mirror of
https://gitlab.ub.uni-bielefeld.de/sfb1288inf/file-setup.git
synced 2024-12-25 10:54:18 +00:00
Use pyFlow for file setup service
This commit is contained in:
Patrick Jentsch
parent
0c8b3421c6
commit
3c9a800886
@ -1,8 +1,5 @@
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image: docker:19.03.13
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variables:
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DOCKER_TLS_CERTDIR: "/certs"
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services:
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- docker:19.03.13-dind
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@ -10,6 +7,10 @@ stages:
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- build
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- push
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variables:
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DOCKER_TLS_CERTDIR: "/certs"
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INTERMEDIATE_IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME-$CI_COMMIT_SHA
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.reg_setup:
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before_script:
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- apk add --no-cache curl
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@ -28,8 +29,6 @@ build_image:
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stage: build
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tags:
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- docker
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variables:
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INTERMEDIATE_IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
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push_master:
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extends:
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@ -47,7 +46,6 @@ push_master:
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- docker
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variables:
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IMAGE_TAG: $CI_REGISTRY_IMAGE:latest
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INTERMEDIATE_IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
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push_other:
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extends:
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@ -68,4 +66,3 @@ push_other:
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- docker
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variables:
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IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_REF_NAME
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INTERMEDIATE_IMAGE_TAG: $CI_REGISTRY_IMAGE:$CI_COMMIT_SHA
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31
Dockerfile
31
Dockerfile
@ -1,7 +1,7 @@
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FROM debian:buster-slim
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LABEL authors="Patrick Jentsch <p.jentsch@uni-bielefeld.de>, Stephan Porada <sporada@uni-bielefeld.de>"
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LABEL authors="Patrick Jentsch <p.jentsch@uni-bielefeld.de>, Stephan Porada <porada@posteo.de>"
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ENV LANG=C.UTF-8
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@ -9,17 +9,38 @@ ENV LANG=C.UTF-8
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RUN apt-get update \
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&& apt-get install --no-install-recommends --yes \
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wget
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# Install the NLP pipeline and it's dependencies #
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## Install pyFlow ##
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ENV PYFLOW_VERSION=1.1.20
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RUN wget --no-check-certificate --quiet \
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"https://github.com/Illumina/pyflow/releases/download/v${PYFLOW_VERSION}/pyflow-${PYFLOW_VERSION}.tar.gz" \
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&& tar -xzf "pyflow-${PYFLOW_VERSION}.tar.gz" \
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&& cd "pyflow-${PYFLOW_VERSION}" \
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&& apt-get install --no-install-recommends --yes \
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python2.7 \
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&& python2.7 setup.py build install \
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&& cd .. \
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&& rm -r "pyflow-${PYFLOW_VERSION}" "pyflow-${PYFLOW_VERSION}.tar.gz"
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## Further dependencies ##
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RUN apt-get install --no-install-recommends --yes \
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imagemagick \
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procps \
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python3.7 \
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zip \
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&& rm -r /var/lib/apt/lists/*
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RUN mv /etc/ImageMagick-6/policy.xml /etc/ImageMagick-6/policy.xml.bak
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&& mv /etc/ImageMagick-6/policy.xml /etc/ImageMagick-6/policy.xml.bak
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## Install Pipeline ##
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COPY file-setup /usr/local/bin
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RUN rm -r /var/lib/apt/lists/*
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ENTRYPOINT ["file-setup"]
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CMD ["--help"]
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37
README.md
37
README.md
@ -0,0 +1,37 @@
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# File setup
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This software implements a parallelized pipeline to setup image files. It is used for nopaque's File setup service but you can also use it standalone, for that purpose a convenient wrapper script is provided.
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## Software used in this pipeline implementation
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- Official Debian Docker image (buster-slim) and programs from its free repositories: https://hub.docker.com/_/debian
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## Use this image
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1. Create input and output directories for the pipeline.
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``` bash
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mkdir -p /<my_data_location>/input /<my_data_location>/output
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```
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2. Place your images files inside a directory in `/<my_data_location>/input`.
