Mercurial > repos > shellac > sam_consensus_v3

annotate env/lib/python3.9/site-packages/planemo/galaxy/profiles.py @ 0:4f3585e2f14b draft default tip

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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
date Mon, 22 Mar 2021 18:12:50 +0000
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1 """This modules describes the abstraction of a Galaxy profile.
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2
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3 This is a workspace with a specific default configuration and shed
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4 tool setup. It is meant to be used with various serve commands.
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5 """
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6 import json
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7 import os
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8 import shutil
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9
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10 from galaxy.util.commands import which
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11
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12 from planemo.database import create_database_source
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13 from planemo.galaxy.api import test_credentials_valid
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14 from .config import DATABASE_LOCATION_TEMPLATE
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15
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16 PROFILE_OPTIONS_JSON_NAME = "planemo_profile_options.json"
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17 ALREADY_EXISTS_EXCEPTION = "Cannot create profile with name [%s], directory [%s] already exists."
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18
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19
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20 def profile_exists(ctx, profile_name, **kwds):
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21 """Return a truthy value iff the specified profile already exists."""
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22 profile_directory = _profile_directory(ctx, profile_name)
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23 return os.path.exists(profile_directory)
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24
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25
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26 def list_profiles(ctx, **kwds):
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27 """Return a list of current profile names."""
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28 return os.listdir(ctx.galaxy_profiles_directory)
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29
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30
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31 def delete_profile(ctx, profile_name, **kwds):
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32 """Delete profile with the specified name."""
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33 profile_directory = _profile_directory(ctx, profile_name)
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34 profile_options = _read_profile_options(profile_directory)
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35 profile_options, profile_options_path = _load_profile_to_json(ctx, profile_name)
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36 if profile_options["engine"] != 'external_galaxy':
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37 database_type = profile_options.get("database_type")
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38 kwds["database_type"] = database_type
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39 if database_type != "sqlite":
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40 database_source = create_database_source(**kwds)
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41 database_identifier = _profile_to_database_identifier(profile_name)
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42 database_source.delete_database(
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43 database_identifier,
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44 )
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45 shutil.rmtree(profile_directory)
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46
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47
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48 def create_profile(ctx, profile_name, **kwds):
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49 """Create a profile with the specified name."""
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50 engine_type = kwds.get("engine", "galaxy")
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51 profile_directory = _profile_directory(ctx, profile_name)
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52 if profile_exists(ctx, profile_name, **kwds):
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53 message = ALREADY_EXISTS_EXCEPTION % (
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54 profile_name, profile_directory
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55 )
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56 raise Exception(message)
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57
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58 os.makedirs(profile_directory)
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59
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60 if engine_type == "docker_galaxy":
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61 create_for_engine = _create_profile_docker
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62 elif engine_type == "external_galaxy" or kwds.get("galaxy_url"):
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63 create_for_engine = _create_profile_external
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64 else:
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65 create_for_engine = _create_profile_local
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66
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67 stored_profile_options = create_for_engine(ctx, profile_directory, profile_name, kwds)
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68
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69 profile_options_path = _stored_profile_options_path(profile_directory)
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70 with open(profile_options_path, "w") as f:
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71 json.dump(stored_profile_options, f)
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72
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73
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74 def _create_profile_docker(ctx, profile_directory, profile_name, kwds):
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75 export_directory = os.path.join(profile_directory, "export")
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76 os.makedirs(export_directory)
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77 return {
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78 "engine": "docker_galaxy",
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79 }
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80
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81
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82 def _create_profile_local(ctx, profile_directory, profile_name, kwds):
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83 database_type = kwds.get("database_type", "auto")
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84 if database_type == "auto":
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85 if which("psql"):
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86 database_type = "postgres"
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87 elif which("docker"):
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88 database_type = "postgres_docker"
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89 else:
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90 database_type = "sqlite"
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91
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92 if database_type != "sqlite":
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93 database_source = create_database_source(**kwds)
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94 database_identifier = _profile_to_database_identifier(profile_name)
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95 database_source.create_database(
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96 database_identifier,
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97 )
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98 database_connection = database_source.sqlalchemy_url(database_identifier)
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99 else:
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100 database_location = os.path.join(profile_directory, "galaxy.sqlite")
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101 database_connection = DATABASE_LOCATION_TEMPLATE % database_location
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102
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103 return {
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104 "database_type": database_type,
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105 "database_connection": database_connection,
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106 "engine": "galaxy",
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107 }
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108
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109
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110 def _create_profile_external(ctx, profile_directory, profile_name, kwds):
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111 url = kwds.get("galaxy_url")
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112 api_key = kwds.get("galaxy_admin_key") or kwds.get("galaxy_user_key")
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113 if test_credentials_valid(url=url, key=api_key, is_admin=kwds.get("galaxy_admin_key")):
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114 return {
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115 "galaxy_url": url,
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116 "galaxy_user_key": kwds.get("galaxy_user_key"),
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117 "galaxy_admin_key": kwds.get("galaxy_admin_key"),
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118 "engine": "external_galaxy",
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119 }
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120 else:
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121 raise ConnectionError('The credentials provided for an external Galaxy instance are not valid.')
