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tool_shed.tools package

Submodules

tool_shed.tools.data_table_manager module

tool_shed.tools.tool_validator module

class tool_shed.tools.tool_validator.ToolValidator(app)[source]

Bases: galaxy.tool_shed.tools.tool_validator.ToolValidator

can_use_tool_config_disk_file(repository, repo, file_path, changeset_revision)[source]

Determine if repository’s tool config file on disk can be used. This method is restricted to tool config files since, with the exception of tool config files, multiple files with the same name will likely be in various directories in the repository and we’re comparing file names only (not relative paths).

concat_messages(msg1, msg2)[source]
copy_disk_sample_files_to_dir(repo_files_dir, dest_path)[source]

Copy all files currently on disk that end with the .sample extension to the directory to which dest_path refers.

get_latest_tool_config_revision_from_repository_manifest(repo, filename, changeset_revision)[source]

Get the latest revision of a tool config file named filename from the repository manifest up to the value of changeset_revision. This method is restricted to tool_config files rather than any file since it is likely that, with the exception of tool config files, multiple files will have the same name in various directories within the repository.

get_list_of_copied_sample_files(repo, changeset_revision, dir)[source]

Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to changeset_revision. Copy each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in order to load the tools and generate metadata for them.

handle_sample_files_and_load_tool_from_disk(repo_files_dir, repository_id, tool_config_filepath, work_dir)[source]

Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories.

handle_sample_files_and_load_tool_from_tmp_config(repo, repository_id, changeset_revision, tool_config_filename, work_dir)[source]
load_tool_from_changeset_revision(repository_id, changeset_revision, tool_config_filename)[source]

Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision is a valid (downloadable) changeset revision. The tool config will be located in the repository manifest between the received valid changeset revision and the first changeset revision in the repository, searching backwards.

load_tool_from_tmp_config(repo, repository_id, ctx, ctx_file, work_dir)[source]

tool_shed.tools.tool_version_manager module

class tool_shed.tools.tool_version_manager.ToolVersionManager(app)[source]

Bases: object

__init__(app)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_tool_version(tool_id)[source]
get_tool_version_association(parent_tool_version, tool_version)[source]

Return a ToolVersionAssociation if one exists that associates the two received tool_versions. This function is called only from Galaxy.

get_version_lineage_for_tool(repository_id, repository_metadata, guid)[source]

Return the tool version lineage chain in descendant order for the received guid contained in the received repsitory_metadata.tool_versions. This function is called only from the Tool Shed.