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annotate planemo/lib/python3.7/site-packages/ephemeris/shed_tools.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 """
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2 A tool to automate installation of tool repositories from a Galaxy Tool Shed
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3 into an instance of Galaxy.
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4
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5 Shed-tools has three commands: update, test and install.
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6
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7 Update simply updates all the tools in a Galaxy given connection details on the command line.
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8
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9 Test tests the specified tools in the Galaxy Instance.
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10
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11 Install allows installation of tools in multiple ways.
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12 Galaxy instance details and the installed tools can be provided in one of three
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13 ways:
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14
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15 1. In the YAML format via dedicated files (a sample can be found
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16 `here <https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample>`_).
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17 2. On the command line as dedicated script options (see the usage help).
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18 3. As a single composite parameter to the script. The parameter must be a
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19 single, YAML-formatted string with the keys corresponding to the keys
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20 available for use in the YAML formatted file (for example:
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21 `--yaml_tool "{'owner': 'kellrott', 'tool_shed_url':
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22 'https://testtoolshed.g2.bx.psu.edu', 'tool_panel_section_id':
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23 'peak_calling', 'name': 'synapse_interface'}"`).
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24
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25 Only one of the methods can be used with each invocation of the script but if
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26 more than one are provided are provided, precedence will correspond to order
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27 of the items in the list above.
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28 When installing tools, Galaxy expects any `tool_panel_section_id` provided when
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29 installing a tool to already exist in the configuration. If the section
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30 does not exist, the tool will be installed outside any section. See
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31 `shed_tool_conf.xml.sample` in this directory for a sample of such file. Before
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32 running this script to install the tools, make sure to place such file into
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33 Galaxy's configuration directory and set Galaxy configuration option
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34 `tool_config_file` to include it.
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35 """
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36 import datetime as dt
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37 import json
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38 import os
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39 import re
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40 import time
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41 from collections import namedtuple
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42 from concurrent.futures import thread, ThreadPoolExecutor
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43
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44 import requests
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45 import yaml
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46 from bioblend.galaxy.client import ConnectionError
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47 from bioblend.galaxy.toolshed import ToolShedClient
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48 from galaxy.tool_util.verify.interactor import (
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49 GalaxyInteractorApi,
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50 verify_tool,
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51 )
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52 from galaxy.util import unicodify
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53
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54 from . import get_galaxy_connection, load_yaml_file
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55 from .ephemeris_log import disable_external_library_logging, setup_global_logger
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56 from .get_tool_list_from_galaxy import GiToToolYaml, the_same_repository, tools_for_repository
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57 from .shed_tools_args import parser
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58 from .shed_tools_methods import complete_repo_information, flatten_repo_info, VALID_KEYS
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59
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60 NON_TERMINAL_REPOSITORY_STATES = {
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61 'New',
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62 'Cloning',
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63 'Setting tool versions',
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64 'Installing repository dependencies',
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65 'Installing tool dependencies',
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66 'Loading proprietary datatypes'
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67 }
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68
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69
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70 class InstallRepositoryManager(object):
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71 """Manages the installation of new repositories on a galaxy instance"""
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72
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73 def __init__(self,
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74 galaxy_instance):
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75 """Initialize a new tool manager"""
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76 self.gi = galaxy_instance
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77 self.tool_shed_client = ToolShedClient(self.gi)
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78
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79 def installed_repositories(self):
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80 """Get currently installed tools"""
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81 return GiToToolYaml(
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82 gi=self.gi,
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83 skip_tool_panel_section_name=False,
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84 get_data_managers=True,
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85 get_all_tools=True
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86 ).tool_list.get("tools")
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87
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88 def filter_installed_repos(self, repos, check_revision=True):
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89 # TODO: Find a speedier algorithm.
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90 """This filters a list of repositories"""
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91 not_installed_repos = []
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92 already_installed_repos = []
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93 if check_revision:
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94 # If we want to check if revisions are equal, flatten the list,
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95 # so each repository - revision combination has its own entry
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96 installed_repos = flatten_repo_info(self.installed_repositories())
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97 else:
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98 # If we do not care about revision equality, do not do the flatten
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99 # action to limit the number of comparisons.
