Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/galaxy/config.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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0
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1 """Abstractions for setting up a Galaxy instance."""
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2 from __future__ import absolute_import
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3 from __future__ import print_function
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4
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5 import abc
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6 import contextlib
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7 import os
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8 import random
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9 import shutil
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10 from string import Template
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11 from tempfile import mkdtemp
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12
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13 from galaxy.containers.docker_model import DockerVolume
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14 from galaxy.tool_util.deps import docker_util
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15 from galaxy.tool_util.deps.commands import argv_to_str
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16 from pkg_resources import parse_version
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17 from six import (
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18 add_metaclass,
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19 iteritems
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20 )
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21 from six.moves import shlex_quote
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22
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23 from planemo import git
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24 from planemo.config import OptionSource
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25 from planemo.deps import ensure_dependency_resolvers_conf_configured
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26 from planemo.docker import docker_host_args
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27 from planemo.io import (
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28 communicate,
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29 kill_pid_file,
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30 shell,
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31 shell_join,
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32 untar_to,
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33 wait_on,
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34 warn,
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35 write_file,
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36 )
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37 from planemo.mulled import build_involucro_context
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38 from planemo.shed import tool_shed_url
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39 from planemo.virtualenv import DEFAULT_PYTHON_VERSION
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40 from .api import (
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41 DEFAULT_MASTER_API_KEY,
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42 gi,
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43 user_api_key,
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44 )
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45 from .distro_tools import (
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46 DISTRO_TOOLS_ID_TO_PATH
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47 )
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48 from .run import (
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49 setup_common_startup_args,
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50 setup_venv,
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51 )
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52 from .workflows import (
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53 find_tool_ids,
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54 import_workflow,
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55 install_shed_repos,
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56 )
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57
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58
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59 NO_TEST_DATA_MESSAGE = (
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60 "planemo couldn't find a target test-data directory, you should likely "
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61 "create a test-data directory or pass an explicit path using --test_data."
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62 )
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63
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64 WEB_SERVER_CONFIG_TEMPLATE = """
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65 [server:${server_name}]
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66 use = egg:Paste#http
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67 port = ${port}
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68 host = ${host}
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69 use_threadpool = True
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70 threadpool_kill_thread_limit = 10800
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71 [app:main]
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72 paste.app_factory = galaxy.web.buildapp:app_factory
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73 """
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74
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75 TOOL_CONF_TEMPLATE = """<toolbox>
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76 <tool file="data_source/upload.xml" />
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77 ${tool_definition}
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78 </toolbox>
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79 """
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80
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81 SHED_TOOL_CONF_TEMPLATE = """<?xml version="1.0"?>
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82 <toolbox tool_path="${shed_tool_path}">
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83 </toolbox>
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84 """
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85
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86 SHED_DATA_MANAGER_CONF_TEMPLATE = """<?xml version="1.0"?>
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87 <data_managers>
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88 </data_managers>
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89 """
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90
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91 EMPTY_JOB_METRICS_TEMPLATE = """<?xml version="1.0"?>
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92 <job_metrics>
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93 </job_metrics>
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94 """
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95
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96 TOOL_SHEDS_CONF = """<tool_sheds>
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97 <tool_shed name="Target Shed" url="${shed_target_url}" />
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98 </tool_sheds>
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99 """
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100
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101 JOB_CONFIG_LOCAL = """<job_conf>
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102 <plugins>
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103 <plugin id="planemo_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
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104 </plugins>
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105 <handlers>
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106 <handler id="main"/>
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107 </handlers>
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108 <destinations default="planemo_dest">
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109 <destination id="planemo_dest" runner="planemo_runner">
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110 <param id="require_container">${require_container}</param>
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111 <param id="docker_enabled">${docker_enable}</param>
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112 <param id="docker_sudo">${docker_sudo}</param>
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113 <param id="docker_sudo_cmd">${docker_sudo_cmd}</param>
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114 <param id="docker_cmd">${docker_cmd}</param>
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115 ${docker_host_param}
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116 </destination>
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117 <destination id="upload_dest" runner="planemo_runner">
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118 <param id="docker_enable">false</param>
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119 </destination>
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120 </destinations>
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121 <tools>
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122 <tool id="upload1" destination="upload_dest" />
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123 </tools>
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124 </job_conf>
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125 """
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126
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127 LOGGING_TEMPLATE = """
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128 ## Configure Python loggers.
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129 [loggers]
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130 keys = root,paste,displayapperrors,galaxydeps,galaxymasterapikey,galaxy
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131
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132 [handlers]
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133 keys = console
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134
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135 [formatters]
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136 keys = generic
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137
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138 [logger_root]
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139 level = WARN
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140 handlers = console
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141
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142 [logger_paste]
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143 level = WARN
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144 handlers = console
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145 qualname = paste
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146 propagate = 0
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147
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148 [logger_galaxydeps]
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149 level = DEBUG
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150 handlers = console
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151 qualname = galaxy.tools.deps
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152 propagate = 0
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153
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154 [logger_galaxymasterapikey]
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155 level = WARN
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156 handlers = console
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157 qualname = galaxy.web.framework.webapp
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158 propagate = 0
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159
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160 [logger_displayapperrors]
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161 level = ERROR
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162 handlers =
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163 qualname = galaxy.datatypes.display_applications.application
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164 propagate = 0
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165
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166 [logger_galaxy]
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167 level = ${log_level}
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168 handlers = console
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169 qualname = galaxy
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170 propagate = 0
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171
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172 [handler_console]
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173 class = StreamHandler
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174 args = (sys.stderr,)
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175 level = DEBUG
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176 formatter = generic
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177
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178 [formatter_generic]
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179 format = %(asctime)s %(levelname)-5.5s [%(name)s] %(message)s
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180 """
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181
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182
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183 EMPTY_TOOL_CONF_TEMPLATE = """<toolbox></toolbox>"""
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184
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185 DEFAULT_GALAXY_BRANCH = "master"
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186 DEFAULT_GALAXY_SOURCE = "https://github.com/galaxyproject/galaxy"
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187 CWL_GALAXY_SOURCE = "https://github.com/common-workflow-language/galaxy"
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188
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189 DATABASE_LOCATION_TEMPLATE = "sqlite:///%s?isolation_level=IMMEDIATE"
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190
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191 COMMAND_STARTUP_COMMAND = "./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}"
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192
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193 CLEANUP_IGNORE_ERRORS = True
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194 DEFAULT_GALAXY_BRAND = 'Configured by Planemo'
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195
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196
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197 @contextlib.contextmanager
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198 def galaxy_config(ctx, runnables, **kwds):
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199 """Set up a ``GalaxyConfig`` in an auto-cleaned context."""
