Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/views.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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: |
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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 resolver.read_only: |
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148 raise exceptions.RequestParameterInvalidException("Attempted to install on a read_only dependency resolver.") |
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149 if resolver.disabled: |
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150 raise exceptions.RequestParameterInvalidException("Attempted to install on a disabled dependency resolver.") |
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151 |
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152 name, version, type, extra_kwds = self._parse_dependency_info(payload) |
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153 return resolver.install_dependency( |
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154 name=name, |
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155 version=version, |
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156 type=type, |
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157 **extra_kwds |
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158 ) |
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159 |
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160 def _dependency(self, index=None, **kwds): |
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161 if index is not None: |
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162 index = int(index) |
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163 |
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164 name, version, type, extra_kwds = self._parse_dependency_info(kwds) |
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165 resolve_kwds = dict( |
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166 job_directory=None, |
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167 index=index, |
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168 **extra_kwds |
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169 ) |
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170 dependency = self._dependency_manager.find_dep( |
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171 name, version=version, type=type, **resolve_kwds |
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172 ) |
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173 return dependency.to_dict() |
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174 |
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175 def _parse_dependency_info(self, kwds): |
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176 extra_kwds = kwds.copy() |
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177 name = extra_kwds.pop("name", None) |
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178 if name is None: |
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179 raise exceptions.RequestParameterMissingException("Missing 'name' parameter required for resolution.") |
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180 version = extra_kwds.pop("version", None) |
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181 type = extra_kwds.pop("type", "package") |
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182 return name, version, type, extra_kwds |
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183 |
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184 def _dependency_resolver(self, index): |
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185 index = int(index) |
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186 return self._dependency_resolvers[index] |
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187 |
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188 @property |
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189 def _dependency_manager(self): |
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190 return self._app.toolbox.dependency_manager |
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191 |
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192 @property |
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193 def _dependency_resolvers(self): |
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194 dependency_manager = self._dependency_manager |
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195 dependency_resolvers = dependency_manager.dependency_resolvers |
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196 return dependency_resolvers |
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197 |
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198 @property |
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199 def installable_resolvers(self): |
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200 """ |
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201 List index for all active resolvers that have the 'install_dependency' attribute. |
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202 """ |
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203 return [index for index, resolver in enumerate(self._dependency_resolvers) if not resolver.read_only and not resolver.disabled] |
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204 |
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205 @property |
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206 def uninstallable_resolvers(self): |
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207 """ |
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208 List index for all active resolvers that can uninstall dependencies that have been installed through this resolver. |
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209 """ |
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210 return [index for index, resolver in enumerate(self._dependency_resolvers) if resolver.can_uninstall_dependencies and not resolver.disabled] |
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211 |
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212 @property |
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213 def tool_ids_by_requirements(self): |
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214 """Dictionary with requirements as keys, and tool_ids as values.""" |
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215 tool_ids_by_requirements = {} |
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216 if not self._app.toolbox.tools_by_id: |
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217 return {} |
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218 for tid, tool in self._app.toolbox.tools_by_id.items(): |
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219 if tool.tool_requirements not in tool_ids_by_requirements: |
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220 tool_ids_by_requirements[tool.tool_requirements] = [tid] |
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221 else: |
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222 tool_ids_by_requirements[tool.tool_requirements].append(tid) |
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223 return tool_ids_by_requirements |
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224 |
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225 @property |
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226 def toolbox_requirements_status(self): |
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227 return self.summarize_requirements() |
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228 |
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229 def summarize_requirements(self, **kwds): |
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230 summary_kwds = {} |
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231 if 'index' in kwds: |
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232 summary_kwds['index'] = int(kwds['index']) |
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233 if 'include_containers' in kwds: |
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234 summary_kwds['include_containers'] = asbool(kwds['include_containers']) |
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235 if 'container_type' in kwds: |
