Adding REST API for small variants (#332)

.github/workflows/ci.yml

@@ -63,10 +63,9 @@ jobs:
         uses: actions/checkout@v2
       - name: install project Python dependencies
         run: |
-          pip install wheel==0.36.2
+          pip install wheel==0.37.1
           pip install -r requirements/local.txt
           pip install -r requirements/test.txt
-          pip install -U 'celery >4.2'
           pip freeze
       - name: Build and run Vue app
         run: |

HISTORY.rst

@@ -46,6 +46,7 @@ End-User Summary
 - Fix issue with variant annotation export (#328)
 - Allowing direct update of variant annotations and ACMG ratings on case annotations details (#344)
 - Fixing problem with ACMD classifiction where VUS-3 was given but should be LB-2 (#359)
+- Adding REST API for creating small variant queries (#332)
 
 Full Change List
 ================
@@ -93,14 +94,16 @@ Full Change List
 - Fixing CADD annotation (#319)
 - Adding mitochondrial inheritance to case phenotype annotation (#325)
 - Fix issue with variant annotation export (#328)
-- Adding REST API versioning to (#333)
+- Adding REST API versioning (#333)
 - Adding more postgres versions to CI (#337)
 - Make migrations compatible with Postgres 14 (#338)
 - DgvSvs and DgvGoldStandardSvs are two different data sources now
 - Adding deep linking into case details tab (#344)
 - Allowing direct update of variant annotations and ACMG ratings on case annotations details (#344)
 - Removing `display_hgmd_public_membership` (#363)
 - Fixing problem with ACMD classifiction where VUS-3 was given but should be LB-2 (#359)
+- Adding REST API for creating small variant queries (#332)
+- Upgrading sodar-core dependency to 0.10.10
 
 -------
 v0.23.9

beaconsite/tests/test_views.py

@@ -2,23 +2,8 @@
 from Crypto.PublicKey import RSA
 from django.urls import reverse
 
-from test_plus.test import TestCase
-
 from beaconsite.models import Consortium, Site
-from beaconsite.tests.factories import ConsortiumFactory, SiteFactory
-from variants.tests.factories import ProjectFactory
-
-
-class TestViewsBase(TestCase):
-    def setUp(self):
-        self.superuser = self.make_user("superuser")
-        self.superuser.is_superuser = True
-        self.superuser.is_staff = True
-        self.superuser.save()
-
-        self.project = ProjectFactory()
-        self.consortium = ConsortiumFactory()
-        self.site = SiteFactory(role=Site.LOCAL, state=Site.ENABLED)
+from variants.tests.helpers import TestViewsBase
 
 
 class TestIndexView(TestViewsBase):

beaconsite/tests/test_views_api.py

@@ -1,15 +1,15 @@
 import cattr
 from django.shortcuts import reverse
-from projectroles.tests.test_views_api import TestAPIViewsBase
 
 from variants.tests.factories import SmallVariantFactory
+from variants.tests.helpers import ApiViewTestBase
 from .test_permissions_api import AcceptHeaderMixin
 from ..models import Site
 from .factories import ConsortiumWithLocalAndRemoteSiteFactory, ConsortiumAssignmentFactory
 from ..models_api import BeaconAlleleRequest
 
 
-class TestBeaconInfoApiView(AcceptHeaderMixin, TestAPIViewsBase):
+class TestBeaconInfoApiView(AcceptHeaderMixin, ApiViewTestBase):
     def setUp(self):
         super().setUp()
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
@@ -20,7 +20,7 @@ def setUp(self):
         )
 
     def test_get_info(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             extra = self.get_accept_header(None, None)
             response = self.client.get(reverse("beaconsite:beacon-api-info"), **extra)
         self.assertEqual(response.status_code, 200)
@@ -47,7 +47,7 @@ def test_get_info(self):
         )
 
