add wheel path in task collect cmd

fractal-analytics-platform · Dec 4, 2024 · 06d62b6 · 06d62b6
1 parent 77f04f9
commit 06d62b6
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Showing 4 changed files with 110 additions and 36 deletions.
diff --git a/fractal_client/cmd/__init__.py b/fractal_client/cmd/__init__.py
@@ -307,7 +307,9 @@ def version(client: Client, **kwargs) -> Interface:
     try:
         res = client.get(f"{settings.FRACTAL_SERVER}/api/alive/")
         data = res.json()
-        server_str = f"\turl: {settings.FRACTAL_SERVER}\tversion: {data['version']}"
+        server_str = (
+            f"\turl: {settings.FRACTAL_SERVER}\tversion: {data['version']}"
+        )
     except ConnectError:
         server_str = f"\tConnection to '{settings.FRACTAL_SERVER}' refused"
 
@@ -320,7 +322,9 @@ def version(client: Client, **kwargs) -> Interface:
     )
 
 
-def user(client: AuthClient, subcmd: str, batch: bool = False, **kwargs) -> Interface:
+def user(
+    client: AuthClient, subcmd: str, batch: bool = False, **kwargs
+) -> Interface:
     if subcmd == "register":
         parameters = [
             "new_email",
@@ -372,7 +376,9 @@ def user(client: AuthClient, subcmd: str, batch: bool = False, **kwargs) -> Inte
     return iface
 
 
-def group(client: AuthClient, subcmd: str, batch: bool = False, **kwargs) -> Interface:
+def group(
+    client: AuthClient, subcmd: str, batch: bool = False, **kwargs
+) -> Interface:
     if subcmd == "list":
         parameters = ["user_ids"]
         function_kwargs = get_kwargs(parameters, kwargs)

diff --git a/fractal_client/cmd/_task_collection.py b/fractal_client/cmd/_task_collection.py
@@ -1,8 +1,8 @@
 import json
 import logging
 import sys
-
 from pathlib import Path
+
 from fractal_client.authclient import AuthClient
 from fractal_client.config import settings
 from fractal_client.interface import Interface
@@ -47,7 +47,11 @@ def task_collect_pip(
     if wheel_path is None:
         with open(wheel_path, "rb") as wheel_buffer:
             file = {
-                "file": (Path(wheel_path).name, wheel_buffer.read(), "application/zip")
+                "file": (
+                    Path(wheel_path).name,
+                    wheel_buffer.read(),
+                    "application/zip",
+                )
             }
         res = client.post(
             f"{settings.BASE_URL}/task/collect/pip/{is_private}",
@@ -107,7 +111,9 @@ def task_collect_custom(
         data=task_collect,
     )
 
-    task_list = check_response(res, expected_status_code=201, redact_long_payload=True)
+    task_list = check_response(
+        res, expected_status_code=201, redact_long_payload=True
+    )
 
     if batch:
         task_ids = [str(task["id"]) for task in task_list]

diff --git a/fractal_client/parser.py b/fractal_client/parser.py
@@ -13,7 +13,6 @@
 Institute for Biomedical Research and Pelkmans Lab from the University of
 Zurich.
 """
-
 import argparse as ap
 
 
@@ -80,7 +79,9 @@
     description="Show details of single project.",
     allow_abbrev=False,
 )
-project_show_parser.add_argument("project_id", type=int, help="ID of project to show.")
+project_show_parser.add_argument(
+    "project_id", type=int, help="ID of project to show."
+)
 
 # project delete
 project_delete_parser = project_subparsers.add_parser(
@@ -127,7 +128,9 @@
 project_edit_parser.add_argument(
     "project_id", type=int, help="ID of the project to edit."
 )
-project_edit_parser.add_argument("--new-name", help="New project name.", required=False)
+project_edit_parser.add_argument(
+    "--new-name", help="New project name.", required=False
+)
 
 
 # DATASET GROUP
@@ -197,7 +200,9 @@
 # task collect
 task_collect_parser = task_subparsers.add_parser(
     "collect",
-    description=("Install and collect all tasks from a pip-installable package."),
+    description=(
+        "Install and collect all tasks from a pip-installable package."
+    ),
     allow_abbrev=False,
 )
 task_collect_parser.add_argument(
@@ -254,7 +259,9 @@
 )
 task_collect_custom_parser.add_argument(
     "python_interpreter",
-    help=("Absolute path to the Python interpreter to be used for running tasks."),
+    help=(
+        "Absolute path to the Python interpreter to be used for running tasks."
+    ),
 )
 task_collect_custom_parser.add_argument(
     "manifest", help="Local path of the Manifest of the Fractal task package."
@@ -313,7 +320,9 @@
     argument_default=ap.SUPPRESS,
     allow_abbrev=False,
 )
-task_new_parser.add_argument("name", help="A human readable name for the task.")
+task_new_parser.add_argument(
+    "name", help="A human readable name for the task."
+)
 task_new_parser.add_argument(
     "--command-non-parallel",
     help="The non parallel command that executes the task.",
@@ -369,12 +378,15 @@
 task_edit_id_or_name_group.add_argument(
     "--id", help="ID of the task to edit.", type=int
 )
-task_edit_id_or_name_group.add_argument("--name", help="Name of the task to edit.")
+task_edit_id_or_name_group.add_argument(
+    "--name", help="Name of the task to edit."
+)
 
