Update models and test files

tes/models.py

@@ -74,7 +74,7 @@ def strconv(value: Any) -> Any:
     """
     if isinstance(value, (tuple, list)):
         if all([isinstance(n, str) for n in value]):
-            return [str(n) for n in value]
+            return type(value)(str(n) for n in value)
         else:
             return value
     elif isinstance(value, str):
@@ -110,6 +110,8 @@ def timestampconv(value: Optional[str]) -> Optional[datetime]:
     """
     if value is None:
         return value
+    if isinstance(value, datetime):
+        return value
     return dateutil.parser.parse(value)
 
 

tes/utils.py

@@ -56,7 +56,7 @@ def unmarshal(j: Any, o: Type, convert_camel_case=True) -> Any:
         try:
             m = json.loads(j)
         except json.decoder.JSONDecodeError:
-            pass
+            raise UnmarshalError("Unable to decode JSON string: %s" % j)
     elif j is None:
         return None
     else:

tests/integration/test_funnel.py

@@ -9,14 +9,7 @@ def tes_client():
 
 @pytest.fixture
 def task():
-    return tes.Task(
-        executors=[
-            tes.Executor(
-                image="alpine",
-                command=["echo", "hello"]
-            )
-        ]
-    )
+    return tes.Task(executors=[tes.Executor(image="alpine", command=["echo", "hello"])])
 
 
 def test_service_info(tes_client):
@@ -39,7 +32,16 @@ def test_task_status(tes_client, task):
     assert task_id is not None
 
     status = tes_client.get_task(task_id, view="MINIMAL").state
-    assert status in ["QUEUED", "INITIALIZING", "RUNNING", "COMPLETE", "CANCELED", "EXECUTOR_ERROR", "SYSTEM_ERROR", "UNKNOWN"]
+    assert status in [
+        "QUEUED",
+        "INITIALIZING",
+        "RUNNING",
+        "COMPLETE",
+        "CANCELED",
+        "EXECUTOR_ERROR",
+        "SYSTEM_ERROR",
+        "UNKNOWN",
+    ]
 
 
 def test_task_logs(tes_client, task):

tests/test_client.py

@@ -5,21 +5,14 @@
 
 import pytest
 
-from tes.client import HTTPClient
+from tes.client import append_suffixes_to_url, HTTPClient, send_request
 from tes.models import Task, Executor
 from tes.utils import TimeoutError
 
 
 @pytest.fixture
 def task():
-    return Task(
-        executors=[
-            Executor(
-                image="alpine",
-                command=["echo", "hello"]
-            )
-        ]
-    )
+    return Task(executors=[Executor(image="alpine", command=["echo", "hello"])])
 
 
 @pytest.fixture
@@ -43,7 +36,7 @@ def test_cli():
     assert cli.urls == [
         "http://fakehost:8000/ga4gh/tes/v1",
         "http://fakehost:8000/v1",
-        "http://fakehost:8000"
+        "http://fakehost:8000",
     ]
     assert cli.timeout == 5
 
@@ -62,24 +55,17 @@ def test_cli():
 
 def test_create_task(cli, task, mock_id, mock_url):
     with requests_mock.Mocker() as m:
-        m.post(
-            f"{mock_url}/ga4gh/tes/v1/tasks",
-            status_code=200,
-            json={"id": mock_id}
-        )
+        m.post(f"{mock_url}/ga4gh/tes/v1/tasks", status_code=200, json={"id": mock_id})
         cli.create_task(task)
         assert m.last_request.text == task.as_json()
         assert m.last_request.timeout == cli.timeout
 
-        m.post(
-            f"{mock_url}/ga4gh/tes/v1/tasks",
-            status_code=500
-        )
+        m.post(f"{mock_url}/ga4gh/tes/v1/tasks", status_code=500)
         with pytest.raises(requests.HTTPError):
             cli.create_task(task)
 
         with pytest.raises(TypeError):
-            cli.create_task('not_a_task_object')  # type: ignore
+            cli.create_task("not_a_task_object")  # type: ignore
 
 
 def test_get_task(cli, mock_id, mock_url):
@@ -90,92 +76,63 @@ def test_get_task(cli, mock_id, mock_url):
             json={
                 "id": mock_id,
                 "state": "RUNNING",
-            }
+            },
         )
         cli.get_task(mock_id, "MINIMAL")
-        assert m.last_request.url == f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}?view=MINIMAL"
+        assert (
+            m.last_request.url
+            == f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}?view=MINIMAL"
+        )
         assert m.last_request.timeout == cli.timeout
 