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3. Start the pipeline process. Check the pipeline help (`file-setup --help`) for more details.
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```
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# Option one: Use the wrapper script
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## Install the wrapper script (only on first run). Get it from https://gitlab.ub.uni-bielefeld.de/sfb1288inf/file-setup/-/raw/1.0.0/wrapper/file-setup, make it executeable and add it to your ${PATH}
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cd /<my_data_location>
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file-setup -i input -o output
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# Option two: Classic Docker style
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docker run \
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--rm \
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-it \
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-u $(id -u $USER):$(id -g $USER) \
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-v /<my_data_location>/input:/input \
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-v /<my_data_location>/output:/output \
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gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file-setup:1.0.0 \
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-i /input \
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-o /output
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```
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4. Check your results in the `/<my_data_location>/output` directory.
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227
file-setup
227
file-setup
@ -1,79 +1,188 @@
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#!/usr/bin/env python3.7
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#!/usr/bin/env python2.7
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# coding=utf-8
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"""A file setup pipeline for image file merging."""
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"""
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file-setup
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Usage: For usage instructions run with option --help
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Authors: Patrick Jentsch <p.jentsch@uni-bielefeld.de
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Stephan Porada <sporada@uni-bielefeld.de>
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"""
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__author__ = 'Patrick Jentsch <p.jentsch@uni-bielefeld.de>,' \
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'Stephan Porada <porada@posteo.de>'
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__version__ = '1.0.0'
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from argparse import ArgumentParser
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from pyflow import WorkflowRunner
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import os
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import re
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import subprocess
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import sys
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def parse_arguments():
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parser = ArgumentParser(description='Merge images (JPEG, PNG or TIFF) into one PDF file.')
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parser.add_argument('-i', '--input-directory',
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class FileSetupPipelineJob:
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"""An file setup pipeline job class
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Each image containing input directory of the pipeline is represented as an
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file setup pipeline job, which holds all necessary information for the
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pipeline to process it.
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Arguments:
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dir -- Path to the directory
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output_dir -- Path to a directory, where job results a stored
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"""
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def __init__(self, dir, output_dir):
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self.dir = dir
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self.name = os.path.basename(dir)
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self.output_dir = output_dir
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class FileSetupPipeline(WorkflowRunner):
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def __init__(self, input_dir, output_dir, zip):
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self.input_dir = input_dir
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self.output_dir = output_dir
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self.zip = zip
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self.jobs = collect_jobs(self.input_dir, self.output_dir)
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def workflow(self):
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if not self.jobs:
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return
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'''
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' ##################################################
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' # setup output directory #
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' ##################################################
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'''
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setup_output_directory_tasks = []
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for i, job in enumerate(self.jobs):
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cmd = 'mkdir -p "{}"'.format(job.output_dir)
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lbl = 'setup_output_directory_-_{}'.format(i)
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task = self.addTask(command=cmd, label=lbl)
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setup_output_directory_tasks.append(task)
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'''
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' ##################################################
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' # pre file setup #
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' ##################################################
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'''
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pre_file_setup_tasks = []
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for i, job in enumerate(self.jobs):
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input_file = os.path.join(job.output_dir, 'file_setup_input_files.txt') # noqa
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cmd = 'ls -dQv "{}/"* >> "{}"'.format(job.dir, input_file)
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deps = 'setup_output_directory_-_{}'.format(i)
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lbl = 'pre_file_setup_-_{}'.format(i)
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task = self.addTask(command=cmd, dependencies=deps, label=lbl)
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pre_file_setup_tasks.append(task)
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'''
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' ##################################################
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' # file setup #
