planemo.shed package

Submodules

planemo.shed.diff module

Utilities for calculating effective repository diffs.

Some intelligence is required because the tool shed updates attributes that it is beneficial to ignore.

planemo.shed.diff.diff_and_remove(working, label_a, label_b, f)[source]

Remove tool shed XML files and use a smart XML diff on them.

Return 0 if and only if the XML content is the sam after stripping attirbutes the tool shed updates.

planemo.shed.interface module

Interface over bioblend and direct access to ToolShed API via requests.

planemo.shed.interface.api_exception_to_message(e)[source]

Convert API exception to human digestable error message - parsing out the shed generate message if possible.

planemo.shed.interface.download_tar(tsi, repo_id, destination, to_directory)[source]
planemo.shed.interface.find_category_ids(tsi, categories)[source]

Translate human readable category names into their associated IDs.

planemo.shed.interface.find_repository(tsi, owner, name)[source]

Find repository information for given owner and repository name.

planemo.shed.interface.latest_installable_revision(tsi, repository_id)[source]
planemo.shed.interface.tool_shed_instance(url, key, email, password)[source]
planemo.shed.interface.username(tsi)[source]

Fetch current username from shed given API key/auth.

Module contents

Abstractions for shed related interactions used by the rest of planemo.

planemo.shed.api_exception_to_message(e)[source]

Convert API exception to human digestable error message - parsing out the shed generate message if possible.

planemo.shed.diff_repo(ctx, realized_repository, **kwds)[source]

Compare two repositories (local or remote) and check for differences.

Returns 0 if and only the repositories are effectively the same given supplied kwds for comparison description.

planemo.shed.download_tarball(ctx, shed_context, realized_repository, **kwds)[source]
planemo.shed.find_raw_repositories(ctx, paths, **kwds)[source]

Return a list of “raw” repository objects for each repo on paths.

planemo.shed.for_each_repository(ctx, function, paths, **kwds)[source]
planemo.shed.get_shed_context(ctx=None, **kwds)[source]
planemo.shed.path_to_repo_name(path)[source]
planemo.shed.shed_init(ctx, path, **kwds)[source]

Initialize a new shed repository.

planemo.shed.tool_shed_client(ctx=None, **kwds)[source]
planemo.shed.tool_shed_url(ctx, **kwds)[source]