planemo.shed package


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.


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]

Fetch current username from shed given API key/auth.

Module contents

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


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.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]