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100 installed_repos = self.installed_repositories()
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101
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102 for repo in repos:
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103 for installed_repo in installed_repos:
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104 if the_same_repository(installed_repo, repo, check_revision):
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105 already_installed_repos.append(repo)
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106 break
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107 else: # This executes when the for loop completes and no match has been found.
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108 not_installed_repos.append(repo)
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109 FilterResults = namedtuple("FilterResults", ["not_installed_repos", "already_installed_repos"])
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110 return FilterResults(already_installed_repos=already_installed_repos, not_installed_repos=not_installed_repos)
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111
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112 def install_repositories(self,
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113 repositories,
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114 log=None,
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115 force_latest_revision=False,
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116 default_toolshed='https://toolshed.g2.bx.psu.edu/',
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117 default_install_tool_dependencies=False,
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118 default_install_resolver_dependencies=True,
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119 default_install_repository_dependencies=True):
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120 """Install a list of tools on the current galaxy"""
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121 if not repositories:
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122 raise ValueError("Empty list of tools was given")
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123 installation_start = dt.datetime.now()
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124 installed_repositories = []
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125 skipped_repositories = []
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126 errored_repositories = []
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127 counter = 0
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128
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129 # Check repos for invalid keys
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130 for repo in repositories:
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131 for key in repo.keys():
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132 if key not in VALID_KEYS and key != 'revisions':
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133 if log:
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134 log.warning("'{0}' not a valid key. Will be skipped during parsing".format(key))
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135
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136 # Start by flattening the repo list per revision
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137 flattened_repos = flatten_repo_info(repositories)
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138 total_num_repositories = len(flattened_repos)
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139
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140 # Complete the repo information, and make sure each repository has a revision
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141 repository_list = []
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142 for repository in flattened_repos:
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143 start = dt.datetime.now()
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144 try:
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145 complete_repo = complete_repo_information(
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146 repository,
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147 default_toolshed_url=default_toolshed,
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148 require_tool_panel_info=True,
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149 default_install_tool_dependencies=default_install_tool_dependencies,
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150 default_install_resolver_dependencies=default_install_resolver_dependencies,
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151 default_install_repository_dependencies=default_install_repository_dependencies,
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152 force_latest_revision=force_latest_revision)
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153 repository_list.append(complete_repo)
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154 except Exception as e:
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155 # We'll run through the loop come whatever may, we log the errored repositories at the end anyway.
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156 if log:
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157 log_repository_install_error(repository, start, unicodify(e), log)
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158 errored_repositories.append(repository)
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159
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160 # Filter out already installed repos
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161 filtered_repos = self.filter_installed_repos(repository_list)
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162
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163 for skipped_repo in filtered_repos.already_installed_repos:
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164 counter += 1
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165 if log:
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166 log_repository_install_skip(skipped_repo, counter, total_num_repositories, log)
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167 skipped_repositories.append(skipped_repo)
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168
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169 # Install repos
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170 for repository in filtered_repos.not_installed_repos:
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171 counter += 1
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172 if log:
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173 log_repository_install_start(repository, counter=counter, installation_start=installation_start, log=log,
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174 total_num_repositories=total_num_repositories)
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175 result = self.install_repository_revision(repository, log)
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176 if result == "error":
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177 errored_repositories.append(repository)
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178 elif result == "skipped":
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179 skipped_repositories.append(repository)
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180 elif result == "installed":
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181 installed_repositories.append(repository)
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182
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183 # Log results
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184 if log:
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185 log.info("Installed repositories ({0}): {1}".format(
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186 len(installed_repositories),
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187 [(
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188 t['name'],
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189 t.get('changeset_revision')
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190 ) for t in installed_repositories])
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191 )
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192 log.info("Skipped repositories ({0}): {1}".format(
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193 len(skipped_repositories),
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194 [(
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195 t['name'],
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196 t.get('changeset_revision')
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197 ) for t in skipped_repositories])
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198 )
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199 log.info("Errored repositories ({0}): {1}".format(
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200 len(errored_repositories),
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201 [(
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202 t['name'],
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203 t.get('changeset_revision', "")
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204 ) for t in errored_repositories])
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205 )
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206 log.info("All repositories have been installed.")
