Second DRS Fix

CHANGELOG.rst

@@ -6,8 +6,16 @@ snovault
 Change Log
 ----------
 
+
 11.22.0
 =======
+
+* Update ``drs`` validation to remove drs_uri
+
+
+11.22.0
+=======
+
 * 2024-09-03/dmichaels
   - Fix in snovault/tests/elasticsearch_fixture.py (use only for local/dev deploy) for
     strange (new as of 2024-09-02) behavior where it was hanging on startup during

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicsnovault"
-version = "11.22.0"
+version = "11.22.0.1b1"  # TODO: To become 11.23.0
 description = "Storage support for 4DN Data Portals."
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

snovault/drs.py

@@ -1,5 +1,6 @@
 from pyramid.view import view_config
 from pyramid.exceptions import HTTPNotFound
+from pyramid.response import Response
 from .util import debug_log
 
 
@@ -12,7 +13,6 @@
 REQUIRED_FIELDS = [
     'id',
     'created_time',
-    'drs_id',
     'self_uri',
     'size',
     'checksums'
@@ -54,7 +54,8 @@ def get_and_format_drs_object(request, object_uri):
     except Exception:
         raise HTTPNotFound('You accessed a DRS object_uri that either does not exist'
                            ' or you do not have access to it.')
-    drs_object['self_uri'] = f'drs://{request.host}{request.path}'
+    uri = drs_object['id']
+    drs_object['self_uri'] = f'drs://{request.host}/{uri}'
     return drs_object
 
 
@@ -83,13 +84,15 @@ def get_drs_url(request, object_uri):
 
 
 @view_config(
-    route_name='drs_objects', request_method='GET'
+    route_name='drs_objects', request_method=['GET', 'OPTIONS']
 )
 @debug_log
 def drs_objects(context, request):
     """ Implements DRS GET as specified by the API description
     https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.0.0/docs/#_getobject
     """
+    if request.method == 'OPTIONS':
+        return Response(status_code=204)
     drs_object_uri = '/' + request.matchdict['object_id']
     formatted_drs_object = get_and_format_drs_object(request, drs_object_uri)
     try:

snovault/renderers.py

@@ -110,7 +110,7 @@ def validate_request_tween(request):
         if 'X_REQUEST_METHOD' in environ:
             environ['REQUEST_METHOD'] = environ['X_REQUEST_METHOD']
 
-        if request.method in ('GET', 'HEAD'):
+        if request.method in ('GET', 'HEAD', 'OPTIONS'):
             # If GET request, don't need to check `request.content_type`
             # Includes page text/html requests.
             return handler(request)

snovault/resources.py

@@ -528,10 +528,19 @@ def rev_link_atids(self, request, rev_name):
                 self.get_filtered_rev_links(request, rev_name)]
 
     def unique_keys(self, properties):
-        return {
+        """ This function used to only resolve keys from schema, it has been
+            updated to handle both accession and alternate_accession
+        """
+        keys = {
             name: [v for prop in props for v in ensurelist(properties.get(prop, ()))]
             for name, props in self.type_info.schema_keys.items()
         }
+        if 'accession' not in self.schema['properties']:
+            return keys
+        keys.setdefault('accession', []).extend(properties.get('alternate_accessions', []))
+        if properties.get('status') != 'replaced' and 'accession' in properties:
+            keys['accession'].append(properties['accession'])
+        return keys
 
     def add_accession_to_title(self, title):
         if self.properties.get('accession') is not None:

snovault/test_schemas/TestingDownload.json

@@ -3,7 +3,8 @@
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "mixinProperties": [
         { "$ref": "mixins.json#/status" },
-        { "$ref": "mixins.json#/submitted" }
+        { "$ref": "mixins.json#/submitted" },
+        { "$ref": "mixins.json#/accession" }
     ],
     "properties": {
         "attachment": {
@@ -25,6 +26,9 @@
                     "enum": ["image/png"]
                 }
             }
+        },
+        "accession": {
+            "accessionType": "TD"
         }
     }
 }

