Adding tests for updating entities

test/test_update_entities.py

@@ -0,0 +1,221 @@
+from test.helpers.database import create_provenance, get_entity
+from test.helpers.response import mock_response
+
+import pytest
+
+
+@pytest.fixture()
+def app(auth):
+    import app as app_module
+
+    app_module.app.config.update({"TESTING": True})
+    app_module.auth_helper_instance = auth
+    app_module.schema_manager._auth_helper = auth
+    # other setup
+    yield app_module.app
+    # clean up
+
+
+# Update Entity Tests
+
+
+@pytest.mark.usefixtures("lab")
+def test_update_source(app, requests, db_session):
+    # Create provenance in test database
+    test_entities = create_provenance(db_session, ["source"])
+    test_source = test_entities["source"]
+
+    # uuid and search api mock responses
+    uuid_api_url = app.config["UUID_API_URL"]
+    search_api_url = app.config["SEARCH_API_URL"]
+    requests.add_response(
+        f"{uuid_api_url}/uuid/{test_source['uuid']}",
+        "get",
+        mock_response(200, {k: test_source[k] for k in ["uuid", "sennet_id", "base_id"]}),
+    )
+    requests.add_response(f"{search_api_url}/reindex/{test_source['uuid']}", "put", mock_response(202))
+
+    with app.test_client() as client:
+        data = {
+            "description": "New Testing lab notes",
+            "lab_source_id": "new_test_lab_source_id",
+        }
+
+        res = client.put(
+            f"/entities/{test_source['uuid']}?return_all_properties=true",
+            json=data,
+            headers={"Authorization": "Bearer test_token"},
+        )
+
+        assert res.status_code == 200
+        assert res.json["uuid"] == test_source["uuid"]
+        assert res.json["sennet_id"] == test_source["sennet_id"]
+
+        assert res.json["description"] == data["description"]
+        assert res.json["lab_source_id"] == data["lab_source_id"]
+
+        # check database
+        db_entity = get_entity(test_source["uuid"], db_session)
+        assert db_entity["description"] == data["description"]
+        assert db_entity["lab_source_id"] == data["lab_source_id"]
+
+
+@pytest.mark.usefixtures("lab")
+def test_update_organ_sample(app, requests, db_session):
+    # Create provenance in test database
+    test_entities = create_provenance(db_session, ["source", "organ"])
+    test_organ = test_entities["organ"]
+
+    # uuid and search api mock responses
+    uuid_api_url = app.config["UUID_API_URL"]
+    search_api_url = app.config["SEARCH_API_URL"]
+    requests.add_response(
+        f"{uuid_api_url}/uuid/{test_organ['uuid']}",
+        "get",
+        mock_response(200, {k: test_organ[k] for k in ["uuid", "sennet_id", "base_id"]}),
+    )
+    requests.add_response(f"{search_api_url}/reindex/{test_organ['uuid']}", "put", mock_response(202))
+
+    with app.test_client() as client:
+        data = {
+            "description": "New Testing lab notes",
+            "lab_tissue_sample_id": "new_test_lab_tissue_organ_id",
+        }
+
+        res = client.put(
+            f"/entities/{test_organ['uuid']}?return_all_properties=true",
+            json=data,
+            headers={"Authorization": "Bearer test_token"},
+        )
+
+        assert res.status_code == 200
+        assert res.json["uuid"] == test_organ["uuid"]
+        assert res.json["sennet_id"] == test_organ["sennet_id"]
+
+        assert res.json["description"] == data["description"]
+        assert res.json["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+        # check database
+        db_entity = get_entity(test_organ["uuid"], db_session)
+        assert db_entity["description"] == data["description"]
+        assert db_entity["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+
+@pytest.mark.usefixtures("lab")
+def test_update_block_sample(app, requests, db_session):
+    # Create provenance in test database
+    test_entities = create_provenance(db_session, ["source", "organ", "block"])
+    test_block = test_entities["block"]
+
+    # uuid and search api mock responses
+    uuid_api_url = app.config["UUID_API_URL"]
+    search_api_url = app.config["SEARCH_API_URL"]
+    requests.add_response(
+        f"{uuid_api_url}/uuid/{test_block['uuid']}",
+        "get",