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122
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123
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124 def ensure_profile(ctx, profile_name, **kwds):
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125 """Ensure a Galaxy profile exists and return profile defaults."""
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126 if not profile_exists(ctx, profile_name, **kwds):
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127 create_profile(ctx, profile_name, **kwds)
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128
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129 return _profile_options(ctx, profile_name, **kwds)
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130
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131
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132 def create_alias(ctx, alias, obj, profile_name, **kwds):
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133 profile_options, profile_options_path = _load_profile_to_json(ctx, profile_name)
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134
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135 if profile_options.get('aliases'):
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136 profile_options['aliases'][alias] = obj
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137 else: # no aliases yet defined
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138 profile_options['aliases'] = {alias: obj}
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139
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140 with open(profile_options_path, 'w') as f:
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141 json.dump(profile_options, f)
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142
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143 return 0
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144
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145
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146 def list_alias(ctx, profile_name, **kwds):
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147 profile_options, _ = _load_profile_to_json(ctx, profile_name)
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148 return profile_options.get('aliases', {})
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149
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150
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151 def delete_alias(ctx, alias, profile_name, **kwds):
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152 profile_options, profile_options_path = _load_profile_to_json(ctx, profile_name)
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153 if alias not in profile_options.get('aliases', {}):
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154 return 1
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155 else:
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156 del profile_options['aliases'][alias]
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157
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158 with open(profile_options_path, 'w') as f:
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159 json.dump(profile_options, f)
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160
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161 return 0
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162
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163
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164 def translate_alias(ctx, alias, profile_name):
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165 if not profile_name:
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166 return alias
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167 aliases = _load_profile_to_json(ctx, profile_name)[0].get('aliases', {})
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168 return aliases.get(alias, alias)
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169
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170
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171 def _load_profile_to_json(ctx, profile_name):
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172 if not profile_exists(ctx, profile_name):
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173 raise Exception("That profile does not exist. Create it with `planemo profile_create`")
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174 profile_directory = _profile_directory(ctx, profile_name)
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175 profile_options_path = _stored_profile_options_path(profile_directory)
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176 with open(profile_options_path) as f:
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177 profile_options = json.load(f)
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178 return profile_options, profile_options_path
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179
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180
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181 def _profile_options(ctx, profile_name, **kwds):
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182 profile_directory = _profile_directory(ctx, profile_name)
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183 profile_options = _read_profile_options(profile_directory)
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184
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185 if profile_options["engine"] == "docker_galaxy":
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186 engine_options = dict(
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187 export_directory=os.path.join(profile_directory, "export")
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188 )
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189 else:
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190 file_path = os.path.join(profile_directory, "files")
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191 shed_tool_path = os.path.join(profile_directory, "shed_tools")
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192 shed_tool_conf = os.path.join(profile_directory, "shed_tool_conf.xml")
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193 tool_dependency_dir = os.path.join(profile_directory, "deps")
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194
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195 engine_options = dict(
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196 file_path=file_path,
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197 tool_dependency_dir=tool_dependency_dir,
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198 shed_tool_conf=shed_tool_conf,
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199 shed_tool_path=shed_tool_path,
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200 galaxy_brand=profile_name,
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201 )
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202 profile_options.update(engine_options)
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203 profile_options["galaxy_brand"] = profile_name
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204 return profile_options
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205
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206
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207 def _profile_to_database_identifier(profile_name):
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208 char_lst = [c if c.isalnum() else "_" for c in profile_name]
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209 return "plnmoprof_%s" % "".join(char_lst)
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210
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211
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212 def _read_profile_options(profile_directory):
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213 profile_options_path = _stored_profile_options_path(profile_directory)
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214 with open(profile_options_path, "r") as f:
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215 profile_options = json.load(f)
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216 return profile_options
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217
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218
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219 def _stored_profile_options_path(profile_directory):
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220 profile_options_path = os.path.join(
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221 profile_directory, PROFILE_OPTIONS_JSON_NAME
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222 )
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223 return profile_options_path
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224
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225
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226 def _profile_directory(ctx, profile_name):
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227 return os.path.join(ctx.galaxy_profiles_directory, profile_name)
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228
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229
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230 __all__ = (
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231 "create_profile",
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232 "delete_profile",
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233 "ensure_profile",
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234 "list_profiles",
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235 )