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galaxy.tool_shed.metadata package¶
Submodules¶
galaxy.tool_shed.metadata.metadata_generator module¶
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class
galaxy.tool_shed.metadata.metadata_generator.
MetadataGenerator
(app, repository=None, changeset_revision=None, repository_clone_url=None, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False, metadata_dict=None, user=None)[source]¶ Bases:
object
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__init__
(app, repository=None, changeset_revision=None, repository_clone_url=None, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False, metadata_dict=None, user=None)[source]¶
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generate_data_manager_metadata
(repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None)[source]¶ Update the received metadata_dict with information from the parsed data_manager_config_filename.
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generate_datatypes_metadata
(tv, repository_files_dir, datatypes_config, metadata_dict)[source]¶ Update the received metadata_dict with information from the parsed datatypes_config.
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generate_environment_dependency_metadata
(elem, valid_tool_dependencies_dict)[source]¶ The value of env_var_name must match the value of the “set_environment” type in the tool config’s <requirements> tag set, or the tool dependency will be considered an orphan.
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generate_metadata_for_changeset_revision
()[source]¶ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision’s disk files, so the value of self.repository_files_dir will not always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ).
The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config.
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generate_package_dependency_metadata
(elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict)[source]¶ Generate the metadata for a tool dependencies package defined for a repository. The value of package_name must match the value of the “package” type in the tool config’s <requirements> tag set.
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generate_repository_dependency_metadata
(repository_dependencies_config, metadata_dict)[source]¶ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy.
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generate_tool_metadata
(tool_config, tool, metadata_dict)[source]¶ Update the received metadata_dict with changes that have been applied to the received tool.
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generate_tool_dependency_metadata
(tool_dependencies_config, metadata_dict, original_repository_metadata=None)[source]¶ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config.
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generate_workflow_metadata
(relative_path, exported_workflow_dict, metadata_dict)[source]¶ Update the received metadata_dict with changes that have been applied to the received exported_workflow_dict.
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get_relative_path_to_repository_file
(root, name, relative_install_dir, work_dir, shed_config_dict)[source]¶
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get_sample_files_from_disk
(repository_files_dir, tool_path=None, relative_install_dir=None)[source]¶
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handle_repository_elem
(repository_elem, only_if_compiling_contained_td=False)[source]¶ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, we’re generating repository dependencies metadata for a repository in the Tool Shed. If the latter, we’re generating package dependency metadata within Galaxy or the Tool Shed.
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