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' ##################################################
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'''
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file_setup_tasks = []
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n_cores = max(1, int(self.getNCores() / len(self.jobs)))
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for i, job in enumerate(self.jobs):
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input_file = os.path.join(job.output_dir, 'file_setup_input_files.txt') # noqa
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output_file = os.path.join(job.output_dir, '{}.pdf'.format(job.name)) # noqa
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cmd = 'convert "@{}" "{}"'.format(input_file, output_file)
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deps = 'pre_file_setup_-_{}'.format(i)
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lbl = 'file_setup_-_{}'.format(i)
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task = self.addTask(command=cmd, dependencies=deps, label=lbl,
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nCores=n_cores)
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file_setup_tasks.append(task)
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'''
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' ##################################################
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' # post file setup #
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' ##################################################
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'''
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post_file_setup_tasks = []
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for i, job in enumerate(self.jobs):
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input_file = os.path.join(job.output_dir, 'file_setup_input_files.txt') # noqa
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cmd = 'rm "{}"'.format(input_file)
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deps = 'file_setup_-_{}'.format(i)
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lbl = 'post_file_setup_-_{}'.format(i)
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task = self.addTask(command=cmd, dependencies=deps, label=lbl)
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post_file_setup_tasks.append(task)
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'''
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' ##################################################
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' # zip creation #
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' ##################################################
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'''
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zip_creation_tasks = []
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if self.zip is not None:
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cmd = 'cd "{}"'.format(self.output_dir)
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cmd += ' && '
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cmd += 'zip'
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cmd += ' -r'
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cmd += ' "{}.zip" .'.format(self.zip)
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cmd += ' -x "pyflow.data*"'
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cmd += ' -i "*.pdf"'
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cmd += ' && '
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cmd += 'cd -'
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deps = file_setup_tasks
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lbl = 'zip_creation'
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task = self.addTask(command=cmd, dependencies=deps, label=lbl)
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zip_creation_tasks.append(task)
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def collect_jobs(input_dir, output_dir):
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jobs = []
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for dir in os.listdir(input_dir):
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if not os.path.isdir(os.path.join(input_dir, dir)):
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continue
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# TODO: Filter for file types
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if not os.listdir(os.path.join(input_dir, dir)):
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continue
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job = FileSetupPipelineJob(os.path.join(input_dir, dir),
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os.path.join(output_dir, dir))
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jobs.append(job)
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return jobs
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def parse_args():
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parser = ArgumentParser(description='A file setup pipeline for image file merging', # noqa
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prog='File setup pipeline')
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parser.add_argument('-i', '--input-dir',
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help='Input directory',
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required=True)
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parser.add_argument('-o', '--output-directory',
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parser.add_argument('-o', '--output-dir',
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help='Output directory',
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required=True)
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parser.add_argument('-f', '--output-file-base',
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help='output file base',
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required=True)
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parser.add_argument('--log-dir')
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parser.add_argument('--zip')
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return parser.parse_args()
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parser.add_argument('--log-dir',
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help='Logging directory')
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parser.add_argument('--mem-mb',
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help='Amount of system memory to be used (Default: min(--n-cores * 2048, available system memory))', # noqa
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type=int)
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parser.add_argument('--n-cores',
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default=1,
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help='Number of CPU threads to be used (Default: 1)',
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type=int)
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parser.add_argument('--zip',
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help='Create one zip file per filetype')
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parser.add_argument('-v', '--version',
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action='version',
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help='Returns the current version of the file setup pipeline', # noqa
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version='%(prog)s {}'.format(__version__))
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args = parser.parse_args()
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def natural_sorted(iterable):
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""" Sort the given list in the way that humans expect.
