Merge remote-tracking branch 'origin/develop' into refact/scopeable-m…

…odel-base-class

# Conflicts:
#	chord_metadata_service/phenopackets/api_views.py
#	chord_metadata_service/phenopackets/tests/test_api.py
#	chord_metadata_service/restapi/api_renderers.py
#	chord_metadata_service/restapi/tests/test_fhir.py

README.md

@@ -53,7 +53,7 @@ CANARIE funded initial development of the Katsu Metadata service under the CHORD
 Katsu Metadata Service is a service to store epigenomic metadata.
 
 1. Patients service handles anonymized individual’s data (individual id, sex, age or date of birth)
-    * Data model: aggregated profile from GA4GH Phenopackets Individual, and FHIR Patient.
+    * Data model: extended from GA4GH Phenopackets Individual.
 
 2. Phenopackets service handles phenotypic and clinical data
     * Data model: [GA4GH Phenopackets schema](https://github.com/phenopackets/phenopacket-schema)
@@ -81,11 +81,6 @@ To retrieved data in json compliant with phenopackets that uses camelCase append
 
 * Data can be ingested and retrieved in snake_case or camelCase.
 
-* Other available renderers:
-Phenopackets model is mapped to [FHIR](https://www.hl7.org/fhir/) using
-[Phenopackets on FHIR](https://aehrc.github.io/fhir-phenopackets-ig/) implementation guide.
-To retrieve data in fhir append `?format=fhir` .
-
 * Ingest endpoint: `/private/ingest`.
 
 
@@ -378,24 +373,6 @@ Ingested data successfully.
   accepted by the Phenopackets workflow or the Experiments workflow, depending
   on the data type of the table)
 
-#### Patient Commands
-
-```
-$ ./manage.py patients_build_index
-...
-```
-
-Builds an ElasticSearch index for patients in the database.
-
-#### Phenopacket Commands
-
-```
-$ ./manage.py phenopackets_build_index
-...
-```
-
-Builds an ElasticSearch index for Phenopackets in the database.
-
 ### Accessing the Django Shell from inside a Bento Container
 
 #### When running Katsu with `bentoV2`:

chord_metadata_service/chord/ingest/__init__.py

@@ -1,9 +1,7 @@
 from chord_metadata_service.chord.workflows import metadata as wm
 
 from .experiments import ingest_experiments_workflow
-from .fhir import ingest_fhir_workflow
 from .phenopackets import ingest_phenopacket_workflow
-from .readsets import ingest_readset_workflow
 
 from typing import Callable
 
@@ -14,6 +12,4 @@
 WORKFLOW_INGEST_FUNCTION_MAP: dict[str, Callable] = {
     wm.WORKFLOW_EXPERIMENTS_JSON: ingest_experiments_workflow,
     wm.WORKFLOW_PHENOPACKETS_JSON: ingest_phenopacket_workflow,
-    wm.WORKFLOW_FHIR_JSON: ingest_fhir_workflow,
-    wm.WORKFLOW_READSET: ingest_readset_workflow,
 }

chord_metadata_service/chord/tests/constants.py

@@ -19,7 +19,6 @@
     "TEST_SEARCH_QUERY_8",
     "TEST_SEARCH_QUERY_9",
     "TEST_SEARCH_QUERY_10",
-    "TEST_FHIR_SEARCH_QUERY",
 ]
 
 VALID_DATA_USE_1 = {
@@ -253,4 +252,3 @@ def valid_phenotypic_feature(biosample=None, phenopacket=None):
 TEST_SEARCH_QUERY_9 = ["#eq", ["#resolve", "subject", "id"], "patient:1"]
 TEST_SEARCH_QUERY_10 = ["#in", ["#resolve", "biosamples", "[item]", "id"],
                         ["#list", "biosample_id:1", "biosample_id:2"]]
-TEST_FHIR_SEARCH_QUERY = {"query": {"match": {"gender": "FEMALE"}}}

chord_metadata_service/chord/tests/test_api_search.py

@@ -1,7 +1,5 @@
 import json
 
-from unittest.mock import patch
-
 from django.urls import reverse
 from rest_framework import status
 from rest_framework.test import APITestCase
@@ -19,7 +17,6 @@
     valid_experiment, valid_experiment_result, valid_instrument
 )
 
