Mercurial > repos > shellac > guppy_basecaller
annotate env/lib/python3.7/site-packages/planemo/galaxy/config.py @ 0:26e78fe6e8c4 draft
"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author | shellac |
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date | Sat, 02 May 2020 07:14:21 -0400 |
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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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384 database_location = config_join("galaxy.sqlite") |
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385 master_api_key = _get_master_api_key(kwds) |
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386 dependency_dir = os.path.join(config_directory, "deps") |
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387 _ensure_directory(shed_tool_path) |
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388 port = _get_port(kwds) |
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389 template_args = dict( |
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390 port=port, |
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391 host=kwds.get("host", "127.0.0.1"), |
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392 server_name=server_name, |
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393 temp_directory=config_directory, |
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394 shed_tool_path=shed_tool_path, |
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395 database_location=database_location, |
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396 tool_conf=tool_conf, |
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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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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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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="${log_level}", |
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427 debug="${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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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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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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455 env = _build_env_for_galaxy(properties, template_args) |
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456 env.update(install_env) |
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457 _build_test_env(properties, env) |
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458 env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf |
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459 env['GALAXY_TEST_DBURI'] = properties["database_connection"] |
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460 |
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461 env["GALAXY_TEST_UPLOAD_ASYNC"] = "false" |
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462 env["GALAXY_TEST_LOGGING_CONFIG"] = config_join("logging.ini") |
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463 env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1" |
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464 # Following are needed in 18.01 to prevent Galaxy from changing log and pid. |
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465 # https://github.com/galaxyproject/planemo/issues/788 |
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466 env["GALAXY_LOG"] = log_file |
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467 env["GALAXY_PID"] = pid_file |
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468 web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args) |
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469 write_file(config_join("galaxy.ini"), web_config) |
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470 _write_tool_conf(ctx, all_tool_paths, tool_conf) |
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471 write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE) |
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472 |
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473 shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args) |
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474 # Write a new shed_tool_conf.xml if needed. |
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475 write_file(shed_tool_conf, shed_tool_conf_contents, force=False) |
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476 |
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477 write_file(shed_data_manager_config_file, SHED_DATA_MANAGER_CONF_TEMPLATE) |
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478 |
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479 yield LocalGalaxyConfig( |
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480 ctx, |
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481 config_directory, |
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482 env, |
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483 test_data_dir, |
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484 port, |
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485 server_name, |
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486 master_api_key, |
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487 runnables, |
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488 galaxy_root, |
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489 kwds, |
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490 ) |
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491 |
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492 |
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493 def _all_tool_paths(runnables, **kwds): |
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494 tool_paths = [r.path for r in runnables if r.has_tools and not r.data_manager_conf_path] |
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495 all_tool_paths = list(tool_paths) + list(kwds.get("extra_tools", [])) |
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496 for runnable in runnables: |
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497 if runnable.type.name == "galaxy_workflow": |
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498 tool_ids = find_tool_ids(runnable.path) |
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499 for tool_id in tool_ids: |
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500 if tool_id in DISTRO_TOOLS_ID_TO_PATH: |
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501 all_tool_paths.append(DISTRO_TOOLS_ID_TO_PATH[tool_id]) |
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502 |
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503 return all_tool_paths |
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504 |
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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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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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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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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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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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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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566 @contextlib.contextmanager |
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567 def _config_directory(ctx, **kwds): |
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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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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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579 shutil.rmtree(config_directory) |
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580 |
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581 |
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582 @add_metaclass(abc.ABCMeta) |
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583 class GalaxyInterface(object): |
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584 """Abstraction around a Galaxy instance. |
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585 |
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586 Description of a Galaxy instance and how to interact with it - this could |
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587 potentially be a remote, already running instance or an instance Planemo manages |
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588 to execute some task(s). |
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589 """ |
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590 |
