fix unit test

Author: paulineribeyre

.secrets.baseline

@@ -178,9 +178,9 @@
         "filename": "tests/test_s3_endpoint.py",
         "hashed_secret": "08d2e98e6754af941484848930ccbaddfefe13d6",
         "is_verified": false,
-        "line_number": 77
+        "line_number": 82
       }
     ]
   },
-  "generated_at": "2026-03-02T20:27:56Z"
+  "generated_at": "2026-03-03T22:13:17Z"
 }

gen3workflow/routes/s3.py

@@ -284,8 +284,6 @@ async def s3_endpoint(path: str, request: Request):
     # We know this is an UploadPart or CompleteMultipartUpload request if it includes the
     # uploadId query parameter.
     query_params = dict(request.query_params)
-    if "uploadId" in query_params:
-        raise Exception("multipart")
     if (
         config["KMS_ENCRYPTION_ENABLED"]
         and request.method in ["PUT", "POST"]

tests/conftest.py

@@ -226,10 +226,33 @@ def mock_tes_server_request_function(
     return httpx.Response(status_code=status_code, json=out, text=text)
 
 
+def mock_aws_s3_request_function(url: str):
+    """
+    Mock responses from AWS S3
+    """
+    resp_xml = MOCKED_S3_RESPONSE_XML
+    headers = {"content-type": "application/xml"}
+
+    # multipart upload special case:
+    if "test_s3_upload_file_multipart.txt" in url:
+        upload_id = "test-upload-id"
+        # "InitiateMultipartUploadResult" with "UploadId"
+        resp_xml = f"""<?xml version="1.0" encoding="UTF-8"?>\n<InitiateMultipartUploadResult xmlns="http://s3.amazonaws.com/doc/2006-03-01/"><Bucket>gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}</Bucket><Key>test_s3_chunk_upload.txt</Key><UploadId>{upload_id}</UploadId></InitiateMultipartUploadResult>"""
+        if f"?uploadId={upload_id}&partNumber=" in url:
+            headers["etag"] = "test-etag"
+
+    return httpx.Response(
+        status_code=200,
+        text=resp_xml,
+        headers=headers,
+    )
+
+
 # making these functions into mocks allows tests to check the requests that were made, for
 # example: `mock_tes_server_request.assert_called_with(...)`
 mock_tes_server_request = MagicMock(side_effect=mock_tes_server_request_function)
 mock_arborist_request = MagicMock(side_effect=mock_arborist_request_function)
+mock_aws_s3_request = MagicMock(side_effect=mock_aws_s3_request_function)
 
 
 @pytest_asyncio.fixture(scope="function", autouse=True)
@@ -316,20 +339,7 @@ async def handle_request(request: Request):
             f"https://gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}.s3.{config['USER_BUCKETS_REGION']}.amazonaws.com"
         ):
             # mock calls to AWS S3
-            resp_xml = MOCKED_S3_RESPONSE_XML
-            headers = {"content-type": "application/xml"}
-            # multipart upload special case:
-            if "test_s3_upload_file_multipart.txt" in url:
-                upload_id = "test-upload-id"
-                # "InitiateMultipartUploadResult" with "UploadId"
-                resp_xml = f"""<?xml version="1.0" encoding="UTF-8"?>\n<InitiateMultipartUploadResult xmlns="http://s3.amazonaws.com/doc/2006-03-01/"><Bucket>gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}</Bucket><Key>test_s3_chunk_upload.txt</Key><UploadId>{upload_id}</UploadId></InitiateMultipartUploadResult>"""
-                if f"?uploadId={upload_id}&partNumber=" in url:
-                    headers["etag"] = "test-etag"
-            mocked_response = httpx.Response(
-                status_code=200,
-                text=resp_xml,
-                headers=headers,
-            )
+            mocked_response = mock_aws_s3_request(url)
 
         if mocked_response is not None:
             print(f"Mocking request '{request.method} {url}'")

tests/test_s3_endpoint.py

@@ -8,7 +8,12 @@
 from fastapi import HTTPException
 import pytest
 
-from conftest import MOCKED_S3_RESPONSE_DICT, TEST_USER_ID, TEST_USER_TOKEN
+from conftest import (
+    MOCKED_S3_RESPONSE_DICT,
+    TEST_USER_ID,
+    TEST_USER_TOKEN,
+    mock_aws_s3_request,
+)
 from gen3workflow.config import config
 from gen3workflow.routes.s3 import (
     set_access_token_and_get_user_id,
@@ -350,24 +355,33 @@ def test_s3_upload_file(s3_client, access_token_patcher, multipart):
     Test that the boto3 `upload_file` function works with the `/s3` endpoint, both for a small
     file uploaded in 1 part and for a large file uploaded in multiple parts.
     """
+    bucket_name = f"gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}"
+    object_key = f"test_s3_upload_file{'_multipart' if multipart else ''}.txt"
+
     with patch(
         "gen3workflow.aws_utils.get_existing_kms_key_for_bucket",
         lambda _: ("test_kms_key_alias", "test_kms_key_arn"),
     ):
-        with tempfile.NamedTemporaryFile(mode="w+t", delete=True) as file_to_upload:
-            file_to_upload.write("Test file contents\n")
+        with tempfile.NamedTemporaryFile(delete=True) as file_to_upload:
+            file_to_upload.write(b"A" * (6 * 1024 * 1024))  # create a 6MB file
+            file_to_upload.flush()
             s3_client.upload_file(
                 file_to_upload.name,
-                f"gen3wf-{config['HOSTNAME']}-{TEST_USER_ID}",
-                f"test_s3_upload_file{'_multipart' if multipart else ''}.txt",
+                bucket_name,
+                object_key,
                 # to test a multipart upload, set the part size to 1 to force splitting the file
                 # into multiple parts:
-                # TODO this doesn't work
-                Config=boto3.s3.transfer.TransferConfig(
-                    multipart_threshold=1 if multipart else 9999
+                Config=(
+                    boto3.s3.transfer.TransferConfig(multipart_threshold=1)
+                    if multipart
+                    else None
                 ),
             )
 
+    mock_aws_s3_request.assert_called_with(
+        f"https://{bucket_name}.s3.us-east-1.amazonaws.com/{object_key}{'?uploadId=test-upload-id' if multipart else ''}"
+    )
+
 
 def test_chunked_to_non_chunked_body():
     """