-        m.get(
-            requests_mock.ANY,
-            status_code=404
-        )
+        m.get(requests_mock.ANY, status_code=404)
         with pytest.raises(requests.HTTPError):
             cli.get_task(mock_id)
 
 
 def test_list_tasks(cli, mock_url):
     with requests_mock.Mocker() as m:
-        m.get(
-            f"{mock_url}/ga4gh/tes/v1/tasks",
-            status_code=200,
-            json={
-                "tasks": []
-            }
-        )
+        m.get(f"{mock_url}/ga4gh/tes/v1/tasks", status_code=200, json={"tasks": []})
         cli.list_tasks()
         assert m.last_request.url == f"{mock_url}/ga4gh/tes/v1/tasks?view=MINIMAL"
         assert m.last_request.timeout == cli.timeout
 
         # empty response
-        m.get(
-            f"{mock_url}/ga4gh/tes/v1/tasks",
-            status_code=200,
-            json={}
-        )
+        m.get(f"{mock_url}/ga4gh/tes/v1/tasks", status_code=200, json={})
         cli.list_tasks()
         assert m.last_request.url == f"{mock_url}/ga4gh/tes/v1/tasks?view=MINIMAL"
 
-        m.get(
-            f"{mock_url}/ga4gh/tes/v1/tasks",
-            status_code=500
-        )
+        m.get(f"{mock_url}/ga4gh/tes/v1/tasks", status_code=500)
         with pytest.raises(requests.HTTPError):
             cli.list_tasks()
 
 
 def test_cancel_task(cli, mock_id, mock_url):
     with requests_mock.Mocker() as m:
         m.post(
-            f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}:cancel",
-            status_code=200,
-            json={}
+            f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}:cancel", status_code=200, json={}
         )
         cli.cancel_task(mock_id)
         assert m.last_request.url == f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}:cancel"
         assert m.last_request.timeout == cli.timeout
 
-        m.post(
-            f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}:cancel",
-            status_code=500
-        )
+        m.post(f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}:cancel", status_code=500)
         with pytest.raises(requests.HTTPError):
             cli.cancel_task(mock_id)
 
-        m.post(
-            requests_mock.ANY,
-            status_code=404,
-            json={}
-        )
+        m.post(requests_mock.ANY, status_code=404, json={})
         with pytest.raises(requests.HTTPError):
             cli.cancel_task(mock_id)
 
 
 def test_get_service_info(cli, mock_url):
     with requests_mock.Mocker() as m:
-        m.get(
-            f"{mock_url}/ga4gh/tes/v1/service-info",
-            status_code=200,
-            json={}
-        )
+        m.get(f"{mock_url}/ga4gh/tes/v1/service-info", status_code=200, json={})
         cli.get_service_info()
         assert m.last_request.url == f"{mock_url}/ga4gh/tes/v1/service-info"
         assert m.last_request.timeout == cli.timeout
 
-        m.get(
-            f"{mock_url}/ga4gh/tes/v1/service-info",
-            status_code=500
-        )
+        m.get(f"{mock_url}/ga4gh/tes/v1/service-info", status_code=500)
         with pytest.raises(requests.HTTPError):
             cli.get_service_info()
 
@@ -189,21 +146,18 @@ def test_wait(cli, mock_id, mock_url):
                 json={
                     "id": mock_id,
                     "state": "RUNNING",
-                }
+                },
             )
             cli.wait(mock_id, timeout=1)
 
     with requests_mock.Mocker() as m:
         m.get(
             f"{mock_url}/ga4gh/tes/v1/tasks/{mock_id}",
             [
-                {"status_code": 200,
-                 "json": {"id": mock_id, "state": "INITIALIZING"}},
-                {"status_code": 200,
-                 "json": {"id": mock_id, "state": "RUNNING"}},
-                {"status_code": 200,
-                 "json": {"id": mock_id, "state": "COMPLETE"}}
-            ]
+                {"status_code": 200, "json": {"id": mock_id, "state": "INITIALIZING"}},
+                {"status_code": 200, "json": {"id": mock_id, "state": "RUNNING"}},
+                {"status_code": 200, "json": {"id": mock_id, "state": "COMPLETE"}},
+            ],
         )
         cli.wait(mock_id, timeout=2)
 