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200 c = local_galaxy_config
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201 if kwds.get("dockerize", False):
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202 c = docker_galaxy_config
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203 elif kwds.get("external", False):
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204 c = external_galaxy_config
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205
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206 with c(ctx, runnables, **kwds) as config:
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207 yield config
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208
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209
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210 def simple_docker_volume(path):
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211 path = os.path.abspath(path)
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212 return DockerVolume("%s:%s:rw" % (path, path))
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213
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214
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215 @contextlib.contextmanager
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216 def docker_galaxy_config(ctx, runnables, for_tests=False, **kwds):
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217 """Set up a ``GalaxyConfig`` for Docker container."""
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218 test_data_dir = _find_test_data(runnables, **kwds)
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219
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220 with _config_directory(ctx, **kwds) as config_directory:
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221 def config_join(*args):
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222 return os.path.join(config_directory, *args)
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223
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224 ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
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225 _handle_job_metrics(config_directory, kwds)
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226
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227 shed_tool_conf = "config/shed_tool_conf.xml"
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228 all_tool_paths = _all_tool_paths(runnables, **kwds)
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229
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230 tool_directories = set([]) # Things to mount...
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231 for tool_path in all_tool_paths:
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232 directory = os.path.dirname(os.path.normpath(tool_path))
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233 if os.path.exists(directory):
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234 tool_directories.add(directory)
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235
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236 # TODO: remap these.
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237 tool_volumes = []
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238 for tool_directory in tool_directories:
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239 volume = simple_docker_volume(tool_directory)
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240 tool_volumes.append(volume)
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241
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242 empty_tool_conf = config_join("empty_tool_conf.xml")
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243
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244 tool_conf = config_join("tool_conf.xml")
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245
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246 shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
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247 _ensure_directory(shed_tool_path)
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248
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249 sheds_config_path = _configure_sheds_config_file(
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250 ctx, config_directory, **kwds
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251 )
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252 port = _get_port(kwds)
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253 properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
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254 _handle_container_resolution(ctx, kwds, properties)
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255 master_api_key = _get_master_api_key(kwds)
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256
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257 template_args = dict(
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258 shed_tool_path=shed_tool_path,
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259 tool_conf=tool_conf,
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260 )
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261 tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
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262
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263 _write_tool_conf(ctx, all_tool_paths, tool_conf)
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264 write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
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265
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266 properties.update(dict(
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267 tool_config_file=tool_config_file,
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268 tool_sheds_config_file=sheds_config_path,
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269 migrated_tools_config=empty_tool_conf,
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270 ))
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271
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272 server_name = "planemo%d" % random.randint(0, 100000)
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273
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274 # Value substitutions in Galaxy properties - for consistency with
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275 # non-Dockerized version.
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276 template_args = dict(
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277 )
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278 env = _build_env_for_galaxy(properties, template_args)
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279 env["NONUSE"] = "nodejs,proftp,reports"
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280 if ctx.verbose:
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281 env["GALAXY_LOGGING"] = "full"
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282
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283 # TODO: setup FTP upload dir and disable FTP server in container.
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284 _build_test_env(properties, env)
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285
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286 docker_target_kwds = docker_host_args(**kwds)
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287 volumes = tool_volumes + [simple_docker_volume(config_directory)]
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288 export_directory = kwds.get("export_directory", None)
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289 if export_directory is not None:
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290 volumes.append(DockerVolume("%s:/export:rw" % export_directory))
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291
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292 # TODO: Allow this to real Docker volumes and allow multiple.
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293 extra_volume = kwds.get("docker_extra_volume")
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294 if extra_volume:
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295 volumes.append(simple_docker_volume(extra_volume))
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296 yield DockerGalaxyConfig(
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297 ctx,
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298 config_directory,
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299 env,
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300 test_data_dir,
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301 port,
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302 server_name,
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303 master_api_key,
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304 runnables,
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305 docker_target_kwds=docker_target_kwds,
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306 volumes=volumes,
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307 export_directory=export_directory,
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308 kwds=kwds,
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309 )
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310
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311
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312 @contextlib.contextmanager
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313 def local_galaxy_config(ctx, runnables, for_tests=False, **kwds):
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314 """Set up a ``GalaxyConfig`` in an auto-cleaned context."""
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315 test_data_dir = _find_test_data(runnables, **kwds)
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316 tool_data_table = _find_tool_data_table(
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317 runnables,
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318 test_data_dir=test_data_dir,
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319 **kwds
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320 )
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321 data_manager_config_paths = [r.data_manager_conf_path for r in runnables if r.data_manager_conf_path]
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322 galaxy_root = _find_galaxy_root(ctx, **kwds)
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323 install_galaxy = kwds.get("install_galaxy", False)
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324 if galaxy_root is not None:
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325 if os.path.isdir(galaxy_root) and not os.listdir(galaxy_root):
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326 os.rmdir(galaxy_root)
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327 if os.path.isdir(galaxy_root) and install_galaxy:
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328 raise Exception("%s is an existing non-empty directory, cannot install Galaxy again" % galaxy_root)
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329
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330 # Duplicate block in docker variant above.
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331 if kwds.get("mulled_containers", False) and not kwds.get("docker", False):
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332 if ctx.get_option_source("docker") != OptionSource.cli:
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333 kwds["docker"] = True
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334 else:
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335 raise Exception("Specified no docker and mulled containers together.")
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336
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337 with _config_directory(ctx, **kwds) as config_directory:
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338 def config_join(*args):
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339 return os.path.join(config_directory, *args)
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340
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341 install_env = {}
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342 if kwds.get('galaxy_skip_client_build', True):
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343 install_env['GALAXY_SKIP_CLIENT_BUILD'] = '1'
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344 if galaxy_root is None:
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345 galaxy_root = config_join("galaxy-dev")
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346 if not os.path.isdir(galaxy_root):
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347 _build_eggs_cache(ctx, install_env, kwds)
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348 _install_galaxy(ctx, galaxy_root, install_env, kwds)
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349
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350 if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'):
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351 # on python 3 we use gunicorn,
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352 # which requires 'main' as server name
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353 server_name = 'main'
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354 else:
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355 server_name = "planemo%d" % random.randint(0, 100000)
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356 # Once we don't have to support earlier than 18.01 - try putting these files
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357 # somewhere better than with Galaxy.
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358 log_file = "%s.log" % server_name
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359 pid_file = "%s.pid" % server_name
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360 ensure_dependency_resolvers_conf_configured(ctx, kwds, os.path.join(config_directory, "resolvers_conf.xml"))
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361 _handle_job_config_file(config_directory, server_name, kwds)
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362 _handle_job_metrics(config_directory, kwds)
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363 file_path = kwds.get("file_path") or config_join("files")
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364 _ensure_directory(file_path)
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365
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366 tool_dependency_dir = kwds.get("tool_dependency_dir") or config_join("deps")
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367 _ensure_directory(tool_dependency_dir)
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368
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369 shed_tool_conf = kwds.get("shed_tool_conf") or config_join("shed_tools_conf.xml")
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370 all_tool_paths = _all_tool_paths(runnables, **kwds)
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371 empty_tool_conf = config_join("empty_tool_conf.xml")
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372
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373 tool_conf = config_join("tool_conf.xml")
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374
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375 shed_data_manager_config_file = config_join("shed_data_manager_conf.xml")
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376
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377 shed_tool_path = kwds.get("shed_tool_path") or config_join("shed_tools")
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378 _ensure_directory(shed_tool_path)
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379
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380 sheds_config_path = _configure_sheds_config_file(
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381 ctx, config_directory, **kwds
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382 )
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383
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diff changeset
384 database_location = config_join("galaxy.sqlite")
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diff changeset
385 master_api_key = _get_master_api_key(kwds)
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diff changeset
386 dependency_dir = os.path.join(config_directory, "deps")
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diff changeset
387 _ensure_directory(shed_tool_path)
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diff changeset
388 port = _get_port(kwds)
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diff changeset
389 template_args = dict(
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diff changeset
390 port=port,
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diff changeset
391 host=kwds.get("host", "127.0.0.1"),
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diff changeset
392 server_name=server_name,
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diff changeset
393 temp_directory=config_directory,
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diff changeset
394 shed_tool_path=shed_tool_path,
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diff changeset
395 database_location=database_location,
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diff changeset
396 tool_conf=tool_conf,
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diff changeset
397 debug=kwds.get("debug", "true"),
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398 id_secret=kwds.get("id_secret", "test_secret"),
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399 log_level="DEBUG" if ctx.verbose else "INFO",
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400 )
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401 tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
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402 # Setup both galaxy_email and older test user test@bx.psu.edu
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403 # as admins for command_line, etc...
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diff changeset
404 properties = _shared_galaxy_properties(config_directory, kwds, for_tests=for_tests)
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405 properties.update(dict(
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406 server_name="main",
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407 ftp_upload_dir_template="${ftp_upload_dir}",
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408 ftp_upload_purge="False",
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409 ftp_upload_dir=test_data_dir or os.path.abspath('.'),
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410 ftp_upload_site="Test Data",
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411 check_upload_content="False",
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diff changeset
412 tool_dependency_dir=dependency_dir,
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413 file_path=file_path,
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414 new_file_path="${temp_directory}/tmp",
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415 tool_config_file=tool_config_file,
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416 tool_sheds_config_file=sheds_config_path,
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417 manage_dependency_relationships="False",
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418 job_working_directory="${temp_directory}/job_working_directory",
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419 template_cache_path="${temp_directory}/compiled_templates",
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420 citation_cache_type="file",
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421 citation_cache_data_dir="${temp_directory}/citations/data",
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422 citation_cache_lock_dir="${temp_directory}/citations/lock",
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423 database_auto_migrate="True",
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424 enable_beta_tool_formats="True",
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425 id_secret="${id_secret}",
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426 log_level="${log_level}",
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diff changeset
427 debug="${debug}",
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428 watch_tools="auto",
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429 default_job_shell="/bin/bash", # For conda dependency resolution
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430 tool_data_table_config_path=tool_data_table,
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431 data_manager_config_file=",".join(data_manager_config_paths) or None, # without 'or None' may raise IOError in galaxy (see #946)
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432 integrated_tool_panel_config=("${temp_directory}/"
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433 "integrated_tool_panel_conf.xml"),
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434 migrated_tools_config=empty_tool_conf,
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435 test_data_dir=test_data_dir, # TODO: make gx respect this
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436 shed_data_manager_config_file=shed_data_manager_config_file,
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437 ))
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diff changeset
438 _handle_container_resolution(ctx, kwds, properties)
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439 write_file(config_join("logging.ini"), _sub(LOGGING_TEMPLATE, template_args))
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440 properties["database_connection"] = _database_connection(database_location, **kwds)
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441
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diff changeset
442 _handle_kwd_overrides(properties, kwds)
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443
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444 # TODO: consider following property
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445 # watch_tool = False
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446 # datatypes_config_file = config/datatypes_conf.xml
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447 # welcome_url = /static/welcome.html
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448 # logo_url = /
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449 # sanitize_all_html = True
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450 # serve_xss_vulnerable_mimetypes = False
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451 # track_jobs_in_database = None
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452 # outputs_to_working_directory = False
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453 # retry_job_output_collection = 0
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454
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diff changeset
455 env = _build_env_for_galaxy(properties, template_args)
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diff changeset
456 env.update(install_env)
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diff changeset
457 _build_test_env(properties, env)
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diff changeset
458 env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf
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diff changeset
459 env['GALAXY_TEST_DBURI'] = properties["database_connection"]
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diff changeset
460
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diff changeset
461 env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
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diff changeset
462 env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini")
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diff changeset
463 env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
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parents:
diff changeset
464 # Following are needed in 18.01 to prevent Galaxy from changing log and pid.
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parents:
diff changeset
465 # https://github.com/galaxyproject/planemo/issues/788
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diff changeset
466 env["GALAXY_LOG"] = log_file
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diff changeset
467 env["GALAXY_PID"] = pid_file
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parents:
diff changeset
468 web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
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parents:
diff changeset
469 write_file(config_join("galaxy.ini"), web_config)
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diff changeset
470 _write_tool_conf(ctx, all_tool_paths, tool_conf)
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parents:
diff changeset
471 write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
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diff changeset
472
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diff changeset
473 shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args)
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parents:
diff changeset
474 # Write a new shed_tool_conf.xml if needed.
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parents:
diff changeset
475 write_file(shed_tool_conf, shed_tool_conf_contents, force=False)
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diff changeset
476
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parents:
diff changeset
477 write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE)
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diff changeset
478
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diff changeset
479 yield LocalGalaxyConfig(
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parents:
diff changeset
480 ctx,
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parents:
diff changeset
481 config_directory,
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parents:
diff changeset
482 env,
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parents:
diff changeset
483 test_data_dir,
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parents:
diff changeset
484 port,
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parents:
diff changeset
485 server_name,
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diff changeset
486 master_api_key,
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parents:
diff changeset
487 runnables,
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parents:
diff changeset
488 galaxy_root,
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parents:
diff changeset
489 kwds,
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parents:
diff changeset
490 )
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parents:
diff changeset
491
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diff changeset
492
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diff changeset
493 def _all_tool_paths(runnables, **kwds):
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diff changeset
494 tool_paths = [r.path for r in runnables if r.has_tools and not r.data_manager_conf_path]
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parents:
diff changeset
495 all_tool_paths = list(tool_paths) + list(kwds.get("extra_tools", []))
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diff changeset
496 for runnable in runnables:
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parents:
diff changeset
497 if runnable.type.name == "galaxy_workflow":
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parents:
diff changeset
498 tool_ids = find_tool_ids(runnable.path)
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diff changeset
499 for tool_id in tool_ids:
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parents:
diff changeset
500 if tool_id in DISTRO_TOOLS_ID_TO_PATH:
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parents:
diff changeset
501 all_tool_paths.append(DISTRO_TOOLS_ID_TO_PATH[tool_id])
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502
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diff changeset
503 return all_tool_paths
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504
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parents:
diff changeset
505
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506 def _shared_galaxy_properties(config_directory, kwds, for_tests):
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507 """Setup properties useful for local and Docker Galaxy instances.
