From 9392809cd1de2df3500a7e52ee18018ecebf6da8 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 17 Jun 2024 13:27:52 +0200
Subject: [PATCH] [classification.scripts] Move upload script to classification
package
---
src/mednet/libs/classification/scripts/cli.py | 3 +
.../classification}/scripts/upload.py | 58 ++-----------
src/mednet/libs/common/scripts/upload.py | 83 +++++++++++++++++++
src/mednet/scripts/cli.py | 2 -
4 files changed, 93 insertions(+), 53 deletions(-)
rename src/mednet/{ => libs/classification}/scripts/upload.py (79%)
create mode 100644 src/mednet/libs/common/scripts/upload.py
diff --git a/src/mednet/libs/classification/scripts/cli.py b/src/mednet/libs/classification/scripts/cli.py
index 34ba1ff3..f922cd7d 100644
--- a/src/mednet/libs/classification/scripts/cli.py
+++ b/src/mednet/libs/classification/scripts/cli.py
@@ -37,6 +37,9 @@ classification.add_command(
classification.add_command(
importlib.import_module("..experiment", package=__name__).experiment,
)
+classification.add_command(
+ importlib.import_module("..upload", package=__name__).upload,
+)
@click.group(
diff --git a/src/mednet/scripts/upload.py b/src/mednet/libs/classification/scripts/upload.py
similarity index 79%
rename from src/mednet/scripts/upload.py
rename to src/mednet/libs/classification/scripts/upload.py
index a10d6518..f4b0114c 100644
--- a/src/mednet/scripts/upload.py
+++ b/src/mednet/libs/classification/scripts/upload.py
@@ -8,6 +8,7 @@ import click
from clapper.click import ResourceOption, verbosity_option
from clapper.logging import setup
from mednet.libs.common.scripts.click import ConfigCommand
+from mednet.libs.common.scripts.upload import reusable_options
logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
@@ -21,74 +22,29 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- mednet upload --experiment-folder=/path/to/results
+ mednet classification upload --experiment-folder=/path/to/results
2. Upload an existing experiment result with an experiment name:
.. code:: sh
- mednet upload --experiment-folder=/path/to/results --experiment-name=exp-pasa_mc
+ mednet classification upload --experiment-folder=/path/to/results --experiment-name=exp-pasa_mc
3. Upload an existing experiment result with a run name:
.. code:: sh
- mednet upload --experiment-folder=/path/to/results --run-name=run-1
+ mednet classification upload --experiment-folder=/path/to/results --run-name=run-1
4. Upload an existing experiment result with defining a size limit of 20MB for each file:
.. code:: sh
- mednet upload --experiment-folder=/path/to/results --upload-limit-mb=20
+ mednet classification upload --experiment-folder=/path/to/results --upload-limit-mb=20
""",
)
-@click.option(
- "--project-path",
- "-p",
- help="Path to the project where to upload model entries",
- required=True,
- type=str,
- default="biosignal/software/mednet",
- show_default=True,
- cls=ResourceOption,
-)
-@click.option(
- "--experiment-folder",
- "-f",
- help="Directory in which to upload results from",
- required=True,
- type=click.Path(
- file_okay=False,
- dir_okay=True,
- path_type=pathlib.Path,
- ),
- default="results",
- show_default=True,
- cls=ResourceOption,
-)
-@click.option(
- "--experiment-name",
- "-e",
- help='A string indicating the experiment name (e.g. "exp-pasa-mc" or "exp-densenet-mc-ch")',
- cls=ResourceOption,
-)
-@click.option(
- "--run-name",
- "-r",
- help='A string indicating the run name (e.g. "run-1")',
- cls=ResourceOption,
-)
-@click.option(
- "--upload-limit-mb",
- "-l",
- help="Maximim upload size in MB (set to 0 for no limit).",
- show_default=True,
- required=True,
- default=10,
- type=click.IntRange(min=0),
- cls=ResourceOption,
-)
+@reusable_options
@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
def upload(
project_path: str,
@@ -123,8 +79,8 @@ def upload(
)
# get train files
- train_log_file = experiment_folder / "trainlog.pdf"
train_folder = experiment_folder / "model"
+ train_log_file = train_folder / "trainlog.pdf"
train_meta_file = train_folder / "meta.json"
train_model_file = get_checkpoint_to_run_inference(train_folder)
train_files = [train_meta_file, train_model_file, train_log_file]
diff --git a/src/mednet/libs/common/scripts/upload.py b/src/mednet/libs/common/scripts/upload.py
new file mode 100644
index 00000000..5302adbc
--- /dev/null
+++ b/src/mednet/libs/common/scripts/upload.py
@@ -0,0 +1,83 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
+import functools
+import pathlib
+
+import click
+from clapper.click import ResourceOption
+from clapper.logging import setup
+
+# logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+logger = setup("mednet", format="%(levelname)s: %(message)s")
+
+
+def reusable_options(f):
+ """Wrap reusable upload script options.
+
+ This decorator equips the target function ``f`` with all (reusable)
+ ``upload`` script options.
+
+ Parameters
+ ----------
+ f
+ The target function to equip with options. This function must have
+ parameters that accept such options.
+
+ Returns
+ -------
+ The decorated version of function ``f``
+ """
+
+ @click.option(
+ "--project-path",
+ "-p",
+ help="Path to the project where to upload model entries",
+ required=True,
+ type=str,
+ default="biosignal/software/mednet",
+ show_default=True,
+ cls=ResourceOption,
+ )
+ @click.option(
+ "--experiment-folder",
+ "-f",
+ help="Directory in which to upload results from",
+ required=True,
+ type=click.Path(
+ file_okay=False,
+ dir_okay=True,
+ path_type=pathlib.Path,
+ ),
+ default="results",
+ show_default=True,
+ cls=ResourceOption,
+ )
+ @click.option(
+ "--experiment-name",
+ "-e",
+ help='A string indicating the experiment name (e.g. "exp-pasa-mc" or "exp-densenet-mc-ch")',
+ cls=ResourceOption,
+ )
+ @click.option(
+ "--run-name",
+ "-r",
+ help='A string indicating the run name (e.g. "run-1")',
+ cls=ResourceOption,
+ )
+ @click.option(
+ "--upload-limit-mb",
+ "-l",
+ help="Maximim upload size in MB (set to 0 for no limit).",
+ show_default=True,
+ required=True,
+ default=10,
+ type=click.IntRange(min=0),
+ cls=ResourceOption,
+ )
+ @functools.wraps(f)
+ def wrapper_reusable_options(*args, **kwargs):
+ return f(*args, **kwargs)
+
+ return wrapper_reusable_options
diff --git a/src/mednet/scripts/cli.py b/src/mednet/scripts/cli.py
index 3b9beb51..59df4ef6 100644
--- a/src/mednet/scripts/cli.py
+++ b/src/mednet/scripts/cli.py
@@ -4,7 +4,6 @@ from mednet.libs.classification.scripts.cli import classification
from mednet.libs.segmentation.scripts.cli import segmentation
from .info import info
-from .upload import upload
@click.group(
@@ -19,4 +18,3 @@ def cli():
cli.add_command(classification)
cli.add_command(segmentation)
cli.add_command(info)
-cli.add_command(upload)
--
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