Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/shed_tools_methods.py @ 0:26e78fe6e8c4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 from bioblend.toolshed import ToolShedInstance
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2
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3
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4 VALID_KEYS = [
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5 "name",
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6 "owner",
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7 "changeset_revision",
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8 "tool_panel_section_id",
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9 "tool_panel_section_label",
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10 "tool_shed_url",
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11 "install_repository_dependencies",
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12 "install_resolver_dependencies",
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13 "install_tool_dependencies"
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14 ]
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15
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16
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17 def complete_repo_information(tool,
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18 default_toolshed_url,
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19 require_tool_panel_info,
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20 default_install_tool_dependencies,
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21 default_install_repository_dependencies,
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22 default_install_resolver_dependencies,
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23 force_latest_revision):
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24 repo = dict()
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25 # We need those values. Throw a KeyError when not present
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26 repo['name'] = tool['name']
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27 repo['owner'] = tool['owner']
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28 repo['tool_panel_section_id'] = tool.get('tool_panel_section_id')
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29 repo['tool_panel_section_label'] = tool.get('tool_panel_section_label')
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30 if require_tool_panel_info and repo['tool_panel_section_id'] is None and repo[
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31 'tool_panel_section_label'] is None and 'data_manager' not in repo.get('name'):
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32 raise KeyError("Either tool_panel_section_id or tool_panel_section_name must be defined for tool '{0}'.".format(
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33 repo.get('name')))
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34 repo['tool_shed_url'] = format_tool_shed_url(tool.get('tool_shed_url', default_toolshed_url))
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35 repo['changeset_revision'] = tool.get('changeset_revision')
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36 repo = get_changeset_revisions(repo, force_latest_revision)
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37 repo['install_repository_dependencies'] = tool.get('install_repository_dependencies',
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38 default_install_repository_dependencies)
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39 repo['install_resolver_dependencies'] = tool.get('install_resolver_dependencies',
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40 default_install_resolver_dependencies)
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41 repo['install_tool_dependencies'] = tool.get('install_tool_dependencies', default_install_tool_dependencies)
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42 return repo
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43
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44
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45 def format_tool_shed_url(tool_shed_url):
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46 formatted_tool_shed_url = tool_shed_url
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47 if not formatted_tool_shed_url.endswith('/'):
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48 formatted_tool_shed_url += '/'
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49 if not formatted_tool_shed_url.startswith('http'):
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50 formatted_tool_shed_url = 'https://' + formatted_tool_shed_url
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51 return formatted_tool_shed_url
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52
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53
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54 def get_changeset_revisions(repository, force_latest_revision=False):
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55 """
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56 Select the correct changeset revision for a repository,
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57 and make sure the repository exists
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58 (i.e a request to the tool shed with name and owner returns a list of revisions).
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59 Return repository or None, if the repository could not be found on the specified tool shed.
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60 """
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61 # Do not connect to the internet when not necessary
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62 if repository.get('changeset_revision') is None or force_latest_revision:
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63 ts = ToolShedInstance(url=repository['tool_shed_url'])
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64 # Get the set revision or set it to the latest installable revision
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65 installable_revisions = ts.repositories.get_ordered_installable_revisions(repository['name'],
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66 repository['owner'])
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67 if not installable_revisions: #
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68 raise LookupError("Repo does not exist in tool shed: {0}".format(repository))
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69 repository['changeset_revision'] = installable_revisions[-1]
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70
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71 return repository
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72
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73
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74 def flatten_repo_info(repositories):
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75 """
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76 Flatten the dict containing info about what tools to install.
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77 The tool definition YAML file allows multiple revisions to be listed for
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78 the same tool. To enable simple, iterative processing of the info in this
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79 script, flatten the `tools_info` list to include one entry per tool revision.
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80
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81 :type repositories: list of dicts
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82 :param repositories: Each dict in this list should contain info about a tool.
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83 :rtype: list of dicts
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84 :return: Return a list of dicts that correspond to the input argument such
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85 that if an input element contained `revisions` key with multiple
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86 values, those will be returned as separate list items.
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87 """
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88
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89 flattened_list = []
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90 for repo_info in repositories:
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91 new_repo_info = dict()
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92 for key, value in repo_info.items():
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93 if key in VALID_KEYS:
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94 new_repo_info[key] = value
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95 if 'revisions' in repo_info:
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96 revisions = repo_info.get('revisions', [])
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97 if not revisions: # Revisions are empty list or None
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98 flattened_list.append(new_repo_info)
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99 else:
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100 for revision in revisions:
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101 # A new dictionary must be created, otherwise there will
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102 # be aliasing of dictionaries. Which leads to multiple
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103 # repos with the same revision in the end result.
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104 new_revision_dict = dict(**new_repo_info)
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105 new_revision_dict['changeset_revision'] = revision
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106 flattened_list.append(new_revision_dict)
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107 else: # Revision was not defined at all
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108 flattened_list.append(new_repo_info)
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109 return flattened_list