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@@ -3,11 +3,11 @@ | |
| # FROM ghcr.io/mamba-org/micromamba:1.5.1-focal-cuda-11.3.1 | ||
| FROM docker.io/python:3.12.1-slim-bookworm | ||
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| LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \ | ||
| org.opencontainers.image.title="ChRIS Plugin Title" \ | ||
| org.opencontainers.image.description="A ChRIS plugin that..." | ||
| LABEL org.opencontainers.image.authors="FNNDSC <[email protected]>" \ | ||
| org.opencontainers.image.title="FETA ChRIS Plugin" \ | ||
| org.opencontainers.image.description="code for feta" | ||
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| ARG SRCDIR=/usr/local/src/app | ||
| ARG SRCDIR=/usr/local/src/FeTA_challenge_2024 | ||
| WORKDIR ${SRCDIR} | ||
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| COPY requirements.txt . | ||
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@@ -19,4 +19,4 @@ RUN pip install ".[${extras_require}]" \ | |
| && cd / && rm -rf ${SRCDIR} | ||
| WORKDIR / | ||
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| CMD ["commandname"] | ||
| CMD ["inference"] | ||
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| @@ -0,0 +1,77 @@ | ||
| #!/usr/bin/env python | ||
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| from pathlib import Path | ||
| from argparse import ArgumentParser, Namespace, ArgumentDefaultsHelpFormatter | ||
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| from chris_plugin import chris_plugin, PathMapper | ||
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| __version__ = '1.0.0' | ||
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| DISPLAY_TITLE = r""" | ||
| ______ _____ ___ _ _ _ _____ _____ _____ ___ | ||
| | ___|_ _/ _ \ | | | | | / __ \| _ |/ __ \ / | | ||
| | |_ ___| |/ /_\ \ ___| |__ __ _| | | ___ _ __ __ _ ___ `' / /'| |/' |`' / /'/ /| | | ||
| | _/ _ \ || _ | / __| '_ \ / _` | | |/ _ \ '_ \ / _` |/ _ \ / / | /| | / / / /_| | | ||
| | || __/ || | | || (__| | | | (_| | | | __/ | | | (_| | __/ ./ /___\ |_/ /./ /__\___ | | ||
| \_| \___\_/\_| |_/ \___|_| |_|\__,_|_|_|\___|_| |_|\__, |\___| \_____/ \___/ \_____/ |_/ | ||
| ______ __/ | ______ | ||
| |______| |___/ |______| | ||
| """ | ||
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| parser = ArgumentParser(description='!!!CHANGE ME!!! An example ChRIS plugin which ' | ||
| 'counts the number of occurrences of a given ' | ||
| 'word in text files.', | ||
| formatter_class=ArgumentDefaultsHelpFormatter) | ||
| parser.add_argument('-w', '--word', required=True, type=str, | ||
| help='word to count') | ||
| parser.add_argument('-p', '--pattern', default='**/*.txt', type=str, | ||
| help='input file filter glob') | ||
| parser.add_argument('-V', '--version', action='version', | ||
| version=f'%(prog)s {__version__}') | ||
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| # The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator." | ||
| # Some metadata about the plugin is specified here. There is more metadata specified in setup.py. | ||
| # | ||
| # documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin | ||
| @chris_plugin( | ||
| parser=parser, | ||
| title='FETA ChRIS Plugin', | ||
| category='', # ref. https://chrisstore.co/plugins | ||
| min_memory_limit='100Mi', # supported units: Mi, Gi | ||
| min_cpu_limit='1000m', # millicores, e.g. "1000m" = 1 CPU core | ||
| min_gpu_limit=0 # set min_gpu_limit=1 to enable GPU | ||
| ) | ||
| def main(options: Namespace, inputdir: Path, outputdir: Path): | ||
| """ | ||
| *ChRIS* plugins usually have two positional arguments: an **input directory** containing | ||
| input files and an **output directory** where to write output files. Command-line arguments | ||
| are passed to this main method implicitly when ``main()`` is called below without parameters. | ||
| :param options: non-positional arguments parsed by the parser given to @chris_plugin | ||
| :param inputdir: directory containing (read-only) input files | ||
| :param outputdir: directory where to write output files | ||
| """ | ||
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| print(DISPLAY_TITLE) | ||
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| # Typically it's easier to think of programs as operating on individual files | ||
| # rather than directories. The helper functions provided by a ``PathMapper`` | ||
| # object make it easy to discover input files and write to output files inside | ||
| # the given paths. | ||
| # | ||
| # Refer to the documentation for more options, examples, and advanced uses e.g. | ||
| # adding a progress bar and parallelism. | ||
| mapper = PathMapper.file_mapper(inputdir, outputdir, glob=options.pattern, suffix='.count.txt') | ||
| for input_file, output_file in mapper: | ||
| # The code block below is a small and easy example of how to use a ``PathMapper``. | ||
| # It is recommended that you put your functionality in a helper function, so that | ||
| # it is more legible and can be unit tested. | ||
| data = input_file.read_text() | ||
| frequency = data.count(options.word) | ||
| output_file.write_text(str(frequency)) | ||
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| if __name__ == '__main__': | ||
| main() |
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@@ -19,18 +19,18 @@ def get_version(rel_path: str) -> str: | |
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| setup( | ||
| name='chris-plugin-template', | ||
| version=get_version('app.py'), | ||
| description='A ChRIS DS plugin template', | ||
| name='FeTA_challenge_2024', | ||
| version=get_version('inference.py'), | ||
| description='code for feta', | ||
| author='FNNDSC', | ||
| author_email='[email protected]', | ||
| url='https://github.com/FNNDSC/python-chrisapp-template', | ||
| py_modules=['app'], | ||
| author_email='[email protected]', | ||
| url='https://github.com/FNNDSC/FeTA_challenge_2024', | ||
| py_modules=['inference'], | ||
| install_requires=['chris_plugin'], | ||
| license='MIT', | ||
| entry_points={ | ||
| 'console_scripts': [ | ||
| 'commandname = app:main' | ||
| 'inference = inference:main' | ||
| ] | ||
| }, | ||
| classifiers=[ | ||
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