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207 log.info("Total run time: {0}".format(dt.datetime.now() - installation_start))
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208 InstallResults = namedtuple("InstallResults",
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209 ["installed_repositories", "errored_repositories", "skipped_repositories"])
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210 return InstallResults(installed_repositories=installed_repositories,
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211 skipped_repositories=skipped_repositories,
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212 errored_repositories=errored_repositories)
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213
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214 def update_repositories(self, repositories=None, log=None, **kwargs):
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215 if not repositories: # Repositories None or empty list
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216 repositories = self.installed_repositories()
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217 else:
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218 filtered_repos = self.filter_installed_repos(repositories, check_revision=False)
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219 if filtered_repos.not_installed_repos:
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220 if log:
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221 log.warning("The following tools are not installed and will not be upgraded: {0}".format(
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222 filtered_repos.not_installed_repos))
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223 repositories = filtered_repos.already_installed_repos
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224 return self.install_repositories(repositories, force_latest_revision=True, log=log, **kwargs)
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225
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226 def test_tools(self,
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227 test_json,
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228 repositories=None,
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229 log=None,
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230 test_user_api_key=None,
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231 test_user="ephemeris@galaxyproject.org",
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232 parallel_tests=1,
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233 ):
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234 """Run tool tests for all tools in each repository in supplied tool list or ``self.installed_repositories()``.
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235 """
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236 tool_test_start = dt.datetime.now()
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237 tests_passed = []
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238 test_exceptions = []
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239
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240 if not repositories: # If repositories is None or empty list
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241 # Consider a variant of this that doesn't even consume a tool list YAML? target
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242 # something like installed_repository_revisions(self.gi)
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243 repositories = self.installed_repositories()
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244
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245 target_repositories = flatten_repo_info(repositories)
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246
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247 installed_tools = []
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248 for target_repository in target_repositories:
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249 repo_tools = tools_for_repository(self.gi, target_repository)
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250 installed_tools.extend(repo_tools)
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251
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252 all_test_results = []
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253 galaxy_interactor = self._get_interactor(test_user, test_user_api_key)
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254 test_history = galaxy_interactor.new_history()
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255
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256 with ThreadPoolExecutor(max_workers=parallel_tests) as executor:
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257 try:
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258 for tool in installed_tools:
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259 self._test_tool(executor=executor,
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260 tool=tool,
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261 galaxy_interactor=galaxy_interactor,
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262 test_history=test_history,
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263 log=log,
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264 tool_test_results=all_test_results,
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265 tests_passed=tests_passed,
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266 test_exceptions=test_exceptions,
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267 )
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268 finally:
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269 # Always write report, even if test was cancelled.
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270 try:
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271 executor.shutdown(wait=True)
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272 except KeyboardInterrupt:
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273 executor._threads.clear()
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274 thread._threads_queues.clear()
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275 n_passed = len(tests_passed)
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276 n_failed = len(test_exceptions)
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277 report_obj = {
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278 'version': '0.1',
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279 'suitename': 'Ephemeris tool tests targeting %s' % self.gi.base_url,
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280 'results': {
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281 'total': n_passed + n_failed,
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282 'errors': n_failed,
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283 'failures': 0,
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284 'skips': 0,
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285 },
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286 'tests': sorted(all_test_results, key=lambda el: el['id']),
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287 }
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288 with open(test_json, "w") as f:
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289 json.dump(report_obj, f)
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290 if log:
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291 log.info("Report written to '%s'", os.path.abspath(test_json))
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292 log.info("Passed tool tests ({0}): {1}".format(
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293 n_passed,
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294 [t for t in tests_passed])
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295 )
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296 log.info("Failed tool tests ({0}): {1}".format(
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297 n_failed,
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298 [t[0] for t in test_exceptions])
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299 )
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300 log.info("Total tool test time: {0}".format(dt.datetime.now() - tool_test_start))
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301
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302 def _get_interactor(self, test_user, test_user_api_key):
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303 if test_user_api_key is None:
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304 whoami = self.gi.make_get_request(self.gi.url + "/whoami").json()
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305 if whoami is not None:
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306 test_user_api_key = self.gi.key
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307 galaxy_interactor_kwds = {