+        mock_response(200, {k: test_block[k] for k in ["uuid", "sennet_id", "base_id"]}),
+    )
+    requests.add_response(f"{search_api_url}/reindex/{test_block['uuid']}", "put", mock_response(202))
+
+    with app.test_client() as client:
+        data = {
+            "description": "New Testing lab notes",
+            "lab_tissue_sample_id": "new_test_lab_tissue_block_id",
+        }
+
+        res = client.put(
+            f"/entities/{test_block['uuid']}?return_all_properties=true",
+            json=data,
+            headers={"Authorization": "Bearer test_token"},
+        )
+
+        assert res.status_code == 200
+        assert res.json["uuid"] == test_block["uuid"]
+        assert res.json["sennet_id"] == test_block["sennet_id"]
+
+        assert res.json["description"] == data["description"]
+        assert res.json["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+        # check database
+        db_entity = get_entity(test_block["uuid"], db_session)
+        assert db_entity["description"] == data["description"]
+        assert db_entity["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+
+@pytest.mark.usefixtures("lab")
+def test_update_section_sample(app, requests, db_session):
+    # Create provenance in test database
+    test_entities = create_provenance(db_session, ["source", "organ", "block", "section"])
+    test_section = test_entities["section"]
+
+    # uuid and search api mock responses
+    uuid_api_url = app.config["UUID_API_URL"]
+    search_api_url = app.config["SEARCH_API_URL"]
+    requests.add_response(
+        f"{uuid_api_url}/uuid/{test_section['uuid']}",
+        "get",
+        mock_response(200, {k: test_section[k] for k in ["uuid", "sennet_id", "base_id"]}),
+    )
+    requests.add_response(f"{search_api_url}/reindex/{test_section['uuid']}", "put", mock_response(202))
+
+    with app.test_client() as client:
+        data = {
+            "description": "New Testing lab notes",
+            "lab_tissue_sample_id": "new_test_lab_tissue_section_id",
+        }
+
+        res = client.put(
+            f"/entities/{test_section['uuid']}?return_all_properties=true",
+            json=data,
+            headers={"Authorization": "Bearer test_token"},
+        )
+
+        assert res.status_code == 200
+        assert res.json["uuid"] == test_section["uuid"]
+        assert res.json["sennet_id"] == test_section["sennet_id"]
+
+        assert res.json["description"] == data["description"]
+        assert res.json["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+        # check database
+        db_entity = get_entity(test_section["uuid"], db_session)
+        assert db_entity["description"] == data["description"]
+        assert db_entity["lab_tissue_sample_id"] == data["lab_tissue_sample_id"]
+
+
+@pytest.mark.usefixtures("lab")
+def test_update_dataset(app, requests, db_session):
+    # Create provenance in test database
+    test_entities = create_provenance(db_session, ["source", "organ", "block", "section", "dataset"])
+    test_dataset = test_entities["dataset"]
+
+    # uuid and search api mock responses
+    uuid_api_url = app.config["UUID_API_URL"]
+    search_api_url = app.config["SEARCH_API_URL"]
+    requests.add_response(
+        f"{uuid_api_url}/uuid/{test_dataset['uuid']}",
+        "get",
+        mock_response(200, {k: test_dataset[k] for k in ["uuid", "sennet_id", "base_id"]}),
+    )
+    requests.add_response(f"{search_api_url}/reindex/{test_dataset['uuid']}", "put", mock_response(202))
+
+    with app.test_client() as client:
+        data = {
+            "description": "New Testing lab notes",
+        }
+
+        res = client.put(
+            f"/entities/{test_dataset['uuid']}?return_all_properties=true",
+            json=data,
+            headers={"Authorization": "Bearer test_token"},
+        )
+
+        assert res.status_code == 200
+        assert res.json["uuid"] == test_dataset["uuid"]
+        assert res.json["sennet_id"] == test_dataset["sennet_id"]
+
+        assert res.json["description"] == data["description"]
+
+        # check database
+        db_entity = get_entity(test_dataset["uuid"], db_session)
+        assert db_entity["description"] == data["description"]