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591 @abc.abstractproperty |
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592 def gi(self): |
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593 """Return an admin bioblend Galaxy instance for API interactions.""" |
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594 |
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595 @abc.abstractproperty |
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596 def user_gi(self): |
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597 """Return a user-backed bioblend Galaxy instance for API interactions.""" |
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598 |
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599 @abc.abstractmethod |
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600 def install_repo(self, *args, **kwds): |
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601 """Install specified tool shed repository.""" |
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602 |
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603 @abc.abstractproperty |
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604 def tool_shed_client(self): |
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605 """Return a admin bioblend tool shed client.""" |
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606 |
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607 @abc.abstractmethod |
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608 def wait_for_all_installed(self): |
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609 """Wait for all queued up repositories installs to complete.""" |
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610 |
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611 @abc.abstractmethod |
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612 def install_workflows(self): |
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613 """Install all workflows configured with these planemo arguments.""" |
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614 |
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615 @abc.abstractmethod |
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616 def workflow_id(self, path): |
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617 """Get installed workflow API ID for input path.""" |
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618 |
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619 |
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620 @add_metaclass(abc.ABCMeta) |
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621 class GalaxyConfig(GalaxyInterface): |
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622 """Specialization of GalaxyInterface for Galaxy instances Planemo manages itself. |
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623 |
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624 This assumes more than an API connection is available - Planemo needs to be able to |
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625 start and stop the Galaxy instance, recover logs, etc... There are currently two |
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626 implementations - a locally executed Galaxy and one running inside a Docker containe |
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627 """ |
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628 |
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629 @abc.abstractproperty |
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630 def kill(self): |
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631 """Stop the running instance.""" |
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632 |
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633 @abc.abstractmethod |
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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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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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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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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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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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695 return gi(url=self.galaxy_url, key=key) |
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696 |
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697 def install_repo(self, *args, **kwds): |
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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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703 def tool_shed_client(self): |
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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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710 return None |
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711 if status == "Installed": |
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712 return True |
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713 raise Exception("Error installing repo status is %s" % status) |
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714 |
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715 def ready(): |
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716 repos = self.tool_shed_client.get_repositories() |
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717 ready = all(map(status_ready, repos)) |
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718 return ready or None |
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719 |
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720 wait_on(ready, "galaxy tool installation", timeout=60 * 60 * 1) |
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721 |
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722 def install_workflows(self): |
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723 for runnable in self.runnables: |
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724 if runnable.type.name in ["galaxy_workflow", "cwl_workflow"]: |
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725 self._install_workflow(runnable) |
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726 |
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727 def _install_workflow(self, runnable): |
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728 if self._kwds["shed_install"]: |
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729 install_shed_repos(runnable, self.gi, self._kwds.get("ignore_dependency_problems", False)) |
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730 |
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731 default_from_path = self._kwds.get("workflows_from_path", False) |
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732 # TODO: Allow serialization so this doesn't need to assume a |
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733 # shared filesystem with Galaxy server. |
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734 from_path = default_from_path or (runnable.type.name == "cwl_workflow") |
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735 workflow = import_workflow( |
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736 runnable.path, admin_gi=self.gi, user_gi=self.user_gi, from_path=from_path |
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737 ) |
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738 self._workflow_ids[runnable.path] = workflow["id"] |
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739 |
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740 def workflow_id(self, path): |
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741 return self._workflow_ids[path] |
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742 |
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743 @property |
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744 def use_path_paste(self): |
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745 option = self._kwds.get("paste_test_data_paths") |
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746 if option is None: |
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747 return self.default_use_path_paste |
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748 else: |
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749 return option |
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750 |
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|
751 @property |
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752 def default_use_path_paste(self): |
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753 return False |
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|
754 |
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|
755 |
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|
756 class BaseManagedGalaxyConfig(BaseGalaxyConfig): |
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757 |
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758 def __init__( |
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759 self, |
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760 ctx, |
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761 config_directory, |
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|
762 env, |
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|
763 test_data_dir, |
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|
764 port, |
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|
765 server_name, |
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766 master_api_key, |
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|
767 runnables, |
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|
768 kwds, |
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769 ): |
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770 galaxy_url = "http://localhost:%d" % port |
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771 super(BaseManagedGalaxyConfig, self).__init__( |
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772 ctx=ctx, |
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773 galaxy_url=galaxy_url, |
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774 master_api_key=master_api_key, |
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775 user_api_key=None, |
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776 runnables=runnables, |
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777 kwds=kwds |
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778 ) |
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779 self.config_directory = config_directory |
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780 self.env = env |
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781 self.test_data_dir = test_data_dir |
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782 self.port = port |
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783 self.server_name = server_name |
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784 |
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|
785 |
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|
786 class DockerGalaxyConfig(BaseManagedGalaxyConfig): |
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787 """A :class:`GalaxyConfig` description of a Dockerized Galaxy instance.""" |
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788 |
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789 def __init__( |
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|
790 self, |
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791 ctx, |
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|
792 config_directory, |
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|
793 env, |
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|
794 test_data_dir, |
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795 port, |
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796 server_name, |
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797 master_api_key, |
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798 runnables, |
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799 docker_target_kwds, |
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800 volumes, |
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801 export_directory, |
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802 kwds, |
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803 ): |
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804 super(DockerGalaxyConfig, self).__init__( |
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805 ctx, |
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806 config_directory, |
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807 env, |
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808 test_data_dir, |
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809 port, |
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810 server_name, |
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811 master_api_key, |
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812 runnables, |
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813 kwds, |
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814 ) |
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815 self.docker_target_kwds = docker_target_kwds |
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816 self.volumes = volumes |
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817 self.export_directory = export_directory |
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818 |
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819 def kill(self): |
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820 """Kill planemo container...""" |
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821 kill_command = docker_util.kill_command( |
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822 self.server_name, |
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823 **self.docker_target_kwds |
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824 ) |
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825 return shell(kill_command) |
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826 |
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827 def startup_command(self, ctx, **kwds): |
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828 """Return a shell command used to startup this instance. |
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829 |
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830 Among other common planmo kwds, this should respect the |
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831 ``daemon`` keyword. |
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832 """ |
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833 daemon = kwds.get("daemon", False) |
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834 daemon_str = "" if not daemon else " -d" |
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835 docker_run_extras = "-p %s:80%s" % (self.port, daemon_str) |
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836 env_directives = ["%s='%s'" % item for item in self.env.items()] |
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837 image = kwds.get("docker_galaxy_image", "bgruening/galaxy-stable") |
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838 run_command = docker_util.build_docker_run_command( |
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839 "", image, |
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840 interactive=False, |
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841 env_directives=env_directives, |
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842 working_directory=None, |
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843 name=self.server_name, |
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844 run_extra_arguments=docker_run_extras, |
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845 set_user=False, |
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846 volumes=self.volumes, |
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847 **self.docker_target_kwds |
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848 ) |
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849 chmod_command = [ |
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850 "chmod", |
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851 "-R", |
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852 "o+rwx", |
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853 self.config_directory, |
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854 ] |
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855 if self.export_directory: |
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856 chmod_command.append(self.export_directory) |
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857 |
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858 return shell_join( |
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859 argv_to_str(chmod_command), |
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860 run_command, |
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861 ) |
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862 |
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863 @property |
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864 def log_contents(self): |
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865 logs_command = docker_util.logs_command( |
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866 self.server_name, |
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867 **self.docker_target_kwds |
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868 ) |
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869 output, _ = communicate( |
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870 logs_command |
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871 ) |
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872 return output |
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873 |
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874 def cleanup(self): |
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875 shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS) |
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876 |
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877 |
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878 class LocalGalaxyConfig(BaseManagedGalaxyConfig): |
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879 """A local, non-containerized implementation of :class:`GalaxyConfig`.""" |
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880 |
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881 def __init__( |
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882 self, |
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883 ctx, |
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884 config_directory, |
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885 env, |
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886 test_data_dir, |
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887 port, |
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888 server_name, |
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889 master_api_key, |
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890 runnables, |
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891 galaxy_root, |
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892 kwds, |
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893 ): |
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894 super(LocalGalaxyConfig, self).__init__( |
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895 ctx, |
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896 config_directory, |
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897 env, |
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898 test_data_dir, |
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899 port, |
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900 server_name, |
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901 master_api_key, |
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902 runnables, |
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903 kwds, |
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904 ) |
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905 self.galaxy_root = galaxy_root |
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906 |
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907 def kill(self): |
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908 kill_pid_file(self.pid_file) |
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909 |
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910 def startup_command(self, ctx, **kwds): |
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911 """Return a shell command used to startup this instance. |
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912 |
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913 Among other common planemo kwds, this should respect the |
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914 ``daemon`` keyword. |
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915 """ |
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|
916 daemon = kwds.get("daemon", False) |
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917 # TODO: Allow running dockerized Galaxy here instead. |
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918 setup_venv_command = setup_venv(ctx, kwds) |
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919 run_script = "%s $COMMON_STARTUP_ARGS" % shlex_quote(os.path.join(self.galaxy_root, "run.sh")) |
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|
920 if daemon: |
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921 run_script += " --daemon" |
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922 self.env["GALAXY_RUN_ALL"] = "1" |
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923 else: |
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924 run_script += " --server-name %s" % shlex_quote(self.server_name) |
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925 server_ini = os.path.join(self.config_directory, "galaxy.ini") |
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926 self.env["GALAXY_CONFIG_FILE"] = server_ini |
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927 if parse_version(kwds.get('galaxy_python_version') or DEFAULT_PYTHON_VERSION) >= parse_version('3'): |
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928 # We need to start under gunicorn |
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929 self.env['APP_WEBSERVER'] = 'gunicorn' |
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930 self.env['GUNICORN_CMD_ARGS'] = "--bind={host}:{port} --name={server_name}".format( |
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931 host=kwds.get('host', '127.0.0.1'), |
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932 port=kwds['port'], |
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933 server_name=self.server_name, |
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|
934 ) |
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935 cd_to_galaxy_command = ['cd', self.galaxy_root] |
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936 return shell_join( |
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|
937 cd_to_galaxy_command, |
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938 setup_venv_command, |
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939 setup_common_startup_args(), |
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940 run_script, |
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|
941 ) |
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|
942 |
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|
943 @property |
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944 def log_file(self): |
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945 """Log file used when planemo serves this Galaxy instance.""" |
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946 file_name = "%s.log" % self.server_name |
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947 return os.path.join(self.galaxy_root, file_name) |
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|
948 |
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|
949 @property |
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950 def pid_file(self): |
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951 pid_file_name = "%s.pid" % self.server_name |
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952 return os.path.join(self.galaxy_root, pid_file_name) |
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|
953 |
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|
954 @property |
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|
955 def log_contents(self): |
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956 if not os.path.exists(self.log_file): |
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|
957 return "" |
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|
958 with open(self.log_file, "r") as f: |
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959 return f.read() |
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|
960 |
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|
961 def cleanup(self): |
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962 shutil.rmtree(self.config_directory, CLEANUP_IGNORE_ERRORS) |
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|
963 |
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|
964 @property |
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965 def default_use_path_paste(self): |
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966 # If Planemo started a local, native Galaxy instance assume files URLs can be |
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967 # pasted. |
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|
968 return True |
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|
969 |
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|
970 |
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|
971 def _database_connection(database_location, **kwds): |
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972 default_connection = DATABASE_LOCATION_TEMPLATE % database_location |
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973 database_connection = kwds.get("database_connection") or default_connection |
