Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/__init__.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 """ |
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2 Dependency management for tools. |
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3 """ |
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4 |
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5 import json |
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6 import logging |
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7 import os.path |
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8 import shutil |
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9 |
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10 from galaxy.util import ( |
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11 hash_util, |
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12 plugin_config, |
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13 string_as_bool, |
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14 ) |
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15 from galaxy.util.oset import OrderedSet |
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16 from .container_resolvers import ContainerResolver |
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17 from .dependencies import ToolInfo |
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18 from .requirements import ( |
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19 ContainerDescription, |
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20 ToolRequirement, |
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21 ToolRequirements |
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22 ) |
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23 from .resolvers import ( |
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24 ContainerDependency, |
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25 NullDependency, |
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26 ) |
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27 from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver |
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28 |
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29 log = logging.getLogger(__name__) |
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30 |
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31 CONFIG_VAL_NOT_FOUND = object() |
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32 |
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33 |
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34 def build_dependency_manager(app_config_dict=None, resolution_config_dict=None, conf_file=None, default_tool_dependency_dir=None): |
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35 """Build a DependencyManager object from app and/or resolution config. |
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36 |
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37 If app_config_dict is specified, it should be application configuration information |
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38 and configuration options are generally named to identify the context of dependency |
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39 management (e.g. conda_prefix not prefix or use_cached_dependency_manager not cache). |
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40 resolution_config_dict if specified is assumed to be the to_dict() version of a |
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41 DependencyManager and should only contain dependency configuration options. |
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42 """ |
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43 |
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44 if app_config_dict is None: |
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45 app_config_dict = {} |
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46 else: |
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47 app_config_dict = app_config_dict.copy() |
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48 |
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49 tool_dependency_dir = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) |
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50 if tool_dependency_dir and tool_dependency_dir.lower() == "none": |
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51 app_config_dict["tool_dependency_dir"] = None |
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52 |
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53 if resolution_config_dict is None and "dependency_resolution" in app_config_dict: |
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54 resolution_config_dict = app_config_dict["dependency_resolution"] |
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55 |
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56 if resolution_config_dict: |
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57 # Convert local to_dict options into global ones. |
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58 |
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59 # to_dict() has "cache", "cache_dir", "use", "default_base_path", "resolvers", "precache" |
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60 app_config_props_from_resolution_config = { |
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61 "use_tool_dependencies": resolution_config_dict.get("use", None), |
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62 "tool_dependency_dir": resolution_config_dict.get("default_base_path", None), |
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63 "dependency_resolvers": resolution_config_dict.get("resolvers", None), |
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64 "tool_dependency_cache_dir": resolution_config_dict.get("cache_dir", None), |
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65 "precache_dependencies": resolution_config_dict.get("precache", None), |
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66 "use_cached_dependency_manager": resolution_config_dict.get("cache", None), |
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67 } |
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68 |
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69 for key, value in app_config_props_from_resolution_config.items(): |
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70 if value is not None: |
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71 app_config_dict[key] = value |
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72 |
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73 use_tool_dependencies = app_config_dict.get("use_tool_dependencies", None) |
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74 # if we haven't set an explicit True or False, try to infer from config... |
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75 if use_tool_dependencies is None: |
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76 use_tool_dependencies = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) is not None or \ |
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77 app_config_dict.get("dependency_resolvers") or \ |
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78 (conf_file and os.path.exists(conf_file)) |
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79 |
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80 if use_tool_dependencies: |
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81 dependency_manager_kwds = { |
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82 "default_base_path": app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir), |
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83 "conf_file": conf_file, |
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84 "app_config": app_config_dict, |
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85 } |
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86 if string_as_bool(app_config_dict.get("use_cached_dependency_manager")): |
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87 dependency_manager = CachedDependencyManager(**dependency_manager_kwds) |
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88 else: |
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89 dependency_manager = DependencyManager(**dependency_manager_kwds) |