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508
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509 Most things related to paths, etc... are very different between Galaxy
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diff changeset
510 modalities and many taken care of internally to the container in that mode.
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511 But this method sets up API stuff, tool, and job stuff that can be shared.
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512 """
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513 master_api_key = _get_master_api_key(kwds)
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514 user_email = _user_email(kwds)
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515 properties = {
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516 'master_api_key': master_api_key,
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517 'admin_users': "%s,test@bx.psu.edu" % user_email,
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518 'expose_dataset_path': "True",
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519 'cleanup_job': 'never',
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520 'collect_outputs_from': "job_working_directory",
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521 'allow_path_paste': "True",
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522 'check_migrate_tools': "False",
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523 'use_cached_dependency_manager': str(kwds.get("conda_auto_install", False)),
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524 'brand': kwds.get("galaxy_brand", DEFAULT_GALAXY_BRAND),
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525 'strict_cwl_validation': str(not kwds.get("non_strict_cwl", False)),
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526 }
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527 if kwds.get("galaxy_single_user", True):
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diff changeset
528 properties['single_user'] = user_email
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529
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530 if for_tests:
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531 empty_dir = os.path.join(config_directory, "empty")
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532 _ensure_directory(empty_dir)
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533 properties["tour_config_dir"] = empty_dir
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534 properties["interactive_environment_plugins_directory"] = empty_dir
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535 properties["visualization_plugins_directory"] = empty_dir
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536 return properties
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537
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538
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diff changeset
539 @contextlib.contextmanager
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540 def external_galaxy_config(ctx, runnables, for_tests=False, **kwds):
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541 yield BaseGalaxyConfig(
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542 ctx=ctx,
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543 galaxy_url=kwds.get("galaxy_url", None),
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544 master_api_key=_get_master_api_key(kwds),
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545 user_api_key=kwds.get("galaxy_user_key", None),
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546 runnables=runnables,
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diff changeset
547 kwds=kwds
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548 )
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549
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550
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551 def _get_master_api_key(kwds):
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552 master_api_key = kwds.get("galaxy_admin_key") or DEFAULT_MASTER_API_KEY
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553 return master_api_key
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554
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555
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556 def _get_port(kwds):
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557 port = int(kwds.get("port", 9090))
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558 return port
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559
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diff changeset
560
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561 def _user_email(kwds):
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562 user_email = kwds.get("galaxy_email")
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563 return user_email
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564
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565
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diff changeset
566 @contextlib.contextmanager
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diff changeset
567 def _config_directory(ctx, **kwds):
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diff changeset
568 config_directory = kwds.get("config_directory", None)
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569 created_config_directory = False
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570 if not config_directory:
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571 created_config_directory = True
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572 config_directory = os.path.realpath(mkdtemp())
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573 ctx.vlog("Created directory for Galaxy configuration [%s]" % config_directory)
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diff changeset
574 try:
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575 yield config_directory
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576 finally:
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577 cleanup = not kwds.get("no_cleanup", False)
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578 if created_config_directory and cleanup:
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parents:
diff changeset
579 shutil.rmtree(config_directory)
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diff changeset
580
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diff changeset
581
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parents:
diff changeset
582 @add_metaclass(abc.ABCMeta)
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parents:
diff changeset
583 class GalaxyInterface(object):
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parents:
diff changeset
584 """Abstraction around a Galaxy instance.
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diff changeset
585
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parents:
diff changeset
586 Description of a Galaxy instance and how to interact with it - this could
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diff changeset
587 potentially be a remote, already running instance or an instance Planemo manages
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parents:
diff changeset
588 to execute some task(s).
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589 """
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590
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diff changeset
591 @abc.abstractproperty
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diff changeset
592 def gi(self):
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diff changeset
593 """Return an admin bioblend Galaxy instance for API interactions."""
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diff changeset
594
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parents:
diff changeset
595 @abc.abstractproperty
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diff changeset
596 def user_gi(self):
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diff changeset
597 """Return a user-backed bioblend Galaxy instance for API interactions."""
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parents:
diff changeset
598
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parents:
diff changeset
599 @abc.abstractmethod
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parents:
diff changeset
600 def install_repo(self, *args, **kwds):
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parents:
diff changeset
601 """Install specified tool shed repository."""
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parents:
diff changeset
602
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parents:
diff changeset
603 @abc.abstractproperty
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parents:
diff changeset
604 def tool_shed_client(self):
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parents:
diff changeset
605 """Return a admin bioblend tool shed client."""
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parents:
diff changeset
606
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parents:
diff changeset
607 @abc.abstractmethod
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parents:
diff changeset
608 def wait_for_all_installed(self):
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parents:
diff changeset
609 """Wait for all queued up repositories installs to complete."""
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parents:
diff changeset
610
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parents:
diff changeset
611 @abc.abstractmethod
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parents:
diff changeset
612 def install_workflows(self):
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parents:
diff changeset
613 """Install all workflows configured with these planemo arguments."""
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parents:
diff changeset
614
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parents:
diff changeset
615 @abc.abstractmethod
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diff changeset
616 def workflow_id(self, path):
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parents:
diff changeset
617 """Get installed workflow API ID for input path."""
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parents:
diff changeset
618
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diff changeset
619
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diff changeset
620 @add_metaclass(abc.ABCMeta)
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parents:
diff changeset
621 class GalaxyConfig(GalaxyInterface):
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parents:
diff changeset
622 """Specialization of GalaxyInterface for Galaxy instances Planemo manages itself.
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parents:
diff changeset
623
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diff changeset
624 This assumes more than an API connection is available - Planemo needs to be able to
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parents:
diff changeset
625 start and stop the Galaxy instance, recover logs, etc... There are currently two
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parents:
diff changeset
626 implementations - a locally executed Galaxy and one running inside a Docker containe
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diff changeset
627 """
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diff changeset
628
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parents:
diff changeset
629 @abc.abstractproperty
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diff changeset
630 def kill(self):
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diff changeset
631 """Stop the running instance."""
