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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/deps/views.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 from galaxy import exceptions
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2 from galaxy.util import asbool, listify
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3 from .dependencies import ToolInfo
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4 from .resolvers import (
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5 ContainerDependency,
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6 NullDependency,
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7 )
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8
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9
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10 class DependencyResolversView(object):
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11 """ Provide a RESTfulish/JSONy interface to a galaxy.tool_util.deps.DependencyResolver
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12 object. This can be adapted by the Galaxy web framework or other web apps.
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13 """
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14
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15 def __init__(self, app):
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16 self._app = app
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17
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18 def index(self):
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19 return [r.to_dict() for r in self._dependency_resolvers]
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20
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21 def show(self, index):
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22 return self._dependency_resolver(index).to_dict()
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23
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24 def reload(self):
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25 self.toolbox.reload_dependency_manager()
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26
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27 def manager_requirements(self):
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28 requirements = []
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29 for index, resolver in enumerate(self._dependency_resolvers):
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30 if not hasattr(resolver, "list_dependencies"):
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31 continue
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32 for requirement in resolver.list_dependencies():
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33 requirements.append({"index": index, "requirement": requirement.to_dict()})
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34 return requirements
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35
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36 def resolver_requirements(self, index):
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37 requirements = []
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38 resolver = self._dependency_resolver(index)
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39 if not hasattr(resolver, "list_dependencies"):
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40 raise exceptions.NotImplemented()
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41 for requirement in resolver.list_dependencies():
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42 requirements.append(requirement.to_dict())
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43 return requirements
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44
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45 def manager_dependency(self, **kwds):
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46 return self._dependency(**kwds)
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47
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48 def resolver_dependency(self, index, **kwds):
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49 return self._dependency(**kwds)
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50
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51 def show_dependencies(self, tool_requirements_d, installed_tool_dependencies=None, **kwd):
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52 """
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53 Resolves dependencies to build a requirements status in the admin panel/API
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54 """
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55 to_deps_kwds = {
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56 'install': False,
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57 'return_null': True,
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58 'installed_tool_dependencies': installed_tool_dependencies
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59 }
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60 to_deps_kwds.update(kwd)
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61 dependencies_per_tool = {tool: self._dependency_manager.requirements_to_dependencies(requirements,
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62 **to_deps_kwds)
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63 for tool, requirements in tool_requirements_d.items()}
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64 return dependencies_per_tool
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65
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66 def uninstall_dependencies(self, index=None, resolver_type=None, container_type=None, **payload):
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67 """Attempt to uninstall requirements. Returns 0 if successfull, else None."""
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68 requirements = payload.get('requirements')
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69 if not requirements:
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70 return None
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71 if index:
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72 resolver = self._dependency_resolvers[index]
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73 if resolver.can_uninstall_dependencies:
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74 return resolver.uninstall(requirements)
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75 elif resolver_type:
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76 for resolver in self._dependency_resolvers:
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77 if resolver.resolver_type == resolver_type and resolver.can_uninstall_dependencies:
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78 return resolver.uninstall(requirements)
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79 elif container_type:
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80 for resolver in self._dependency_resolvers:
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81 if getattr(resolver, "container_type", None) == container_type and resolver.can_uninstall_dependencies:
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82 return resolver.uninstall(requirements)
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83 else:
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84 for index in self.uninstallable_resolvers:
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85 return_code = self._dependency_resolvers[index].uninstall(requirements)
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86 if return_code == 0:
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87 return return_code
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88 return None
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89
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90 @property
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91 def unused_dependency_paths(self):
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92 """List dependencies that are not currently installed."""
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93 unused_dependencies = []
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94 toolbox_requirements_status = self.toolbox_requirements_status
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95 for resolver in self._dependency_resolvers:
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96 if hasattr(resolver, 'unused_dependency_paths'):
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97 unused_dependencies.extend(resolver.unused_dependency_paths(toolbox_requirements_status))
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98 return set(unused_dependencies)
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99
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100 def remove_unused_dependency_paths(self, envs):
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101 """
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102 Remove dependencies that are not currently used.
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103
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104 Returns a list of all environments that have been successfully removed.