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90 else: |
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91 dependency_manager = NullDependencyManager() |
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92 |
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93 return dependency_manager |
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94 |
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95 |
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96 class DependencyManager: |
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97 """ |
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98 A DependencyManager attempts to resolve named and versioned dependencies by |
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99 searching for them under a list of directories. Directories should be |
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100 of the form: |
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101 |
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102 $BASE/name/version/... |
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103 |
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104 and should each contain a file 'env.sh' which can be sourced to make the |
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105 dependency available in the current shell environment. |
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106 """ |
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107 cached = False |
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108 |
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109 def __init__(self, default_base_path, conf_file=None, app_config=None): |
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110 """ |
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111 Create a new dependency manager looking for packages under the paths listed |
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112 in `base_paths`. The default base path is app.config.tool_dependency_dir. |
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113 """ |
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114 if app_config is None: |
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115 app_config = {} |
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116 if not os.path.exists(default_base_path): |
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117 log.warning("Path '%s' does not exist, ignoring", default_base_path) |
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118 if not os.path.isdir(default_base_path): |
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119 log.warning("Path '%s' is not directory, ignoring", default_base_path) |
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120 self.__app_config = app_config |
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121 self.default_base_path = os.path.abspath(default_base_path) |
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122 self.resolver_classes = self.__resolvers_dict() |
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123 |
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124 plugin_source = None |
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125 dependency_resolver_dicts = app_config.get("dependency_resolvers") |
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126 if dependency_resolver_dicts is not None: |
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127 plugin_source = plugin_config.PluginConfigSource('dict', dependency_resolver_dicts) |
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128 else: |
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129 plugin_source = self.__build_dependency_resolvers_plugin_source(conf_file) |
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130 self.dependency_resolvers = self.__parse_resolver_conf_plugins(plugin_source) |
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131 self._enabled_container_types = [] |
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132 self._destination_for_container_type = {} |
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133 |
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134 def set_enabled_container_types(self, container_types_to_destinations): |
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135 """Set the union of all enabled container types.""" |
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136 self._enabled_container_types = [container_type for container_type in container_types_to_destinations.keys()] |
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137 # Just pick first enabled destination for a container type, probably covers the most common deployment scenarios |
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138 self._destination_for_container_type = container_types_to_destinations |
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139 |
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140 def get_destination_info_for_container_type(self, container_type, destination_id=None): |
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141 if destination_id is None: |
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142 return next(iter(self._destination_for_container_type[container_type])).params |
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143 else: |
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144 for destination in self._destination_for_container_type[container_type]: |
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145 if destination.id == destination_id: |
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146 return destination.params |
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147 |
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148 @property |
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149 def enabled_container_types(self): |
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150 """Returns the union of enabled container types.""" |
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151 return self._enabled_container_types |
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152 |
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153 def get_resolver_option(self, resolver, key, explicit_resolver_options=None): |
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154 """Look in resolver-specific settings for option and then fallback to global settings. |
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155 """ |
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156 if explicit_resolver_options is None: |
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157 explicit_resolver_options = {} |
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158 default = resolver.config_options.get(key) |
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159 config_prefix = resolver.resolver_type |
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160 global_key = f"{config_prefix}_{key}" |
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161 value = explicit_resolver_options.get(key, CONFIG_VAL_NOT_FOUND) |
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162 if value is CONFIG_VAL_NOT_FOUND: |
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163 value = self.get_app_option(global_key, default) |
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164 |
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165 return value |
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166 |
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167 def get_app_option(self, key, default=None): |
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168 value = CONFIG_VAL_NOT_FOUND |
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169 if isinstance(self.__app_config, dict): |
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170 value = self.__app_config.get(key, CONFIG_VAL_NOT_FOUND) |
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171 else: |
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172 value = getattr(self.__app_config, key, CONFIG_VAL_NOT_FOUND) |
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173 if value is CONFIG_VAL_NOT_FOUND and hasattr(self.__app_config, "config_dict"): |
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174 value = self.__app_config.config_dict.get(key, CONFIG_VAL_NOT_FOUND) |