snovault/test_schemas/mixins.json

@@ -69,5 +69,33 @@
             "pattern": "^[a-zA-Z0-9_\\-][a-zA-Z0-9_\\-\\s]+[a-zA-Z0-9_\\-]$"
         }
     }
-  } 
+  },
+   "accession": {
+        "accession": {
+            "title": "Accession",
+            "description": "A unique identifier to be used to reference the object.",
+            "internal_comment": "Only admins are allowed to set or update this value.",
+            "exclude_from": [
+                "FFedit-create"
+            ],
+            "type": "string",
+            "format": "accession",
+            "permission": "restricted_fields",
+            "serverDefault": "accession"
+        },
+        "alternate_accessions": {
+            "title": "Alternate Accessions",
+            "description": "Accessions previously assigned to objects that have been merged with this object.",
+            "type": "array",
+            "lookup": 1000,
+            "internal_comment": "Only admins are allowed to set or update this value.",
+            "items": {
+                "title": "Alternate Accession",
+                "description": "An accession previously assigned to an object that has been merged with this object.",
+                "type": "string",
+                "permission": "restricted_fields",
+                "format": "accession"
+            }
+        }
+    }
 }

snovault/tests/test_drs.py

@@ -12,13 +12,17 @@ class TestDRSAPI:
     def test_drs_get_object(self, testapp, testing_download):  # noQA fixture
         """ Tests basic structure about a drs object """
         res = testapp.get(testing_download)
-        drs_object_uri = res.json['uuid']
+        drs_object_uri = res.json['accession']
+        drs_object_uuid = res.json['uuid']
+        testapp.options(f'/ga4gh/drs/v1/objects/{drs_object_uri}',
+                        headers={'Content-Type': 'application/json'}, status=204)
         drs_object_1 = testapp.get(f'/ga4gh/drs/v1/objects/{drs_object_uri}').json
         for key in REQUIRED_FIELDS:
             assert key in drs_object_1
-        assert drs_object_1['self_uri'] == f'drs://localhost:80/ga4gh/drs/v1/objects/{drs_object_uri}'
+        assert drs_object_1['self_uri'] == f'drs://localhost:80/{drs_object_uri}'
         assert (drs_object_1['access_methods'][0]['access_url']['url']
-                == f'{self.BASE_URL}{drs_object_uri}/@@download')
+                == f'{self.BASE_URL}{drs_object_uuid}/@@download')
+        assert (drs_object_1['access_methods'][0]['access_id'] == 'http')
 
         # failure cases
         testapp.get(f'/ga4gh/drs/v1/objects/not_a_uri', status=404)

snovault/tests/testing_views.py

@@ -228,15 +228,6 @@ def __ac_local_roles__(self):
             #     roles[viewing_group_members] = 'role.viewing_group_member'
         return roles
 
-    def unique_keys(self, properties):
-        keys = super(Item, self).unique_keys(properties)
-        if 'accession' not in self.schema['properties']:
-            return keys
-        keys.setdefault('accession', []).extend(properties.get('alternate_accessions', []))
-        if properties.get('status') != 'replaced' and 'accession' in properties:
-            keys['accession'].append(properties['accession'])
-        return keys
-
     @calculated_property(schema={
         "title": "Display Title",
         "description": "A calculated title for every object in 4DN",
@@ -418,6 +409,7 @@ class NestedObjectLinkTarget(Item):
 
 @collection(
     'testing-downloads',
+    unique_key='accession',
     properties={
         'title': 'Test download collection',
         'description': 'Testing. Testing. 1, 2, 3.',
@@ -436,11 +428,11 @@ def drs(context, request):
         downstream API (see drs.py).
     """
     rendered_object = request.embed(str(context.uuid), '@@object', as_user=True)
+    accession = rendered_object['accession']
     drs_object = {
-        'id': rendered_object['@id'],
+        'id': accession,
         'created_time': rendered_object['date_created'],
-        'drs_id': rendered_object['uuid'],
-        'self_uri': f'drs://{request.host}{request.path}',
+        'self_uri': f'drs://{request.host}/{accession}',
         'size': 0,
         'checksums': [
             {
@@ -453,7 +445,8 @@ def drs(context, request):
                 'access_url': {
                     'url': f'http://{request.host}/{context.uuid}/@@download'
                 },
-                'type': 'http'
+                'type': 'http',
+                'access_id': 'http'
             },
         ]
     }