Merge pull request #9 from smaht-dac/wrr_schema

Schema updates

CHANGELOG.rst

@@ -7,6 +7,13 @@ smaht-portal
 Change Log
 ----------
 
+0.0.6
+=====
+
+* Removes ``jsonschema_serialize_fork``, use new schema draft version
+* Implement ``$merge`` referential schema fields
+
+
 0.0.5
 =====
 
@@ -15,6 +22,7 @@ Change Log
 * Allow testing with ES in GA with smaht-development credentials
 * Build Docker as part of GA
 
+
 0.0.4
 =====
 
@@ -23,6 +31,7 @@ Change Log
 * Update to use Webpack 5
 * Do some light adjustments to be more compatible with Google Analytics 4 down the line
 
+
 0.0.3
 =====
 
@@ -34,9 +43,10 @@ Change Log
 
 * Implement base level permissioning scheme working with ``consortia`` and ``submission_center``
 
+
 0.0.1
 =====
 
 * Initial version
 * TODO: update base.ini, various other ini file templates once new AWS is provisioned
-* TOOD: build GLOBAL_ENV_BUCKET for testing (conftest.py)
+* TOOD: build GLOBAL_ENV_BUCKET for testing (conftest.py)

Dockerfile

@@ -23,7 +23,7 @@ ENV NGINX_USER=nginx \
     NVM_VERSION=v0.39.1 \
     NODE_VERSION=16.14.0
 
-# Configure Python3.7 venv
+# Configure Python3.9 venv
 ENV VIRTUAL_ENV=/opt/venv
 RUN python -m venv /opt/venv
 ENV PATH="$VIRTUAL_ENV/bin:$PATH"

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.0.5"
+version = "0.0.6"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -42,17 +42,15 @@ certifi = ">=2021.5.30"
 chardet = "3.0.4"
 codeguru-profiler-agent = "^1.2.4"
 colorama = "0.3.3"
-dcicsnovault = "8.2.0.1b45"
-dcicutils = "7.5.1.1b0"
-encoded-core = "^0.0.2"
+dcicsnovault = "^10.0.0"
+dcicutils = "^7.7.0"
+encoded-core = "^0.0.3"
 elasticsearch = "7.13.4"
 execnet = "1.4.1"
-# html5lib = "0.9999999"
 humanfriendly = "^1.44.9"
 hupper = "1.5"
 idna = ">=2.10,<3"
 jmespath = "0.9.0"
-jsonschema_serialize_fork = "^2.1.1"
 loremipsum = "1.0.5"
 netaddr = ">=0.8.0,<1"
 openpyxl = "^3.0.7,!=3.0.8"  # a version 3.0.8 appeared but then got withdrawn, for now just pin 3.0.7. try again later.
@@ -77,7 +75,6 @@ pyramid-retry = "^1.0"
 pyramid-tm = "^2.4"
 pyramid_translogger = "^0.1"
 python-dateutil = "^2.8.2"
-# python-magic is presently pinned to 0.4.15 in lockstep with dcicsnovault's requirements. See explanation there.
 python_magic = ">=0.4.24,<1"
 pytz = ">=2021.3"
 rdflib = "^4.2.2"
@@ -88,12 +85,10 @@ requests = "^2.23.0"
 rfc3986 = "^1.4.0"
 rsa = "3.3"
 rutter = ">=0.3,<1"
-# We don't use this directly. It's part of boto3. It slows down solving to pin.
-# s3transfer = ">=0.3.7,<0.4.0"
 sentry-sdk = "^1.5.6"
 simplejson = "^3.17.0"
 SPARQLWrapper = "^1.8.5"
-SQLAlchemy = "1.4.41"  # Pinned because >=1.3.17 is broken for us (circular constraints prevent deletes)
+SQLAlchemy = "1.4.41"
 structlog = ">=19.2.0,<20"
 #submit4dn = "0.9.7"
 subprocess-middleware = "^0.3.0"

src/encoded/project/authentication.py

@@ -8,7 +8,7 @@ def login(self, context, request, *, samesite):
 
     def namespaced_authentication_policy_authenticated_userid(self, namespaced_authentication_policy, request,
                                                               set_user_info_property):
-        set_user_info_property = False
+        set_user_info_property = True
         return super().namespaced_authentication_policy_authenticated_userid(namespaced_authentication_policy, request,
                                                                              set_user_info_property)
 

src/encoded/schema_formats.py

@@ -1,6 +1,6 @@
 import re
 from pyramid.threadlocal import get_current_request
-from jsonschema_serialize_fork import FormatChecker
+from snovault.schema_validation import FormatChecker
 from snovault.server_defaults import test_accession
 from .server_defaults import (
     ACCESSION_FACTORY,

