Automatically validate oraganise configs

arteria-project · Sep 15, 2023 · 7777dd1 · 7777dd1
1 parent f649b10
commit 7777dd1
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Showing 3 changed files with 49 additions and 38 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,9 +18,15 @@ jobs:
         python -m pip install --upgrade pip
         pip install wheel
         pip install -r requirements/dev .
+        npm install -g pajv
     - name: Launch tests
       run: |
         nosetests ./tests
     - name: Lint config files
       run: |
         yamllint -c .yamllint.yml config/organise_configs/*.yml
+    - name: Validate config files
+      run: >
+        pajv
+        -s config/organise_configs/schema.json
+        -d config/organise_configs/*.yml
diff --git a/config/organise_configs/schema.json b/config/organise_configs/schema.json
@@ -0,0 +1,34 @@
+{
+    "type": "object",
+    "required": ["variables", "files_to_organise"],
+    "properties": {
+        "variables": {
+            "type": "object",
+            "additionalProperties": {"type": "string"}
+        },
+        "files_to_organise": {
+            "type": "array",
+            "items": {
+                "type": "object",
+                "required": ["source", "destination", "options"],
+                "properties": {
+                    "source": {"type": "string"},
+                    "destination": {"type": "string"},
+                    "options": {
+                        "type": "object",
+                        "properties": {
+                            "required": {"type": "boolean"},
+                            "link_type": {
+                                "type": "string",
+                                "enum": ["softlink", "hardlink", "copy"]
+                            },
+                            "filter": {"type": "string"}
+                        },
+                        "additionalProperties": false
+                    }
+                }
+            }
+        }
+    },
+    "additionalProperties": false
+}
diff --git a/delivery/handlers/organise_handlers.py b/delivery/handlers/organise_handlers.py
@@ -12,41 +12,6 @@
 
 log = logging.getLogger(__name__)
 
-ORGANISE_CONFIG_SCHEMA = {
-    "type": "object",
-    "required": ["variables", "files_to_organise"],
-    "properties": {
-        "variables": {
-            "type": "object",
-            "additionalProperties": {"type": "string"},
-        },
-        "files_to_organise": {
-            "type": "array",
-            "items": {
-                "type": "object",
-                "required": ["source", "destination", "options"],
-                "properties": {
-                    "source": {"type": "string"},
-                    "destination": {"type": "string"},
-                    "options": {
-                        "type": "object",
-                        "properties": {
-                            "required": {"type": "boolean"},
-                            "link_type": {
-                                "type": "string",
-                                "enum": ["softlink", "hardlink", "copy"],
-                            },
-                            "filter": {"type": "string"},
-                        },
-                        "additionalProperties": False,
-                    }
-                }
-            }
-        }
-    },
-    "additionalProperties": False,
-}
-
 
 class BaseOrganiseHandler(BaseRestHandler):
     pass
@@ -145,7 +110,9 @@ def post(self, analysis_pipeline, project):
                 f"Config file not found at {organise_config_path}")
         with open(organise_config_path, 'r') as organise_config_file:
             config = yaml.load(organise_config_file, Loader=yaml.CLoader)
-            jsonschema.validate(config, ORGANISE_CONFIG_SCHEMA)
+        with open(organise_config_dir / "schema.json", 'r') as organise_config_schema:
+            schema = json.load(organise_config_schema)
+        jsonschema.validate(config, schema)
 
         if not project_path.is_dir():
             raise FileNotFoundError(
@@ -176,7 +143,9 @@ def post(self, project):
                 f"Config file not found at {organise_config_path}")
         with open(organise_config_path, 'r') as organise_config_file:
             config = yaml.load(organise_config_file, Loader=yaml.CLoader)
-            jsonschema.validate(config, ORGANISE_CONFIG_SCHEMA)
+        with open(pathlib.Path(self.config["organise_config_dir"]) / "schema.json", 'r') as organise_config_schema:
+            schema = json.load(organise_config_schema)
+        jsonschema.validate(config, schema)
 
         if not project_path.is_dir():
             raise FileNotFoundError(
@@ -211,7 +180,9 @@ def post(self, runfolder):
                 f"Config file not found at {organise_config_path}")
         with open(organise_config_path, 'r') as organise_config_file:
             config = yaml.load(organise_config_file, Loader=yaml.CLoader)
-            jsonschema.validate(config, ORGANISE_CONFIG_SCHEMA)
+        with open(organise_config_dir / "schema.json", 'r') as organise_config_schema:
+            schema = json.load(organise_config_schema)
+        jsonschema.validate(config, schema)
 
         if not runfolder_path.is_dir():
             raise FileNotFoundError(