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974 return database_connection |
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|
975 |
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|
976 |
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977 def _find_galaxy_root(ctx, **kwds): |
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978 root_prop = "galaxy_root" |
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979 cwl = kwds.get("cwl", False) |
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980 if cwl: |
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981 root_prop = "cwl_galaxy_root" |
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982 galaxy_root = kwds.get(root_prop, None) |
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983 if galaxy_root: |
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984 return galaxy_root |
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985 else: |
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986 par_dir = os.getcwd() |
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987 while True: |
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988 run = os.path.join(par_dir, "run.sh") |
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989 config = os.path.join(par_dir, "config") |
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990 if os.path.isfile(run) and os.path.isdir(config): |
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991 return par_dir |
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992 new_par_dir = os.path.dirname(par_dir) |
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993 if new_par_dir == par_dir: |
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994 break |
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995 par_dir = new_par_dir |
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996 return None |
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|
997 |
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998 |
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999 def _find_test_data(runnables, **kwds): |
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1000 test_data_search_path = "." |
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1001 runnables = [r for r in runnables if r.has_tools] |
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1002 if len(runnables) > 0: |
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1003 test_data_search_path = runnables[0].test_data_search_path |
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1004 |
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|
1005 # Find test data directory associated with path. |
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1006 test_data = kwds.get("test_data", None) |
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1007 if test_data: |
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1008 return os.path.abspath(test_data) |
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1009 else: |
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1010 test_data = _search_tool_path_for(test_data_search_path, "test-data") |
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1011 if test_data: |
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1012 return test_data |
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1013 warn(NO_TEST_DATA_MESSAGE) |
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1014 return None |
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1015 |
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|
1016 |
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1017 def _find_tool_data_table(runnables, test_data_dir, **kwds): |
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1018 tool_data_search_path = "." |
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1019 runnables = [r for r in runnables if r.has_tools] |
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1020 if len(runnables) > 0: |
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1021 tool_data_search_path = runnables[0].tool_data_search_path |
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1022 |
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1023 tool_data_table = kwds.get("tool_data_table", None) |
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1024 if tool_data_table: |
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1025 return os.path.abspath(tool_data_table) |
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1026 else: |
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1027 extra_paths = [test_data_dir] if test_data_dir else [] |
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1028 return _search_tool_path_for( |
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1029 tool_data_search_path, |
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1030 "tool_data_table_conf.xml.test", |
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1031 extra_paths, |
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1032 ) or _search_tool_path_for( # if all else fails just use sample |
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1033 tool_data_search_path, |
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1034 "tool_data_table_conf.xml.sample" |
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1035 ) |
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1036 |
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1037 |
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1038 def _search_tool_path_for(path, target, extra_paths=[]): |
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1039 """Check for presence of a target in different artifact directories.""" |
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1040 if not os.path.isdir(path): |
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1041 tool_dir = os.path.dirname(path) |
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1042 else: |
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1043 tool_dir = path |
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1044 possible_dirs = [tool_dir, "."] + extra_paths |
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1045 for possible_dir in possible_dirs: |
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1046 possible_path = os.path.join(possible_dir, target) |
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1047 if os.path.exists(possible_path): |
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1048 return os.path.abspath(possible_path) |
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1049 return None |
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1050 |
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1051 |
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1052 def _configure_sheds_config_file(ctx, config_directory, **kwds): |
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1053 if "shed_target" not in kwds: |
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1054 kwds = kwds.copy() |
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1055 kwds["shed_target"] = "toolshed" |
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1056 shed_target_url = tool_shed_url(ctx, **kwds) |
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1057 contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url}) |
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1058 tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml") |
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1059 write_file(tool_sheds_conf, contents) |
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1060 return tool_sheds_conf |
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1061 |
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1062 |
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1063 def _tool_conf_entry_for(tool_paths): |
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1064 tool_definitions = "" |
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1065 for tool_path in tool_paths: |
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1066 if os.path.isdir(tool_path): |
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1067 tool_definitions += '''<tool_dir dir="%s" />''' % tool_path |
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1068 else: |
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1069 tool_definitions += '''<tool file="%s" />''' % tool_path |
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1070 return tool_definitions |
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1071 |
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1072 |
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1073 def _install_galaxy(ctx, galaxy_root, env, kwds): |
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1074 if not kwds.get("no_cache_galaxy", False): |
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1075 _install_galaxy_via_git(ctx, galaxy_root, env, kwds) |
