Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/resolvers/modules.py @ 0:4f3585e2f14b draft default tip
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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 This file contains the outline of an implementation to load environment modules |
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3 (http://modules.sourceforge.net/). |
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4 |
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5 This is a community contributed feature and the core Galaxy team does utilize |
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6 it, hence support for it will be minimal. The Galaxy team eagerly welcomes |
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7 community contribution and maintenance however. |
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8 """ |
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9 import logging |
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10 from io import StringIO |
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11 from os import ( |
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12 environ, |
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13 pathsep |
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14 ) |
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15 from os.path import ( |
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16 exists, |
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17 isdir, |
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18 join |
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19 ) |
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20 from subprocess import ( |
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21 PIPE, |
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22 Popen |
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23 ) |
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24 |
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25 from . import ( |
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26 Dependency, |
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27 DependencyResolver, |
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28 MappableDependencyResolver, |
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29 NullDependency, |
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30 ) |
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31 |
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32 log = logging.getLogger(__name__) |
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33 |
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34 DEFAULT_MODULECMD_PATH = "modulecmd" # Just check path |
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35 DEFAULT_MODULE_PATH = '/usr/share/modules/modulefiles' |
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36 DEFAULT_INDICATOR = '(default)' |
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37 DEFAULT_MODULE_PREFETCH = "true" |
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38 DEFAULT_MAPPING_FILE = 'config/environment_modules_mapping.yml' |
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39 UNKNOWN_FIND_BY_MESSAGE = "ModuleDependencyResolver does not know how to find modules by [%s], find_by should be one of %s" |
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40 |
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41 |
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42 class ModuleDependencyResolver(DependencyResolver, MappableDependencyResolver): |
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43 dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['base_path', 'modulepath', 'modulecmd', 'prefetch', 'default_indicator', 'find_by'] |
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44 resolver_type = "modules" |
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45 |
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46 def __init__(self, dependency_manager, **kwds): |
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47 # Mapping file management |
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48 self._set_default_mapping_file(kwds) |
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49 self._setup_mapping(dependency_manager, **kwds) |
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50 self.versionless = _string_as_bool(kwds.get('versionless', 'false')) |
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51 find_by = kwds.get('find_by', 'avail') |
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52 self.find_by = find_by |
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53 prefetch = _string_as_bool(kwds.get('prefetch', DEFAULT_MODULE_PREFETCH)) |
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54 self.modulecmd = kwds.get('modulecmd', DEFAULT_MODULECMD_PATH) |
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55 self.modulepath = kwds.get('modulepath', self.__default_modulespath()) |
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56 self.default_indicator = kwds.get('default_indicator', DEFAULT_INDICATOR) |
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57 if find_by == 'directory': |
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58 self.module_checker = DirectoryModuleChecker(self, self.modulepath, prefetch) |
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59 elif find_by == 'avail': |
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60 self.module_checker = AvailModuleChecker(self, self.modulepath, prefetch, self.default_indicator) |
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61 else: |
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62 raise Exception(UNKNOWN_FIND_BY_MESSAGE % (find_by, ["avail", "directory"])) |
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63 |
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64 def __default_modulespath(self): |
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65 if 'MODULEPATH' in environ: |
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66 module_path = environ['MODULEPATH'] |
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67 elif 'MODULESHOME' in environ: |
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68 module_path = join(environ['MODULESHOME'], 'modulefiles') |
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69 else: |
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70 module_path = DEFAULT_MODULE_PATH |
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71 return module_path |
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72 |
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73 def _set_default_mapping_file(self, resolver_attributes): |
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74 if 'mapping_files' not in resolver_attributes: |
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75 if exists(DEFAULT_MAPPING_FILE): |
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76 resolver_attributes['mapping_files'] = DEFAULT_MAPPING_FILE |
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77 |
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78 def resolve(self, requirement, **kwds): |
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79 requirement = self._expand_mappings(requirement) |
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80 name, version, type = requirement.name, requirement.version, requirement.type |
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81 |
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82 if type != "package": |
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83 return NullDependency(version=version, name=name) |
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84 |
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85 if self.__has_module(name, version): |
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86 return ModuleDependency(self, name, version, exact=True, dependency_resolver=self) |
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87 elif self.versionless and self.__has_module(name, None): |
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88 return ModuleDependency(self, name, None, exact=False, dependency_resolver=self) |
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89 |
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90 return NullDependency(version=version, name=name) |
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91 |
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92 def __has_module(self, name, version): |
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93 return self.module_checker.has_module(name, version) |
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94 |
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95 |
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96 class DirectoryModuleChecker: |
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97 """Finds module by path. |
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98 |
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99 Searches the paths listed in modulepath to for a file or directory matching the module name. |
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100 If the version=True, searches for files named module/version.""" |
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101 |
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102 def __init__(self, module_dependency_resolver, modulepath, prefetch): |
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103 self.module_dependency_resolver = module_dependency_resolver |
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104 self.directories = modulepath.split(pathsep) |
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105 if prefetch: |
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106 log.warning("Created module dependency resolver with prefetch enabled, but directory module checker does not support this.") |
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107 |
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108 def has_module(self, module, version): |
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109 has_module = False |
