Improved tests and included rocrate validator

.github/workflows/pytest.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install pytest rocrate jsonschema
+          pip install pytest rocrate jsonschema rocrateValidator
       - name: Test with pytest
         run: |
           pytest --tb=no -s

tests/test_00_pypi_rocrate.py

@@ -13,6 +13,7 @@
 from rocrate.rocrate import ROCrate
 
 LABEL = 'pypi_rocrate'
+verbose = False
 
 class Test_1(unittest.TestCase):
     """
@@ -43,7 +44,8 @@ def test_main(self):
                         tempPath= [i for i in dirpath.iterdir() if i.is_dir()][0]
                         crate = ROCrate(tempPath)
                         for e in crate.get_entities():
-                            print(f'  {e.id}: {e.type}')
+                            if verbose:
+                                print(f'  {e.id}: {e.type}')
                         if fileName not in logJson:
                             logJson[fileName] = {LABEL:True}
                         else:

tests/test_01_params_metadata_json.py

@@ -27,7 +27,7 @@ def test_main(self):
         # runtime global variables
         METADATA_FILE = 'ro-crate-metadata.json'
         OUTPUT_INFO = False
-        OUTPUT_COUNTS = True
+        OUTPUT_COUNTS = False
         KNOWN_KEYS = DATASET_MANDATORY+DATASET_SUGGESTED+FILE_MANDATORY+FILE_SUGGESTED+['@id', '@type']
         LABEL = 'params_metadata_json'
 

tests/test_03_validator.py

@@ -0,0 +1,65 @@
+#!/usr/bin/python3
+"""
+Validate if rocrate of pypi can open and parse it. This is a test if we follow general ro-crate guidelines.
+https://pypi.org/project/rocrate/
+"""
+import os
+import json
+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
+
+LABEL = 'validator'
+METADATA_FILE = 'ro-crate-metadata.json'
+
+class Test_1(unittest.TestCase):
+    """
+    derived class for this test
+    """
+    def test_main(self):
+        """
+        main function
+        """
+        # log-file
+        if Path('tests/logging.json').exists():
+            logJson = json.load(open('tests/logging.json'))
+        else:
+            logJson = {}
+
+        for root, _, files in os.walk(".", topdown=False):
+            for name in files:
+                if not name.endswith('.eln'):
+                  continue
+                fileName = os.path.join(root, name)
+                print(f'\n\nTry to parse: {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']:
+                        success = True
+                    else:
+                        print(f'{fileName} is not valid')
+                        print(result_dict)
+                        success = False
+                logJson[fileName] = logJson.get(fileName,{}) | {LABEL: success}
+            json.dump(logJson, open('tests/logging.json', 'w'))
+        assert success

tests/test_99_logging.py

@@ -4,7 +4,7 @@
 import json
 import unittest
 
-COLUMNS = ['params_metadata_json', 'pypi_rocrate','schema']
+COLUMNS = ['pypi_rocrate','validator','schema','params_metadata_json']
 HEADER  = "## Results of verification\nautomatically created\n\n"
 
 
@@ -31,9 +31,10 @@ def test_main(self):
                     resultStr   = ' | '.join([':white_check_mark:' if 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; aka if eln file conforms to rocrate convention.\n")
-                output.write("- **params_metadata_json**: tests if the conventions of the consortium are fulfilled, aka parameters exist and are consistent with convention.\n")
-                output.write("- **schema**: tests if the conventions of the consortium are fulfilled using a schema description.\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")
+                output.write("- **validator**: tests if the ro-crate conventions fulfilled using pypi's rocrateValidator.\n")
+                output.write("- **schema**: tests if the conventions of the ELN-consortium are fulfilled using a schema description.\n")
+                output.write("- **params_metadata_json**: tests if the conventions of the ELN-consortium are fulfilled, aka parameters exist and are consistent with convention.\n")
                 output.close()
             print('Created logging markdown')
         else: