Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/galaxy_packages.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 import logging |
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2 from os import listdir |
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3 from os.path import ( |
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4 basename, |
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5 exists, |
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6 isdir, |
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7 islink, |
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8 join, |
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9 realpath, |
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10 ) |
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11 |
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12 from . import ( |
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13 Dependency, |
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14 DependencyResolver, |
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15 ListableDependencyResolver, |
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16 MappableDependencyResolver, |
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17 NullDependency, |
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18 ) |
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19 from .resolver_mixins import UsesToolDependencyDirMixin |
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20 |
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21 log = logging.getLogger(__name__) |
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22 |
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23 |
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24 class GalaxyPackageDependency(Dependency): |
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25 dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['script', 'path', 'version', 'name', 'dependency_resolver'] |
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26 dependency_type = 'galaxy_package' |
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27 |
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28 def __init__(self, script, path, name, type, version, exact=True, dependency_resolver=None): |
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29 self.script = script |
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30 self.path = path |
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31 self.name = name |
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32 self.type = type |
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33 self.version = version |
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34 self._exact = exact |
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35 assert self.script is not None or self.path is not None |
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36 self.dependency_resolver = dependency_resolver |
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37 |
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38 @property |
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39 def exact(self): |
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40 return self._exact |
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41 |
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42 def shell_commands(self): |
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43 base_path = self.path |
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44 if self.type == 'package' and self.script is None: |
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45 commands = f'PACKAGE_BASE={base_path}; export PACKAGE_BASE; PATH="{base_path}/bin:$PATH"; export PATH' |
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46 else: |
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47 commands = f'PACKAGE_BASE={base_path}; export PACKAGE_BASE; . {self.script}' |
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48 return commands |
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49 |
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50 |
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51 class ToolShedDependency(GalaxyPackageDependency): |
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52 dependency_type = 'tool_shed_package' |
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53 |
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54 |
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55 class BaseGalaxyPackageDependencyResolver(DependencyResolver, UsesToolDependencyDirMixin): |
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56 dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'versionless'] |
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57 dependency_type = GalaxyPackageDependency |
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58 |
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59 def __init__(self, dependency_manager, **kwds): |
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60 # Galaxy tool shed requires explicit versions on XML elements, |
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61 # this in inconvient for testing or Galaxy instances not utilizing |
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62 # the tool shed so allow a fallback version of the Galaxy package |
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63 # resolver that will just grab 'default' version of exact version |
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64 # unavailable. |
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65 self.versionless = str(kwds.get('versionless', "false")).lower() == "true" |
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66 self._init_base_path(dependency_manager, **kwds) |
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67 |
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68 def resolve(self, requirement, **kwds): |
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69 """ |
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70 Attempt to find a dependency named `name` at version `version`. If version is None, return the "default" version as determined using a |
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71 symbolic link (if found). Returns a triple of: env_script, base_path, real_version |
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72 """ |
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73 name, version, type = requirement.name, requirement.version, requirement.type |
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74 |
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75 if version is None or self.versionless: |
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76 exact = not self.versionless or version is None |
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77 return self._find_dep_default(name, type=type, exact=exact, **kwds) |
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78 else: |
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79 return self._find_dep_versioned(name, version, type=type, **kwds) |
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80 |
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81 def _find_dep_versioned(self, name, version, type='package', **kwds): |
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82 base_path = self.base_path |
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83 path = join(base_path, name, version) |
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84 return self._galaxy_package_dep(path, version, name, type, True) |
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85 |
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86 def _find_dep_default(self, name, type='package', exact=True, **kwds): |
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87 base_path = self.base_path |
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88 path = join(base_path, name, 'default') |
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89 if islink(path): |
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90 real_path = realpath(path) |
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91 real_version = basename(real_path) |
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92 return self._galaxy_package_dep(real_path, real_version, name, type, exact) |
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93 else: |
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94 return NullDependency(version=None, name=name) |
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95 |
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96 def _galaxy_package_dep(self, path, version, name, type, exact): |
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97 script = join(path, 'env.sh') |
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98 if exists(script): |
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99 return self.dependency_type(script, path, name, type, version, exact, dependency_resolver=self) |
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100 elif exists(join(path, 'bin')): |
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101 return self.dependency_type(None, path, name, type, version, exact, dependency_resolver=self) |
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102 return NullDependency(version=version, name=name) |
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103 |
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104 |
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105 class GalaxyPackageDependencyResolver(BaseGalaxyPackageDependencyResolver, ListableDependencyResolver, MappableDependencyResolver): |
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106 resolver_type = "galaxy_packages" |
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107 |
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108 def __init__(self, dependency_manager, **kwds): |
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109 super().__init__(dependency_manager, **kwds) |
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110 self._setup_mapping(dependency_manager, **kwds) |
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111 |
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112 def resolve(self, requirement, **kwds): |
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113 requirement = self._expand_mappings(requirement) |
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114 return super().resolve(requirement, **kwds) |
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115 |
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116 def list_dependencies(self): |
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117 base_path = self.base_path |
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118 for package_name in listdir(base_path): |
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119 package_dir = join(base_path, package_name) |
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120 if isdir(package_dir): |
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121 for version in listdir(package_dir): |
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122 version_dir = join(package_dir, version) |
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123 if version == "default": |
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124 version = None |
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125 valid_dependency = _is_dependency_directory(version_dir) |
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126 if valid_dependency: |
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127 yield self._to_requirement(package_name, version) |
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128 |
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129 |
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130 def _is_dependency_directory(directory): |
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131 return exists(join(directory, 'env.sh')) or exists(join(directory, 'bin')) |
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132 |
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133 |
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134 __all__ = ( |
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135 'GalaxyPackageDependency', |
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136 'GalaxyPackageDependencyResolver', |
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137 'ToolShedDependency' |
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138 ) |