 
-class TestBeaconQueryApiView(AcceptHeaderMixin, TestAPIViewsBase):
+class TestBeaconQueryApiView(AcceptHeaderMixin, ApiViewTestBase):
     def setUp(self):
         super().setUp()
         self.consortium = ConsortiumWithLocalAndRemoteSiteFactory()
@@ -71,7 +71,7 @@ def test_query(self):
             "%s=%s" % (k, v) for k, v in cattr.unstructure(self.beacon_allele_request).items()
         )
 
-        with self.login(self.user):
+        with self.login(self.superuser):
             extra = self.get_accept_header(None, None)
             response = self.client.get(url, **extra)
         self.assertEqual(response.status_code, 200)

config/settings/base.py

@@ -11,9 +11,11 @@
 import logging
 import os
 import environ
+import re
 import sys
 
 from dotenv import load_dotenv
+from varfish import __version__ as varfish_version
 
 logger = logging.getLogger(__name__)
 
@@ -594,8 +596,12 @@ def set_logging(level=None):
 PROJECTROLES_ENABLE_SEARCH = not KIOSK_MODE
 PROJECTROLES_SEARCH_PAGINATION = 5
 
-SODAR_API_DEFAULT_VERSION = "0.1"
-SODAR_API_MEDIA_TYPE = "application/vnd.bihealth.sodar+json"
+SODAR_API_MEDIA_TYPE = "application/vnd.bihealth.varfish+json"
+SODAR_API_DEFAULT_VERSION = re.match(r"^([0-9.]+)(?:[+|\-][\S]+)?$", varfish_version)[1]
+SODAR_API_ALLOWED_VERSIONS = [
+    "0.23.9",
+]
+
 
 PROJECTROLES_SITE_MODE = env.str("PROJECTROLES_SITE_MODE", "TARGET")
 PROJECTROLES_TARGET_CREATE = env.bool("PROJECTROLES_TARGET_CREATE", True)

docs_manual/api_case.rst

@@ -0,0 +1,62 @@
+.. _api_case:
+
+================
+Case & Query API
+================
+
+The REST API for case access and is described in this section.
+Cases are not managed directly but through the :ref:`api_importer`.
+
+
+----------
+Versioning
+----------
+
+For accept header versioning, the following media type and version are expected in the current VarFish version:
+
+.. code-block:: console
+
+    Accept: application/vnd.bihealth.varfish+json; version=0.23.9
+
+
+-----------
+Return Data
+-----------
+
+The return data for each request will be a JSON document unless otherwise
+specified.
+
+If return data is not specified in the documentation of an API view, it will
+return the appropriate HTTP status code along with an optional ``detail`` JSON
+field upon a successfully processed request.
+
+For creation views, the ``sodar_uuid`` of the created object is returned
+along with other object fields.
+
+--------------
+Query Settings
+--------------
+
+The query follows a :ref:`JSON Schema <api_json_schemas>`.
+
+---------
+API Views
+---------
+
+.. currentmodule:: variants.views_api
+
+.. autoclass:: CaseListApiView
+
+.. autoclass:: CaseRetrieveApiView
+
+.. autoclass:: SmallVariantQueryApiView
+
+.. autoclass:: SmallVariantQueryCreateApiView
+
+.. autoclass:: SmallVariantQueryRetrieveApiView
+
+.. autoclass:: SmallVariantQueryStatusApiView
+
+.. autoclass:: SmallVariantQueryUpdateApiView
+
+.. autoclass:: SmallVariantQueryFetchResultsApiView

docs_manual/api_importer.rst

@@ -0,0 +1,27 @@
+.. _api_importer:
+
+===============
+Case Import API
+===============
+
+The REST API for case import functionality is documented in this section.
+
+
+---------
+API Views
+---------
+
+.. note::
+
+    This is currently not implemented.
+
+
+----------
+Versioning
+----------
+
+For accept header versioning, the following media type and version are expected in the current VarFish version:
+
+.. code-block:: console
+
+    Accept: application/vnd.bihealth.varfish+json; version=0.23.9

docs_manual/api_json_schemas.rst

@@ -0,0 +1,16 @@
+.. _api_json_schemas:
+
+===========
+JSON Schema
+===========
+
+This section contains the JSON schemas used in the VarFish Server API.
+
+.. _api_json_schemas_case_query_v1:
+
+--------------------
+Case Query Schema V1
+--------------------
+
+.. jsonschema:: ../variants/schemas/case-query-v1.json
+

docs_manual/api_overview.rst

@@ -35,7 +35,7 @@ Add the token in the ``Authorization`` header of your HTTP request as follows:
 Versioning
 ==========
 
