Merge pull request #59 from AustralianBioCommons/fix-dont-script-program-proj-rule-validate

Fix dont script program proj rule validate

Author: JoshuaHarris391

jupyter/protoyping.ipynb

@@ -17,18 +17,20 @@
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "True"
-      ]
-     },
-     "execution_count": 3,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "ValueError",
+     "evalue": "Schema 'project' property 'consent_codes' with type 'array' must include an 'items' property. Please add an 'items' property to the 'properties' section.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
+      "\u001b[31mValueError\u001b[39m                                Traceback (most recent call last)",
+      "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[3]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m      1\u001b[39m lipid_schema = g.utils.load_yaml(\u001b[33m\"\u001b[39m\u001b[33m/Users/harrijh/projects/gen3schemadev/src/gen3schemadev/schema/schema_templates/project.yaml\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m      2\u001b[39m rule_val = g.validators.rule_validator.RuleValidator(lipid_schema)\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m \u001b[43mrule_val\u001b[49m\u001b[43m.\u001b[49m\u001b[43mtype_array_needs_items\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n",
+      "\u001b[36mFile \u001b[39m\u001b[32m~/projects/gen3schemadev/src/gen3schemadev/validators/rule_validator.py:226\u001b[39m, in \u001b[36mRuleValidator.type_array_needs_items\u001b[39m\u001b[34m(self)\u001b[39m\n\u001b[32m    224\u001b[39m     \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(value, \u001b[38;5;28mdict\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m value.get(\u001b[33m\"\u001b[39m\u001b[33mtype\u001b[39m\u001b[33m\"\u001b[39m) == \u001b[33m\"\u001b[39m\u001b[33marray\u001b[39m\u001b[33m\"\u001b[39m:\n\u001b[32m    225\u001b[39m         \u001b[38;5;28;01mif\u001b[39;00m \u001b[33m\"\u001b[39m\u001b[33mitems\u001b[39m\u001b[33m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m value:\n\u001b[32m--> \u001b[39m\u001b[32m226\u001b[39m             \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[32m    227\u001b[39m                 \u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mSchema \u001b[39m\u001b[33m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m.schema.get(\u001b[33m'\u001b[39m\u001b[33mid\u001b[39m\u001b[33m'\u001b[39m)\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m'\u001b[39m\u001b[33m property \u001b[39m\u001b[33m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m'\u001b[39m\u001b[33m with type \u001b[39m\u001b[33m'\u001b[39m\u001b[33marray\u001b[39m\u001b[33m'\u001b[39m\u001b[33m must include an \u001b[39m\u001b[33m'\u001b[39m\u001b[33mitems\u001b[39m\u001b[33m'\u001b[39m\u001b[33m property. \u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m    228\u001b[39m                 \u001b[33m\"\u001b[39m\u001b[33mPlease add an \u001b[39m\u001b[33m'\u001b[39m\u001b[33mitems\u001b[39m\u001b[33m'\u001b[39m\u001b[33m property to the \u001b[39m\u001b[33m'\u001b[39m\u001b[33mproperties\u001b[39m\u001b[33m'\u001b[39m\u001b[33m section.\u001b[39m\u001b[33m\"\u001b[39m\n\u001b[32m    229\u001b[39m             )\n\u001b[32m    230\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m\n",
+      "\u001b[31mValueError\u001b[39m: Schema 'project' property 'consent_codes' with type 'array' must include an 'items' property. Please add an 'items' property to the 'properties' section."
+     ]
     }
    ],
    "source": [
-    "lipid_schema = g.utils.load_yaml(\"../output/lipidomics_file.yaml\")\n",
+    "lipid_schema = g.utils.load_yaml(\"/Users/harrijh/projects/gen3schemadev/src/gen3schemadev/schema/schema_templates/project.yaml\")\n",
     "rule_val = g.validators.rule_validator.RuleValidator(lipid_schema)\n",
     "rule_val.type_array_needs_items()"
    ]

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "Gen3SchemaDev"
-version = "2.3.1"
+version = "2.3.2"
 description = "Tool for data modelling in Gen3"
 authors = [
     {name = "JoshuaHarris391",email = "[email protected]"}

src/gen3schemadev/cli.py

@@ -205,9 +205,10 @@ def main():
 
         # Exclusion list
         exclude_schema_list = [
-            'project', '_definitions', '_settings',
-            '_terms', 'core_metadata_collection',
-            'program'
+            '_definitions',
+            '_settings',
+            '_terms',
+            'core_metadata_collection',
         ]
         if args.no_exclude:
             print(f"Validation now includes: {exclude_schema_list}")

src/gen3schemadev/schema/schema_templates/project.yaml

@@ -126,6 +126,34 @@ properties:
       \ and/or material might be removed, stored or used. \\n\n        Based on the\
       \ Data Use Ontology : see http://www.obofoundry.org/ontology/duo.html"
     type: array
+    items:
+      type: string
+      enum:
+      - General Research Use
+      - Health or Biomedical Research
+      - Disease Specific Research
+      - not for profit, non commercial user only
+      - ethics approval required
+      - user specific restriction
+      enumDef:
+      - enumeration: General Research Use
+        source: duo
+        term_id: DUO:0000042
+      - enumeration: Health or Biomedical Research
+        source: duo
+        term_id: DUO:0000006
+      - enumeration: Disease Specific Research
+        source: duo
+        term_id: DUO:0000007
+      - enumeration: not for profit, non commercial user only
+        source: duo
+        term_id: DUO:0000018
+      - enumeration: ethics approval required
+        source: duo
+        term_id: DUO:0000021
+      - enumeration: user specific restriction
+        source: duo
+        term_id: DUO:0000026
   data_access_url:
     description: A URL link that takes you to a page that explains how to gain access
       to the project