Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/deps/containers.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import collections
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2 import logging
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3 import os
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4
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5 from galaxy.util import (
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6 asbool,
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7 plugin_config
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8 )
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9 from .container_classes import (
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10 CONTAINER_CLASSES,
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11 DOCKER_CONTAINER_TYPE,
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12 NULL_CONTAINER,
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13 SINGULARITY_CONTAINER_TYPE,
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14 )
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15 from .container_resolvers import ResolutionCache
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16 from .container_resolvers.explicit import (
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17 ExplicitContainerResolver,
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18 ExplicitSingularityContainerResolver,
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19 )
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20 from .container_resolvers.mulled import (
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21 BuildMulledDockerContainerResolver,
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22 BuildMulledSingularityContainerResolver,
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23 CachedMulledDockerContainerResolver,
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24 CachedMulledSingularityContainerResolver,
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25 MulledDockerContainerResolver,
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26 MulledSingularityContainerResolver,
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27 )
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28 from .requirements import (
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29 ContainerDescription,
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30 )
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31
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32 log = logging.getLogger(__name__)
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33
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34
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35 DEFAULT_CONTAINER_TYPE = DOCKER_CONTAINER_TYPE
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36 ALL_CONTAINER_TYPES = [DOCKER_CONTAINER_TYPE, SINGULARITY_CONTAINER_TYPE]
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37
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38 ResolvedContainerDescription = collections.namedtuple('ResolvedContainerDescription', ['container_resolver', 'container_description'])
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39
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40
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41 class ContainerFinder(object):
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42
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43 def __init__(self, app_info, mulled_resolution_cache=None):
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44 self.app_info = app_info
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45 self.container_registry = ContainerRegistry(app_info, mulled_resolution_cache=mulled_resolution_cache)
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46
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47 def _enabled_container_types(self, destination_info):
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48 return [t for t in ALL_CONTAINER_TYPES if self.__container_type_enabled(t, destination_info)]
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49
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50 def find_best_container_description(self, enabled_container_types, tool_info, **kwds):
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51 """Regardless of destination properties - find best container for tool.
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52
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53 Given container types and container.ToolInfo description of the tool."""
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54 return self.container_registry.find_best_container_description(enabled_container_types, tool_info, **kwds)
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55
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56 def resolve(self, enabled_container_types, tool_info, **kwds):
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57 """Regardless of destination properties - find ResolvedContainerDescription for tool."""
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58 return self.container_registry.resolve(enabled_container_types, tool_info, **kwds)
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59
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60 def find_container(self, tool_info, destination_info, job_info):
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61 enabled_container_types = self._enabled_container_types(destination_info)
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62
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63 # Short-cut everything else and just skip checks if no container type is enabled.
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64 if not enabled_container_types:
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65 return NULL_CONTAINER
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66
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67 def __destination_container(container_description=None, container_id=None, container_type=None):
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68 if container_description:
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69 container_id = container_description.identifier
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70 container_type = container_description.type
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71 container = self.__destination_container(
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72 container_id,
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73 container_type,
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74 tool_info,
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75 destination_info,
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76 job_info,
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77 container_description,
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78 )
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79 return container
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80
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81 def container_from_description_from_dicts(destination_container_dicts):
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82 for destination_container_dict in destination_container_dicts:
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83 container_description = ContainerDescription.from_dict(destination_container_dict)
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84 if container_description:
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85 container = __destination_container(container_description)
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86 if container:
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87 return container
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88
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89 if "container_override" in destination_info:
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90 container = container_from_description_from_dicts(destination_info["container_override"])
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91 if container:
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92 return container
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93
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94 # If destination forcing Galaxy to use a particular container do it,
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95 # this is likely kind of a corner case. For instance if deployers
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96 # do not trust the containers annotated in tools.
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97 for container_type in CONTAINER_CLASSES.keys():
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98 container_id = self.__overridden_container_id(container_type, destination_info)
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99 if container_id:
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100 container = __destination_container(container_type=container_type, container_id=container_id)
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101 if container:
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102 return container
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103
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104 # Otherwise lets see if we can find container for the tool.
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105 container_description = self.find_best_container_description(enabled_container_types, tool_info)
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106 container = __destination_container(container_description)
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107 if container:
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108 return container
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109
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110 # If we still don't have a container, check to see if any container
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111 # types define a default container id and use that.
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112 if "container" in destination_info:
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113 container = container_from_description_from_dicts(destination_info["container"])
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114 if container:
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115 return container
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116
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117 for container_type in CONTAINER_CLASSES.keys():
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118 container_id = self.__default_container_id(container_type, destination_info)
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119 if container_id:
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120 container = __destination_container(container_type=container_type, container_id=container_id)
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121 if container:
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122 return container
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123
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124 return NULL_CONTAINER
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125
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126 def resolution_cache(self):
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127 cache = ResolutionCache()
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128 if self.container_registry.mulled_resolution_cache is not None:
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129 cache.mulled_resolution_cache = self.container_registry.mulled_resolution_cache
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130 return cache
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131
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132 def __overridden_container_id(self, container_type, destination_info):
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133 if not self.__container_type_enabled(container_type, destination_info):
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134 return None
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135 if "%s_container_id_override" % container_type in destination_info:
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136 return destination_info.get("%s_container_id_override" % container_type)
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137 if "%s_image_override" % container_type in destination_info:
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138 return self.__build_container_id_from_parts(container_type, destination_info, mode="override")
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139
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140 def __build_container_id_from_parts(self, container_type, destination_info, mode):
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141 repo = ""
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142 owner = ""
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143 repo_key = "%s_repo_%s" % (container_type, mode)
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144 owner_key = "%s_owner_%s" % (container_type, mode)
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145 if repo_key in destination_info:
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146 repo = destination_info[repo_key] + "/"
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147 if owner_key in destination_info:
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148 owner = destination_info[owner_key] + "/"
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149 cont_id = repo + owner + destination_info["%s_image_%s" % (container_type, mode)]
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150 tag_key = "%s_tag_%s" % (container_type, mode)
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151 if tag_key in destination_info:
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152 cont_id += ":" + destination_info[tag_key]
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153 return cont_id
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154
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155 def __default_container_id(self, container_type, destination_info):
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156 if not self.__container_type_enabled(container_type, destination_info):
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157 return None
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158 key = "%s_default_container_id" % container_type
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159 # Also allow docker_image...
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160 if key not in destination_info:
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161 key = "%s_image" % container_type
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162 if key in destination_info:
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163 return destination_info.get(key)
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164 elif "%s_image_default" % container_type in destination_info:
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165 return self.__build_container_id_from_parts(container_type, destination_info, mode="default")
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166 return None
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167
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168 def __destination_container(self, container_id, container_type, tool_info, destination_info, job_info, container_description=None):
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169 # TODO: ensure destination_info is dict-like
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170 if not self.__container_type_enabled(container_type, destination_info):
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171 return NULL_CONTAINER
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172
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173 # TODO: Right now this assumes all containers available when a
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174 # container type is - there should be more thought put into this.
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175 # Checking which are available - settings policies for what can be
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176 # auto-fetched, etc....
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177 return CONTAINER_CLASSES[container_type](container_id, self.app_info, tool_info, destination_info, job_info, container_description)
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178
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179 def __container_type_enabled(self, container_type, destination_info):
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180 return asbool(destination_info.get("%s_enabled" % container_type, False))
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181
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182
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183 class NullContainerFinder(object):
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184
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185 def find_container(self, tool_info, destination_info, job_info):
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186 return []
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187
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188
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189 class ContainerRegistry(object):
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190 """Loop through enabled ContainerResolver plugins and find first match."""
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191
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192 def __init__(self, app_info, mulled_resolution_cache=None):
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193 self.resolver_classes = self.__resolvers_dict()
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194 self.enable_mulled_containers = app_info.enable_mulled_containers
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195 self.app_info = app_info
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196 self.container_resolvers = self.__build_container_resolvers(app_info)
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197 self.mulled_resolution_cache = mulled_resolution_cache
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198
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199 def __build_container_resolvers(self, app_info):
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200 conf_file = getattr(app_info, 'containers_resolvers_config_file', None)
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201 if not conf_file:
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202 return self.__default_containers_resolvers()
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203 if not os.path.exists(conf_file):
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204 log.debug("Unable to find config file '%s'", conf_file)
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205 return self.__default_containers_resolvers()
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206 plugin_source = plugin_config.plugin_source_from_path(conf_file)
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207 return self._parse_resolver_conf(plugin_source)
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208
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209 def _parse_resolver_conf(self, plugin_source):
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210 extra_kwds = {
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211 'app_info': self.app_info
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212 }
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213 return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds)
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214
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215 def __default_containers_resolvers(self):
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216 default_resolvers = [
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217 ExplicitContainerResolver(self.app_info),
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218 ExplicitSingularityContainerResolver(self.app_info),
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219 ]
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220 if self.enable_mulled_containers:
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221 default_resolvers.extend([
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222 CachedMulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
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223 CachedMulledDockerContainerResolver(self.app_info, namespace="local"),
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224 CachedMulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
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225 CachedMulledSingularityContainerResolver(self.app_info, namespace="local"),
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226 MulledDockerContainerResolver(self.app_info, namespace="biocontainers"),
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227 MulledSingularityContainerResolver(self.app_info, namespace="biocontainers"),
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228 BuildMulledDockerContainerResolver(self.app_info),
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229 BuildMulledSingularityContainerResolver(self.app_info),
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230 ])
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231 return default_resolvers
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232
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233 def __resolvers_dict(self):
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234 import galaxy.tool_util.deps.container_resolvers
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235 return plugin_config.plugins_dict(galaxy.tool_util.deps.container_resolvers, 'resolver_type')
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236
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237 def find_best_container_description(self, enabled_container_types, tool_info, **kwds):
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238 """Yield best container description of supplied types matching tool info."""
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239 try:
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240 resolved_container_description = self.resolve(enabled_container_types, tool_info, **kwds)
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241 except Exception:
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242 log.exception("Could not get container description for tool '%s'", tool_info.tool_id)
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243 return None
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244 return None if resolved_container_description is None else resolved_container_description.container_description
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245
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246 def resolve(self, enabled_container_types, tool_info, index=None, resolver_type=None, install=True, resolution_cache=None):
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247 for i, container_resolver in enumerate(self.container_resolvers):
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248 if index is not None and i != index:
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249 continue
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250
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251 if resolver_type is not None and resolver_type != container_resolver.resolver_type:
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252 continue
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253
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254 if hasattr(container_resolver, "container_type"):
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255 if container_resolver.container_type not in enabled_container_types:
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256 continue
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257
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258 if not install and container_resolver.builds_on_resolution:
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259 continue
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260
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261 container_description = container_resolver.resolve(enabled_container_types, tool_info, resolution_cache=resolution_cache)
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262 log.info("Checking with container resolver [%s] found description [%s]" % (container_resolver, container_description))
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263 if container_description:
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264 assert container_description.type in enabled_container_types
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265 return ResolvedContainerDescription(container_resolver, container_description)
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266
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267 return None