 task_edit_parser.add_argument(
     "--version",
     help=(
-        "Version of the task to edit " "(only accepted in combination with `--name`)."
+        "Version of the task to edit "
+        "(only accepted in combination with `--name`)."
     ),
 )
 task_edit_parser.add_argument("--new-version", help="New task version.")
@@ -456,7 +468,9 @@
     allow_abbrev=False,
 )
 workflow_delete_parser.add_argument("project_id", type=int, help="Project ID.")
-workflow_delete_parser.add_argument("workflow_id", type=int, help="Workflow ID.")
+workflow_delete_parser.add_argument(
+    "workflow_id", type=int, help="Workflow ID."
+)
 
 
 # workflow add task
@@ -465,7 +479,9 @@
     description="Add new task to specific workflow.",
     allow_abbrev=False,
 )
-workflow_add_task_parser.add_argument("project_id", type=int, help="Project ID.")
+workflow_add_task_parser.add_argument(
+    "project_id", type=int, help="Project ID."
+)
 workflow_add_task_parser.add_argument(
     "workflow_id",
     type=int,
@@ -483,7 +499,10 @@
 )
 workflow_add_task_parser.add_argument(
     "--task-version",
-    help=("Version of task to add " "(only accepted in combination with --task-name)."),
+    help=(
+        "Version of task to add "
+        "(only accepted in combination with --task-name)."
+    ),
 )
 workflow_add_task_parser.add_argument(
     "--order", help="Order of this task within the workflow's task list."
@@ -493,7 +512,9 @@
     "--args-non-parallel", help="Args for non parallel tasks"
 )
 
-workflow_add_task_parser.add_argument("--args-parallel", help="Args for parallel tasks")
+workflow_add_task_parser.add_argument(
+    "--args-parallel", help="Args for parallel tasks"
+)
 
 workflow_add_task_parser.add_argument(
     "--meta-non-parallel", help="Metadata file fornon parallel tasks"
@@ -515,7 +536,9 @@
     description="Edit task within specific workflow.",
     allow_abbrev=False,
 )
-workflow_edit_task_parser.add_argument("project_id", type=int, help="Project ID.")
+workflow_edit_task_parser.add_argument(
+    "project_id", type=int, help="Project ID."
+)
 workflow_edit_task_parser.add_argument(
     "workflow_id",
     type=int,
@@ -556,7 +579,9 @@
     description="Remove task from a specific workflow.",
     allow_abbrev=False,
 )
-workflow_remove_task_parser.add_argument("project_id", type=int, help="Project ID.")
+workflow_remove_task_parser.add_argument(
+    "project_id", type=int, help="Project ID."
+)
 workflow_remove_task_parser.add_argument(
     "workflow_id",
     type=int,
@@ -655,7 +680,9 @@
     description="Download full folder of workflow-execution job.",
     allow_abbrev=False,
 )
-job_download_logs_parser.add_argument("project_id", type=int, help="Project ID.")
+job_download_logs_parser.add_argument(
+    "project_id", type=int, help="Project ID."
+)
 job_download_logs_parser.add_argument("job_id", type=int, help="Job ID.")
 job_download_logs_parser.add_argument(
     "--output",
@@ -689,14 +716,20 @@
     "--start",
     dest="first_task_index",
     type=int,
-    help=("Positional index of the first task to be executed" " (starting from 0)."),
+    help=(
+        "Positional index of the first task to be executed"
+        " (starting from 0)."
+    ),
     required=False,
 )
 job_submit_parser.add_argument(
     "--end",
     dest="last_task_index",
     type=int,
-    help=("Positional index of the last task to be executed" " (starting from 0)."),
+    help=(
+        "Positional index of the last task to be executed"
+        " (starting from 0)."
+    ),
     required=False,
 )
 job_submit_parser.add_argument(
@@ -747,8 +780,12 @@
     ),
     allow_abbrev=False,
 )
-user_register_parser.add_argument("new_email", help="Email to be used as username.")
-user_register_parser.add_argument("new_password", help="Password for the new user.")
+user_register_parser.add_argument(
+    "new_email", help="Email to be used as username."
+)
+user_register_parser.add_argument(
+    "new_password", help="Password for the new user."
+)
 user_register_parser.add_argument(
     "--project-dir",
     help="User-writeable base folder, used e.g. for default `zarr_dir` paths.",
@@ -806,8 +843,12 @@
     allow_abbrev=False,
 )
 user_edit_parser.add_argument("user_id", help="ID of the user.", type=int)
-user_edit_parser.add_argument("--new-email", help="New email address.", required=False)
-user_edit_parser.add_argument("--new-password", help="New password.", required=False)
+user_edit_parser.add_argument(
+    "--new-email", help="New email address.", required=False
+)
+user_edit_parser.add_argument(
+    "--new-password", help="New password.", required=False
+)
 user_edit_parser.add_argument(
     "--new-username", help="New user username.", required=False
 )
@@ -864,7 +905,9 @@
     description=("Reset user-group membership for an existing user."),
     allow_abbrev=False,
 )
-user_set_groups_parser.add_argument("user_id", help="ID of the user.", type=int)
+user_set_groups_parser.add_argument(
+    "user_id", help="ID of the user.", type=int
+)
 user_set_groups_parser.add_argument(
     "group_ids",
     help=(
@@ -903,7 +946,9 @@
 group_get_parser = group_subparsers.add_parser(
     "get", description="Get single group.", allow_abbrev=False
 )
-group_get_parser.add_argument("group_id", help="ID of the group to get.", type=int)
+group_get_parser.add_argument(
+    "group_id", help="ID of the group to get.", type=int
+)
 