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parents:
diff changeset
632
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parents:
diff changeset
633 @abc.abstractmethod
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diff changeset
634 def startup_command(self, ctx, **kwds):
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635 """Return a shell command used to startup this instance.
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636
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637 Among other common planmo kwds, this should respect the
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638 ``daemon`` keyword.
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639 """
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640
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641 @abc.abstractproperty
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642 def log_contents(self):
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diff changeset
643 """Retrieve text of log for running Galaxy instance."""
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644
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645 @abc.abstractmethod
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646 def cleanup(self):
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diff changeset
647 """Cleanup allocated resources to run this instance."""
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648
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649 @abc.abstractproperty
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650 def use_path_paste(self):
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diff changeset
651 """Use path paste to upload data."""
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652
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653
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654 class BaseGalaxyConfig(GalaxyInterface):
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655
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656 def __init__(
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657 self,
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658 ctx,
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659 galaxy_url,
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660 master_api_key,
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661 user_api_key,
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662 runnables,
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663 kwds,
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664 ):
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665 self._ctx = ctx
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666 self.galaxy_url = galaxy_url
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667 self.master_api_key = master_api_key
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668 self._user_api_key = user_api_key
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669 self.runnables = runnables
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670 self._kwds = kwds
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671 self._workflow_ids = {}
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672
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673 @property
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674 def gi(self):
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675 assert self.galaxy_url
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676 return gi(url=self.galaxy_url, key=self.master_api_key)
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677
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678 @property
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679 def user_gi(self):
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680 user_api_key = self.user_api_key
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681 assert user_api_key
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682 return self._gi_for_key(user_api_key)
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683
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684 @property
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685 def user_api_key(self):
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parents:
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686 # TODO: thread-safe
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687 if self._user_api_key is None:
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688 # TODO: respect --galaxy_email - seems like a real bug
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689 self._user_api_key = user_api_key(self.gi)
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690
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691 return self._user_api_key
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692
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693 def _gi_for_key(self, key):
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694 assert self.galaxy_url
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diff changeset
695 return gi(url=self.galaxy_url, key=key)
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diff changeset
696
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diff changeset
697 def install_repo(self, *args, **kwds):
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parents:
diff changeset
698 self.tool_shed_client.install_repository_revision(
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699 *args, **kwds
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700 )
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701
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702 @property
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parents:
diff changeset
703 def tool_shed_client(self):
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parents:
diff changeset
704 return self.gi.toolShed
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705
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706 def wait_for_all_installed(self):
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707 def status_ready(repo):
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708 status = repo["status"]
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709 if status in ["Installing", "New"]:
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diff changeset
710 return None
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diff changeset
711 if status == "Installed":
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diff changeset
712 return True
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713 raise Exception("Error installing repo status is %s" % status)
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parents:
diff changeset
714
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parents:
diff changeset
715 def ready():
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parents:
diff changeset
716 repos = self.tool_shed_client.get_repositories()
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parents:
diff changeset
717 ready = all(map(status_ready, repos))
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parents:
diff changeset
718 return ready or None
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parents:
diff changeset
719
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parents:
diff changeset
720 wait_on(ready, "galaxy tool installation", timeout=60 * 60 * 1)
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parents:
diff changeset
721
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parents:
diff changeset
722 def install_workflows(self):
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parents:
diff changeset
723 for runnable in self.runnables:
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parents:
diff changeset
724 if runnable.type.name in ["galaxy_workflow", "cwl_workflow"]:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
725 self._install_workflow(runnable)
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parents:
diff changeset
726
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parents:
diff changeset
727 def _install_workflow(self, runnable):
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parents:
diff changeset
728 if self._kwds["shed_install"]:
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shellac
parents:
diff changeset
729 install_shed_repos(runnable, self.gi, self._kwds.get("ignore_dependency_problems", False))
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parents:
diff changeset
730
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parents:
diff changeset
731 default_from_path = self._kwds.get("workflows_from_path", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
732 # TODO: Allow serialization so this doesn't need to assume a
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parents:
diff changeset
733 # shared filesystem with Galaxy server.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
734 from_path = default_from_path or (runnable.type.name == "cwl_workflow")
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parents:
diff changeset
735 workflow = import_workflow(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
736 runnable.path, admin_gi=self.gi, user_gi=self.user_gi, from_path=from_path
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parents:
diff changeset
737 )
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parents:
diff changeset
738 self._workflow_ids[runnable.path] = workflow["id"]
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parents:
diff changeset
739
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
740 def workflow_id(self, path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
741 return self._workflow_ids[path]
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parents:
diff changeset
742
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parents:
diff changeset
743 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
744 def use_path_paste(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
745 option = self._kwds.get("paste_test_data_paths")
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parents:
diff changeset
746 if option is None:
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parents:
diff changeset
747 return self.default_use_path_paste
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parents:
diff changeset
748 else:
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parents:
diff changeset
749 return option
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parents:
diff changeset
750
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parents:
diff changeset
751 @property
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parents:
diff changeset
752 def default_use_path_paste(self):
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parents:
diff changeset
753 return False
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shellac
parents:
diff changeset
754
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parents:
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755
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parents:
diff changeset
756 class BaseManagedGalaxyConfig(BaseGalaxyConfig):
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parents:
diff changeset
757
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parents:
diff changeset
758 def __init__(
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parents:
diff changeset
759 self,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
760 ctx,
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parents:
diff changeset
761 config_directory,
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parents:
diff changeset
762 env,
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parents:
diff changeset
763 test_data_dir,
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parents:
diff changeset
764 port,
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parents:
diff changeset
765 server_name,
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parents:
diff changeset
766 master_api_key,
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parents:
diff changeset
767 runnables,
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parents:
diff changeset
768 kwds,
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parents:
diff changeset
769 ):
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parents:
diff changeset
770 galaxy_url = "http://localhost:%d" % port
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parents:
diff changeset
771 super(BaseManagedGalaxyConfig, self).__init__(
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parents:
diff changeset
772 ctx=ctx,
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parents:
diff changeset
773 galaxy_url=galaxy_url,
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parents:
diff changeset
774 master_api_key=master_api_key,
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parents:
diff changeset
775 user_api_key=None,
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parents:
diff changeset
776 runnables=runnables,
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parents:
diff changeset
777 kwds=kwds
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parents:
diff changeset
778 )
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parents:
diff changeset
779 self.config_directory = config_directory
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parents:
diff changeset
780 self.env = env
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parents:
diff changeset
781 self.test_data_dir = test_data_dir
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parents:
diff changeset
782 self.port = port
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parents:
diff changeset
783 self.server_name = server_name
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parents:
diff changeset
784
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parents:
diff changeset
785
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parents:
diff changeset
786 class DockerGalaxyConfig(BaseManagedGalaxyConfig):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
787 """A :class:`GalaxyConfig` description of a Dockerized Galaxy instance."""