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175 if value is CONFIG_VAL_NOT_FOUND: |
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176 value = default |
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177 return value |
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178 |
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179 @property |
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180 def precache(self): |
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181 return string_as_bool(self.get_app_option("precache_dependencies", True)) |
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182 |
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183 def dependency_shell_commands(self, requirements, **kwds): |
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184 requirements_to_dependencies = self.requirements_to_dependencies(requirements, **kwds) |
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185 ordered_dependencies = OrderedSet(requirements_to_dependencies.values()) |
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186 return [dependency.shell_commands() for dependency in ordered_dependencies if not isinstance(dependency, ContainerDependency)] |
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187 |
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188 def requirements_to_dependencies(self, requirements, **kwds): |
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189 """ |
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190 Takes a list of requirements and returns a dictionary |
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191 with requirements as key and dependencies as value caching |
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192 these on the tool instance if supplied. |
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193 """ |
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194 requirement_to_dependency = self._requirements_to_dependencies_dict(requirements, **kwds) |
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195 |
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196 if 'tool_instance' in kwds: |
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197 kwds['tool_instance'].dependencies = [dep.to_dict() for dep in requirement_to_dependency.values()] |
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198 |
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199 return requirement_to_dependency |
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200 |
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201 def _requirements_to_dependencies_dict(self, requirements, search=False, **kwds): |
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202 """Build simple requirements to dependencies dict for resolution.""" |
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203 requirement_to_dependency = {} |
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204 index = kwds.get('index') |
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205 install = kwds.get('install', False) |
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206 resolver_type = kwds.get('resolver_type') |
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207 include_containers = kwds.get('include_containers', False) |
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208 container_type = kwds.get('container_type') |
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209 require_exact = kwds.get('exact', False) |
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210 return_null_dependencies = kwds.get('return_null', False) |
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211 |
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212 resolvable_requirements = requirements.resolvable |
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213 |
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214 tool_info_kwds = dict(requirements=resolvable_requirements) |
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215 if 'tool_instance' in kwds: |
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216 tool = kwds['tool_instance'] |
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217 tool_info_kwds['tool_id'] = tool.id |
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218 tool_info_kwds['tool_version'] = tool.version |
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219 tool_info_kwds['container_descriptions'] = tool.containers |
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220 tool_info_kwds['requires_galaxy_python_environment'] = tool.requires_galaxy_python_environment |
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221 |
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222 tool_info = ToolInfo(**tool_info_kwds) |
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223 |
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224 for i, resolver in enumerate(self.dependency_resolvers): |
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225 |
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226 if index is not None and i != index: |
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227 continue |
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228 |
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229 if resolver_type is not None and resolver.resolver_type != resolver_type: |
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230 continue |
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231 |
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232 if container_type is not None and getattr(resolver, "container_type", None) != container_type: |
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233 continue |
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234 |
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235 _requirement_to_dependency = {k: v for k, v in requirement_to_dependency.items() if not isinstance(v, NullDependency)} |
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236 |
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237 if len(_requirement_to_dependency) == len(resolvable_requirements): |
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238 # Shortcut - resolution complete. |
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239 break |
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240 |
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241 # Check requirements all at once |
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242 all_unmet = len(_requirement_to_dependency) == 0 |
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243 if hasattr(resolver, "resolve_all"): |
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244 resolve = resolver.resolve_all |
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245 elif isinstance(resolver, ContainerResolver): |
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246 if not include_containers: |
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247 continue |
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248 if not install and resolver.builds_on_resolution: |
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249 # don't want to build images here |
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250 continue |
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251 if not resolver.resolver_type.startswith(('cached', 'explicit', 'fallback')) and not (search or install): |
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252 # These would look up available containers using the quay API, |
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253 # we only want to do this if we search for containers |
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254 continue |
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255 resolve = resolver.resolve |
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256 else: |
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257 resolve = None |
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258 if all_unmet and resolve is not None: |
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259 # TODO: Handle specs. |
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260 dependencies = resolve(requirements=resolvable_requirements, |