-The SODAR REST API uses accept header versioning.
+The VarFish REST API uses accept header versioning.
 While specifying the desired API version in your HTTP requests is optional, it is **strongly recommended**.
 This ensures you will get the appropriate return data and avoid running into unexpected incompatibility issues.
 

docs_manual/api_projectroles.rst

@@ -0,0 +1,26 @@
+.. _api_projectroles:
+
+======================
+Project Management API
+======================
+
+The REST API for project access and management operations is described in this section.
+
+
+---------
+API Views
+---------
+
+The project management API is provided by the SODAR Core package.
+The documentation for the REST API views can be found in the `SODAR Core Documentation <https://sodar-core.readthedocs.io/en/latest/app_projectroles_api_rest.html#api-views>`_.
+
+
+----------
+Versioning
+----------
+
+For accept header versioning, the following media type and version are expected in the current VarFish version:
+
+.. code-block:: console
+
+    Accept: application/vnd.bihealth.sodar-core+json; version=0.10.7

docs_manual/conf.py

@@ -12,7 +12,11 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.abspath("."))
+import django
+
+sys.path.insert(0, os.path.abspath("../"))
+os.environ["DJANGO_SETTINGS_MODULE"] = "config.settings.local"
+django.setup()
 
 # Get the project root dir, which is the parent dir of this
 cwd = os.getcwd()
@@ -37,7 +41,7 @@
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = []
+extensions = ["sphinx.ext.autodoc", "sphinx.ext.viewcode", "sphinx-jsonschema"]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]

docs_manual/index.rst

@@ -129,6 +129,10 @@ Currently, the main focus is on small/sequence variants called from high-througp
     :titlesonly:
 
     api_overview
+    api_projectroles
+    api_importer
+    api_case
+    api_json_schemas
 
 .. raw:: latex
 

geneinfo/tests/_test_views.py

@@ -79,23 +79,23 @@ class TestGeneView(TestViewBase):
     setup_case_in_db = fixture_setup_geneinfo
 
     def test_geneinfo_ensembl(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             project = Project.objects.first()
             response = self.client.get(
                 reverse("geneinfo:gene", kwargs={"project": project.sodar_uuid, "gene_id": "ENSG1"})
             )
             self.assertEquals(response.status_code, 200)
 
     def test_geneinfo_refseq(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             project = Project.objects.first()
             response = self.client.get(
                 reverse("geneinfo:gene", kwargs={"project": project.sodar_uuid, "gene_id": "123"})
             )
             self.assertEquals(response.status_code, 200)
 
     def test_geneinfo_render_complete(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             project = Project.objects.first()
             response = self.client.get(
                 reverse("geneinfo:gene", kwargs={"project": project.sodar_uuid, "gene_id": "456"})
@@ -112,7 +112,7 @@ def test_geneinfo_render_complete(self):
             self.assertEquals(response.context["hgncomim"]["2"][0]["hpo_id"], "HP:002")
 
     def test_geneinfo_render_empty(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             project = Project.objects.first()
             response = self.client.get(
                 reverse("geneinfo:gene", kwargs={"project": project.sodar_uuid, "gene_id": "000"})
@@ -129,7 +129,7 @@ class TestGeneViewIncomplete(TestViewBase):
     setup_case_in_db = fixture_setup_geneinfo_incomplete
 
     def test_geneinfo_render_missing_omim(self):
-        with self.login(self.user):
+        with self.login(self.superuser):
             project = Project.objects.first()
             response = self.client.get(
                 reverse("geneinfo:gene", kwargs={"project": project.sodar_uuid, "gene_id": "456"})