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236 summary_kwds['container_type'] = kwds['container_type'] |
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237 if 'resolver_type' in kwds: |
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238 summary_kwds['resolver_type'] = kwds['resolver_type'] |
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239 if 'search' in kwds: |
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240 summary_kwds['search'] = asbool(kwds['search']) |
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241 if 'install' in kwds: |
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242 summary_kwds['install'] = asbool(kwds['install']) |
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243 |
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244 tool_ids_by_requirements = self.tool_ids_by_requirements |
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245 statuses = {r: self.get_requirements_status(tool_requirements_d={tids[0]: r}, |
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246 installed_tool_dependencies=self._app.toolbox.tools_by_id[tids[0]].installed_tool_dependencies, **summary_kwds) |
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247 for r, tids in tool_ids_by_requirements.items()} |
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248 if kwds.get("for_json", False): |
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249 # All public attributes of this class should be returning JSON - this is meant to mimic a restful API. |
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250 rval = [] |
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251 for requirements, status in statuses.items(): |
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252 item = {} |
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253 item["requirements"] = requirements.to_dict() |
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254 item["status"] = status |
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255 item["tool_ids"] = tool_ids_by_requirements[requirements] |
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256 rval.append(item) |
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257 statuses = rval |
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258 return statuses |
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259 |
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260 def summarize_tools(self, **kwds): |
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261 summary_kwds = {} |
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262 if 'index' in kwds: |
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263 summary_kwds['index'] = int(kwds['index']) |
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264 if 'include_containers' in kwds: |
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265 summary_kwds['include_containers'] = asbool(kwds['include_containers']) |
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266 if 'container_type' in kwds: |
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267 summary_kwds['container_type'] = kwds['container_type'] |
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268 if 'resolver_type' in kwds: |
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269 summary_kwds['resolver_type'] = kwds['resolver_type'] |
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270 if 'search' in kwds: |
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271 summary_kwds['search'] = asbool(kwds['search']) |
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272 if 'install' in kwds: |
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273 summary_kwds['install'] = asbool(kwds['install']) |
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274 |
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275 tool_ids = pop_tool_ids(kwds) |
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276 |
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277 rval = [] |
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278 for tid, tool in self._app.toolbox.tools_by_id.items(): |
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279 if tool_ids and tid not in tool_ids: |
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280 continue |
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281 |
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282 requirements = tool.tool_requirements |
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283 status = self.get_requirements_status(tool_requirements_d={tid: requirements}, |
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284 installed_tool_dependencies=tool.installed_tool_dependencies, |
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285 tool_instance=tool, **summary_kwds) |
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286 item = {} |
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287 item["requirements"] = requirements.to_dict() |
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288 item["status"] = status |
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289 item["tool_ids"] = [tid] |
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290 rval.append(item) |
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291 return rval |
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292 |
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293 def get_requirements_status(self, tool_requirements_d, installed_tool_dependencies=None, **kwd): |
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294 dependencies = self.show_dependencies(tool_requirements_d, installed_tool_dependencies, **kwd) |
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295 # dependencies is a dict keyed on tool_ids, value is a ToolRequirements object for that tool. |
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296 # We use the union of resolvable ToolRequirements to get resolved dependencies without duplicates. |
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297 requirements = [r.resolvable for r in tool_requirements_d.values()] |
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298 flat_tool_requirements = set().union(*requirements) |
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299 flat_dependencies = [] |
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300 for requirements_odict in dependencies.values(): |
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301 for requirement in requirements_odict: |
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302 if requirement in flat_tool_requirements: |
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303 flat_dependencies.append(requirements_odict[requirement]) |
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304 flat_tool_requirements.remove(requirement) |
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305 return [d.to_dict() for d in flat_dependencies] |
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306 |
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307 def clean(self, index=None, **kwds): |
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308 if index: |
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309 resolver = self._dependency_resolver(index) |
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310 if not hasattr(resolver, "clean"): |
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311 raise exceptions.NotImplemented() |
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312 else: |
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313 resolver.clean() |
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314 return "OK" |
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315 else: |
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316 [resolver.clean(**kwds) for resolver in self._dependency_resolvers if hasattr(resolver, 'clean')] |
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317 return "OK" |
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318 |
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319 |
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320 class ContainerResolutionView: |
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321 """ |
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322 """ |
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323 |
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324 def __init__(self, app): |
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325 self._app = app |
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326 |
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327 def index(self): |
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328 return [r.to_dict() for r in self._container_resolvers] |
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329 |
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330 def show(self, index): |
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331 return self._container_resolver(index).to_dict() |
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332 |
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333 def resolve(self, **kwds): |
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334 find_best_kwds = { |
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335 'install': False, |
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336 'enabled_container_types': ['docker', 'singularity'], |
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337 'resolution_cache': kwds.get("resolution_cache"), |
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338 'session': kwds.get('session'), |
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339 } |
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340 |
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341 if 'index' in kwds: |
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342 find_best_kwds['index'] = int(kwds['index']) |
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343 if 'container_type' in kwds: |
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344 find_best_kwds['enabled_container_types'] = [kwds['container_type']] |
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345 if 'resolver_type' in kwds: |
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346 find_best_kwds['resolver_type'] = kwds['resolver_type'] |
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347 if 'install' in kwds: |
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348 find_best_kwds['install'] = asbool(kwds['install']) |
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349 |
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350 tool_info_kwds = {} |
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351 tool_id = kwds["tool_id"] |
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352 tool = self._app.toolbox.tools_by_id[tool_id] |
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353 |
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354 requirements = tool.tool_requirements |
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355 tool_info_kwds = dict(requirements=requirements) |
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356 requirements_only = asbool(kwds.get("requirements_only", False)) |
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357 # If requirements_only, simply use the tool to load a requirement set from, |
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358 # mimics the default behavior of searching for containers through the dependency resolution |
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359 # component. Not useful for tool execution but perhaps when summarizing mulled containers for requirements. |
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360 if not requirements_only: |
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361 tool_info_kwds['container_descriptions'] = tool.containers |
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362 tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment |
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363 tool_info_kwds['tool_id'] = tool.id |
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364 tool_info_kwds['tool_version'] = tool.version |
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365 |
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366 find_best_kwds["tool_info"] = ToolInfo(**tool_info_kwds) |
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367 |
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368 # Consider implementing 'search' to match dependency resolution API. |
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369 resolved_container_description = self._app.container_finder.resolve( |
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370 **find_best_kwds |
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371 ) |
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372 if resolved_container_description: |
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373 status = ContainerDependency(resolved_container_description.container_description, container_resolver=resolved_container_description.container_resolver).to_dict() |
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374 else: |
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375 status = NullDependency().to_dict() |
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376 return { |
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377 "tool_id": kwds["tool_id"], |
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378 "status": status, |
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379 "requirements": requirements.to_dict() |
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380 } |
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381 |
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382 def resolve_toolbox(self, **kwds): |
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383 rval = [] |
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384 resolve_kwds = kwds.copy() |
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385 tool_ids = pop_tool_ids(resolve_kwds) |
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386 resolve_kwds["resolution_cache"] = self._app.container_finder.resolution_cache() |
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387 if tool_ids is not None: |
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388 tool_ids = listify(tool_ids) |
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389 for tool_id, tool in self._app.toolbox.tools_by_id.items(): |
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390 if tool_ids is not None and tool_id not in tool_ids: |
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391 continue |
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392 |
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393 if tool.tool_action.produces_real_jobs: |
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394 rval.append(self.resolve(tool_id=tool_id, **resolve_kwds)) |
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395 return rval |
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396 |
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397 @property |
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398 def _container_resolvers(self): |
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399 return self._app.container_finder.container_resolvers |
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400 |
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401 def _container_resolver(self, index): |
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402 index = int(index) |
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403 return self._container_resolvers[index] |
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404 |
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405 |
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406 def pop_tool_ids(kwds): |
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407 tool_ids = None |
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408 if "tool_ids" in kwds: |
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409 tool_ids = listify(kwds.pop("tool_ids")) |
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410 if "tool_ids[]" in kwds: |
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411 tool_ids = listify(kwds.pop("tool_ids[]")) |
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412 if "tool_id" in kwds: |
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413 tool_ids = [kwds.pop("tool_id")] |
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414 return tool_ids |