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105 """
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106 envs_to_remove = set(envs)
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107 toolbox_requirements_status = self.toolbox_requirements_status
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108 removed_environments = set()
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109 for resolver in self._dependency_resolvers:
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110 if hasattr(resolver, 'unused_dependency_paths') and hasattr(resolver, 'uninstall_environments'):
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111 unused_dependencies = resolver.unused_dependency_paths(toolbox_requirements_status)
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112 can_remove = envs_to_remove & set(unused_dependencies)
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113 exit_code = resolver.uninstall_environments(can_remove)
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114 if exit_code == 0:
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115 removed_environments = removed_environments.union(can_remove)
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116 envs_to_remove = envs_to_remove.difference(can_remove)
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117 return list(removed_environments)
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118
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119 def install_dependencies(self, requirements, **kwds):
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120 kwds['install'] = True
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121 return self._dependency_manager._requirements_to_dependencies_dict(requirements, **kwds)
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122
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123 def install_dependency(self, index=None, **payload):
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124 """
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125 Installs dependency using highest priority resolver that supports dependency installation
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126 (Currently only the conda resolver supports this). If index is given, attempt
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127 installation directly using the corresponding resolver.
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128 Returns True on success, False on failure.
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129 payload is dictionary that must container name, version and type,
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130 e.g. {'name': 'numpy', version='1.9.1', type='package'}
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131 """
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132 if index:
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133 return self._install_dependency(index, **payload)
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134 else:
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135 for index in self.installable_resolvers:
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136 success = self._install_dependency(index, **payload)
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137 if success:
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138 return success
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139 return False
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140
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141 def _install_dependency(self, index, **payload):
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142 """
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143 Resolver install dependency should return True when installation succeeds,
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144 False if not successful
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145 """
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146 resolver = self._dependency_resolver(index)
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147 if not hasattr(resolver, "install_dependency"):
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148 raise exceptions.NotImplemented()
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149
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150 name, version, type, extra_kwds = self._parse_dependency_info(payload)
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151 return resolver.install_dependency(
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152 name=name,
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153 version=version,
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154 type=type,
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155 **extra_kwds
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156 )
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157
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158 def _dependency(self, index=None, **kwds):
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159 if index is not None:
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160 index = int(index)
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161
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162 name, version, type, extra_kwds = self._parse_dependency_info(kwds)
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163 resolve_kwds = dict(
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164 job_directory=None,
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165 index=index,
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166 **extra_kwds
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167 )
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168 dependency = self._dependency_manager.find_dep(
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169 name, version=version, type=type, **resolve_kwds
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170 )
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171 return dependency.to_dict()
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172
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173 def _parse_dependency_info(self, kwds):
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174 extra_kwds = kwds.copy()
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175 name = extra_kwds.pop("name", None)
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176 if name is None:
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177 raise exceptions.RequestParameterMissingException("Missing 'name' parameter required for resolution.")
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178 version = extra_kwds.pop("version", None)
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179 type = extra_kwds.pop("type", "package")
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180 return name, version, type, extra_kwds
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181
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182 def _dependency_resolver(self, index):
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183 index = int(index)
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184 return self._dependency_resolvers[index]
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185
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186 @property
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187 def _dependency_manager(self):
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188 return self._app.toolbox.dependency_manager
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189
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190 @property
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191 def _dependency_resolvers(self):
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192 dependency_manager = self._dependency_manager
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193 dependency_resolvers = dependency_manager.dependency_resolvers
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194 return dependency_resolvers
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195
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196 @property
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197 def installable_resolvers(self):
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198 """
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199 List index for all active resolvers that have the 'install_dependency' attribute.
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200 """
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201 return [index for index, resolver in enumerate(self._dependency_resolvers) if hasattr(resolver, "install_dependency") and not resolver.disabled]
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202
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203 @property
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204 def uninstallable_resolvers(self):
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205 """
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206 List index for all active resolvers that can uninstall dependencies that have been installed through this resolver.
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207 """
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208 return [index for index, resolver in enumerate(self._dependency_resolvers) if resolver.can_uninstall_dependencies and not resolver.disabled]
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209
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210 @property
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211 def tool_ids_by_requirements(self):
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212 """Dictionary with requirements as keys, and tool_ids as values."""
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213 tool_ids_by_requirements = {}
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214 if not self._app.toolbox.tools_by_id:
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215 return {}
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216 for tid, tool in self._app.toolbox.tools_by_id.items():
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217 if tool.tool_requirements not in tool_ids_by_requirements:
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218 tool_ids_by_requirements[tool.tool_requirements] = [tid]
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219 else:
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220 tool_ids_by_requirements[tool.tool_requirements].append(tid)
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221 return tool_ids_by_requirements
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222
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223 @property
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224 def toolbox_requirements_status(self):
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225 return self.summarize_requirements()
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226
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227 def summarize_requirements(self, **kwds):
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228 summary_kwds = {}
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229 if 'index' in kwds:
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230 summary_kwds['index'] = int(kwds['index'])
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231 if 'include_containers' in kwds:
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232 summary_kwds['include_containers'] = asbool(kwds['include_containers'])
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233 if 'container_type' in kwds:
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234 summary_kwds['container_type'] = kwds['container_type']
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235 if 'resolver_type' in kwds:
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236 summary_kwds['resolver_type'] = kwds['resolver_type']
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237 if 'search' in kwds:
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238 summary_kwds['search'] = asbool(kwds['search'])
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239 if 'install' in kwds:
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240 summary_kwds['install'] = asbool(kwds['install'])
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241
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242 tool_ids_by_requirements = self.tool_ids_by_requirements
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243 statuses = {r: self.get_requirements_status(tool_requirements_d={tids[0]: r},
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244 installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies, **summary_kwds)
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245 for r, tids in tool_ids_by_requirements.items()}
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246 if kwds.get("for_json", False):
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247 # All public attributes of this class should be returning JSON - this is meant to mimic a restful API.
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248 rval = []
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249 for requirements, status in statuses.items():
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250 item = {}
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251 item["requirements"] = requirements.to_dict()
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252 item["status"] = status
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253 item["tool_ids"] = tool_ids_by_requirements[requirements]
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254 rval.append(item)
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255 statuses = rval
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256 return statuses
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257
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258 def summarize_tools(self, **kwds):
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259 summary_kwds = {}
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260 if 'index' in kwds:
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261 summary_kwds['index'] = int(kwds['index'])
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262 if 'include_containers' in kwds:
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263 summary_kwds['include_containers'] = asbool(kwds['include_containers'])
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264 if 'container_type' in kwds:
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265 summary_kwds['container_type'] = kwds['container_type']
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266 if 'resolver_type' in kwds:
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267 summary_kwds['resolver_type'] = kwds['resolver_type']
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268 if 'search' in kwds:
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269 summary_kwds['search'] = asbool(kwds['search'])
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270 if 'install' in kwds:
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271 summary_kwds['install'] = asbool(kwds['install'])
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272
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273 tool_ids = pop_tool_ids(kwds)
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274
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275 rval = []
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276 for tid, tool in self._app.toolbox.tools_by_id.items():
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277 if tool_ids and tid not in tool_ids:
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278 continue
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279
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280 requirements = tool.tool_requirements
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281 status = self.get_requirements_status(tool_requirements_d={tid: requirements},
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282 installed_tool_dependencies=tool.installed_tool_dependencies,
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283 tool_instance=tool, **summary_kwds)
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284 item = {}
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285 item["requirements"] = requirements.to_dict()
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286 item["status"] = status
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287 item["tool_ids"] = [tid]
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288 rval.append(item)
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289 return rval
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290
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291 def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies=None, **kwd):
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292 dependencies = self.show_dependencies(tool_requirements_d, installed_tool_dependencies, **kwd)
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293 # dependencies is a dict keyed on tool_ids, value is a ToolRequirements object for that tool.
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294 # We use the union of resolvable ToolRequirements to get resolved dependencies without duplicates.