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308 "galaxy_url": re.sub('/api', '', self.gi.url),
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309 "master_api_key": self.gi.key,
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310 "api_key": test_user_api_key, # TODO
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311 "keep_outputs_dir": '',
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312 }
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313 if test_user_api_key is None:
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314 galaxy_interactor_kwds["test_user"] = test_user
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315 galaxy_interactor = GalaxyInteractorApi(**galaxy_interactor_kwds)
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316 return galaxy_interactor
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317
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318 @staticmethod
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319 def _test_tool(executor,
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320 tool,
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321 galaxy_interactor,
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322 tool_test_results,
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323 tests_passed,
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324 test_exceptions,
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325 log,
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326 test_history=None,
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327 ):
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328 if test_history is None:
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329 test_history = galaxy_interactor.new_history()
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330 tool_id = tool["id"]
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331 tool_version = tool["version"]
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332 try:
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333 tool_test_dicts = galaxy_interactor.get_tool_tests(tool_id, tool_version=tool_version)
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334 except Exception as e:
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335 if log:
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336 log.warning("Fetching test definition for tool '%s' failed", tool_id, exc_info=True)
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337 test_exceptions.append((tool_id, e))
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338 Results = namedtuple("Results", ["tool_test_results", "tests_passed", "test_exceptions"])
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339 return Results(tool_test_results=tool_test_results,
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340 tests_passed=tests_passed,
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341 test_exceptions=test_exceptions)
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342 test_indices = list(range(len(tool_test_dicts)))
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343
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344 for test_index in test_indices:
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345 test_id = tool_id + "-" + str(test_index)
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346
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347 def run_test(index, test_id):
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348
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349 def register(job_data):
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350 tool_test_results.append({
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351 'id': test_id,
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352 'has_data': True,
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353 'data': job_data,
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354 })
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355
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356 try:
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357 if log:
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358 log.info("Executing test '%s'", test_id)
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359 verify_tool(
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360 tool_id, galaxy_interactor, test_index=index, tool_version=tool_version,
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361 register_job_data=register, quiet=True, test_history=test_history,
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362 )
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363 tests_passed.append(test_id)
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364 if log:
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365 log.info("Test '%s' passed", test_id)
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diff changeset
366 except Exception as e:
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diff changeset
367 if log:
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368 log.warning("Test '%s' failed", test_id, exc_info=True)
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369 test_exceptions.append((test_id, e))
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370
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371 executor.submit(run_test, test_index, test_id)
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372
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373 def install_repository_revision(self, repository, log):
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374 default_err_msg = ('All repositories that you are attempting to install '
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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375 'have been previously installed.')
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376 start = dt.datetime.now()
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377 try:
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378 repository['new_tool_panel_section_label'] = repository.pop('tool_panel_section_label')
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379 response = self.tool_shed_client.install_repository_revision(**repository)
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380 if isinstance(response, dict) and response.get('status', None) == 'ok':
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381 # This rare case happens if a repository is already installed but
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382 # was not recognised as such in the above check. In such a
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383 # case the return value looks like this:
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384 # {u'status': u'ok', u'message': u'No repositories were
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guerler
parents:
diff changeset
385 # installed, possibly because the selected repository has
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
386 # already been installed.'}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
387 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
388 log.debug("\tRepository {0} is already installed.".format(repository['name']))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
389 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
390 log_repository_install_success(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
391 repository=repository,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
392 start=start,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
393 log=log)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
394 return "installed"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
395 except (ConnectionError, requests.exceptions.ConnectionError) as e:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
396 if default_err_msg in unicodify(e):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
397 # THIS SHOULD NOT HAPPEN DUE TO THE CHECKS EARLIER
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
398 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
399 log.debug("\tRepository %s already installed (at revision %s)" %
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
400 (repository['name'], repository['changeset_revision']))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
401 return "skipped"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
402 elif "504" in unicodify(e) or 'Connection aborted' in unicodify(e):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
403 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
404 log.debug("Timeout during install of %s, extending wait to 1h", repository['name'])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
405 success = self.wait_for_install(repository=repository, log=log, timeout=3600)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
406 if success:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
407 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
408 log_repository_install_success(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
