Mercurial > repos > bcclaywell > argo_navis

annotate venv/lib/python2.7/site-packages/planemo/galaxy_config.py @ 0:d67268158946 draft

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planemo upload commit a3f181f5f126803c654b3a66dd4e83a48f7e203b
author bcclaywell
date Mon, 12 Oct 2015 17:43:33 -0400
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1 from __future__ import absolute_import
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2 from __future__ import print_function
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3
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4 import contextlib
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5 import os
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6 import random
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7 import shutil
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8 import time
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9 from six.moves.urllib.request import urlopen
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10 from six import iteritems
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11 from string import Template
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12 from tempfile import mkdtemp
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13 from six.moves.urllib.request import urlretrieve
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14
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15 import click
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16
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17 from planemo import galaxy_run
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18 from planemo.io import warn
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19 from planemo.io import shell
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20 from planemo.io import write_file
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21 from planemo.io import kill_pid_file
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22 from planemo import git
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23 from planemo.shed import tool_shed_url
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24 from planemo.bioblend import (
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25 galaxy,
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26 ensure_module,
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27 )
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28
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29
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30 NO_TEST_DATA_MESSAGE = (
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31 "planemo couldn't find a target test-data directory, you should likely "
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32 "create a test-data directory or pass an explicit path using --test_data."
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33 )
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34
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35 WEB_SERVER_CONFIG_TEMPLATE = """
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36 [server:${server_name}]
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37 use = egg:Paste#http
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38 port = ${port}
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39 host = ${host}
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40 use_threadpool = True
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41 threadpool_kill_thread_limit = 10800
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42 [app:main]
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43 paste.app_factory = galaxy.web.buildapp:app_factory
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44 """
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45
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46 TOOL_CONF_TEMPLATE = """<toolbox>
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47 <tool file="data_source/upload.xml" />
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48 ${tool_definition}
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49 </toolbox>
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50 """
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51
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52 SHED_TOOL_CONF_TEMPLATE = """<?xml version="1.0"?>
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53 <toolbox tool_path="${shed_tools_path}">
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54 </toolbox>
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55 """
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56
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57
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58 EMPTY_JOB_METRICS_TEMPLATE = """<?xml version="1.0"?>
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59 <job_metrics>
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60 </job_metrics>
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61 """
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62
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63
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64 BREW_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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65 <homebrew />
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66 <!--
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67 <homebrew versionless="true" />
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68 -->
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69 </dependency_resolvers>
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70 """
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71
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72 SHED_DEPENDENCY_RESOLUTION_CONF = """<dependency_resolvers>
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73 <tool_shed_tap />
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74 </dependency_resolvers>
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75 """
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76
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77 TOOL_SHEDS_CONF = """<tool_sheds>
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78 <tool_shed name="Target Shed" url="${shed_target_url}" />
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79 </tool_sheds>
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80 """
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81
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82 # Provide some shortcuts for simple/common dependency resolutions strategies.
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83 STOCK_DEPENDENCY_RESOLUTION_STRATEGIES = {
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84 "brew_dependency_resolution": BREW_DEPENDENCY_RESOLUTION_CONF,
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85 "shed_dependency_resolution": SHED_DEPENDENCY_RESOLUTION_CONF,
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86 }
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87
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88 EMPTY_TOOL_CONF_TEMPLATE = """<toolbox></toolbox>"""
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89
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90 DOWNLOADS_URL = ("https://raw.githubusercontent.com/"
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91 "jmchilton/galaxy-downloads/master/")
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92 DOWNLOADABLE_MIGRATION_VERSIONS = [127, 120, 117]
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93 LATEST_URL = DOWNLOADS_URL + "latest.sqlite"
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94
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95 FAILED_TO_FIND_GALAXY_EXCEPTION = (
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96 "Failed to find Galaxy root directory - please explicitly specify one "
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97 "with --galaxy_root."
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98 )
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99
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100
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101 @contextlib.contextmanager
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102 def galaxy_config(ctx, tool_paths, for_tests=False, **kwds):
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103 test_data_dir = _find_test_data(tool_paths, **kwds)
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104 tool_data_table = _find_tool_data_table(
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105 tool_paths,
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106 test_data_dir=test_data_dir,
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107 **kwds
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108 )
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109 galaxy_root = _check_galaxy(ctx, **kwds)
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110 install_galaxy = galaxy_root is None
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111 config_directory = kwds.get("config_directory", None)
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112
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113 def config_join(*args):
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114 return os.path.join(config_directory, *args)
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115
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116 created_config_directory = False
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117 if not config_directory:
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118 created_config_directory = True
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119 config_directory = mkdtemp()
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120 try:
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121 latest_galaxy = False
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122 if install_galaxy:
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123 _install_galaxy(ctx, config_directory, kwds)
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124 latest_galaxy = True
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125 galaxy_root = config_join("galaxy-dev")
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126
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127 _handle_dependency_resolution(config_directory, kwds)
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128 _handle_job_metrics(config_directory, kwds)
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129 tool_definition = _tool_conf_entry_for(tool_paths)
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130 empty_tool_conf = config_join("empty_tool_conf.xml")
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131 shed_tool_conf = _shed_tool_conf(install_galaxy, config_directory)
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132 tool_conf = config_join("tool_conf.xml")
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133 database_location = config_join("galaxy.sqlite")
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134 shed_tools_path = config_join("shed_tools")
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135 sheds_config_path = _configure_sheds_config_file(
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136 ctx, config_directory, **kwds
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137 )
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138 preseeded_database = True
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139 master_api_key = kwds.get("master_api_key", "test_key")
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140 dependency_dir = os.path.join(config_directory, "deps")
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141
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142 try:
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143 _download_database_template(
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144 galaxy_root,
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145 database_location,
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146 latest=latest_galaxy
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147 )
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148 except Exception as e:
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149 print(e)
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150 # No network access - just roll forward from null.
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151 preseeded_database = False
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152
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153 os.makedirs(shed_tools_path)
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154 server_name = "planemo%d" % random.randint(0, 100000)
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155 port = kwds.get("port", 9090)
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156 template_args = dict(
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157 port=port,
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158 host=kwds.get("host", "127.0.0.1"),
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159 server_name=server_name,
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160 temp_directory=config_directory,
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161 shed_tools_path=shed_tools_path,
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162 database_location=database_location,
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163 tool_definition=tool_definition,
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164 tool_conf=tool_conf,
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165 debug=kwds.get("debug", "true"),
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166 master_api_key=master_api_key,
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167 id_secret=kwds.get("id_secret", "test_secret"),
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168 log_level=kwds.get("log_level", "DEBUG"),
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169 )
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170 tool_config_file = "%s,%s" % (tool_conf, shed_tool_conf)
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171 properties = dict(
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172 tool_dependency_dir=dependency_dir,
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173 file_path="${temp_directory}/files",
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174 new_file_path="${temp_directory}/tmp",
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175 tool_config_file=tool_config_file,
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176 tool_sheds_config_file=sheds_config_path,
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177 check_migrate_tools="False",
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178 manage_dependency_relationships="False",
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179 job_working_directory="${temp_directory}/job_working_directory",
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180 template_cache_path="${temp_directory}/compiled_templates",
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181 citation_cache_type="file",
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182 citation_cache_data_dir="${temp_directory}/citations/data",
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183 citation_cache_lock_dir="${temp_directory}/citations/lock",
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184 collect_outputs_from="job_working_directory",
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185 database_auto_migrate="True",
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186 cleanup_job="never",
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187 master_api_key="${master_api_key}",
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188 id_secret="${id_secret}",
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189 log_level="${log_level}",
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190 debug="${debug}",
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191 watch_tools="auto",
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192 tool_data_table_config_path=tool_data_table,
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193 integrated_tool_panel_config=("${temp_directory}/"
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194 "integrated_tool_panel_conf.xml"),
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195 # Use in-memory database for kombu to avoid database contention
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196 # during tests.
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197 amqp_internal_connection="sqlalchemy+sqlite://",
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198 migrated_tools_config=empty_tool_conf,
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199 test_data_dir=test_data_dir, # TODO: make gx respect this
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200 )
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201 if not for_tests:
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202 properties["database_connection"] = \
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203 "sqlite:///${database_location}?isolation_level=IMMEDIATE"
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204
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205 _handle_kwd_overrides(properties, kwds)
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206
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207 # TODO: consider following property
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208 # watch_tool = False
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209 # datatypes_config_file = config/datatypes_conf.xml
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210 # welcome_url = /static/welcome.html
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211 # logo_url = /
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212 # sanitize_all_html = True
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213 # serve_xss_vulnerable_mimetypes = False
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214 # track_jobs_in_database = None
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215 # outputs_to_working_directory = False
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216 # retry_job_output_collection = 0
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217
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218 env = _build_env_for_galaxy(properties, template_args)
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219 if install_galaxy:
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220 _build_eggs_cache(ctx, env, kwds)
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221 _build_test_env(properties, env)
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222 env['GALAXY_TEST_SHED_TOOL_CONF'] = shed_tool_conf
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223
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224 # No need to download twice - would GALAXY_TEST_DATABASE_CONNECTION
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225 # work?
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226 if preseeded_database:
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227 env["GALAXY_TEST_DB_TEMPLATE"] = os.path.abspath(database_location)
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228 env["GALAXY_TEST_UPLOAD_ASYNC"] = "false"
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229 env["GALAXY_DEVELOPMENT_ENVIRONMENT"] = "1"
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230 web_config = _sub(WEB_SERVER_CONFIG_TEMPLATE, template_args)
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231 write_file(config_join("galaxy.ini"), web_config)
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232 tool_conf_contents = _sub(TOOL_CONF_TEMPLATE, template_args)
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233 write_file(tool_conf, tool_conf_contents)
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234 write_file(empty_tool_conf, EMPTY_TOOL_CONF_TEMPLATE)
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235
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236 shed_tool_conf_contents = _sub(SHED_TOOL_CONF_TEMPLATE, template_args)
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237 write_file(shed_tool_conf, shed_tool_conf_contents)
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238
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239 yield GalaxyConfig(
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240 galaxy_root,
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241 config_directory,
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242 env,
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243 test_data_dir,
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244 port,
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245 server_name,
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246 master_api_key,
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247 )
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248 finally:
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249 cleanup = not kwds.get("no_cleanup", False)
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250 if created_config_directory and cleanup:
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251 shutil.rmtree(config_directory)
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252
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253
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254 class GalaxyConfig(object):
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255
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256 def __init__(
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257 self,
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258 galaxy_root,
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259 config_directory,
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260 env,
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261 test_data_dir,
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262 port,
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263 server_name,
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264 master_api_key,
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265 ):
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266 self.galaxy_root = galaxy_root
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267 self.config_directory = config_directory
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268 self.env = env
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269 self.test_data_dir = test_data_dir
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270 # Runtime server configuration stuff not used if testing...
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271 # better design might be GalaxyRootConfig and GalaxyServerConfig
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272 # as two separate objects.
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273 self.port = port
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274 self.server_name = server_name
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275 self.master_api_key = master_api_key
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276
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277 def kill(self):
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278 kill_pid_file(self.pid_file)
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279
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280 @property
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281 def pid_file(self):
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282 return os.path.join(self.galaxy_root, "%s.pid" % self.server_name)
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283
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284 @property
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285 def gi(self):
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286 ensure_module(galaxy)
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287 return galaxy.GalaxyInstance(
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288 url="http://localhost:%d" % self.port,
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289 key=self.master_api_key
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290 )
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291
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292 def install_repo(self, *args, **kwds):
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293 self.tool_shed_client.install_repository_revision(
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294 *args, **kwds
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295 )
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296
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297 @property
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298 def tool_shed_client(self):
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299 return self.gi.toolShed
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300
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301 def wait_for_all_installed(self):
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302 def status_ready(repo):
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303 status = repo["status"]
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304 if status in ["Installing", "New"]:
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305 return False
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306 if status == "Installed":
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307 return True
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308 raise Exception("Error installing repo status is %s" % status)
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309
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310 def not_ready():
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311 repos = self.tool_shed_client.get_repositories()
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312 return not all(map(status_ready, repos))
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313
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314 self._wait_for(not_ready)
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315
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316 # Taken from Galaxy's twilltestcase.
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317 def _wait_for(self, func, **kwd):
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318 sleep_amount = 0.2
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319 slept = 0
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320 walltime_exceeded = 1086400
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321 while slept <= walltime_exceeded:
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322 result = func()
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323 if result:
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324 time.sleep(sleep_amount)
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325 slept += sleep_amount
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326 sleep_amount *= 1.25
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327 if slept + sleep_amount > walltime_exceeded:
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328 sleep_amount = walltime_exceeded - slept
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329 else:
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330 break
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331 assert slept < walltime_exceeded, "Action taking too long."
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332
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333 def cleanup(self):
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334 shutil.rmtree(self.config_directory)
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335
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336
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337 def _download_database_template(galaxy_root, database_location, latest=False):
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338 if latest:
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339 template_url = DOWNLOADS_URL + urlopen(LATEST_URL).read()
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340 urlretrieve(template_url, database_location)
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341 return True
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342
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343 newest_migration = _newest_migration_version(galaxy_root)
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344 download_migration = None
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345 for migration in DOWNLOADABLE_MIGRATION_VERSIONS:
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346 if newest_migration > migration:
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347 download_migration = migration
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348 break
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349
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350 if download_migration:
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351 download_name = "db_gx_rev_0%d.sqlite" % download_migration
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352 download_url = DOWNLOADS_URL + download_name
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353 urlretrieve(download_url, database_location)
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354 return True
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355 else:
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356 return False
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357
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358
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359 def _newest_migration_version(galaxy_root):
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360 versions = os.path.join(galaxy_root, "lib/galaxy/model/migrate/versions")
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361 version = max(map(_file_name_to_migration_version, os.listdir(versions)))
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362 return version
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363
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364
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365 def _file_name_to_migration_version(name):
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366 try:
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367 return int(name[0:4])
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368 except ValueError:
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369 return -1
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370
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371
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372 def _check_galaxy(ctx, **kwds):
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373 """ Find Galaxy root, return None to indicate it should be
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374 installed automatically.
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375 """
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376 install_galaxy = kwds.get("install_galaxy", None)
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377 galaxy_root = None
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378 if not install_galaxy:
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379 galaxy_root = _find_galaxy_root(ctx, **kwds)
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parents:
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380 return galaxy_root
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parents:
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381
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382
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parents:
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383 def _find_galaxy_root(ctx, **kwds):
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384 galaxy_root = kwds.get("galaxy_root", None)
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parents:
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385 if galaxy_root:
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386 return galaxy_root
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parents:
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387 elif ctx.global_config.get("galaxy_root", None):
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388 return ctx.global_config["galaxy_root"]
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389 else:
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390 par_dir = os.getcwd()
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391 while True:
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392 run = os.path.join(par_dir, "run.sh")
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393 config = os.path.join(par_dir, "config")
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394 if os.path.isfile(run) and os.path.isdir(config):
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395 return par_dir
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parents:
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396 new_par_dir = os.path.dirname(par_dir)
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397 if new_par_dir == par_dir:
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parents:
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398 break
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399 par_dir = new_par_dir
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400 return None
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parents:
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401
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402
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403 def _find_test_data(tool_paths, **kwds):
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404 path = "."
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405 if len(tool_paths) > 0:
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406 path = tool_paths[0]
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407
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408 # Find test data directory associated with path.
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409 test_data = kwds.get("test_data", None)
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410 if test_data:
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411 return os.path.abspath(test_data)
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412 else:
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413 test_data = _search_tool_path_for(path, "test-data")
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parents:
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414 if test_data:
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parents:
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415 return test_data
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parents:
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416 warn(NO_TEST_DATA_MESSAGE)
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417 return None
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418
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parents:
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419
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420 def _find_tool_data_table(tool_paths, test_data_dir, **kwds):
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421 path = "."
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422 if len(tool_paths) > 0:
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423 path = tool_paths[0]
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424
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425 tool_data_table = kwds.get("tool_data_table", None)
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parents:
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426 if tool_data_table:
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parents:
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427 return os.path.abspath(tool_data_table)
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428 else:
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parents:
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429 extra_paths = [test_data_dir] if test_data_dir else []
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parents:
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430 return _search_tool_path_for(
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parents:
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431 path,
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parents:
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432 "tool_data_table_conf.xml.test",
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parents:
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433 extra_paths,
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parents:
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434 ) or _search_tool_path_for( # if all else fails just use sample
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parents:
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435 path,
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parents:
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436 "tool_data_table_conf.xml.sample"
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parents:
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437 )
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parents:
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438
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parents:
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439
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parents:
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440 def _search_tool_path_for(path, target, extra_paths=[]):
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441 if not os.path.isdir(path):
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442 tool_dir = os.path.dirname(path)
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parents:
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443 else:
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444 tool_dir = path
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parents:
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445 possible_dirs = [tool_dir, "."] + extra_paths
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parents:
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446 for possible_dir in possible_dirs:
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parents:
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447 possible_path = os.path.join(possible_dir, target)
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parents:
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448 if os.path.exists(possible_path):
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parents:
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449 return os.path.abspath(possible_path)
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parents:
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450 return None
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parents:
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451
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parents:
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452
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parents:
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453 def _configure_sheds_config_file(ctx, config_directory, **kwds):
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parents:
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454 if "shed_target" not in kwds:
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parents:
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455 kwds = kwds.copy()
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parents:
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456 kwds["shed_target"] = "toolshed"
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parents:
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457 shed_target_url = tool_shed_url(ctx, **kwds)
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parents:
diff changeset
458 contents = _sub(TOOL_SHEDS_CONF, {"shed_target_url": shed_target_url})
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parents:
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459 tool_sheds_conf = os.path.join(config_directory, "tool_sheds_conf.xml")
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parents:
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460 write_file(tool_sheds_conf, contents)
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parents:
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461 return tool_sheds_conf
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parents:
diff changeset
462
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parents:
diff changeset
463
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parents:
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464 def _tool_conf_entry_for(tool_paths):
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parents:
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465 tool_definitions = ""
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parents:
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466 for tool_path in tool_paths:
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parents:
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467 if os.path.isdir(tool_path):
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parents:
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468 tool_definitions += '''<tool_dir dir="%s" />''' % tool_path
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parents:
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469 else:
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parents:
diff changeset
470 tool_definitions += '''<tool file="%s" />''' % tool_path
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parents:
diff changeset
471 return tool_definitions
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bcclaywell
parents:
diff changeset
472
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bcclaywell
parents:
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473
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parents:
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474 def _shed_tool_conf(install_galaxy, config_directory):
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diff changeset
475 # TODO: There is probably a reason this is split up like this but I have
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parents:
diff changeset
476 # no clue why I did it and not documented on the commit message.
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parents:
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477 if install_galaxy:
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parents:
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478 config_dir = os.path.join(config_directory, "galaxy-dev", "config")
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parents:
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479 else:
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parents:
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480 config_dir = config_directory
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parents:
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481 return os.path.join(config_dir, "shed_tool_conf.xml")
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parents:
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482
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bcclaywell
parents:
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483
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parents:
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484 def _install_galaxy(ctx, config_directory, kwds):
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parents:
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485 if not kwds.get("no_cache_galaxy", False):
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parents:
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486 _install_galaxy_via_git(ctx, config_directory, kwds)
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parents:
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487 else:
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parents:
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488 _install_galaxy_via_download(config_directory, kwds)
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parents:
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489
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bcclaywell
parents:
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490
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parents:
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491 def _install_galaxy_via_download(config_directory, kwds):
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parents:
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492 command = galaxy_run.DOWNLOAD_GALAXY + "; tar -zxvf dev | tail"
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493 _install_with_command(config_directory, command)
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parents:
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494
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parents:
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495
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parents:
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496 def _install_galaxy_via_git(ctx, config_directory, kwds):
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parents:
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497 _ensure_galaxy_repository_available(ctx)
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parents:
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498 workspace = ctx.workspace
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parents:
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499 gx_repo = os.path.join(workspace, "gx_repo")
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parents:
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500 command = git.command_clone(ctx, gx_repo, "galaxy-dev")
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parents:
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501 _install_with_command(config_directory, command)
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parents:
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502
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bcclaywell
parents:
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503
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bcclaywell
parents:
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504 def _build_eggs_cache(ctx, env, kwds):
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505 if kwds.get("no_cache_galaxy", False):
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506 return None
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507 workspace = ctx.workspace
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508 eggs_path = os.path.join(workspace, "gx_eggs")
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509 if not os.path.exists(eggs_path):
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510 os.makedirs(eggs_path)
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parents:
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511 env["GALAXY_EGGS_PATH"] = eggs_path
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512
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parents:
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513
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514 def _install_with_command(config_directory, command):
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515 install_cmds = [
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516 "cd %s" % config_directory,
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517 command,
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518 "cd galaxy-dev",
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519 "type virtualenv >/dev/null 2>&1 && virtualenv .venv",
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520 galaxy_run.ACTIVATE_COMMAND,
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521 ]
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522 shell(";".join(install_cmds))
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523
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524
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525 def _ensure_galaxy_repository_available(ctx):
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526 workspace = ctx.workspace
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527 gx_repo = os.path.join(workspace, "gx_repo")
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528 if os.path.exists(gx_repo):
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529 # Attempt fetch - but don't fail if not interweb, etc...
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parents:
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530 shell("git --git-dir %s fetch >/dev/null 2>&1" % gx_repo)
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parents:
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531 else:
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532 remote_repo = "https://github.com/galaxyproject/galaxy"
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parents:
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533 command = git.command_clone(ctx, remote_repo, gx_repo, bare=True)
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534 shell(command)
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535
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parents:
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536
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parents:
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537 def _build_env_for_galaxy(properties, template_args):
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538 env = {}
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539 for key, value in iteritems(properties):
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540 var = "GALAXY_CONFIG_OVERRIDE_%s" % key.upper()
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parents:
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541 value = _sub(value, template_args)
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542 env[var] = value
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543 return env
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parents:
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544
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parents:
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545
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parents:
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546 def _build_test_env(properties, env):
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547 # Keeping these environment variables around for a little while but they
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parents:
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548 # many are probably not needed as of the following commit.
