diff --git a/Dockerfile b/Dockerfile index a171797..79d0463 100644 --- a/Dockerfile +++ b/Dockerfile @@ -11,7 +11,7 @@ ARG SRCDIR=/usr/local/src/pl-spleendatads WORKDIR ${SRCDIR} COPY requirements.txt . -RUN --mount=type=cache,sharing=private,target=/root/.cache/pip pip install -r requirements.txt +RUN pip install -r requirements.txt COPY . . ARG extras_require=none diff --git a/requirements.txt b/requirements.txt index 96d114d..4db5b5c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,3 @@ chris_plugin==0.4.0 -monai-weekly tqdm twine diff --git a/spleendatads.py b/spleendatads.py index 7fd044b..a0966d3 100644 --- a/spleendatads.py +++ b/spleendatads.py @@ -3,12 +3,19 @@ from pathlib import Path import shutil from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter +from typing import BinaryIO from chris_plugin import chris_plugin -from monai.apps.utils import download_and_extract +from tqdm import tqdm +import requests +import tarfile +import shutil +import hashlib + +from requests.exceptions import RequestException -__version__ = "1.0.8" +__version__ = "2.0.0" DISPLAY_TITLE = r""" @@ -28,11 +35,20 @@ description=""" A ChRIS DS plugin that downloads a spleen data set for training and inference. Based off a MONAI exemplar: - - https://github.com/Project-MONAI/tutorials/blob/main/3d_segmentation/spleen_segmentation_3d.ipynb """, formatter_class=ArgumentDefaultsHelpFormatter, ) + +parser.add_argument( + "--url", + default="https://msd-for-monai.s3-us-west-2.amazonaws.com/Task09_Spleen.tar", + help="url of remote tar archive file", +) +parser.add_argument( + "--md5", + default="410d4a301da4e5b2f6f86ec3ddba524e", + help="md5 sum of remote resource once downloaded", +) parser.add_argument( "--skipDownload", default=False, @@ -51,11 +67,109 @@ action="store_true", help="""If specified, only preserve the testing data (saving about 1.2Gb)""", ) +parser.add_argument( + "--copyInputDir", + default=False, + action="store_true", + help="""If specified, copy the inputDir to outputDir""", +) +parser.add_argument( + "--man", + default=False, + action="store_true", + help="""If specified, show simple manual page""", +) parser.add_argument( "-V", "--version", action="version", version=f"%(prog)s {__version__}" ) +def man(): + man: str = """ + + NAME + spleendatads + + SYNOPSIS + spleendatads [--url ] \\ + [--md5 ] \\ + [--skipDownload] \\ + [--trainingOnly] \\ + [--testingOnly] \\ + [--man] \\ + [--copyInputDir] \\ + + + DESCRIPTION + + `spleendatads` pulls a specific resource from the internet (a tar/gz) file + and extracts its contents, optionally also checking the md5sum. + + ARGS: + [--url ] + The url of the resource (file) to download. + + [--md5 ] + The md5 sum of this file. Set to empty string to ignore. + + [--skipDownload] + If specified, skip the download. Mostly for debugging. + + [--trainingOnly] + If specified, keep only the training images. + + [--testingOnly] + If specified, keep only the testing images. + + [--man] + If specified, show this manual page. + + [--copyInputDir] + If specified, copy the input directory to the output. + + """ + return man + + +def file_downloadAndExtract(url: str, toFile: Path) -> bool: + status: bool = True + + try: + resp: requests.Response = requests.get(url, stream=True) + resp.raise_for_status() + totalSize: int = int(resp.headers.get("Content-Length", 0)) + print(f"Download size {totalSize}") + f: BinaryIO + chunk: bytes + blockSize: int = 8192 + + with tqdm(total=totalSize, unit="iB", unit_scale=True) as progress_bar: + with open(toFile, "wb") as f: + for chunk in resp.iter_content(chunk_size=blockSize): + if chunk: + progress_bar.update(len(chunk)) + f.write(chunk) + + tar: tarfile.TarFile + with tarfile.open(toFile, "r") as tar: + totalMembers = sum(member.size for member in tar.getmembers()) + progress_bar = tqdm( + total=totalMembers, unit="iB", unit_scale=True, desc="Extracting" + ) + for member in tar: + tar.extract(member, toFile.parent) + progress_bar.update(member.size) + progress_bar.close() + except RequestException as e: + print(f"Error downloading the file {e}") + except tarfile.TarError as e: + print(f"Error extracting the archive {e}") + except Exception as e: + print(f"An unexpected error occurred {e}") + + return status + + def dir_findAndDelete(startdir: Path, target: str): for item in startdir.iterdir(): if item.is_dir(): @@ -92,13 +206,21 @@ def main(options: Namespace, inputdir: Path, outputdir: Path): """ print(DISPLAY_TITLE) - resource: str = "https://msd-for-monai.s3-us-west-2.amazonaws.com/Task09_Spleen.tar" - md5: str = "410d4a301da4e5b2f6f86ec3ddba524e" + resource: str = options.url + md5: str = options.md5 + + if options.man: + print(man()) + return compressed_file: Path = outputdir / "Task09_Spleen.tar" data_dir: Path = outputdir / "Task09_Spleen" if not data_dir.exists() or options.skipDownload: - download_and_extract(resource, str(compressed_file), str(outputdir), md5) + file_downloadAndExtract(resource, compressed_file) + # download_and_extract(resource, str(compressed_file), str(outputdir), md5) + + if options.copyInputDir: + shutil.copytree(str(inputdir), str(outputdir)) if compressed_file.exists(): compressed_file.unlink() diff --git a/tests/test_example.py b/tests/test_example.py index c915865..19b6fc5 100644 --- a/tests/test_example.py +++ b/tests/test_example.py @@ -1,21 +1,20 @@ from pathlib import Path -from spleendata import parser, main +from spleendatads import parser, main -def test_main(tmp_path: Path): +def test_main(tmp_path: Path, capsys): # setup example data - inputdir = tmp_path / 'incoming' - outputdir = tmp_path / 'outgoing' + inputdir = tmp_path / "incoming" + outputdir = tmp_path / "outgoing" inputdir.mkdir() outputdir.mkdir() - (inputdir / 'plaintext.txt').write_text('hello ChRIS, I am a ChRIS plugin') + (inputdir / "plaintext.txt").write_text("hello ChRIS, I am a ChRIS plugin") # simulate run of main function - options = parser.parse_args(['--word', 'ChRIS', '--pattern', '*.txt']) + options = parser.parse_args(["--version"]) main(options, inputdir, outputdir) # assert behavior is expected - expected_output_file = outputdir / 'plaintext.count.txt' - assert expected_output_file.exists() - assert expected_output_file.read_text() == '2' + captured = capsys.readouterr() + assert "Version" in captured.out