Merge pull request #507 from ISA-tools/issue-497-fix

Issue 497 fix
ISA-tools · Oct 23, 2023 · d246d77 · d246d77
2 parents b2ecfb0 + 4f41ecd
commit d246d77
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Showing 7 changed files with 21 additions and 11 deletions.
diff --git a/isatools/convert/isatab2json.py b/isatools/convert/isatab2json.py
@@ -19,7 +19,7 @@
 log = logging.getLogger('isatools')
 
 SCHEMAS_PATH = join(os.path.dirname(os.path.realpath(__file__)),
-                    "../resources/schemas/v1.0.1/")
+                    "..", "resources", "schemas", "isa_model_version_1_0_schemas", "core")
 INVESTIGATION_SCHEMA = "investigation_schema.json"
 
 # REGEXES

diff --git a/isatools/model/context.py b/isatools/model/context.py
@@ -145,6 +145,7 @@ def __init__(self) -> None:
     def gen_id(self) -> str:
         """ Generate an identifier for the object. """
         prepend = self.context.prepend_url if self.context.prepend_url else ''
+
         if isinstance(self, Identifiable):
             return self.id if self.id.startswith('http') else prepend + self.id
         return prepend + gen_id(self.__class__.__name__)

diff --git a/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json b/isatools/resources/schemas/isa_model_version_1_0_schemas/core/process_schema.json
@@ -7,8 +7,8 @@
     "type": "object",
     "properties": {
         "@id": { "type": "string", "format": "uri-reference" },
-      "@context": { "type": "string", "format": "uri-reference"},
-      "@type" : { "type": "string", "enum": ["Process"] },
+        "@context": { "type": "string", "format": "uri-reference"},
+        "@type" : { "type": "string", "enum": ["Process"] },
         "name": {
             "type": "string"
         },

diff --git a/isatools/resources/schemas/v1.0.1/study_schema.json b/isatools/resources/schemas/v1.0.1/study_schema.json
@@ -91,6 +91,12 @@
         "$ref": "factor_schema.json#"
       }
     },
+    "study_groups": {
+      "type": "array",
+      "items": {
+        "$ref": "study_group.json#"
+      }
+    },
     "characteristicCategories": {
       "description": "List of all the characteristics categories (or material attributes) defined in the study, used to avoid duplication of their declaration when each material_attribute_value is created. ",
       "type": "array",
@@ -105,6 +111,10 @@
         "$ref": "ontology_annotation_schema.json#"
       }
     },
+    "license": {
+      "type": "string",
+      "enum": [""]
+    },
     "comments" : {
       "type": "array",
       "items": {

diff --git a/tests/convert/test_isatab2w4m.py b/tests/convert/test_isatab2w4m.py
@@ -46,7 +46,7 @@ def plain_test(self, study, test_dir):
             output_file = os.path.join(self._tmp_dir, '.'.join(
                 ['-'.join([study, 'w4m', x]), 'tsv']))
             self.assertTrue(os.path.exists(output_file))
-            self.assertTrue(filecmp.cmp(output_file, ref_file),
+            self.assertTrue(filecmp.cmp(output_file, ref_file, shallow=False),
                             'Output file "{0}" differs from reference file "{1}".'.format(output_file, ref_file))
 
     # Test MTBLS30

diff --git a/tests/model/test_to_dict.py b/tests/model/test_to_dict.py
@@ -177,7 +177,7 @@ def test_study_to_dict(self):
 
         # Test study design descriptors
         study.design_descriptors = [
-            OntologyAnnotation(term_accession='accession1', term_source='source1', term='name1', id_='id1',
+            OntologyAnnotation(term_accession='accession1', term_source=OntologySource(name='source1'), term='name1', id_='id1',
                                comments=comments)
         ]
         expected_dict['studyDesignDescriptors'] = [
@@ -261,7 +261,6 @@ def setUp(self):
 
     def test_to_ld(self):
 
-
         self.maxDiff = None
 
         comment_1 = Comment(name='comment_1', value='value_1')
@@ -312,13 +311,10 @@ def test_to_ld(self):
         self.investigation.publications = [publication]
         self.investigation.studies = [study]
 
-        inv_ld = self.investigation.to_ld()
-        investigation = Investigation()
-        investigation.from_dict(inv_ld)
-        self.assertEqual(investigation.to_dict(), self.investigation.to_dict())
-
         set_context(vocab='wd', all_in_one=False, local=False)
+
         inv_ld = self.investigation.to_ld()
         investigation = Investigation()
         investigation.from_dict(inv_ld)
         self.assertEqual(investigation.to_dict(), self.investigation.to_dict())
+
diff --git a/tests/validators/test_validate_test_data.py b/tests/validators/test_validate_test_data.py
@@ -354,9 +354,12 @@ def test_validate_testdata_treatment_sequence_json(self):
 class TestPerformerValidation(unittest.TestCase):
     def test_ptx(self):
         filepath = os.path.join(utils.TAB_DATA_DIR, 'TEST-PTX', 'i_investigation.txt')
+
         with open(filepath) as fp:
             investigation = isatab.load(fp)
             print(investigation.title)
+
+        with open(filepath) as fp:
             report = isatab.validate(fp)
             print(report["errors"])