DIG-1272: Clinical ingest integration tests (#329)

* Update candigv2-ingest * sometimes you clean up a thing and it doesn't exist. That's OK. * add basic clinical ingest test * Update candigv2-ingest * (temporary until merged) * Update candigv2-ingest * Revert "(temporary until merged)"
CanDIG · Nov 13, 2023 · 19de81d · 19de81d
1 parent c603ff5
commit 19de81d
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diff --git a/etc/tests/test_integration.py b/etc/tests/test_integration.py
@@ -445,7 +445,7 @@ def clean_up_program(test_id):
         headers=get_headers(is_admin=True),
     )
     assert (
-        delete_response.status_code == HTTPStatus.NO_CONTENT
+        delete_response.status_code == HTTPStatus.NO_CONTENT or delete_response.status_code == HTTPStatus.NOT_FOUND
     ), f"CLEAN_UP_PROGRAM Expected status code {HTTPStatus.NO_CONTENT}, but got {delete_response.status_code}."
     f" Response content: {delete_response.content}"
 
@@ -797,6 +797,46 @@ def test_katsu_users_data_access():
 
 # =========================|| KATSU TEST END ||=============================== #
 
+def test_ingest_permissions():
+    clean_up_program("SYNTHETIC-2")
+    clean_up_program("TEST_2")
+
+    test_loc = "https://raw.githubusercontent.com/CanDIG/candigv2-ingest/develop/tests/single_ingest.json"
+    test_data = requests.get(test_loc).json()
+
+    token = get_token(
+        username=ENV["CANDIG_NOT_ADMIN_USER"],
+        password=ENV["CANDIG_NOT_ADMIN_PASSWORD"],
+    )
+    headers = {
+        "Authorization": f"Bearer {token}",
+        "Content-Type": "application/json; charset=utf-8",
+    }
+
+    response = requests.post(f"{ENV['CANDIG_URL']}/ingest/ingest/clinical_donors", headers=headers, json=test_data)
+    # when the user has no admin access, they should not be allowed
+    assert response.status_code == 403
+
+    token = get_token(
+        username=ENV["CANDIG_SITE_ADMIN_USER"],
+        password=ENV["CANDIG_SITE_ADMIN_PASSWORD"],
+    )
+    headers = {
+        "Authorization": f"Bearer {token}",
+        "Content-Type": "application/json; charset=utf-8",
+    }
+    response = requests.post(f"{ENV['CANDIG_URL']}/ingest/ingest/clinical_donors", headers=headers, json=test_data)
+    # when the user has admin access, they should be allowed
+    print(response.json())
+    assert response.status_code == 201
+    assert len(response.json()["SYNTHETIC-2"]["errors"]) == 0
+    assert len(response.json()["TEST_2"]["errors"]) == 0
+    assert len(response.json()["SYNTHETIC-2"]["results"]) == 12
+    assert len(response.json()["TEST_2"]["results"]) == 5
+
+    clean_up_program("SYNTHETIC-2")
+    clean_up_program("TEST_2")
+
 
 ## HTSGet + katsu:
 def test_add_sample_to_genomic():

diff --git a/lib/candig-ingest/candigv2-ingest b/lib/candig-ingest/candigv2-ingest
+3 −0		Dockerfile
+2 −2		auth.py
+120 −3		htsget_ingest.py
+0 −148		htsget_methods.py
+3 −4		ingest_operations.py
+4 −1		ingest_result.py
+98 −121		katsu_ingest.py
+0 −0		tests/__init__.py
+0 −0		tests/single_ingest.json
+14 −0		tests/test_ingest.py