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parents:
diff changeset
788
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parents:
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789 def __init__(
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parents:
diff changeset
790 self,
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parents:
diff changeset
791 ctx,
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parents:
diff changeset
792 config_directory,
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parents:
diff changeset
793 env,
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parents:
diff changeset
794 test_data_dir,
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parents:
diff changeset
795 port,
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parents:
diff changeset
796 server_name,
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shellac
parents:
diff changeset
797 master_api_key,
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parents:
diff changeset
798 runnables,
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parents:
diff changeset
799 docker_target_kwds,
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parents:
diff changeset
800 volumes,
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parents:
diff changeset
801 export_directory,
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parents:
diff changeset
802 kwds,
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parents:
diff changeset
803 ):
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parents:
diff changeset
804 super(DockerGalaxyConfig, self).__init__(
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parents:
diff changeset
805 ctx,
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parents:
diff changeset
806 config_directory,
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shellac
parents:
diff changeset
807 env,
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parents:
diff changeset
808 test_data_dir,
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parents:
diff changeset
809 port,
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parents:
diff changeset
810 server_name,
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parents:
diff changeset
811 master_api_key,
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parents:
diff changeset
812 runnables,
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parents:
diff changeset
813 kwds,
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parents:
diff changeset
814 )
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parents:
diff changeset
815 self.docker_target_kwds = docker_target_kwds
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parents:
diff changeset
816 self.volumes = volumes
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parents:
diff changeset
817 self.export_directory = export_directory
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parents:
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818
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parents:
diff changeset
819 def kill(self):
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parents:
diff changeset
820 """Kill planemo container..."""
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parents:
diff changeset
821 kill_command = docker_util.kill_command(
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parents:
diff changeset
822 self.server_name,
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parents:
diff changeset
823 **self.docker_target_kwds
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
824 )
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parents:
diff changeset
825 return shell(kill_command)
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parents:
diff changeset
826
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parents:
diff changeset
827 def startup_command(self, ctx, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
828 """Return a shell command used to startup this instance.
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parents:
diff changeset
829
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parents:
diff changeset
830 Among other common planmo kwds, this should respect the
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parents:
diff changeset
831 ``daemon`` keyword.
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parents:
diff changeset
832 """
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parents:
diff changeset
833 daemon = kwds.get("daemon", False)
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parents:
diff changeset
834 daemon_str = "" if not daemon else " -d"
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parents:
diff changeset
835 docker_run_extras = "-p %s:80%s" % (self.port, daemon_str)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
836 env_directives = ["%s='%s'" % item for item in self.env.items()]
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parents:
diff changeset
837 image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable")
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parents:
diff changeset
838 run_command = docker_util.build_docker_run_command(
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parents:
diff changeset
839 "", image,
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parents:
diff changeset
840 interactive=False,
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parents:
diff changeset
841 env_directives=env_directives,
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parents:
diff changeset
842 working_directory=None,
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parents:
diff changeset
843 name=self.server_name,
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parents:
diff changeset
844 run_extra_arguments=docker_run_extras,
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parents:
diff changeset
845 set_user=False,
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parents:
diff changeset
846 volumes=self.volumes,
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parents:
diff changeset
847 **self.docker_target_kwds
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parents:
diff changeset
848 )
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parents:
diff changeset
849 chmod_command = [
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parents:
diff changeset
850 "chmod",
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parents:
diff changeset
851 "-R",
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parents:
diff changeset
852 "o+rwx",
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parents:
diff changeset
853 self.config_directory,
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parents:
diff changeset
854 ]
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parents:
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855 if self.export_directory:
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parents:
diff changeset
856 chmod_command.append(self.export_directory)
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parents:
diff changeset
857
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parents:
diff changeset
858 return shell_join(
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parents:
diff changeset
859 argv_to_str(chmod_command),
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parents:
diff changeset
860 run_command,
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parents:
diff changeset
861 )
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parents:
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862
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parents:
diff changeset
863 @property
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parents:
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864 def log_contents(self):
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parents:
diff changeset
865 logs_command = docker_util.logs_command(
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parents:
diff changeset
866 self.server_name,
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parents:
diff changeset
867 **self.docker_target_kwds
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parents:
diff changeset
868 )
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parents:
diff changeset
869 output, _ = communicate(
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parents:
diff changeset
870 logs_command
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parents:
diff changeset
871 )
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parents:
diff changeset
872 return output
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parents:
diff changeset
873
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parents:
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874 def cleanup(self):
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parents:
diff changeset
875 shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS)
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parents:
diff changeset
876
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parents:
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877
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
878 class LocalGalaxyConfig(BaseManagedGalaxyConfig):
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parents:
diff changeset
879 """A local, non-containerized implementation of :class:`GalaxyConfig`."""