src/encoded/schemas/consortium.json

@@ -1,7 +1,7 @@
 {
     "title": "Consortium",
-    "id": "/profiles/consortium.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/consortium.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "required": [
         "name",
         "title"

src/encoded/schemas/submission_center.json

@@ -1,7 +1,7 @@
 {
     "title": "SubmissionCenter",
-    "id": "/profiles/submission_center.json",
-    "$schema": "http://json-schema.org/draft-04/schema#",
+    "$id": "/profiles/submission_center.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
     "required": [
         "name",
         "title"

src/encoded/server_defaults.py

@@ -1,5 +1,5 @@
 from dcicutils.misc_utils import ignored
-from jsonschema_serialize_fork import NO_DEFAULT
+from snovault.schema_validation import NO_DEFAULT
 from snovault.schema_utils import server_default
 from snovault.server_defaults import get_user_resource
 

src/encoded/tests/test_merge_schemas.py

@@ -0,0 +1,23 @@
+import pytest
+from snovault.schema_utils import load_schema
+from .testing_views import TestingLinkedSchemaField
+
+
+class TestMergedSchemas:
+    """ Class that contains tests that validate $merge refs are correctly resolved within repo
+        and across repos
+    """
+
+    @staticmethod
+    def test_merged_schemas():
+        """ Checks that we can resolve multiple different schema $ref types """
+        schema = load_schema(TestingLinkedSchemaField.schema)
+        props = schema['properties']
+        for key in ['access_key_id', 'file_format', 'title']:
+            assert key in props
+        # check access key id
+        assert props['access_key_id']['comment'] == 'Only admins are allowed to set this value.'
+        # check file_format
+        assert props['file_format']['linkTo'] == 'FileFormat'
+        # check title
+        assert props['title']['description'] == 'A title for the Consortium.'

src/encoded/tests/test_permissions.py

@@ -52,6 +52,20 @@ def consortium_file(testapp, fastq_format, test_consortium):
     return res.json['@graph'][0]
 
 
+class TestAdminPermissions:
+    """ Tests admins can do various actions, including purging items """
+
+    @staticmethod
+    def test_admin_can_purge(testapp, fastq_format):
+        testapp.patch_json(f'/{fastq_format["uuid"]}', {'status': 'deleted'}, status=200)
+        testapp.delete_json(f'/{fastq_format["uuid"]}/?purge=True', {}, status=200)
+
+    @staticmethod
+    def test_non_admin_cannot_purge(submitter_testapp, fastq_format):
+        submitter_testapp.patch_json(f'/{fastq_format["uuid"]}', {'status': 'deleted'}, status=422)
+        submitter_testapp.delete_json(f'/{fastq_format["uuid"]}/?purge=True', {}, status=403)
+
+
 class TestPermissionsHelper:
 
     @staticmethod

src/encoded/tests/test_schemas.py

@@ -99,7 +99,7 @@ def test_load_schema(schema, master_mixins, registry, testapp):
 
     if schema not in ['namespaces.json', 'mixins.json']:
         # check that schema.id is same as /profiles/schema
-        idtag = loaded_schema['id']
+        idtag = loaded_schema['$id']
         idtag = idtag.replace('/profiles/', '')
         # special case for access_key.json
         if schema == 'access_key.json':

src/encoded/tests/testing_views.py

@@ -62,3 +62,37 @@ class TestingPostPutPatch(Item):
             },
         }
     }
+
+
+@collection(
+    'testing-linked-schema-fields',
+    acl=[
+        (Allow, 'group.submitter', ['add', 'edit', 'view']),
+    ],
+)
+class TestingLinkedSchemaField(Item):
+    item_type = 'testing_linked_schema_field'
+    schema = {
+        'type': 'object',
+        'additionalProperties': False,
+        'properties': {
+            "schema_version": {
+                "type": "string",
+                "pattern": "^\\d+(\\.\\d+)*$",
+                "requestMethod": [],
+                "default": "1",
+            },
+            # link from snovault field
+            'access_key_id': {
+                '$merge': 'snovault:schemas/access_key.json#/properties/access_key_id'
+            },
+            # link from encoded-core field
+            'file_format': {
+                '$merge': 'encoded_core:schemas/file.json#/properties/file_format'
+            },
+            # link from this repo
+            'title': {
+                '$merge': 'encoded:schemas/consortium.json#/properties/title'
+            }
+        }
+    }