Mercurial > repos > shellac > guppy_basecaller

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

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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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.tool_util.deps.commands import which
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11
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12 from planemo.config import (
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13 OptionSource,
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14 )
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15 from planemo.database import create_database_source
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16 from .config import DATABASE_LOCATION_TEMPLATE
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17
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18 PROFILE_OPTIONS_JSON_NAME = "planemo_profile_options.json"
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19 ALREADY_EXISTS_EXCEPTION = "Cannot create profile with name [%s], directory [%s] already exists."
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20
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21
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22 def profile_exists(ctx, profile_name, **kwds):
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23 """Return a truthy value iff the specified profile already exists."""
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24 profile_directory = _profile_directory(ctx, profile_name)
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25 return os.path.exists(profile_directory)
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26
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27
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28 def list_profiles(ctx, **kwds):
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29 """Return a list of current profile names."""
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30 return os.listdir(ctx.galaxy_profiles_directory)
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31
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32
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33 def delete_profile(ctx, profile_name, **kwds):
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34 """Delete profile with the specified name."""
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35 profile_directory = _profile_directory(ctx, profile_name)
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36 profile_options = _read_profile_options(profile_directory)
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37 database_type = profile_options.get("database_type")
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38 if database_type != "sqlite":
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39 database_source = create_database_source(**kwds)
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40 database_identifier = _profile_to_database_identifier(profile_name)
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41 database_source.delete_database(
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42 database_identifier,
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43 )
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44 shutil.rmtree(profile_directory)
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45
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46
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47 def create_profile(ctx, profile_name, **kwds):
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48 """Create a profile with the specified name."""
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49 engine_type = kwds.get("engine", "galaxy")
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50 profile_directory = _profile_directory(ctx, profile_name)
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51 if profile_exists(ctx, profile_name, **kwds):
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52 message = ALREADY_EXISTS_EXCEPTION % (
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53 profile_name, profile_directory
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54 )
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55 raise Exception(message)
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56
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57 os.makedirs(profile_directory)
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58 create_for_engine = _create_profile_docker if engine_type == "docker_galaxy" else _create_profile_local
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59 stored_profile_options = create_for_engine(ctx, profile_directory, profile_name, kwds)
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60
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61 profile_options_path = _stored_profile_options_path(profile_directory)
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62 with open(profile_options_path, "w") as f:
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63 json.dump(stored_profile_options, f)
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64
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65
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66 def _create_profile_docker(ctx, profile_directory, profile_name, kwds):
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67 export_directory = os.path.join(profile_directory, "export")
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68 os.makedirs(export_directory)
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69 return {
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70 "engine": "docker_galaxy",
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71 }
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72
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73
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74 def _create_profile_local(ctx, profile_directory, profile_name, kwds):
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75 database_type = kwds.get("database_type", "auto")
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76 if database_type == "auto":
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77 if which("psql"):
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78 database_type = "postgres"
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79 elif which("docker"):
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80 database_type = "postgres_docker"
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81 else:
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82 database_type = "sqlite"
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83
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84 if database_type != "sqlite":
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85 database_source = create_database_source(**kwds)
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86 database_identifier = _profile_to_database_identifier(profile_name)
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87 database_source.create_database(
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88 database_identifier,
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89 )
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90 database_connection = database_source.sqlalchemy_url(database_identifier)
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91 else:
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92 database_location = os.path.join(profile_directory, "galaxy.sqlite")
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93 database_connection = DATABASE_LOCATION_TEMPLATE % database_location
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94
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95 return {
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96 "database_type": database_type,
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97 "database_connection": database_connection,
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98 "engine": "galaxy",
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99 }
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100
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101
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102 def ensure_profile(ctx, profile_name, **kwds):
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103 """Ensure a Galaxy profile exists and return profile defaults."""
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104 if not profile_exists(ctx, profile_name, **kwds):
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105 create_profile(ctx, profile_name, **kwds)
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106
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107 return _profile_options(ctx, profile_name, **kwds)
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108
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109
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110 def _profile_options(ctx, profile_name, **kwds):
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111 profile_directory = _profile_directory(ctx, profile_name)
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112 profile_options = _read_profile_options(profile_directory)
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113 specified_engine_type = kwds.get("engine", "galaxy")
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114 profile_engine_type = profile_options["engine"]
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115 if specified_engine_type != profile_engine_type:
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116 if ctx.get_option_source("engine") == OptionSource.cli:
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117 raise Exception("Configured profile engine type [%s] does not match specified engine type [%s].")
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118
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119 if profile_engine_type == "docker_galaxy":
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120 engine_options = dict(
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121 export_directory=os.path.join(profile_directory, "export")
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122 )
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123 else:
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124 file_path = os.path.join(profile_directory, "files")
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125 shed_tool_path = os.path.join(profile_directory, "shed_tools")
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126 shed_tool_conf = os.path.join(profile_directory, "shed_tool_conf.xml")
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127 tool_dependency_dir = os.path.join(profile_directory, "deps")
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128
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129 engine_options = dict(
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130 file_path=file_path,
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131 tool_dependency_dir=tool_dependency_dir,
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132 shed_tool_conf=shed_tool_conf,
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133 shed_tool_path=shed_tool_path,
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134 galaxy_brand=profile_name,
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135 )
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136 profile_options.update(engine_options)
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137 profile_options["galaxy_brand"] = profile_name
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138 return profile_options
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139
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140
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141 def _profile_to_database_identifier(profile_name):
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142 char_lst = [c if c.isalnum() else "_" for c in profile_name]
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143 return "plnmoprof_%s" % "".join(char_lst)
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144
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145
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146 def _read_profile_options(profile_directory):
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147 profile_options_path = _stored_profile_options_path(profile_directory)
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148 with open(profile_options_path, "r") as f:
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149 profile_options = json.load(f)
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150 return profile_options
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151
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152
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153 def _stored_profile_options_path(profile_directory):
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154 profile_options_path = os.path.join(
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155 profile_directory, PROFILE_OPTIONS_JSON_NAME
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156 )
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157 return profile_options_path
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158
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159
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160 def _profile_directory(ctx, profile_name):
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161 return os.path.join(ctx.galaxy_profiles_directory, profile_name)
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162
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163
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164 __all__ = (
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165 "create_profile",
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166 "delete_profile",
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167 "ensure_profile",
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168 "list_profiles",
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169 )