 # group new
 group_new_parser = group_subparsers.add_parser(
@@ -912,7 +957,10 @@
 group_new_parser.add_argument("name", help="Name of the new group.", type=str)
 group_new_parser.add_argument(
     "--viewer-paths",
-    help=("List of group's `viewer_paths` (e.g " "`--viewer-paths /something /else`)",),
+    help=(
+        "List of group's `viewer_paths` (e.g "
+        "`--viewer-paths /something /else`)",
+    ),
     required=False,
     type=str,
     nargs="+",
@@ -945,7 +993,9 @@
 group_add_user_parser.add_argument(
     "group_id", help="ID of the group to which to add the user.", type=int
 )
-group_add_user_parser.add_argument("user_id", help="ID of the user to add.", type=int)
+group_add_user_parser.add_argument(
+    "user_id", help="ID of the user to add.", type=int
+)
 
 # group remove-user
 group_remove_user_parser = group_subparsers.add_parser(

diff --git a/tests/test_task_collection.py b/tests/test_task_collection.py
@@ -1,9 +1,10 @@
 import json
+import logging
 import sys
 import time
 from urllib.request import urlopen
 from urllib.request import urlretrieve
-import logging
+
 import pytest
 from devtools import debug
 
@@ -52,7 +53,13 @@ def test_task_collection_invalid_pinned_dependency(invoke, caplog):
     """
     PACKAGE = "devtools"
     with pytest.raises(SystemExit):
-        invoke(("task collect " f"{PACKAGE} " "--pinned-dependency invalid-string"))
+        invoke(
+            (
+                "task collect "
+                f"{PACKAGE} "
+                "--pinned-dependency invalid-string"
+            )
+        )
     # Check that payload was prepared correctly
     log_lines = [record.message for record in caplog.records]
     debug(log_lines)
@@ -84,15 +91,18 @@ def test_task_collection(invoke_as_custom_user, user_factory, new_name):
     initial_task_list = len(res.data)
 
     res0 = invoke_as_custom_user(
-        f"task collect --private {PACKAGE_PATH} --wheel-path {PACKAGE_PATH}", **new_user
+        f"task collect --private {PACKAGE_PATH} --wheel-path {PACKAGE_PATH}",
+        **new_user,
     )
     debug(res0.data)
     activity_id = res0.data["id"]
 
     # Wait until collection is complete
     starting_time = time.perf_counter()
     while True:
-        res1 = invoke_as_custom_user(f"task check-collection {activity_id}", **new_user)
+        res1 = invoke_as_custom_user(
+            f"task check-collection {activity_id}", **new_user
+        )
         assert res1.retcode == 0
         time.sleep(0.1)
         if res1.data["status"] == "OK":
@@ -101,7 +111,9 @@ def test_task_collection(invoke_as_custom_user, user_factory, new_name):
         assert time.perf_counter() - starting_time < COLLECTION_TIMEOUT
 
     # Check successful status and no logs
-    res2 = invoke_as_custom_user(f"task check-collection {activity_id}", **new_user)
+    res2 = invoke_as_custom_user(
+        f"task check-collection {activity_id}", **new_user
+    )
     assert res2.retcode == 0
     assert res2.data["status"] == "OK"
     assert res2.data["log"] is None