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295 requirements = [r.resolvable for r in tool_requirements_d.values()]
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296 flat_tool_requirements = set().union(*requirements)
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297 flat_dependencies = []
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298 for requirements_odict in dependencies.values():
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299 for requirement in requirements_odict:
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300 if requirement in flat_tool_requirements:
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301 flat_dependencies.append(requirements_odict[requirement])
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302 flat_tool_requirements.remove(requirement)
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303 return [d.to_dict() for d in flat_dependencies]
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304
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305 def clean(self, index=None, **kwds):
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306 if index:
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307 resolver = self._dependency_resolver(index)
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308 if not hasattr(resolver, "clean"):
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309 raise exceptions.NotImplemented()
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310 else:
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311 resolver.clean()
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312 return "OK"
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313 else:
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314 [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, 'clean')]
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315 return "OK"
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316
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317
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318 class ContainerResolutionView(object):
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319 """
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320 """
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321
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322 def __init__(self, app):
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323 self._app = app
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324
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325 def index(self):
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326 return [r.to_dict() for r in self._container_resolvers]
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327
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328 def show(self, index):
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329 return self._container_resolver(index).to_dict()
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330
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331 def resolve(self, **kwds):
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332 find_best_kwds = {
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333 'install': False,
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334 'enabled_container_types': ['docker', 'singularity'],
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335 'resolution_cache': kwds.get("resolution_cache"),
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336 }
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337
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338 if 'index' in kwds:
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339 find_best_kwds['index'] = int(kwds['index'])
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340 if 'container_type' in kwds:
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341 find_best_kwds['enabled_container_types'] = [kwds['container_type']]
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342 if 'resolver_type' in kwds:
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343 find_best_kwds['resolver_type'] = kwds['resolver_type']
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344 if 'install' in kwds:
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345 find_best_kwds['install'] = asbool(kwds['install'])
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346
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347 tool_info_kwds = {}
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348 tool_id = kwds["tool_id"]
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349 tool = self._app.toolbox.tools_by_id[tool_id]
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350
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351 requirements = tool.tool_requirements
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352 tool_info_kwds = dict(requirements=requirements)
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353 requirements_only = asbool(kwds.get("requirements_only", False))
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354 # If requirements_only, simply use the tool to load a requirement set from,
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355 # mimics the default behavior of searching for containers through the dependency resolution
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356 # component. Not useful for tool execution but perhaps when summarizing mulled containers for requirements.
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357 if not requirements_only:
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358 tool_info_kwds['container_descriptions'] = tool.containers
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359 tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment
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360 tool_info_kwds['tool_id'] = tool.id
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361 tool_info_kwds['tool_version'] = tool.version
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362
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363 find_best_kwds["tool_info"] = ToolInfo(**tool_info_kwds)
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364
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365 # Consider implementing 'search' to match dependency resolution API.
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366 resolved_container_description = self._app.container_finder.resolve(
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367 **find_best_kwds
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368 )
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369 if resolved_container_description:
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370 status = ContainerDependency(resolved_container_description.container_description, container_resolver=resolved_container_description.container_resolver).to_dict()
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371 else:
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372 status = NullDependency().to_dict()
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373 return {
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374 "tool_id": kwds["tool_id"],
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375 "status": status,
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376 "requirements": requirements.to_dict()
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377 }
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378
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379 def resolve_toolbox(self, **kwds):
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380 rval = []
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381 resolve_kwds = kwds.copy()
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382 tool_ids = pop_tool_ids(resolve_kwds)
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383 resolve_kwds["resolution_cache"] = self._app.container_finder.resolution_cache()
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384 if tool_ids is not None:
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385 tool_ids = listify(tool_ids)
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386 for tool_id, tool in self._app.toolbox.tools_by_id.items():
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387 if tool_ids is not None and tool_id not in tool_ids:
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388 continue
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389
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390 if tool.tool_action.produces_real_jobs:
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391 rval.append(self.resolve(tool_id=tool_id, **resolve_kwds))
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392 return rval
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393
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394 @property
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395 def _container_resolvers(self):
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396 return self._app.container_finder.container_resolvers
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397
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398 def _container_resolver(self, index):
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399 index = int(index)
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400 return self._container_resolvers[index]
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401
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402
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403 def pop_tool_ids(kwds):
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404 tool_ids = None
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405 if "tool_ids" in kwds:
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406 tool_ids = listify(kwds.pop("tool_ids"))
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407 if "tool_ids[]" in kwds:
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408 tool_ids = listify(kwds.pop("tool_ids[]"))
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409 if "tool_id" in kwds:
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410 tool_ids = [kwds.pop("tool_id")]
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411 return tool_ids