https://github.com/afgane/bioblend
Tip revision: f041b823cff00b80918f66f68fe5e8ab03c16d32 authored by Enis Afgan on 14 September 2015, 14:20:32 UTC
Add more method implementations for openstack; abstract some common methods into the interface class
Add more method implementations for openstack; abstract some common methods into the interface class
Tip revision: f041b82
CHANGELOG.md
### 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](https://github.com/galaxyproject/bioblend/commit/19e168f5342f4c791d37694d7039a85f2669df71)
and [442ae98](https://github.com/galaxyproject/bioblend/commit/442ae98037be7455d57be15542553dc848d99431).
* 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](https://tox.readthedocs.org/) and
[flake8](https://gitlab.com/pycqa/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.