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261 enabled_container_types=self.enabled_container_types, |
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262 destination_for_container_type=self.get_destination_info_for_container_type, |
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263 tool_info=tool_info, |
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264 **kwds) |
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265 if dependencies: |
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266 if isinstance(dependencies, ContainerDescription): |
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267 dependencies = [ContainerDependency(dependencies, name=r.name, version=r.version, container_resolver=resolver) for r in resolvable_requirements] |
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268 assert len(dependencies) == len(resolvable_requirements) |
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269 for requirement, dependency in zip(resolvable_requirements, dependencies): |
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270 log.debug(dependency.resolver_msg) |
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271 requirement_to_dependency[requirement] = dependency |
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272 |
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273 # Shortcut - resolution complete. |
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274 break |
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275 |
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276 if not isinstance(resolver, ContainerResolver): |
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277 |
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278 # Check individual requirements |
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279 for requirement in resolvable_requirements: |
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280 if requirement in _requirement_to_dependency: |
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281 continue |
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282 |
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283 dependency = resolver.resolve(requirement, **kwds) |
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284 if require_exact and not dependency.exact: |
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285 continue |
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286 |
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287 if not isinstance(dependency, NullDependency): |
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288 log.debug(dependency.resolver_msg) |
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289 requirement_to_dependency[requirement] = dependency |
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290 elif return_null_dependencies: |
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291 log.debug(dependency.resolver_msg) |
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292 dependency.version = requirement.version |
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293 requirement_to_dependency[requirement] = dependency |
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294 |
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295 return requirement_to_dependency |
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296 |
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297 def uses_tool_shed_dependencies(self): |
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298 return any(map(lambda r: isinstance(r, ToolShedPackageDependencyResolver), self.dependency_resolvers)) |
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299 |
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300 def find_dep(self, name, version=None, type='package', **kwds): |
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301 log.debug(f'Find dependency {name} version {version}') |
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302 requirements = ToolRequirements([ToolRequirement(name=name, version=version, type=type)]) |
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303 dep_dict = self._requirements_to_dependencies_dict(requirements, **kwds) |
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304 if len(dep_dict) > 0: |
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305 return next(iter(dep_dict.values())) # get first dep |
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306 else: |
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307 return NullDependency(name=name, version=version) |
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308 |
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309 def __build_dependency_resolvers_plugin_source(self, conf_file): |
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310 if not conf_file: |
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311 return self.__default_dependency_resolvers_source() |
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312 if not os.path.exists(conf_file): |
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313 log.debug("Unable to find config file '%s'", conf_file) |
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314 return self.__default_dependency_resolvers_source() |
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315 plugin_source = plugin_config.plugin_source_from_path(conf_file) |
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316 return plugin_source |
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317 |
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318 def __default_dependency_resolvers_source(self): |
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319 return plugin_config.PluginConfigSource('dict', [ |
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320 {"type": "tool_shed_packages"}, |
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321 {"type": "galaxy_packages"}, |
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322 {"type": "conda"}, |
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323 {"type": "galaxy_packages", "versionless": True}, |
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324 {"type": "conda", "versionless": True}, |
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325 ]) |
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326 |
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327 def __parse_resolver_conf_plugins(self, plugin_source): |
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328 """ |
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329 """ |
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330 extra_kwds = dict(dependency_manager=self) |
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331 # Use either 'type' from YAML definition or 'resolver_type' from to_dict definition. |
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332 return plugin_config.load_plugins(self.resolver_classes, plugin_source, extra_kwds, plugin_type_keys=['type', 'resolver_type']) |
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333 |
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334 def __resolvers_dict(self): |
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335 import galaxy.tool_util.deps.resolvers |
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336 return plugin_config.plugins_dict(galaxy.tool_util.deps.resolvers, 'resolver_type') |
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337 |
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338 def to_dict(self): |
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339 return { |
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340 "use": True, |
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341 "cache": self.cached, |
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342 "precache": self.precache, |
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343 "cache_dir": getattr(self, "tool_dependency_cache_dir", None), |
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344 "default_base_path": self.default_base_path, |
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345 "resolvers": [m.to_dict() for m in self.dependency_resolvers], |
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346 } |
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347 |
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348 |
