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Adding new script to update CWL dockerpull key
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,2 @@ | ||
| requests~=2.24.0 | ||
| requests~=2.24.0 | ||
| PyYAML~=5.3.1 |
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src/bioconda2biocontainer/entry_point_update_cwl_docker.py
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,27 @@ | ||
| #!/usr/bin/env python | ||
| import argparse | ||
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| import yaml | ||
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| from bioconda2biocontainer.update_cwl_docker_image import update_cwl_docker_from_tool_name | ||
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| def main(): | ||
| parser = argparse.ArgumentParser( | ||
| description='Replace Docker image in CWL from conda env yaml file') | ||
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| parser.add_argument('--conda_env_file', help='Conda env yaml file', | ||
| required=True) | ||
| parser.add_argument('--cwl_path', help='Path to the CWL directory', | ||
| required=True) | ||
| args = parser.parse_args() | ||
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| with open(args.conda_env_file) as fin: | ||
| conda_env = yaml.load(fin, Loader=yaml.FullLoader) | ||
| if 'dependencies' in conda_env: | ||
| for d in conda_env['dependencies']: | ||
| update_cwl_docker_from_tool_name(d, args.cwl_path) | ||
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| if __name__ == '__main__': | ||
| main() |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,84 @@ | ||
| import os | ||
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| import yaml | ||
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| from bioconda2biocontainer.biocontainer import find_latest_image | ||
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| PRINT_HEADER = True | ||
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| def __replace_docker_image(f, old, new, package_name, package_version): | ||
| global PRINT_HEADER | ||
| if PRINT_HEADER: | ||
| print('{} with version {} update image to: {}'.format( | ||
| package_name, package_version, | ||
| new)) | ||
| PRINT_HEADER = False | ||
| print('\t{} with old image replaced: {}'.format(f, old)) | ||
| with open(f) as fin: | ||
| list_of_lines = fin.readlines() | ||
| with open(f, 'w') as fout: | ||
| for line in list_of_lines: | ||
| if old in line: | ||
| line = line.replace(old, new) | ||
| fout.write(line) | ||
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| def __load_cwl(f, package_name, package_version, image_name): | ||
| with open(f) as fin: | ||
| try: | ||
| y = yaml.load(fin, Loader=yaml.FullLoader) | ||
| return y | ||
| except yaml.scanner.ScannerError: | ||
| pass | ||
| return None | ||
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| def __replace_in_cwl(f, package_name, package_version, image_name): | ||
| y = __load_cwl(f, package_name, package_version, image_name) | ||
| if y: | ||
| if 'hints' in y and 'DockerRequirement' in y['hints'] and \ | ||
| 'dockerPull' in y['hints']['DockerRequirement'] and \ | ||
| y['hints']['DockerRequirement']['dockerPull'].split(':')[0] == \ | ||
| image_name.split(':')[0] and \ | ||
| y['hints']['DockerRequirement']['dockerPull'] != image_name: | ||
| __replace_docker_image(f, | ||
| y['hints']['DockerRequirement']['dockerPull'], image_name, | ||
| package_name, package_version) | ||
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| def __replace_in_yml(f, package_name, package_version, image_name): | ||
| y = __load_cwl(f, package_name, package_version, image_name) | ||
| if y: | ||
| if 'dockerPull' in y and y['dockerPull'].split(':')[0] == image_name.split(':')[0] and \ | ||
| y['dockerPull'] != image_name: | ||
| __replace_docker_image(f, | ||
| y['dockerPull'], image_name, | ||
| package_name, package_version) | ||
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| def update_cwl_docker_from_biocontainers(package_name, package_version, cwl_path): | ||
| biocontainer_image = find_latest_image(package_name, package_version, False, | ||
| False, False, 'Docker', None) | ||
| if isinstance(biocontainer_image, dict): | ||
| for root, dirs, files in os.walk(cwl_path): | ||
| for f in files: | ||
| f = os.path.join(root, f) | ||
| if f.endswith('.cwl'): | ||
| __replace_in_cwl(f, package_name, package_version, | ||
| biocontainer_image['image_name']) | ||
| elif f.endswith('.yml') or f.endswith('.yaml'): | ||
| __replace_in_yml(f, package_name, package_version, | ||
| biocontainer_image['image_name']) | ||
| else: | ||
| print('There is not biocontainer image for {} version {}'.format( | ||
| package_name, package_version)) | ||
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| def update_cwl_docker_from_tool_name(tool, cwl_path): | ||
| global PRINT_HEADER | ||
| PRINT_HEADER = True | ||
| if isinstance(tool, str) and '=' in tool: | ||
| tool_version = tool.split('=') | ||
| update_cwl_docker_from_biocontainers( | ||
| tool_version[0], tool_version[1], cwl_path) |