409 repository=repository,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
410 start=start,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
411 log=log)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
412 return "installed"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
413 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
414 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
415 log_repository_install_error(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
416 repository=repository,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
417 start=start, msg=e.body,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
418 log=log)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
419 return "error"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
420 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
421 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
422 log_repository_install_error(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
423 repository=repository,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
424 start=start, msg=e.body,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
425 log=log)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
426 return "error"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
427
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
428 def wait_for_install(self, repository, log=None, timeout=3600):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
429 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
430 If nginx times out, we look into the list of installed repositories
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
431 and try to determine if a repository of the same namer/owner is still installing.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
432 Returns True if install finished successfully,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
433 returns False when timeout is exceeded or installation has failed.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
434 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
435 # We request a repository revision, but Galaxy may decide to install the next downloable revision.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
436 # This ensures we have a revision to track, and if not, finds the revision that is actually being installed
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
437 name = repository['name']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
438 owner = repository['owner']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
439 changeset_revision = repository['changeset_revision']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
440 installed_repos = self.tool_shed_client.get_repositories()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
441 non_terminal = [r for r in installed_repos if r['name'] == name and r['owner'] == owner and r['status'] in NON_TERMINAL_REPOSITORY_STATES]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
442 assert len(non_terminal) > 0, "Repository '%s' from owner '%s' not in currently installling Repositories" % (name, owner)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
443 installing_repo_id = None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
444 if len(non_terminal) == 1:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
445 # Unambiguous, we wait for this repo
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
446 installing_repo_id = non_terminal[0]['id']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
447 if len(non_terminal) > 1:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
448 # More than one repo with the requested name and owner in installing status.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
449 # If any repo is of the requested changeset revision we wait for this repo.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
450 for installing_repo in non_terminal:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
451 if installing_repo['changeset_revision'] == changeset_revision:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
452 installing_repo_id = installing_repo['id']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
453 break
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
454 if not installing_repo_id:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
455 # We may have a repo that is permanently in a non-terminal state (e.g because of restart during installation).
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
456 # Raise an exception and continue with the remaining repos.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
457 msg = "Multiple repositories for name '%s', owner '%s' found in non-terminal states. Please uninstall all non-terminal repositories."
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
458 raise AssertionError(msg % (name, owner))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
459 start = dt.datetime.now()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
460 while (dt.datetime.now() - start) < dt.timedelta(seconds=timeout):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
461 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
462 installed_repo = self.tool_shed_client.show_repository(installing_repo_id)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
463 status = installed_repo['status']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
464 if status == 'Installed':
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
465 return True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
466 elif status == 'Error':
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
467 return False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 elif status in NON_TERMINAL_REPOSITORY_STATES:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
469 time.sleep(10)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
470 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
471 raise AssertionError("Repository name '%s', owner '%s' in unknown status '%s'" % (name, owner, status))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
472 except ConnectionError as e:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
473 if log:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
474 log.warning('Failed to get repositories list: %s', unicodify(e))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
475 time.sleep(10)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
476 return False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
477
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
478
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
479 def log_repository_install_error(repository, start, msg, log):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
480 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
481 Log failed repository installations. Return a dictionary with information
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
482 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
483 end = dt.datetime.now()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
484 log.error(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
485 "\t* Error installing a repository (after %s seconds)! Name: %s," "owner: %s, ""revision: %s, error: %s",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
486 str(end - start),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
487 repository.get('name', ""),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
488 repository.get('owner', ""),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
489 repository.get('changeset_revision', ""),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 msg)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
493 def log_repository_install_success(repository, start, log):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
494 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 Log successful repository installation.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
496 Repositories that finish in error still count as successful installs currently.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
497 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
498 end = dt.datetime.now()
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 log.debug(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 "\trepository %s installed successfully (in %s) at revision %s" % (
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 repository['name'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
502 str(end - start),
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
503 repository['changeset_revision']
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
504 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
507
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 def log_repository_install_skip(repository, counter, total_num_repositories, log):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 log.debug(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
510 "({0}/{1}) repository {2} already installed at revision {3}. Skipping."
