Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/mulled/mulled_list.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 #!/usr/bin/env python |
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2 |
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3 import argparse |
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4 import logging |
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5 from glob import glob |
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6 from html.parser import HTMLParser |
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7 |
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8 import requests |
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9 |
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10 QUAY_API_ENDPOINT = 'https://quay.io/api/v1/repository' |
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11 |
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12 |
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13 def get_quay_containers(repository='biocontainers'): |
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14 """ |
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15 Get all quay containers in the biocontainers repo |
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16 """ |
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17 containers = [] |
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18 |
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19 repos_parameters = {'public': 'true', 'namespace': repository} |
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20 repos_headers = {'Accept-encoding': 'gzip', 'Accept': 'application/json'} |
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21 repos_response = requests.get( |
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22 QUAY_API_ENDPOINT, headers=repos_headers, params=repos_parameters, timeout=12) |
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23 |
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24 repos = repos_response.json()['repositories'] |
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25 |
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26 for repo in repos: |
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27 logging.info(repo) |
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28 tags_response = requests.get( |
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29 "{}/{}/{}".format(QUAY_API_ENDPOINT, repository, repo['name'])) |
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30 tags = tags_response.json()['tags'] |
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31 for tag in tags: |
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32 containers.append('{}:{}'.format(repo['name'], tag)) |
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33 |
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34 return containers |
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35 |
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36 |
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37 def get_singularity_containers(): |
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38 """ |
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39 Get all existing singularity containers from "https://depot.galaxyproject.org/singularity/" |
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40 """ |
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41 class GetContainerNames(HTMLParser): # small parser which gets list of containers |
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42 def __init__(self): |
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43 HTMLParser.__init__(self) |
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44 self.containers = [] |
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45 |
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46 def handle_starttag(self, tag, attrs): |
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47 try: |
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48 for attr in attrs: |
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49 if attr[0] == 'href' and attr[1] != '../': |
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50 self.containers.append(attr[1].replace('%3A', ':')) |
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51 except IndexError: |
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52 pass |
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53 |
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54 parser = GetContainerNames() |
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55 index = requests.get("https://depot.galaxyproject.org/singularity/") |
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56 parser.feed(index.text) |
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57 return parser.containers |
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58 |
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59 |
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60 def get_conda_envs(filepath): |
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61 """ |
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62 Get list of already existing envs |
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63 """ |
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64 return [n.split('__')[-1].replace('@', ':') for n in glob('%s/*' % filepath)] |
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65 |
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66 |
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67 def get_missing_containers(quay_list, singularity_list, blocklist_file=None): |
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68 r""" |
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69 Return list of quay containers that do not exist as singularity containers. Files stored in a blocklist will be ignored |
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70 """ |
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71 blocklist = [] |
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72 if blocklist_file: |
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73 with open(blocklist_file) as fh: |
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74 blocklist = fh.read().split('\n') |
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75 return [n for n in quay_list if n not in singularity_list and n not in blocklist] |
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76 |
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77 |
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78 def get_missing_envs(quay_list, conda_list, blocklist_file=None): |
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79 r""" |
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80 Compares list of conda envs and docker containers and returns missing conda envs |
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81 """ |
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82 blocklist = [] |
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83 if blocklist_file: |
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84 with open(blocklist_file) as fh: |
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85 blocklist = fh.read().split('\n') |
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86 |
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87 return [n for n in quay_list if n.split('--')[0] not in conda_list and n.split('--')[0] not in blocklist] |
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88 |
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89 |
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90 def main(): |
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91 parser = argparse.ArgumentParser( |
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92 description='Returns list of Docker containers in the quay.io biocontainers repository.') |
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93 parser.add_argument('--source', '-s', |
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94 help="Docker, Singularity or Conda.") |
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95 parser.add_argument('--not-singularity', dest='not_singularity', action="store_true", |
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96 help="Exclude Docker containers from which Singularity containers have already been built.") |
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97 parser.add_argument('--not-conda', dest='not_conda', action="store_true", |
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98 help="Exclude Docker containers from which Conda environments have already been extracted.") |
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99 parser.add_argument('--conda-filepath', dest='conda_filepath', default=None, |
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100 help="If searching for conda environments or employing the --not-conda option, a filepath where the environments are located.") |
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101 parser.add_argument('-b', '--blocklist', '--blacklist', dest='blocklist', default=None, |
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102 help="Provide a 'blocklist file' containing containers which should be excluded from the list.") |
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103 parser.add_argument('-f', '--file', dest='output', default=None, |
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104 help="File to write list to. If not given output will be returned on the command line.") |
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105 |
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106 args = parser.parse_args() |
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107 |
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108 if args.source == 'docker': |
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109 containers = get_quay_containers() |
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110 if args.not_singularity: |
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111 containers = get_missing_containers( |
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112 containers, get_singularity_containers(), args.blocklist) |
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113 if args.not_conda: |
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114 containers = get_missing_envs(containers, get_conda_envs( |
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115 args.conda_filepath), args.blocklist) |
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116 elif args.source == 'singularity': |
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117 containers = get_singularity_containers() |
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118 elif args.source == 'conda': |
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119 containers = get_conda_envs(args.conda_filepath) |
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120 else: |
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121 print("The 'source' argument was not understood.") |
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122 return |
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123 |
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124 if args.output: |
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125 with open(args.output, 'a') as f: |
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126 for container in containers: |
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127 f.write('%s\n' % container) |
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128 else: |
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129 print(containers) |
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130 |
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131 |
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132 if __name__ == '__main__': |
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133 main() |