@@ -215,7 +169,7 @@ def test_wait_exception(cli, mock_id, mock_url):
             status_code=200,
             json={
                 "Error": "Error",
-            }
+            },
         )
         with pytest.raises(Exception):
             cli.wait(mock_id, timeout=2)
@@ -229,7 +183,7 @@ def test_wait_no_state_change(cli, mock_id, mock_url):
                 {"status_code": 200, "json": {"id": mock_id, "state": "RUNNING"}},
                 {"status_code": 200, "json": {"id": mock_id, "state": "RUNNING"}},
                 # Continues to return RUNNING state
-            ]
+            ],
         )
         with pytest.raises(TimeoutError):
             cli.wait(mock_id, timeout=2)
@@ -249,10 +203,12 @@ def test_request_params():
     with pytest.raises(KeyError):
         _ = vals["params"]
 
-    cli = HTTPClient(url="http://fakehost:8000", user="user",
-                     password="password", token="token")
-    vals = cli._request_params(data='{"json": "string"}',
-                               params={"query_param": "value"})
+    cli = HTTPClient(
+        url="http://fakehost:8000", user="user", password="password", token="token"
+    )
+    vals = cli._request_params(
+        data='{"json": "string"}', params={"query_param": "value"}
+    )
     assert vals["timeout"] == 10
     assert vals["headers"]["Content-type"] == "application/json"
     assert vals["headers"]["Authorization"] == "Bearer token"
@@ -270,18 +226,18 @@ def test_append_suffixes_to_url():
 
     results = append_suffixes_to_url(urls=urls, suffixes=suffixes)
     assert len(results) == len(urls) * len(suffixes)
-    assert all(url == 'http://example.com/foo' for url in results)
+    assert all(url == "http://example.com/foo" for url in results)
 
     results = append_suffixes_to_url(urls=urls, suffixes=no_suffixes)
     assert len(results) == len(urls) * len(no_suffixes)
-    assert all(url == 'http://example.com' for url in results)
+    assert all(url == "http://example.com" for url in results)
 
     results = append_suffixes_to_url(urls=urls_order, suffixes=suffixes_order)
     assert len(results) == len(urls_order) * len(suffixes_order)
-    assert results[0] == 'http://example1.com/1'
-    assert results[1] == 'http://example1.com/2'
-    assert results[2] == 'http://example2.com/1'
-    assert results[3] == 'http://example2.com/2'
+    assert results[0] == "http://example1.com/1"
+    assert results[1] == "http://example1.com/2"
+    assert results[2] == "http://example2.com/1"
+    assert results[3] == "http://example2.com/2"
 
 
 def test_send_request():
@@ -305,7 +261,7 @@ def test_send_request():
         m.get(mock_urls[1], status_code=200)
         response = send_request(paths=mock_urls)
         assert response.status_code == 200
-        assert m.last_request.url.rstrip('/') == f"{mock_url}"
+        assert m.last_request.url.rstrip("/") == f"{mock_url}"
 
     # error on first path, 404 on second
     with requests_mock.Mocker() as m:
@@ -327,14 +283,13 @@ def test_send_request():
         m.get(mock_urls[1], status_code=200)
         response = send_request(paths=mock_urls)
         assert response.status_code == 200
-        assert m.last_request.url.rstrip('/') == f"{mock_url}"
+        assert m.last_request.url.rstrip("/") == f"{mock_url}"
 
     # POST 200
     with requests_mock.Mocker() as m:
         m.post(f"{mock_url}/suffix/foo/{mock_id}:bar", status_code=200)
         paths = append_suffixes_to_url(mock_urls, ["/foo/{id}:bar"])
-        response = send_request(paths=paths, method="post", json={},
-                                id=mock_id)
+        response = send_request(paths=paths, method="post", json={}, id=mock_id)
         assert response.status_code == 200
         assert m.last_request.url == f"{mock_url}/suffix/foo/{mock_id}:bar"