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1076 else: |
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1077 _install_galaxy_via_download(ctx, galaxy_root, env, kwds) |
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1078 |
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1079 |
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1080 def _install_galaxy_via_download(ctx, galaxy_root, env, kwds): |
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1081 branch = _galaxy_branch(kwds) |
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1082 untar_to("https://codeload.github.com/galaxyproject/galaxy/tar.gz/" + branch, tar_args=['-xvzf', '-', 'galaxy-' + branch], dest_dir=galaxy_root) |
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1083 _install_with_command(ctx, galaxy_root, env, kwds) |
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1084 |
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1085 |
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1086 def _install_galaxy_via_git(ctx, galaxy_root, env, kwds): |
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1087 gx_repo = _ensure_galaxy_repository_available(ctx, kwds) |
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1088 branch = _galaxy_branch(kwds) |
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1089 command = git.command_clone(ctx, gx_repo, galaxy_root, branch=branch) |
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1090 shell(command, env=env) |
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1091 _install_with_command(ctx, galaxy_root, env, kwds) |
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1092 |
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1093 |
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1094 def _build_eggs_cache(ctx, env, kwds): |
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1095 if kwds.get("no_cache_galaxy", False): |
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1096 return None |
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1097 workspace = ctx.workspace |
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1098 eggs_path = os.path.join(workspace, "gx_eggs") |
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1099 if not os.path.exists(eggs_path): |
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1100 os.makedirs(eggs_path) |
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1101 env["GALAXY_EGGS_PATH"] = eggs_path |
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1102 |
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1103 |
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1104 def _galaxy_branch(kwds): |
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1105 branch = kwds.get("galaxy_branch", None) |
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1106 if branch is None: |
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1107 cwl = kwds.get("cwl", False) |
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1108 branch = "cwl-1.0" if cwl else None |
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1109 if branch is None: |
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1110 branch = DEFAULT_GALAXY_BRANCH |
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1111 |
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1112 return branch |
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1113 |
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1114 |
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1115 def _galaxy_source(kwds): |
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1116 source = kwds.get("galaxy_source", None) |
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1117 if source is None: |
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1118 cwl = kwds.get("cwl", False) |
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1119 source = CWL_GALAXY_SOURCE if cwl else None |
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1120 if source is None: |
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1121 source = DEFAULT_GALAXY_SOURCE |
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1122 |
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1123 return source |
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1124 |
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1125 |
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1126 def _install_with_command(ctx, galaxy_root, env, kwds): |
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1127 setup_venv_command = setup_venv(ctx, kwds) |
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1128 env['__PYVENV_LAUNCHER__'] = '' |
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1129 install_cmd = shell_join( |
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1130 setup_venv_command, |
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1131 setup_common_startup_args(), |
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1132 COMMAND_STARTUP_COMMAND, |
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1133 ) |
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1134 shell(install_cmd, cwd=galaxy_root, env=env) |
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1135 |
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1136 |
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1137 def _ensure_galaxy_repository_available(ctx, kwds): |
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1138 workspace = ctx.workspace |
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1139 cwl = kwds.get("cwl", False) |
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1140 galaxy_source = kwds.get('galaxy_source') |
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1141 if galaxy_source and galaxy_source != DEFAULT_GALAXY_SOURCE: |
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1142 sanitized_repo_name = "".join(c if c.isalnum() else '_' for c in kwds['galaxy_source']).rstrip()[:255] |
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1143 gx_repo = os.path.join(workspace, "gx_repo_%s" % sanitized_repo_name) |
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1144 else: |
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1145 gx_repo = os.path.join(workspace, "gx_repo") |
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1146 if cwl: |
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1147 gx_repo += "_cwl" |
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1148 if os.path.exists(gx_repo): |
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1149 # Convert the git repository from bare to mirror, if needed |
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1150 shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.fetch', '+refs/*:refs/*']) |
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1151 shell(['git', '--git-dir', gx_repo, 'config', 'remote.origin.mirror', 'true']) |
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1152 # Attempt remote update - but don't fail if not interweb, etc... |
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1153 shell("git --git-dir %s remote update >/dev/null 2>&1" % gx_repo) |
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1154 else: |
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1155 remote_repo = _galaxy_source(kwds) |
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1156 command = git.command_clone(ctx, remote_repo, gx_repo, mirror=True) |
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1157 shell(command) |
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1158 return gx_repo |
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1159 |
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1160 |
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1161 def _build_env_for_galaxy(properties, template_args): |
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1162 env = {} |
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1163 for key, value in iteritems(properties): |
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1164 if value is not None: # Do not override None with empty string |
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1165 var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper() |
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1166 value = _sub(value, template_args) |
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1167 env[var] = value |
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1168 return env |
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1169 |
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1170 |
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1171 def _build_test_env(properties, env): |
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1172 # Keeping these environment variables around for a little while but |
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1173 # many are probably not needed as of the following commit. |
