Merge pull request #117 from SteffenBrinckmann/sb_repairPytests

Repair github actions

.github/workflows/pytest.yml

@@ -22,11 +22,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest rocrate jsonschema roc-validator
+          pip install -r tests/requirements.txt
       - name: Test with pytest
         run: |
           pytest --tb=short -s
-        continue-on-error: true
       - name: Create action summary
         run: |
           cat tests/logging.md >> $GITHUB_STEP_SUMMARY
+        if: always()

tests/requirements.in

@@ -0,0 +1,4 @@
+jsonschema
+pytest
+rocrate
+roc-validator

tests/requirements.txt

@@ -0,0 +1,46 @@
+arcp==0.2.1
+attrs==25.1.0
+cattrs==24.1.2
+certifi==2025.1.31
+charset-normalizer==3.4.1
+click==8.1.8
+colorlog==6.9.0
+enum-tools==0.12.0
+html5lib==1.1
+idna==3.10
+iniconfig==2.0.0
+inquirerpy==0.3.4
+Jinja2==3.1.5
+jsonschema==4.23.0
+jsonschema-specifications==2024.10.1
+markdown-it-py==3.0.0
+MarkupSafe==3.0.2
+mdurl==0.1.2
+owlrl==6.0.2
+packaging==24.2
+pfzy==0.3.4
+platformdirs==4.3.6
+pluggy==1.5.0
+prettytable==3.14.0
+prompt_toolkit==3.0.50
+Pygments==2.19.1
+pyparsing==3.2.1
+pyshacl==0.26.0
+pytest==8.3.4
+python-dateutil==2.9.0.post0
+rdflib==7.1.3
+referencing==0.36.2
+requests==2.32.3
+requests-cache==1.2.1
+rich==13.9.4
+rich-click==1.8.5
+roc-validator==0.5.0
+rocrate==0.13.0
+rpds-py==0.22.3
+six==1.17.0
+toml==0.10.2
+typing_extensions==4.12.2
+url-normalize==1.4.3
+urllib3==2.3.0
+wcwidth==0.2.13
+webencodings==0.5.1

tests/test_00_pypi_rocrate.py

@@ -35,7 +35,7 @@ def test_main(self):
                 if not name.endswith('.eln'):
                   continue
                 fileName = os.path.join(root, name)
-                print(f'\n\nTry to parse: {fileName}')
+                print(f'\n\nTest 00: {fileName}')
                 with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
                     dirName = os.path.splitext(os.path.basename(fileName))[0]
                     try:

tests/test_01_params_metadata_json.py

@@ -89,7 +89,7 @@ def processNode(graph, nodeID):
                 if not name.endswith('.eln'):
                   continue
                 fileName = os.path.join(root, name)
-                print(f'\n\nParse: {fileName}')
+                print(f'\n\nTest 01: {fileName}')
                 with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
                     success = True
                     metadataJsonFile = [i for i in elnFile.namelist() if i.endswith(METADATA_FILE)][0]

tests/test_02_schema.py

@@ -38,7 +38,7 @@ def test_main(self):
                 if not name.endswith('.eln'):
                   continue
                 fileName = os.path.join(root, name)
-                print(f'\nInspect: {name}')
+                print(f'\nTest 02: {name}')
                 with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
                     metadataJsonFile = [i for i in elnFile.namelist() if i.endswith(METADATA_FILE)][0]
                     metadataContent = json.loads(elnFile.read(metadataJsonFile))

tests/test_03_validator.py

@@ -5,14 +5,13 @@
 """
 import os
 import json
+import logging
 import tempfile
 import unittest
 from pathlib import Path
 from zipfile import ZIP_DEFLATED
 from zipfile import ZipFile
-import rocrate_validator
-from rocrate_validator.errors import ValidationError
-import rocrate_validator.services as rvs
+from rocrate_validator import services, models
 
 LABEL = 'validator'
 METADATA_FILE = 'ro-crate-metadata.json'
@@ -26,6 +25,7 @@ def test_main(self):
         main function
         """
         # log-file
+        logging.getLogger('rdflib').setLevel(logging.ERROR) # get rid of verbose rdflib warnings, we concentrate on validator directly
         if Path('tests/logging.json').exists():
             logJson = json.load(open('tests/logging.json'))
         else:
@@ -36,30 +36,28 @@ def test_main(self):
                 if not name.endswith('.eln'):
                   continue
                 fileName = os.path.join(root, name)
-                print(f'\n\nTry to parse: {fileName}')
+                print(f'\n\nTest 03: {fileName}')
                 with ZipFile(fileName, 'r', compression=ZIP_DEFLATED) as elnFile:
                     dirpath = Path(tempfile.mkdtemp())/Path(fileName).parent.name
                     dirpath.mkdir(parents=True, exist_ok=True)
                     elnFile.extractall(dirpath)
                     rocrate_dir= [i for i in dirpath.iterdir() if i.is_dir()][0]
-                    result = rvs.validate({
-                        "profiles_path": rocrate_validator.utils.get_profiles_path(),
-                        "profile_identifier": "ro-crate",
-                        "requirement_severity": rocrate_validator.models.Severity.REQUIRED.name,
-                        "requirement_severity_only": False,
-                        "inherit_profiles": True,
-                        "verbose": True,
-                        "data_path": rocrate_dir,
-                        "ontology_path": None,
-                        "abort_on_first": False
-                        })
-                    result_dict = result.to_dict()
-                    if result_dict['issues'] == [] and result_dict['passed']:
+
+                    # start validation
+                    settings = services.ValidationSettings(
+                        rocrate_uri=rocrate_dir,
+                        profile_identifier='ro-crate-1.1',
+                        requirement_severity=models.Severity.REQUIRED,
+                    )
+                    result = services.validate(settings)
+                    if not result.has_issues():
                         success = True
                     else:
                         print(f'{fileName} is not valid')
-                        print(result_dict)
+                        for issue in result.get_issues():
+                            print(f"Detected issue of severity {issue.severity.name} with check \"{issue.check.identifier}\": {issue.message}")
                         success = False
+
                 logJson[fileName] = logJson.get(fileName,{}) | {LABEL: success}
             json.dump(logJson, open('tests/logging.json', 'w'))
         assert success

tests/test_99_logging.py

@@ -28,7 +28,7 @@ def test_main(self):
                     individualFileName = Path(filename).parts[2]
                     if len(individualFileName)>30:
                         individualFileName=individualFileName[:24]+'...eln'
-                    resultStr   = ' | '.join([':white_check_mark:' if result[col] else ':x:' for col in COLUMNS])
+                    resultStr   = ' | '.join([':white_check_mark:' if col in result and result[col] else ':x:' for col in COLUMNS])
                     output.write(f'| {software} | {individualFileName} | {resultStr} |\n')
                 output.write("\n\nDefinition of tests\n")
                 output.write("- **pypi_rocrate**: tests if eln-file can be opened by pypi's rocrate; if eln file can be easily opened by that library.\n")