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
511 .format(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
512 counter,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
513 total_num_repositories,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 repository['name'],
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diff changeset
515 repository['changeset_revision']
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diff changeset
516 )
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diff changeset
517 )
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518
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519
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520 def log_repository_install_start(repository, counter, total_num_repositories, installation_start, log):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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521 log.debug(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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522 '(%s/%s) Installing repository %s from %s to section "%s" at revision %s (TRT: %s)' % (
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523 counter, total_num_repositories,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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524 repository['name'],
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525 repository['owner'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
526 repository['tool_panel_section_id'] or repository['tool_panel_section_label'],
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parents:
diff changeset
527 repository['changeset_revision'],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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528 dt.datetime.now() - installation_start
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529 )
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530 )
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diff changeset
531
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532
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533 def args_to_repos(args):
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534 if args.tool_list_file:
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535 tool_list = load_yaml_file(args.tool_list_file)
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536 repos = tool_list['tools']
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537 elif args.tool_yaml:
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538 repos = [yaml.safe_load(args.tool_yaml)]
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parents:
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539 elif args.name and args.owner:
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540 repo = dict(
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541 owner=args.owner,
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542 name=args.name,
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543 tool_panel_section_id=args.tool_panel_section_id,
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544 tool_panel_section_label=args.tool_panel_section_label,
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545 revisions=args.revisions
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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546 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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547 if args.tool_shed_url:
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548 repo["tool_shed_url"] = args.tool_shed_url
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549 repos = [repo]
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550 else:
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551 repos = []
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552 return repos
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553
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554
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555 def main():
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556 disable_external_library_logging()
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557 args = parser().parse_args()
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558 log = setup_global_logger(name=__name__, log_file=args.log_file)
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559 gi = get_galaxy_connection(args, file=args.tool_list_file, log=log, login_required=True)
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560 install_repository_manager = InstallRepositoryManager(gi)
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561
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562 repos = args_to_repos(args)
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563
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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564 if args.tool_list_file:
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565 tool_list = load_yaml_file(args.tool_list_file)
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566 else:
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567 tool_list = dict()
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568
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569 # Get some of the other installation arguments
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570 kwargs = dict(
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571 default_install_tool_dependencies=tool_list.get("install_tool_dependencies") or getattr(args,
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572 "install_tool_dependencies",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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573 False),
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574 default_install_repository_dependencies=tool_list.get("install_repository_dependencies") or getattr(args,
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575 "install_repository_dependencies",
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576 False),
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577 default_install_resolver_dependencies=tool_list.get("install_resolver_dependencies") or getattr(args,
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578 "install_resolver_dependencies",
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579 False))
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580
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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581 # Start installing/updating and store the results in install_results.
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582 # Or do testing if the action is `test`
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583 install_results = None
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584 if args.action == "update":
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585 install_results = install_repository_manager.update_repositories(
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586 repositories=repos,
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587 log=log,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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588 **kwargs)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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589 elif args.action == "install":
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590 install_results = install_repository_manager.install_repositories(
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591 repos,
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592 log=log,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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593 force_latest_revision=args.force_latest_revision,
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594 **kwargs)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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595 elif args.action == "test":
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596 install_repository_manager.test_tools(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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597 test_json=args.test_json,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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598 repositories=repos,
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599 log=log,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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600 test_user_api_key=args.test_user_api_key,
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601 test_user=args.test_user,
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diff changeset
602 parallel_tests=args.parallel_tests,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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603 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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604 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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605 raise NotImplementedError("This point in the code should not be reached. Please contact the developers.")
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606
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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607 # Run tests on the install results if required.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
608 if install_results and args.test or args.test_existing:
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609 to_be_tested_repositories = install_results.installed_repositories
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
610 if args.test_existing:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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611 to_be_tested_repositories.extend(install_results.skipped_repositories)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
612 if to_be_tested_repositories:
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613 install_repository_manager.test_tools(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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614 test_json=args.test_json,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
615 repositories=to_be_tested_repositories,
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616 log=log,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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617 test_user_api_key=args.test_user_api_key,
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618 test_user=args.test_user,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
619 parallel_tests=args.parallel_tests,
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620 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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621
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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622
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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623 if __name__ == "__main__":
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624 main()