Utilize a single JSON_SCHEMA_FILE_RESOLVER setting for all defined sc…

…hemas

refinery/analysis_manager/schemas/AnalysisConfig.json

@@ -8,27 +8,21 @@
     "workflow_uuid"
 
   ],
-  "patterns": {
-    "uuid": {
-      "type": "string",
-      "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
-    }
-  },
   "properties": {
     "name": {
       "type": "string"
     },
     "study_uuid": {
-      "$ref": "#/patterns/uuid"
+      "$ref": "core/schemas/Base.json#patterns/uuid"
     },
     "tool_uuid": {
-      "$ref": "#/patterns/uuid"
+      "$ref": "core/schemas/Base.json#patterns/uuid"
     },
     "user_id": {
       "type": "number"
     },
     "workflow_uuid": {
-      "$ref": "#/patterns/uuid"
+      "$ref": "core/schemas/Base.json#patterns/uuid"
     }
   }
 }

refinery/analysis_manager/utils.py

@@ -190,7 +190,11 @@ def validate_analysis_config(analysis_config):
     with open(settings.REFINERY_ANALYSIS_CONFIG_SCHEMA) as f:
         schema = json.loads(f.read())
     try:
-        validate(analysis_config, schema)
+        validate(
+            analysis_config,
+            schema,
+            resolver=settings.JSON_SCHEMA_FILE_RESOLVER
+        )
     except ValidationError as e:
         raise RuntimeError(
             "Analysis Configuration is invalid: {}".format(e)

refinery/config/settings/base.py

@@ -8,6 +8,7 @@
 from django.core.exceptions import ImproperlyConfigured
 
 import djcelery
+from jsonschema import RefResolver
 import yaml
 
 logger = logging.getLogger(__name__)
@@ -690,3 +691,9 @@ def get_setting(name, settings=local_settings, default=None):
     BASE_DIR,
     "refinery/tool_manager/schemas/WorkflowStep.json"
 )
+
+# Allow JSONSchema to find the JSON pointers to our schema files
+JSON_SCHEMA_FILE_RESOLVER = RefResolver(
+    "file://{}/".format(os.path.join(BASE_DIR, "refinery")),
+    None
+)

refinery/tool_manager/schemas/ToolDefinition.json

@@ -16,12 +16,12 @@
           "type": "string"
         },
         "file_relationship": {
-          "$ref": "FileRelationship.json#"
+          "$ref": "tool_manager/schemas/FileRelationship.json#"
         },
         "parameters": {
           "type": "array",
           "items": {
-            "$ref": "GalaxyParameter.json#"
+            "$ref": "tool_manager/schemas/GalaxyParameter.json#"
           }
         },
         "tool_type":{
@@ -48,12 +48,12 @@
           "type": "string"
         },
         "file_relationship": {
-          "$ref": "FileRelationship.json#"
+          "$ref": "tool_manager/schemas/FileRelationship.json#"
         },
         "parameters": {
           "type": "array",
           "items": {
-            "$ref": "Parameter.json#"
+            "$ref": "tool_manager/schemas/Parameter.json#"
           }
         },
         "tool_type":{

refinery/tool_manager/schemas/ToolLaunchConfig.json

@@ -7,8 +7,8 @@
     "file_relationships"
   ],
   "properties": {
-    "dataset_uuid": {"$ref": "Base.json#patterns/uuid"},
-    "tool_definition_uuid": {"$ref": "Base.json#patterns/uuid"},
+    "dataset_uuid": {"$ref": "core/schemas/Base.json#patterns/uuid"},
+    "tool_definition_uuid": {"$ref": "core/schemas/Base.json#patterns/uuid"},
     "file_relationships": {
       "oneOf": [
         {"type": "string"},

refinery/tool_manager/schemas/WorkflowStep.json

@@ -6,7 +6,7 @@
       "type": "array",
       "items": {
         "type": "object",
-        "$ref": "Parameter.json#"
+        "$ref": "tool_manager/schemas/Parameter.json#"
       }
     }
   }

refinery/tool_manager/utils.py

@@ -1,7 +1,6 @@
 import glob
 import json
 import logging
-import os
 import uuid
 
 from django.conf import settings
@@ -10,7 +9,7 @@
 
 from bioblend.galaxy.client import ConnectionError
 from django_docker_engine.docker_utils import DockerClientWrapper
-from jsonschema import RefResolver, ValidationError, validate
+from jsonschema import ValidationError, validate
 
 from core.models import DataSet, Workflow, WorkflowEngine
 from factory_boy.django_model_factories import (FileRelationshipFactory,
@@ -32,13 +31,6 @@
     "https://github.com/refinery-platform/refinery-platform/wiki/"
     "Annotating-&-Importing-Refinery-Tools#importing-refinery-tools"
 )
-# Allow JSON Schema to find the JSON pointers we define in our schemas
-JSON_SCHEMA_FILE_RESOLVER = RefResolver(
-    "file://{}/".format(
-        os.path.join(settings.BASE_DIR, "refinery/tool_manager/schemas")
-    ),
-    None
-)
 
 
 class AdminFieldPopulator(admin.ModelAdmin):
@@ -449,7 +441,6 @@ def validate_tool_annotation(annotation_dictionary):
     properly.
     :param annotation_dictionary: dict containing Tool annotation data
     """
-
     with open(settings.REFINERY_TOOL_DEFINITION_SCHEMA) as f:
         schema = json.loads(f.read())
     annotation_to_validate = annotation_dictionary["annotation"]
@@ -459,7 +450,7 @@ def validate_tool_annotation(annotation_dictionary):
         validate(
             annotation_to_validate,
             schema,
-            resolver=JSON_SCHEMA_FILE_RESOLVER
+            resolver=settings.JSON_SCHEMA_FILE_RESOLVER
         )
     except ValidationError as e:
         raise RuntimeError(
@@ -484,7 +475,7 @@ def validate_workflow_step_annotation(workflow_step_dictionary):
         validate(
             workflow_step_dictionary,
             schema,
-            resolver=JSON_SCHEMA_FILE_RESOLVER
+            resolver=settings.JSON_SCHEMA_FILE_RESOLVER
         )
     except ValidationError as e:
         raise RuntimeError(
@@ -503,7 +494,7 @@ def validate_tool_launch_configuration(tool_launch_config):
         validate(
             tool_launch_config,
             schema,
-            resolver=JSON_SCHEMA_FILE_RESOLVER
+            resolver=settings.JSON_SCHEMA_FILE_RESOLVER
         )
     except ValidationError as e:
         raise RuntimeError(