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CHANGELOG.md

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BioBlend v0.6.1 - July 27, 2015

  • BioBlend.objects: Rename ObjDatasetClient abstract class to ObjDatasetContainerClient.

  • BioBlend.objects: Add ABCMeta metaclass and list() method to ObjClient.

  • BioBlend.objects: Add io_details and link_details parameters to ObjToolClient.get() method.

  • Open port 8800 when launching cloud instances for use by NodeJS proxy for Galaxy IPython Interactive Environments.

  • When launching cloud instances, propagate error messages back to the called. The return types for methods create_cm_security_group, create_key_pair in CloudManLauncher class have changed as a result of this.

BioBlend v0.6.0 - June 30, 2015

  • Add support for Python >= 3.3.

  • Add get_library_permissions() method to LibraryClient.

  • Add update_group(), get_group_users(), get_group_roles(), add_group_user(), add_group_role(), delete_group_user() and delete_group_role() methods to GroupsClient.

  • Add full_details parameter to JobsClient.show_job() (thanks to Rossano Atzeni).

  • BioBlend.objects: add ObjJobClient and Job wrapper (thanks to Rossano Atzeni).

  • BioBlend.objects: add check to verify that all tools in a workflow are installed on the Galaxy instance (thanks to Gianmauro Cuccuru).

  • Remove several deprecated parameters: see commits 19e168f and 442ae98.

  • Verify SSL certificates by default.

  • Add documentation about the Tool Shed and properly link all the docs on ReadTheDocs.

  • Solidify automated testing by using tox and flake8.

BioBlend v0.5.3 - March 18, 2015

  • Project source moved to new URL - https://github.com/galaxyproject/bioblend

  • Huge improvements to automated testing, tests now run against Galaxy release_14.02 and all later versions to ensure backward compatibility (see .travis.yml for details).

  • Many documentation improvements (thanks to Eric Rasche).

  • Add Galaxy clients for the tool data tables, the roles, and library folders (thanks to Anthony Bretaudeau).

  • Add method to get the standard error and standard output for the job corresponding to a Galaxy dataset (thanks to Anthony Bretaudeau).

  • Add get_state() method to JobsClient.

  • Add copy_from_dataset() method to LibraryClient.

  • Add create_repository() method to ToolShedClient (thanks to Eric Rasche).

  • Fix DatasetClient.download_dataset() for certain proxied Galaxy deployments.

  • Make LibraryClient._get_root_folder_id() method safer and faster for Galaxy release_13.06 and later.

  • Deprecate and ignore invalid deleted parameter to WorkflowClient.get_workflows().

  • CloudMan: Add method to fetch instance types.

  • CloudMan: Update cluster options to reflect change to SLURM.

  • BioBlend.objects: Deprecate and ignore invalid deleted parameter to ObjWorkflowClient.list().

  • BioBlend.objects: Add paste_content() method to History objects.

  • BioBlend.objects: Add copy_from_dataset() method and root_folder property to Library objects.

  • BioBlend.objects: Add container and deleted attributes to Folder objects.

  • BioBlend.objects: Set the parent attribute of a Folder object to its parent folder object (thanks to John M. Eppley).

  • BioBlend.objects: Add deleted parameter to list() method of libraries and histories.

  • BioBlend.objects: Add state and state_details attributes to History objects (thanks to Gianmauro Cuccuru).

  • BioBlend.objects: Rename upload_dataset() method to upload_file() for History objects.

  • BioBlend.objects: Rename input_ids and output_ids attributes of Workflow objects to source_ids and sink_ids respectively.

  • Add run_bioblend_tests.sh script (useful for Continuous Integration testing).

BioBlend v0.5.2 - October 17, 2014

  • BioBlend.objects: enable email&password auth

  • Enable Tool Shed tar ball uploads

  • BioBlend.objects: allow deletion of history and library datasets

  • BioBlend.objects: fixed library dataset downloads

  • Fixed the Tool Shed tool installation method

  • Add 'deleted' attribute to DatasetContainer

  • Handle data_type changes in the Oct 2014 Galaxy release

  • Renamed get_current_history() to get_most_recently_used_history()

  • A number of documentation improvements and other small fixes (see the commit messages for more details)

BioBlend v0.5.1 - August 19, 2014

  • Fixed url joining problem described in issue #82

  • Enabled Travis Continuous Inetgration testing

  • Added script to create a user and get its API key

  • Deprecated create_user() method in favor of clearer create_remote_user(). Added create_local_user().

  • Skip instead of fail tests when BIOBLEND_GALAXY_URL and BIOBLEND_GALAXY_API_KEY environment variables are not defined.

  • Added export and download to objects API

  • Added export/download history

  • GalaxyClient: changed make_put_request to return whole requests response object

  • Added Tool wrapper to BioBlend.objects plus methods to list tools and get one

  • Added show_tool() method to ToolClient class

  • Added name, in_panel and trackster filters to get_tools()

  • Added upload_dataset() method to History class.

  • Removed DataInput and Tool classes for workflow steps. Tool is to be used for running single tools.