Optional enriched ontology file with descriptions in JSON format",
     )
     parser.add_argument(
         "--ontology_owl",
@@ -306,10 +317,6 @@ def main():
             print("create-and-exit action requires --unstructured_text argument.\n")
             parser.print_help()
             exit(-1)
-        if args.ontology_json is None:
-            print("create-and-exit action requires --ontology_json argument.\n")
-            parser.print_help()
-            exit(-1)
         if args.ontology_owl is None:
             print("create-and-exit action requires --ontology_owl argument.\n")
             parser.print_help()
@@ -339,12 +346,6 @@ def main():
             )
             parser.print_help()
             exit(-1)
-        if args.ontology_json is None:
-            print(
-                "create-download-kg-delete action requires --ontology_json argument.\n"
-            )
-            parser.print_help()
-            exit(-1)
         if args.ontology_owl is None:
             print(
                 "create-download-kg-delete action requires --ontology_owl argument.\n"
@@ -361,12 +362,6 @@ def main():
             )
             parser.print_help()
             exit(-1)
-        if args.ontology_json is None:
-            print(
-                "create-download-kg-delete action requires --ontology_json argument.\n"
-            )
-            parser.print_help()
-            exit(-1)
         if args.ontology_owl is None:
             print(
                 "create-download-kg-delete action requires --ontology_owl argument.\n"

src/cleverswarm_python_client/libs/cleverswarm_client.py

@@ -595,7 +595,7 @@ class CleverSwarmClient(object):
     def create_unstructured_to_kg_job(
         self,
         unstructured_text_file: Path,
-        ontology_file: Path,
+        ontology_file: Path | None,
         ontology_spec_file: Path,
         force_filetype: FileTypeAPI = FileTypeAPI.AutoDetect,
     ):
@@ -604,7 +604,7 @@ class CleverSwarmClient(object):
         Login is requested if required by the server.
         If the upload is successful, it returns a job ID.
         :param unstructured_text_file: a valid file path containing unstructured text for conversion
-        :param ontology_file: a valid file containing an ontology in JSON format.
+        :param ontology_file: optional file containing an ontology in JSON format.
         :param ontology_spec_file: a valid file path containing the ontology spec in OWL/XML format.
         :param force_filetype: indicate the file type to force for the input file
         :return: the job ID where the files were placed.
@@ -618,11 +618,6 @@ class CleverSwarmClient(object):
                 f"{str(unstructured_text_file)}"
             )
 
-        if not ontology_file.exists() or not ontology_file.is_file():
-            raise InvalidFileException(
-                f"Ontology files does not exist or is not a file: {str(ontology_file)}"
-            )
-
         if not ontology_spec_file.exists() or not ontology_spec_file.is_file():
             raise InvalidFileException(
                 f"OWL/XML ontology file does not exist or is not a file: "
@@ -634,9 +629,11 @@ class CleverSwarmClient(object):
             params = {"file_type": force_filetype}
             files = [
                 ("unstructured", open(unstructured_text_file, "rb")),
-                ("ontology", open(ontology_file, "rb")),
                 ("ontology_spec", open(ontology_spec_file, "rb")),
             ]
+            if ontology_file:
+                files.append(("ontology", open(ontology_file, "rb")))
+
             response = requests.post(
                 self._base_url + "unstructured/with_ontology",
                 headers=headers,
@@ -669,7 +666,7 @@ class CleverSwarmClient(object):
     def create_unstructured_to_kg_wildcards_job(
         self,
         unstructured_text_file: Path,
-        ontology_file: Path,
+        ontology_file: Path | None,
         ontology_spec_file: Path,
         wildcards_query_file: Path,
         force_filetype: FileTypeAPI = FileTypeAPI.AutoDetect,
@@ -679,7 +676,7 @@ class CleverSwarmClient(object):
         Login is requested if required by the server.
         If the upload is successful, it returns a job ID.
         :param unstructured_text_file: a valid file path containing unstructured text for conversion
-        :param ontology_file: a valid file containing an ontology in JSON format.
+        :param ontology_file: optional file containing an ontology in JSON format.
         :param ontology_spec_file: a valid file path containing the ontology spec in OWL/XML format.
         :param wildcards_query_file: a valid file path containing wildcard queries in JSON.
         :param force_filetype: indicate the file type to force for the input file
@@ -694,11 +691,6 @@ class CleverSwarmClient(object):
                 f"{str(unstructured_text_file)}"
             )
 
-        if not ontology_file.exists() or not ontology_file.is_file():
-            raise InvalidFileException(
-                f"Ontology files does not exist or is not a file: {str(ontology_file)}"
-            )
-
         if not ontology_spec_file.exists() or not ontology_spec_file.is_file():
             raise InvalidFileException(
                 f"OWL/XML ontology file does not exist or is not a file: "
@@ -716,10 +708,12 @@ class CleverSwarmClient(object):
             params = {"file_type": force_filetype}
             files = [
                 ("unstructured", open(unstructured_text_file, "rb")),
-                ("ontology", open(ontology_file, "rb")),
                 ("ontology_spec", open(ontology_spec_file, "rb")),
                 ("wildcards", open(wildcards_query_file, "rb")),
             ]
+            if ontology_file:
+                files.append(("ontology", open(ontology_file, "rb")))
+
             response = requests.post(
                 self._base_url + "unstructured/with_wildcards",
                 headers=headers,

tests/test_cswarm_text_to_kg_client.py

@@ -214,18 +214,75 @@ class TestTextoToKGCLIJobCreation:
                 "test.owl"
             )
 