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parents:
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549 # https://bitbucket.org/galaxy/galaxy-central/commits/d7dd1f9
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550 test_property_variants = {
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551 'GALAXY_TEST_MIGRATED_TOOL_CONF': 'migrated_tools_config',
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552 'GALAXY_TEST_TOOL_CONF': 'tool_config_file',
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parents:
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553 'GALAXY_TEST_FILE_DIR': 'test_data_dir',
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parents:
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554 'GALAXY_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
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parents:
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555 # Next line would be required for tool shed tests.
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parents:
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556 # 'GALAXY_TEST_TOOL_DEPENDENCY_DIR': 'tool_dependency_dir',
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parents:
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557 }
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parents:
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558 for test_key, gx_key in test_property_variants.items():
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559 value = properties.get(gx_key, None)
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560 if value is not None:
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561 env[test_key] = value
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562
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parents:
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563
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564 def _handle_dependency_resolution(config_directory, kwds):
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565 resolutions_strategies = [
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566 "brew_dependency_resolution",
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diff changeset
567 "dependency_resolvers_config_file",
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parents:
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568 "shed_dependency_resolution",
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bcclaywell
parents:
diff changeset
569 ]
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parents:
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570
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parents:
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571 selected_strategies = 0
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parents:
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572 for key in resolutions_strategies:
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parents:
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573 if kwds.get(key):
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parents:
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574 selected_strategies += 1
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parents:
diff changeset
575
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parents:
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576 if selected_strategies > 1:
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parents:
diff changeset
577 message = "At most one option from [%s] may be specified"
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578 raise click.UsageError(message % resolutions_strategies)
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parents:
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579
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parents:
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580 for key in STOCK_DEPENDENCY_RESOLUTION_STRATEGIES:
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parents:
diff changeset
581 if kwds.get(key):
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bcclaywell
parents:
diff changeset
582 resolvers_conf = os.path.join(
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bcclaywell
parents:
diff changeset
583 config_directory,
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bcclaywell
parents:
diff changeset
584 "resolvers_conf.xml"
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bcclaywell
parents:
diff changeset
585 )
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bcclaywell
parents:
diff changeset
586 conf_contents = STOCK_DEPENDENCY_RESOLUTION_STRATEGIES[key]
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parents:
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587 open(resolvers_conf, "w").write(conf_contents)
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bcclaywell
parents:
diff changeset
588 kwds["dependency_resolvers_config_file"] = resolvers_conf
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bcclaywell
parents:
diff changeset
589
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bcclaywell
parents:
diff changeset
590
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bcclaywell
parents:
diff changeset
591 def _handle_job_metrics(config_directory, kwds):
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bcclaywell
parents:
diff changeset
592 metrics_conf = os.path.join(config_directory, "job_metrics_conf.xml")
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parents:
diff changeset
593 open(metrics_conf, "w").write(EMPTY_JOB_METRICS_TEMPLATE)
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parents:
diff changeset
594 kwds["job_metrics_config_file"] = metrics_conf
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bcclaywell
parents:
diff changeset
595
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bcclaywell
parents:
diff changeset
596
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parents:
diff changeset
597 def _handle_kwd_overrides(properties, kwds):
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parents:
diff changeset
598 kwds_gx_properties = [
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parents:
diff changeset
599 'job_config_file',
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parents:
diff changeset
600 'job_metrics_config_file',
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parents:
diff changeset
601 'dependency_resolvers_config_file',
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parents:
diff changeset
602 'tool_dependency_dir',
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parents:
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603 ]
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parents:
diff changeset
604 for prop in kwds_gx_properties:
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parents:
diff changeset
605 val = kwds.get(prop, None)
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parents:
diff changeset
606 if val:
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parents:
diff changeset
607 properties[prop] = val
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bcclaywell
parents:
diff changeset
608
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bcclaywell
parents:
diff changeset
609
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bcclaywell
parents:
diff changeset
610 def _sub(template, args):
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bcclaywell
parents:
diff changeset
611 if template is None:
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bcclaywell
parents:
diff changeset
612 return ''
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parents:
diff changeset
613 return Template(template).safe_substitute(args)
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parents:
diff changeset
614
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parents:
diff changeset
615 __all__ = ["galaxy_config"]