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parents:
diff changeset
880
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parents:
diff changeset
881 def __init__(
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shellac
parents:
diff changeset
882 self,
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parents:
diff changeset
883 ctx,
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parents:
diff changeset
884 config_directory,
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shellac
parents:
diff changeset
885 env,
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shellac
parents:
diff changeset
886 test_data_dir,
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shellac
parents:
diff changeset
887 port,
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parents:
diff changeset
888 server_name,
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shellac
parents:
diff changeset
889 master_api_key,
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shellac
parents:
diff changeset
890 runnables,
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shellac
parents:
diff changeset
891 galaxy_root,
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shellac
parents:
diff changeset
892 kwds,
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parents:
diff changeset
893 ):
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parents:
diff changeset
894 super(LocalGalaxyConfig, self).__init__(
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parents:
diff changeset
895 ctx,
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shellac
parents:
diff changeset
896 config_directory,
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shellac
parents:
diff changeset
897 env,
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shellac
parents:
diff changeset
898 test_data_dir,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
899 port,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
900 server_name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
901 master_api_key,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
902 runnables,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
903 kwds,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
904 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
905 self.galaxy_root = galaxy_root
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
906
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
907 def kill(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
908 kill_pid_file(self.pid_file)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
909
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
910 def startup_command(self, ctx, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
911 """Return a shell command used to startup this instance.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
912
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
913 Among other common planemo kwds, this should respect the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
914 ``daemon`` keyword.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
915 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
916 daemon = kwds.get("daemon", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
917 # TODO: Allow running dockerized Galaxy here instead.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
918 setup_venv_command = setup_venv(ctx, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
919 run_script = "%s $COMMON_STARTUP_ARGS" % shlex_quote(os.path.join(self.galaxy_root, "run.sh"))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
920 if daemon:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
921 run_script += " --daemon"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
922 self.env["GALAXY_RUN_ALL"] = "1"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
923 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
924 run_script += " --server-name %s" % shlex_quote(self.server_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
925 server_ini = os.path.join(self.config_directory, "galaxy.ini")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
926 self.env["GALAXY_CONFIG_FILE"] = server_ini
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
927 if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
928 # We need to start under gunicorn
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
929 self.env['APP_WEBSERVER'] = 'gunicorn'
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
930 self.env['GUNICORN_CMD_ARGS'] = "--bind={host}:{port} --name={server_name}".format(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
931 host=kwds.get('host', '127.0.0.1'),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
932 port=kwds['port'],
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
933 server_name=self.server_name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
934 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
935 cd_to_galaxy_command = ['cd', self.galaxy_root]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
936 return shell_join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
937 cd_to_galaxy_command,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
938 setup_venv_command,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
939 setup_common_startup_args(),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
940 run_script,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
941 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
942
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
943 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
944 def log_file(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
945 """Log file used when planemo serves this Galaxy instance."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
946 file_name = "%s.log" % self.server_name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
947 return os.path.join(self.galaxy_root, file_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
948
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
949 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
950 def pid_file(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
951 pid_file_name = "%s.pid" % self.server_name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
952 return os.path.join(self.galaxy_root, pid_file_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
953
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
954 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
955 def log_contents(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
956 if not os.path.exists(self.log_file):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
957 return ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
958 with open(self.log_file, "r") as f:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
959 return f.read()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
960
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
961 def cleanup(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
962 shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
963
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
964 @property
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
965 def default_use_path_paste(self):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
966 # If Planemo started a local, native Galaxy instance assume files URLs can be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
967 # pasted.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
968 return True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
969
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
970
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
971 def _database_connection(database_location, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
972 default_connection = DATABASE_LOCATION_TEMPLATE % database_location
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
973 database_connection = kwds.get("database_connection") or default_connection
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
974 return database_connection
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
975
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
976
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
977 def _find_galaxy_root(ctx, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
978 root_prop = "galaxy_root"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
979 cwl = kwds.get("cwl", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
980 if cwl:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
981 root_prop = "cwl_galaxy_root"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
982 galaxy_root = kwds.get(root_prop, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
983 if galaxy_root:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
984 return galaxy_root
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
985 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
986 par_dir = os.getcwd()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
987 while True:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
988 run = os.path.join(par_dir, "run.sh")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
989 config = os.path.join(par_dir, "config")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
990 if os.path.isfile(run) and os.path.isdir(config):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
991 return par_dir
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
992 new_par_dir = os.path.dirname(par_dir)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
993 if new_par_dir == par_dir:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
994 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
995 par_dir = new_par_dir
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
996 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
997
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
998
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
999 def _find_test_data(runnables, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1000 test_data_search_path = "."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1001 runnables = [r for r in runnables if r.has_tools]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1002 if len(runnables) > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1003 test_data_search_path = runnables[0].test_data_search_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1004
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1005 # Find test data directory associated with path.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1006 test_data = kwds.get("test_data", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1007 if test_data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1008 return os.path.abspath(test_data)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1009 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1010 test_data = _search_tool_path_for(test_data_search_path, "test-data")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1011 if test_data:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1012 return test_data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1013 warn(NO_TEST_DATA_MESSAGE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1014 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1015
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1016
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1017 def _find_tool_data_table(runnables, test_data_dir, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1018 tool_data_search_path = "."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1019 runnables = [r for r in runnables if r.has_tools]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1020 if len(runnables) > 0:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1021 tool_data_search_path = runnables[0].tool_data_search_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1022
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1023 tool_data_table = kwds.get("tool_data_table", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1024 if tool_data_table:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1025 return os.path.abspath(tool_data_table)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1026 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1027 extra_paths = [test_data_dir] if test_data_dir else []
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1028 return _search_tool_path_for(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1029 tool_data_search_path,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1030 "tool_data_table_conf.xml.test",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1031 extra_paths,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1032 ) or _search_tool_path_for( # if all else fails just use sample
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1033 tool_data_search_path,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1034 "tool_data_table_conf.xml.sample"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1035 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1036
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1037
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1038 def _search_tool_path_for(path, target, extra_paths=[]):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1039 """Check for presence of a target in different artifact directories."""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1040 if not os.path.isdir(path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1041 tool_dir = os.path.dirname(path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1042 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1043 tool_dir = path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1044 possible_dirs = [tool_dir, "."] + extra_paths
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1045 for possible_dir in possible_dirs:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1046 possible_path = os.path.join(possible_dir, target)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1047 if os.path.exists(possible_path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1048 return os.path.abspath(possible_path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1049 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1050
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1051
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1052 def _configure_sheds_config_file(ctx, config_directory, **kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1053 if "shed_target" not in kwds:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1054 kwds = kwds.copy()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1055 kwds["shed_target"] = "toolshed"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1056 shed_target_url = tool_shed_url(ctx, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1057 contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1058 tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1059 write_file(tool_sheds_conf, contents)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1060 return tool_sheds_conf
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1061
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1062
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1063 def _tool_conf_entry_for(tool_paths):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1064 tool_definitions = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1065 for tool_path in tool_paths:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1066 if os.path.isdir(tool_path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1067 tool_definitions += '''<tool_dir dir="%s" />''' % tool_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1068 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1069 tool_definitions += '''<tool file="%s" />''' % tool_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1070 return tool_definitions
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1071
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1072
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1073 def _install_galaxy(ctx, galaxy_root, env, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1074 if not kwds.get("no_cache_galaxy", False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1075 _install_galaxy_via_git(ctx, galaxy_root, env, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1076 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1077 _install_galaxy_via_download(ctx, galaxy_root, env, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1078