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"""
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convert = lambda text: int(text) if text.isdigit() else text
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alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', key)]
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return sorted(iterable, key=alphanum_key)
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def merge_images(input_dir, output_dir, output_file_base, zip):
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try:
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os.mkdir(output_dir)
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except FileExistsError:
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pass
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files = filter(lambda x: x.lower().endswith(('.jpg', '.jpeg', '.png', '.tif', '.tiff')),
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os.listdir(input_dir))
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files = natural_sorted(files)
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files = map(lambda x: os.path.join(input_dir, x), files)
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output_file = os.path.join(output_dir, '{}.pdf'.format(output_file_base))
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# Convert input files to a single PDF
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cmd = 'convert "{}" "{}"'.format('" "'.join(files), output_file)
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subprocess.run(cmd, shell=True)
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# zip stuff
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if zip is not None:
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# Set some tricky default values and check for insufficient input
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if args.log_dir is None:
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args.log_dir = args.output_dir
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if args.n_cores < 1:
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raise Exception('--n-cores must be greater or equal 1')
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if args.mem_mb is None:
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max_mem_mb = int(os.popen('free -t -m').readlines()[-1].split()[1:][0])
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args.mem_mb = min(args.n_cores * 2048, max_mem_mb)
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if args.mem_mb < 2048:
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raise Exception('--mem-mb must be greater or equal 2048')
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if args.zip is not None and args.zip.lower().endswith('.zip'):
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# Remove .zip file extension if provided
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if zip.lower().endswith('.zip'):
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zip = zip[:-4]
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zip = zip if zip else 'output'
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cmd = 'cd "{}"'.format(output_dir)
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cmd += ' && '
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cmd += 'zip'
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cmd += ' "{}.zip" "{}.pdf"'.format(zip, output_file_base)
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cmd += ' && '
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cmd += 'cd -'
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subprocess.run(cmd, shell=True)
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args.zip = args.zip[:-4]
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args.zip = args.zip if args.zip else 'output'
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return args
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def main():
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args = parse_arguments()
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merge_images(args.input_directory,
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args.output_directory,
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args.output_file_base,
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args.zip)
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args = parse_args()
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file_setup_pipeline = FileSetupPipeline(args.input_dir, args.output_dir, args.zip) # noqa
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retval = file_setup_pipeline.run(dataDirRoot=args.log_dir, memMb=args.mem_mb, nCores=args.n_cores) # noqa
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sys.exit(retval)
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if __name__ == '__main__':
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@ -4,30 +4,35 @@
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from argparse import ArgumentParser
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import os
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import subprocess
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import sys
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CONTAINER_IMAGE = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file-setup:latest'
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CONTAINER_IMAGE = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file-setup:1.0.0'
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CONTAINER_INPUT_DIR = '/input'
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CONTAINER_OUTPUT_DIR = '/output'
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CONTAINER_LOG_DIR = '/logs'
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UID = str(os.getuid())
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GID = str(os.getgid())
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parser = ArgumentParser(add_help=False)
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parser.add_argument('-i', '--input-directory')
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parser.add_argument('-o', '--output-directory')
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parser.add_argument('-i', '--input-dir')
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parser.add_argument('-o', '--output-dir')
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parser.add_argument('--log-dir')
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args, remaining_args = parser.parse_known_args()
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cmd = ['docker', 'run', '--rm', '-it', '-u', '{}:{}'.format(UID, GID)]
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if args.output_directory is not None:
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cmd += ['-v', '{}:{}'.format(os.path.abspath(args.output_directory),
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CONTAINER_OUTPUT_DIR)]
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remaining_args.insert(0, CONTAINER_OUTPUT_DIR)
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remaining_args.insert(0, '-o')
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if args.input_directory is not None:
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cmd += ['-v', '{}:{}'.format(os.path.abspath(args.input_directory),
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CONTAINER_INPUT_DIR)]
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remaining_args.insert(0, CONTAINER_INPUT_DIR)
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remaining_args.insert(0, '-i')
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if args.input_dir is not None:
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mapping = os.path.abspath(args.input_dir) + ':' + CONTAINER_INPUT_DIR
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cmd += ['-v', mapping]
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remaining_args += ['-i', CONTAINER_INPUT_DIR]
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if args.output_dir is not None:
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mapping = os.path.abspath(args.output_dir) + ':' + CONTAINER_OUTPUT_DIR
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cmd += ['-v', mapping]
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remaining_args += ['-o', CONTAINER_OUTPUT_DIR]
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if args.log_dir is not None:
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mapping = os.path.abspath(args.log_dir) + ':' + CONTAINER_LOG_DIR
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cmd += ['-v', mapping]
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remaining_args += ['--log-dir', CONTAINER_LOG_DIR]
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cmd.append(CONTAINER_IMAGE)
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cmd += remaining_args
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subprocess.run(cmd)
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sys.exit(subprocess.run(cmd).returncode)
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