-from chord_metadata_service.chord.tests.es_mocks import SEARCH_SUCCESS
 from .constants import (
     VALID_PROJECT_1,
     valid_dataset_1,
@@ -34,7 +31,6 @@
     TEST_SEARCH_QUERY_8,
     TEST_SEARCH_QUERY_9,
     TEST_SEARCH_QUERY_10,
-    TEST_FHIR_SEARCH_QUERY,
 )
 from ..models import Project, Dataset
 from ..data_types import (
@@ -105,25 +101,25 @@ def _search_call(self, endpoint, args=None, data=None, method="GET"):
     def test_common_search_1(self):
         # No body
         for method in POST_GET:
-            r = self._search_call("search", method=method)
+            r = self._search_call("private-search", method=method)
             self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_common_search_2(self):
         # No data type
         for method in POST_GET:
-            r = self._search_call("search", data={"query": TEST_SEARCH_QUERY_1}, method=method)
+            r = self._search_call("private-search", data={"query": TEST_SEARCH_QUERY_1}, method=method)
             self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_common_search_3(self):
         # No query
         for method in POST_GET:
-            r = self._search_call("search", data={"data_type": DATA_TYPE_PHENOPACKET}, method=method)
+            r = self._search_call("private-search", data={"data_type": DATA_TYPE_PHENOPACKET}, method=method)
             self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
     def test_common_search_4(self):
         # Bad data type
         for method in POST_GET:
-            r = self._search_call("search", data={
+            r = self._search_call("private-search", data={
                 "data_type": "bad_data_type",
                 "query": TEST_SEARCH_QUERY_1,
             }, method=method)
@@ -132,33 +128,16 @@ def test_common_search_4(self):
     def test_common_search_5(self):
         # Bad syntax for query
         for method in POST_GET:
-            r = self._search_call("search", data={
+            r = self._search_call("private-search", data={
                 "data_type": DATA_TYPE_PHENOPACKET,
                 "query": ["hello", "world"]
             }, method=method)
             self.assertEqual(r.status_code, status.HTTP_400_BAD_REQUEST)
 
-    def test_search_with_result(self):
-        # Valid search with result
-        for method in POST_GET:
-            r = self._search_call("search", data={
-                "data_type": DATA_TYPE_PHENOPACKET,
-                "query": TEST_SEARCH_QUERY_1
-            }, method=method)
-            self.assertEqual(r.status_code, status.HTTP_200_OK)
-
-            c = r.json()
-
-            self.assertEqual(len(c["results"]), 1)
-            self.assertDictEqual(c["results"][0], {
-                "id": str(self.dataset.identifier),
-                "data_type": DATA_TYPE_PHENOPACKET
-            })
-
     def test_search_without_result(self):
         # Valid search without result
         for method in POST_GET:
-            r = self._search_call("search", data={
+            r = self._search_call("private-search", data={
                 "data_type": DATA_TYPE_PHENOPACKET,
                 "query": TEST_SEARCH_QUERY_2
             }, method=method)
@@ -499,37 +478,3 @@ def test_private_search_values_list(self):
             dataset_id = list(c["results"].keys())[0]
             matches = c["results"][dataset_id]["matches"]
             self.assertEqual(len(matches), 2)   # 2 biosamples in list
-
-    @patch('chord_metadata_service.chord.views_search.es')
-    def test_fhir_search(self, mocked_es):
-        mocked_es.search.return_value = SEARCH_SUCCESS
-        # Valid search with result
-        for method in POST_GET:
-            r = self._search_call("fhir-search", data={
-                "query": TEST_FHIR_SEARCH_QUERY
-            }, method=method)
-
-            self.assertEqual(r.status_code, status.HTTP_200_OK)
-            c = r.json()
-
-            self.assertEqual(len(c["results"]), 1)
-            self.assertDictEqual(c["results"][0], {
-                "id": str(self.dataset.identifier),
-                "data_type": DATA_TYPE_PHENOPACKET
-            })
-
-    @patch('chord_metadata_service.chord.views_search.es')
-    def test_private_fhir_search(self, mocked_es):
-        mocked_es.search.return_value = SEARCH_SUCCESS
-        # Valid search with result
-        for method in POST_GET:
-            r = self._search_call("fhir-private-search", data={
-                "query": TEST_FHIR_SEARCH_QUERY
-            }, method=method)
-
-            self.assertEqual(r.status_code, status.HTTP_200_OK)
-            c = r.json()
-
-            self.assertIn(str(self.dataset.identifier), c["results"])
-            self.assertEqual(c["results"][str(self.dataset.identifier)]["data_type"], DATA_TYPE_PHENOPACKET)
-            self.assertEqual(self.phenopacket.id, c["results"][str(self.dataset.identifier)]["matches"][0]["id"])

chord_metadata_service/chord/urls.py

@@ -24,9 +24,6 @@
     path('data-types/<str:data_type>/metadata_schema', views_data_types.data_type_metadata_schema,
          name="data-type-metadata-schema"),
 
-    path('search', views_search.chord_search, name="search"),
-    path('fhir-search', views_search.fhir_public_search, name="fhir-search"),
-    path('private/fhir-search', views_search.fhir_private_search, name="fhir-private-search"),
     path('private/search', views_search.chord_private_search, name="private-search"),
 
     path('datasets', DatasetViewSet.as_view({'get': 'list'}), name="chord-dataset-list"),