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1079
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1080 def _install_galaxy_via_download(ctx, galaxy_root, env, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1081 branch = _galaxy_branch(kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1082 untar_to("https://codeload.github.com/galaxyproject/galaxy/tar.gz/" + branch, tar_args=['-xvzf', '-', 'galaxy-' + branch], dest_dir=galaxy_root)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1083 _install_with_command(ctx, galaxy_root, env, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1084
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1085
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1086 def _install_galaxy_via_git(ctx, galaxy_root, env, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1087 gx_repo = _ensure_galaxy_repository_available(ctx, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1088 branch = _galaxy_branch(kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1089 command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1090 shell(command, env=env)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1091 _install_with_command(ctx, galaxy_root, env, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1092
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1093
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1094 def _build_eggs_cache(ctx, env, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1095 if kwds.get("no_cache_galaxy", False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1096 return None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1097 workspace = ctx.workspace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1098 eggs_path = os.path.join(workspace, "gx_eggs")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1099 if not os.path.exists(eggs_path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1100 os.makedirs(eggs_path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1101 env["GALAXY_EGGS_PATH"] = eggs_path
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1102
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1103
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1104 def _galaxy_branch(kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1105 branch = kwds.get("galaxy_branch", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1106 if branch is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1107 cwl = kwds.get("cwl", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1108 branch = "cwl-1.0" if cwl else None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1109 if branch is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1110 branch = DEFAULT_GALAXY_BRANCH
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1111
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1112 return branch
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1113
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1114
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1115 def _galaxy_source(kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1116 source = kwds.get("galaxy_source", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1117 if source is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1118 cwl = kwds.get("cwl", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1119 source = CWL_GALAXY_SOURCE if cwl else None
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1120 if source is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1121 source = DEFAULT_GALAXY_SOURCE
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1122
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1123 return source
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1124
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1125
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1126 def _install_with_command(ctx, galaxy_root, env, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1127 setup_venv_command = setup_venv(ctx, kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1128 env['__PYVENV_LAUNCHER__'] = ''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1129 install_cmd = shell_join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1130 setup_venv_command,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1131 setup_common_startup_args(),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1132 COMMAND_STARTUP_COMMAND,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1133 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1134 shell(install_cmd, cwd=galaxy_root, env=env)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1135
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1136
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1137 def _ensure_galaxy_repository_available(ctx, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1138 workspace = ctx.workspace
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1139 cwl = kwds.get("cwl", False)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1140 galaxy_source = kwds.get('galaxy_source')
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1141 if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1142 sanitized_repo_name = "".join(c if c.isalnum() else '_' for c in kwds['galaxy_source']).rstrip()[:255]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1143 gx_repo = os.path.join(workspace, "gx_repo_%s" % sanitized_repo_name)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1144 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1145 gx_repo = os.path.join(workspace, "gx_repo")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1146 if cwl:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1147 gx_repo += "_cwl"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1148 if os.path.exists(gx_repo):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1149 # Convert the git repository from bare to mirror, if needed
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1150 shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.fetch', '+refs/*:refs/*'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1151 shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.mirror', 'true'])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1152 # Attempt remote update - but don't fail if not interweb, etc...
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1153 shell("git --git-dir %s remote update >/dev/null 2>&1" % gx_repo)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1154 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1155 remote_repo = _galaxy_source(kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1156 command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1157 shell(command)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1158 return gx_repo
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1159
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1160
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1161 def _build_env_for_galaxy(properties, template_args):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1162 env = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1163 for key, value in iteritems(properties):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1164 if value is not None: # Do not override None with empty string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1165 var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1166 value = _sub(value, template_args)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1167 env[var] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1168 return env
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1169
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shellac
parents:
diff changeset
1170
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1171 def _build_test_env(properties, env):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1172 # Keeping these environment variables around for a little while but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1173 # many are probably not needed as of the following commit.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1174 # https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f9
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1175 test_property_variants = {
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1176 'GALAXY_TEST_JOB_CONFIG_FILE': 'job_config_file',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1177 'GALAXY_TEST_MIGRATED_TOOL_CONF': 'migrated_tools_config',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1178 'GALAXY_TEST_TOOL_CONF': 'tool_config_file',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1179 'GALAXY_TEST_FILE_DIR': 'test_data_dir',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1180 'GALAXY_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1181 # Next line would be required for tool shed tests.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1182 # 'GALAXY_TEST_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1183 }
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1184 for test_key, gx_key in test_property_variants.items():
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1185 value = properties.get(gx_key, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1186 if value is not None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1187 env[test_key] = value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1188
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1189
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1190 def _handle_job_config_file(config_directory, server_name, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1191 job_config_file = kwds.get("job_config_file", None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1192 if not job_config_file:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1193 template_str = JOB_CONFIG_LOCAL
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1194 job_config_file = os.path.join(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1195 config_directory,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1196 "job_conf.xml",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1197 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1198 docker_enable = str(kwds.get("docker", False))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1199 docker_host = str(kwds.get("docker_host", docker_util.DEFAULT_HOST))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1200 docker_host_param = ""
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1201 if docker_host:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1202 docker_host_param = """<param id="docker_host">%s</param>""" % docker_host
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1203
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1204 conf_contents = Template(template_str).safe_substitute({
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1205 "server_name": server_name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1206 "docker_enable": docker_enable,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1207 "require_container": "false",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1208 "docker_sudo": str(kwds.get("docker_sudo", False)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1209 "docker_sudo_cmd": str(kwds.get("docker_sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1210 "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1211 "docker_host": docker_host_param,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1212 })
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1213 write_file(job_config_file, conf_contents)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1214 kwds["job_config_file"] = job_config_file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1215
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1216
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1217 def _write_tool_conf(ctx, tool_paths, tool_conf_path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1218 tool_definition = _tool_conf_entry_for(tool_paths)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1219 tool_conf_template_kwds = dict(tool_definition=tool_definition)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1220 tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, tool_conf_template_kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1221 write_file(tool_conf_path, tool_conf_contents)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1222 ctx.vlog(
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1223 "Writing tool_conf to path %s with contents [%s]",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1224 tool_conf_path,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1225 tool_conf_contents,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1226 )
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1227
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1228
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1229 def _handle_container_resolution(ctx, kwds, galaxy_properties):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1230 if kwds.get("mulled_containers", False):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1231 galaxy_properties["enable_beta_mulled_containers"] = "True"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1232 involucro_context = build_involucro_context(ctx, **kwds)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1233 galaxy_properties["involucro_auto_init"] = "False" # Use planemo's
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1234 galaxy_properties["involucro_path"] = involucro_context.involucro_bin
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1235
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1236
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1237 def _handle_job_metrics(config_directory, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1238 metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml")
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1239 with open(metrics_conf, "w") as fh:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1240 fh.write(EMPTY_JOB_METRICS_TEMPLATE)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1241 kwds["job_metrics_config_file"] = metrics_conf
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1242
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1243
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1244 def _handle_kwd_overrides(properties, kwds):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1245 kwds_gx_properties = [
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1246 'job_config_file',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1247 'job_metrics_config_file',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1248 'dependency_resolvers_config_file',
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1249 ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1250 for prop in kwds_gx_properties:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1251 val = kwds.get(prop, None)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1252 if val:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1253 properties[prop] = val
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1254
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1255
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1256 def _sub(template, args):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1257 if template is None:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1258 return ''
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1259 return Template(template).safe_substitute(args)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1260
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1261
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1262 def _ensure_directory(path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1263 if path is not None and not os.path.exists(path):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1264 os.makedirs(path)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1265
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1266
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1267 __all__ = (
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1268 "DATABASE_LOCATION_TEMPLATE",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1269 "galaxy_config",
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
1270 )