Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/container_resolvers/explicit.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """This module describes the :class:`ExplicitContainerResolver` ContainerResolver plugin.""" |
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2 import logging |
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3 |
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4 from ..container_resolvers import ( |
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5 ContainerResolver, |
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6 ) |
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7 from ..requirements import ContainerDescription |
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8 |
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9 log = logging.getLogger(__name__) |
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10 |
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11 DEFAULT_SHELL = "/bin/bash" |
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12 |
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13 |
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14 class ExplicitContainerResolver(ContainerResolver): |
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15 """Find explicit containers referenced in the tool description (e.g. tool XML file) if present.""" |
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16 |
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17 resolver_type = "explicit" |
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18 |
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19 def resolve(self, enabled_container_types, tool_info, **kwds): |
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20 """Find a container explicitly mentioned in tool description. |
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21 |
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22 This ignores the tool requirements and assumes the tool author crafted |
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23 a correct container. |
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24 """ |
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25 for container_description in tool_info.container_descriptions: |
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26 if self._container_type_enabled(container_description, enabled_container_types): |
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27 container_description.explicit = True |
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28 return container_description |
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29 |
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30 return None |
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31 |
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32 |
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33 class ExplicitSingularityContainerResolver(ExplicitContainerResolver): |
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34 |
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35 resolver_type = 'explicit_singularity' |
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36 container_type = 'singularity' |
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37 |
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38 def resolve(self, enabled_container_types, tool_info, **kwds): |
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39 """Find a container explicitly mentioned in tool description. |
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40 |
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41 This ignores the tool requirements and assumes the tool author crafted |
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42 a correct container. We use singularity here to fetch docker containers, |
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43 hence the container_description hack here. |
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44 """ |
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45 for container_description in tool_info.container_descriptions: |
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46 if container_description.type == 'docker': |
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47 desc_dict = container_description.to_dict() |
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48 desc_dict['type'] = self.container_type |
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49 desc_dict['identifier'] = "docker://%s" % container_description.identifier |
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50 container_description = container_description.from_dict(desc_dict) |
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51 if self._container_type_enabled(container_description, enabled_container_types): |
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52 return container_description |
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53 |
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54 return None |
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55 |
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56 |
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57 class BaseAdminConfiguredContainerResolver(ContainerResolver): |
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58 |
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59 def __init__(self, app_info=None, shell=DEFAULT_SHELL, **kwds): |
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60 super().__init__(app_info, **kwds) |
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61 self.shell = shell |
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62 |
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63 def _container_description(self, identifier, container_type): |
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64 container_description = ContainerDescription( |
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65 identifier, |
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66 type=container_type, |
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67 shell=self.shell, |
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68 ) |
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69 return container_description |
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70 |
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71 |
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72 class FallbackContainerResolver(BaseAdminConfiguredContainerResolver): |
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73 """Specify an explicit, identified container as a Docker container resolver.""" |
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74 |
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75 resolver_type = "fallback" |
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76 container_type = 'docker' |
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77 |
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78 def __init__(self, app_info=None, identifier="", **kwds): |
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79 super().__init__(app_info, **kwds) |
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80 assert identifier, "fallback container resolver must be specified with non-empty identifier" |
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81 self.identifier = identifier |
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82 |
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83 def _match(self, enabled_container_types, tool_info, container_description): |
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84 if self._container_type_enabled(container_description, enabled_container_types): |
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85 return True |
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86 return False |
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87 |
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88 def resolve(self, enabled_container_types, tool_info, **kwds): |
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89 container_description = self._container_description(self.identifier, self.container_type) |
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90 if self._match(enabled_container_types, tool_info, container_description): |
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91 return container_description |
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92 |
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93 |
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94 class FallbackSingularityContainerResolver(FallbackContainerResolver): |
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95 """Specify an explicit, identified container as a Singularity container resolver.""" |
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96 |
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97 resolver_type = "fallback_singularity" |
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98 container_type = 'singularity' |
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99 |
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100 |
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101 class FallbackNoRequirementsContainerResolver(FallbackContainerResolver): |
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102 |
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103 resolver_type = "fallback_no_requirements" |
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104 |
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105 def _match(self, enabled_container_types, tool_info, container_description): |
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106 type_matches = super()._match(enabled_container_types, tool_info, container_description) |
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107 return type_matches and (tool_info.requirements is None or len(tool_info.requirements) == 0) |
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108 |
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109 |
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110 class FallbackNoRequirementsSingularityContainerResolver(FallbackNoRequirementsContainerResolver): |
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111 |
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112 resolver_type = "fallback_no_requirements_singularity" |
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113 container_type = 'singularity' |
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114 |
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115 |
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116 class RequiresGalaxyEnvironmentContainerResolver(FallbackContainerResolver): |
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117 |
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118 resolver_type = "requires_galaxy_environment" |
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119 |
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120 def _match(self, enabled_container_types, tool_info, container_description): |
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121 type_matches = super()._match(enabled_container_types, tool_info, container_description) |
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122 return type_matches and tool_info.requires_galaxy_python_environment |
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123 |
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124 |
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125 class RequiresGalaxyEnvironmentSingularityContainerResolver(RequiresGalaxyEnvironmentContainerResolver): |
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126 |
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127 resolver_type = "requires_galaxy_environment_singularity" |
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128 container_type = 'singularity' |
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129 |
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130 |
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131 class MappingContainerResolver(BaseAdminConfiguredContainerResolver): |
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132 resolver_type = "mapping" |
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133 |
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134 def __init__(self, app_info=None, **kwds): |
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135 super().__init__(app_info, **kwds) |
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136 mappings = self.resolver_kwds["mappings"] |
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137 assert isinstance(mappings, list), "mapping container resolver must be specified with mapping list" |
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138 self.mappings = mappings |
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139 |
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140 def resolve(self, enabled_container_types, tool_info, **kwds): |
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141 tool_id = tool_info.tool_id |
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142 # If resolving against dependencies and not a specific tool, skip over this resolver |
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143 if not tool_id: |
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144 return |
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145 |
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146 tool_version = tool_info.tool_version |
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147 |
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148 for mapping in self.mappings: |
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149 if mapping.get("tool_id") != tool_id: |
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150 continue |
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151 |
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152 mapping_tool_version = mapping.get("tool_version") |
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153 if mapping_tool_version is not None and tool_version != mapping_tool_version: |
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154 continue |
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155 |
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156 container_description = self._container_description(mapping["identifier"], mapping.get("container_type")) |
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157 if not self._container_type_enabled(container_description, enabled_container_types): |
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158 continue |
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159 return container_description |
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160 |
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161 |
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162 __all__ = ( |
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163 "ExplicitContainerResolver", |
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164 "ExplicitSingularityContainerResolver", |
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165 "FallbackContainerResolver", |
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166 "FallbackSingularityContainerResolver", |
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167 "FallbackNoRequirementsContainerResolver", |
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168 "FallbackNoRequirementsSingularityContainerResolver", |
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169 "MappingContainerResolver", |
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170 "RequiresGalaxyEnvironmentContainerResolver", |
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171 "RequiresGalaxyEnvironmentSingularityContainerResolver", |
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172 ) |