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349 class CachedDependencyManager(DependencyManager): |
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350 cached = True |
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351 |
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352 def __init__(self, default_base_path, **kwd): |
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353 super().__init__(default_base_path=default_base_path, **kwd) |
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354 self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") or os.path.join(default_base_path, "_cache") |
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355 |
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356 def build_cache(self, requirements, **kwds): |
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357 resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) |
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358 cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable] |
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359 hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies) |
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360 if os.path.exists(hashed_dependencies_dir): |
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361 if kwds.get('force_rebuild', False): |
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362 try: |
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363 shutil.rmtree(hashed_dependencies_dir) |
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364 except Exception: |
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365 log.warning("Could not delete cached dependencies directory '%s'" % hashed_dependencies_dir) |
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366 raise |
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367 else: |
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368 log.debug("Cached dependencies directory '%s' already exists, skipping build", hashed_dependencies_dir) |
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369 return |
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370 [dep.build_cache(hashed_dependencies_dir) for dep in cacheable_dependencies] |
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371 |
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372 def dependency_shell_commands(self, requirements, **kwds): |
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373 """ |
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374 Runs a set of requirements through the dependency resolvers and returns |
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375 a list of commands required to activate the dependencies. If dependencies |
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376 are cacheable and the cache does not exist, will try to create it. |
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377 If cached environment exists or is successfully created, will generate |
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378 commands to activate it. |
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379 """ |
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380 resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) |
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381 cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable] |
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382 hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies) |
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383 if not os.path.exists(hashed_dependencies_dir) and self.precache: |
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384 # Cache not present, try to create it |
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385 self.build_cache(requirements, **kwds) |
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386 if os.path.exists(hashed_dependencies_dir): |
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387 [dep.set_cache_path(hashed_dependencies_dir) for dep in cacheable_dependencies] |
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388 commands = [dep.shell_commands() for dep in resolved_dependencies.values()] |
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389 return commands |
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390 |
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391 def hash_dependencies(self, resolved_dependencies): |
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392 """Return hash for dependencies""" |
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393 resolved_dependencies = [(dep.name, dep.version, dep.exact, dep.dependency_type) for dep in resolved_dependencies] |
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394 hash_str = json.dumps(sorted(resolved_dependencies)) |
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395 return hash_util.new_secure_hash(hash_str)[:8] # short hash |
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396 |
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397 def get_hashed_dependencies_path(self, resolved_dependencies): |
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398 """ |
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399 Returns the path to the hashed dependencies directory (but does not evaluate whether the path exists). |
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400 |
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401 :param resolved_dependencies: list of resolved dependencies |
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402 :type resolved_dependencies: list |
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403 |
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404 :return: path |
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405 :rtype: str |
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406 """ |
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407 req_hashes = self.hash_dependencies(resolved_dependencies) |
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408 return os.path.abspath(os.path.join(self.tool_dependency_cache_dir, req_hashes)) |
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409 |
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410 |
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411 class NullDependencyManager(DependencyManager): |
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412 cached = False |
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413 |
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414 def __init__(self, default_base_path=None, conf_file=None, app_config=None): |
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415 if app_config is None: |
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416 app_config = {} |
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417 self.__app_config = app_config |
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418 self.resolver_classes = set() |
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419 self.dependency_resolvers = [] |
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420 self._enabled_container_types = [] |
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421 self._destination_for_container_type = {} |
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422 self.default_base_path = None |
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423 |
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424 def uses_tool_shed_dependencies(self): |
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425 return False |
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426 |
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427 def dependency_shell_commands(self, requirements, **kwds): |
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428 return [] |
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429 |
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430 def find_dep(self, name, version=None, type='package', **kwds): |
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431 return NullDependency(version=version, name=name) |
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432 |
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433 def to_dict(self): |
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434 return {"use": False} |