Merge pull request #60 from AustralianBioCommons/fix-project-program-allowed-system-props

Fix project program allowed system props

Author: JoshuaHarris391

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "Gen3SchemaDev"
-version = "2.3.2"
+version = "2.3.3"
 description = "Tool for data modelling in Gen3"
 authors = [
     {name = "JoshuaHarris391",email = "[email protected]"}

src/gen3schemadev/validators/rule_validator.py

@@ -129,6 +129,15 @@ def _system_props(self):
         return system_props
 
     def props_cannot_be_system_props(self):
+        
+        if self.schema.get('id', '') == 'project':
+            logger.info("Skipping system property check for project schema.")
+            return True
+        
+        if self.schema.get('id', '') == 'program':
+            logger.info("Skipping system property check for program schema.")
+            return True
+        
         props = self._get_props()
         prop_keys = list(props.keys())
         schema_id = self.schema.get("id", "<unknown id>")

tests/test_converter.py

@@ -19,7 +19,6 @@ def test_get_node_names(fixture_input_yaml_pass):
     node_names = get_node_names(fixture_input_yaml_pass)
     assert 'lipidomics_file' in node_names
     assert 'sample' in node_names
-    assert 'project' in node_names
     assert 'assay' in node_names
 
 def test_get_node_data(fixture_input_yaml_pass):
@@ -214,22 +213,22 @@ def test_create_link_prop():
 
 
 def test_get_properties(fixture_input_yaml_pass):
-    result = get_properties("project", fixture_input_yaml_pass)
+    result = get_properties("lipidomics_file", fixture_input_yaml_pass)
     expected = [
         {
-            'project_id': {
-                'type': 'string',
-                'description': 'Synthetic_Dataset_1',
-                'required': True,
-                'enums': None
+            "cv": {
+                "type": "number",
+                "description": "Coefficient of variation (%)",
+                "enums": None,
+                "required": True
             }
         },
         {
-            'description': {
-                'type': 'string',
-                'description': 'Project containing synthetic data',
-                'required': False,
-                'enums': None
+            "lipid_species": {
+                "type": "array",
+                "enums": None,
+                "description": "List of lipid species",
+                "required": False
             }
         }
     ]