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110 for directory in self.directories: |
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111 module_directory = join(directory, module) |
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112 has_module_directory = isdir(module_directory) |
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113 if not version: |
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114 has_module = has_module_directory or exists(module_directory) # could be a bare modulefile |
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115 else: |
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116 modulefile = join(module_directory, version) |
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117 has_modulefile = exists(modulefile) |
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118 has_module = has_module_directory and has_modulefile |
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119 if has_module: |
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120 break |
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121 return has_module |
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122 |
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123 |
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124 class AvailModuleChecker: |
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125 """Finds modules by searching output of 'module avail'. |
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126 |
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127 Parses the Environment Modules 'module avail' output, splitting |
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128 module names into module and version on '/' and discarding a postfix matching default_indicator |
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129 (by default '(default)'. Matching is done using the module and |
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130 (if version=True) the module version.""" |
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131 |
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132 def __init__(self, module_dependency_resolver, modulepath, prefetch, default_indicator=DEFAULT_INDICATOR): |
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133 self.module_dependency_resolver = module_dependency_resolver |
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134 self.modulepath = modulepath |
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135 self.default_indicator = default_indicator |
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136 if prefetch: |
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137 prefetched_modules = [] |
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138 for module in self.__modules(): |
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139 prefetched_modules.append(module) |
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140 else: |
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141 prefetched_modules = None |
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142 self.prefetched_modules = prefetched_modules |
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143 |
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144 def has_module(self, module, version): |
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145 module_generator = self.prefetched_modules |
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146 if module_generator is None: |
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147 module_generator = self.__modules() |
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148 |
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149 for module_name, module_version in module_generator: |
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150 names_match = module == module_name |
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151 module_match = names_match and (version is None or module_version == version) |
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152 if module_match: |
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153 return True |
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154 return False |
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155 |
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156 def __modules(self): |
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157 raw_output = self.__module_avail_output().decode("utf-8") |
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158 for line in StringIO(raw_output): |
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159 line = line and line.strip() |
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160 if not line or line.startswith("-"): |
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161 continue |
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162 |
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163 line_modules = line.split() |
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164 for module in line_modules: |
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165 if module.endswith(self.default_indicator): |
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166 module = module[0:-len(self.default_indicator)].strip() |
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167 module_parts = module.split('/') |
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168 module_version = None |
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169 if len(module_parts) == 2: |
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170 module_version = module_parts[1] |
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171 module_name = module_parts[0] |
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172 yield module_name, module_version |
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173 |
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174 def __module_avail_output(self): |
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175 avail_command = [self.module_dependency_resolver.modulecmd, 'sh', 'avail'] |
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176 return Popen(avail_command, stderr=PIPE, env={'MODULEPATH': self.modulepath}).communicate()[1] |
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177 |
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178 |
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179 class ModuleDependency(Dependency): |
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180 """Converts module dependencies into shell expressions using modulecmd. |
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181 |
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182 Using Environment Modules' 'modulecmd' (specifically 'modulecmd sh load') to |
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183 convert module specifications into shell expressions for inclusion in |
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184 the script used to run a tool in Galaxy.""" |
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185 dict_collection_visible_keys = Dependency.dict_collection_visible_keys + ['module_name', 'module_version', 'dependency_resolver'] |
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186 dependency_type = 'module' |
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187 |
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188 def __init__(self, module_dependency_resolver, module_name, module_version=None, exact=True, dependency_resolver=None): |
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189 self.module_dependency_resolver = module_dependency_resolver |
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190 self.module_name = module_name |
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191 self.module_version = module_version |
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192 self._exact = exact |
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193 self.dependency_resolver = dependency_resolver |
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194 |
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195 @property |
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196 def name(self): |
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197 return self.module_name |
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198 |
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199 @property |
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200 def version(self): |
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201 return self.module_version |
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202 |
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203 @property |
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204 def exact(self): |
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205 return self._exact |
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206 |
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207 def shell_commands(self): |
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208 module_to_load = self.module_name |
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209 if self.module_version: |
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210 module_to_load = f'{self.module_name}/{self.module_version}' |
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211 command = 'MODULEPATH={}; export MODULEPATH; eval `{} sh load {}`'.format(self.module_dependency_resolver.modulepath, |
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212 self.module_dependency_resolver.modulecmd, |
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213 module_to_load) |
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214 return command |
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215 |
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216 |
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217 def _string_as_bool(value): |
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218 return str(value).lower() == "true" |
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219 |
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220 |
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221 __all__ = ('ModuleDependencyResolver', ) |