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1174 # https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f9 |
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1175 test_property_variants = { |
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1176 'GALAXY_TEST_JOB_CONFIG_FILE': 'job_config_file', |
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1177 'GALAXY_TEST_MIGRATED_TOOL_CONF': 'migrated_tools_config', |
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1178 'GALAXY_TEST_TOOL_CONF': 'tool_config_file', |
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1179 'GALAXY_TEST_FILE_DIR': 'test_data_dir', |
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1180 'GALAXY_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir', |
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1181 # Next line would be required for tool shed tests. |
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1182 # 'GALAXY_TEST_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir', |
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1183 } |
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1184 for test_key, gx_key in test_property_variants.items(): |
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1185 value = properties.get(gx_key, None) |
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1186 if value is not None: |
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1187 env[test_key] = value |
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1188 |
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1189 |
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1190 def _handle_job_config_file(config_directory, server_name, kwds): |
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1191 job_config_file = kwds.get("job_config_file", None) |
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1192 if not job_config_file: |
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1193 template_str = JOB_CONFIG_LOCAL |
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1194 job_config_file = os.path.join( |
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1195 config_directory, |
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1196 "job_conf.xml", |
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1197 ) |
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1198 docker_enable = str(kwds.get("docker", False)) |
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1199 docker_host = str(kwds.get("docker_host", docker_util.DEFAULT_HOST)) |
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1200 docker_host_param = "" |
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1201 if docker_host: |
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1202 docker_host_param = """<param id="docker_host">%s</param>""" % docker_host |
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1203 |
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1204 conf_contents = Template(template_str).safe_substitute({ |
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1205 "server_name": server_name, |
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1206 "docker_enable": docker_enable, |
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1207 "require_container": "false", |
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1208 "docker_sudo": str(kwds.get("docker_sudo", False)), |
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1209 "docker_sudo_cmd": str(kwds.get("docker_sudo_cmd", docker_util.DEFAULT_SUDO_COMMAND)), |
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1210 "docker_cmd": str(kwds.get("docker_cmd", docker_util.DEFAULT_DOCKER_COMMAND)), |
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1211 "docker_host": docker_host_param, |
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1212 }) |
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1213 write_file(job_config_file, conf_contents) |
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1214 kwds["job_config_file"] = job_config_file |
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1215 |
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1216 |
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1217 def _write_tool_conf(ctx, tool_paths, tool_conf_path): |
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1218 tool_definition = _tool_conf_entry_for(tool_paths) |
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1219 tool_conf_template_kwds = dict(tool_definition=tool_definition) |
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1220 tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, tool_conf_template_kwds) |
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1221 write_file(tool_conf_path, tool_conf_contents) |
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1222 ctx.vlog( |
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1223 "Writing tool_conf to path %s with contents [%s]", |
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1224 tool_conf_path, |
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1225 tool_conf_contents, |
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1226 ) |
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1227 |
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1228 |
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1229 def _handle_container_resolution(ctx, kwds, galaxy_properties): |
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1230 if kwds.get("mulled_containers", False): |
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1231 galaxy_properties["enable_beta_mulled_containers"] = "True" |
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1232 involucro_context = build_involucro_context(ctx, **kwds) |
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1233 galaxy_properties["involucro_auto_init"] = "False" # Use planemo's |
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1234 galaxy_properties["involucro_path"] = involucro_context.involucro_bin |
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1235 |
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1236 |
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1237 def _handle_job_metrics(config_directory, kwds): |
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1238 metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml") |
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1239 with open(metrics_conf, "w") as fh: |
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1240 fh.write(EMPTY_JOB_METRICS_TEMPLATE) |
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1241 kwds["job_metrics_config_file"] = metrics_conf |
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1242 |
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1243 |
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1244 def _handle_kwd_overrides(properties, kwds): |
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1245 kwds_gx_properties = [ |
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1246 'job_config_file', |
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1247 'job_metrics_config_file', |
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1248 'dependency_resolvers_config_file', |
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1249 ] |
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1250 for prop in kwds_gx_properties: |
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1251 val = kwds.get(prop, None) |
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1252 if val: |
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1253 properties[prop] = val |
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1254 |
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1255 |
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1256 def _sub(template, args): |
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1257 if template is None: |
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1258 return '' |
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1259 return Template(template).safe_substitute(args) |
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1260 |
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1261 |
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1262 def _ensure_directory(path): |
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1263 if path is not None and not os.path.exists(path): |
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1264 os.makedirs(path) |
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1265 |
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1266 |
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1267 __all__ = ( |
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1268 "DATABASE_LOCATION_TEMPLATE", |
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1269 "galaxy_config", |
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1270 ) |