-    def test_create_job_invalid_json_file(self):
-        """Test job creation with invalid JSON file."""
+    def test_create_job_with_invalid_json_file(self):
+        """Test job creation with invalid (non-existent) JSON file - should raise exception if JSON is provided."""
         with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.txt') as text_file:
             text_file.write("Test text content")
             text_file.flush()
             
-            with pytest.raises(ClientException, match="Input ontology JSON file does not exist"):
-                self.cli.create_job(
-                    text_file.name,
-                    "nonexistent.json",
-                    "test.owl"
-                )
+            with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.owl') as owl_file:
+                owl_file.write('<rdf:RDF>test</rdf:RDF>')
+                owl_file.flush()
+                
+                # If ontology_json is provided but file doesn't exist, should raise exception
+                with pytest.raises(ClientException, match="Specified optional Ontology JSON file does not exist"):
+                    self.cli.create_job(
+                        text_file.name,
+                        "nonexistent.json",  # Non-existent JSON file - should raise exception
+                        owl_file.name
+                    )
+
+    def test_create_job_without_json_file(self):
+        """Test job creation without JSON file - should work since JSON is optional."""
+        with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.txt') as text_file:
+            text_file.write("Test text content")
+            text_file.flush()
+            
+            with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.owl') as owl_file:
+                owl_file.write('<rdf:RDF>test</rdf:RDF>')
+                owl_file.flush()
+                
+                with patch.object(self.cli._client, 'create_unstructured_to_kg_job') as mock_create:
+                    mock_create.return_value = "test_job_123"
+                    
+                    # Job creation should work without JSON file since it's optional
+                    result = self.cli.create_job(
+                        text_file.name,
+                        None,  # No JSON file provided - should work
+                        owl_file.name
+                    )
+                    
+                    assert result == "test_job_123"
+                    mock_create.assert_called_once()
+                    # Verify that None was passed for ontology_file since it wasn't provided
+                    call_args = mock_create.call_args
+                    assert call_args[0][1] is None  # ontology_file parameter should be None
+
+    def test_create_job_with_empty_json_file_string(self):
+        """Test job creation with empty string for JSON file - should work since JSON is optional."""
+        with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.txt') as text_file:
+            text_file.write("Test text content")
+            text_file.flush()
+            
+            with tempfile.NamedTemporaryFile(mode='w', delete=False, suffix='.owl') as owl_file:
+                owl_file.write('<rdf:RDF>test</rdf:RDF>')
+                owl_file.flush()
+                
+                with patch.object(self.cli._client, 'create_unstructured_to_kg_job') as mock_create:
+                    mock_create.return_value = "test_job_123"
+                    
+                    # Job creation should work with empty string for JSON file since it's optional
+                    result = self.cli.create_job(
+                        text_file.name,
+                        "",  # Empty string for JSON file - should work
+                        owl_file.name
+                    )
+                    
+                    assert result == "test_job_123"
+                    mock_create.assert_called_once()
+                    # Verify that None was passed for ontology_file since empty string is falsy
+                    call_args = mock_create.call_args
+                    assert call_args[0][1] is None  # ontology_file parameter should be None
 
     def test_create_job_invalid_owl_file(self):
         """Test job creation with invalid OWL file."""

tox.ini

@@ -10,8 +10,11 @@ deps =
     pytest-html>=4.1.1
     requests>=2.32.4
     httmock>=1.3.0
+# Isolate coverage database per environment to prevent conflicts in parallel runs
+setenv =
+    COVERAGE_FILE = {envdir}/.coverage.{envname}
 commands =
-    pytest {posargs:tests} --html=unit_tests_report.html --self-contained-html --junitxml=unit_tests_report.xml --cov=cleverswarm_python_client
+    pytest {posargs:tests} --html=unit_tests_report.html --self-contained-html --junitxml=unit_tests_report.xml --cov=src/cleverswarm_python_client --cov-config=.coveragerc
 
 [testenv:lint]
 deps =
@@ -36,8 +39,11 @@ deps =
     coverage>=5.5
     requests>=2.32.4
     httmock>=1.3.0
+# Use a dedicated coverage database for the coverage environment
+setenv =
+    COVERAGE_FILE = {envdir}/.coverage
 commands =
-    pytest {posargs:tests} --cov=cleverswarm_python_client --cov-report=term --cov-report=xml:coverage_report.xml --cov-report=html
+    pytest {posargs:tests} --cov=src/cleverswarm_python_client --cov-config=.coveragerc --cov-report=term --cov-report=xml:coverage_report.xml --cov-report=html
     coverage report --fail-under=85
 
 [testenv:format]