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BioBlend v0.12.0 - 2018-12-17

  • Added supported for Python 3.7. Added support for Galaxy releases 18.05 and 18.09.

  • Added update_library_dataset() method to LibraryClient (thanks to Anthony Bretaudeau).

  • Added preserve_dirs and tag_using_filenames parameters to upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient (thanks to Anthony Bretaudeau).

  • Removed deprecated wait_for_completion parameter of DatasetClient.download_dataset() method.

  • BioBlend.objects: added genome_build and misc_info attributes to Dataset objects. Moved deleted attribute from Dataset to HistoryDatasetAssociation and LibraryDatasetDatasetAssociation objects. Moved purged attribute from Dataset to HistoryDatasetAssociation objects.

  • BioBlend.objects: added update() method to LibraryDataset (thanks to Anthony Bretaudeau).

  • Run tests with pytest instead of nose

BioBlend v0.11.0 - 2018-04-18

  • Dropped supported for Python 3.3. Added support for Galaxy release 18.01.

  • Always wait for terminal state when downloading a dataset.

  • Deprecated wait_for_completion parameter of DatasetClient.download_dataset() method.

  • Fixed downloading of datasets receiving a HTTP 500 status code (thanks to Eric Rasche).

  • Added wait_for_dataset() method to LibraryClient.

  • Added verify parameter to GalaxyInstance.__init__() method (thanks to Devon Ryan).

  • Improvements to tests and documentation.

BioBlend v0.10.0 - 2017-09-26

  • Dropped support for Python 2.6. Added support for Galaxy release 17.09.

  • Added contents parameter to FoldersClient.show_folder() method (thanks to Eric Rasche).

  • Exposed the verify attribute of GalaxyInstance and ToolShedInstance objects as __init__() parameter.

  • Added create_role() method to RolesClient (thanks to Ashok Varadharajan).

  • Added timeout parameter to GalaxyClient.__init__() method.

  • Added publish parameter to import_workflow_dict() and import_workflow_from_local_path() methods of WorkflowClient (thanks to Marco Enrico Piras).

  • BioBlend.objects: added publish parameter to ObjWorkflowClient.import_new() method (thanks to Marco Enrico Piras).

  • Do not check for mismatching content size when streaming a dataset to file (reported by Jorrit Boekel).

  • Fixed delete requests when Galaxy uses external authentication (thanks to Eric Rasche).

  • Fixed retrieval of the API key when a GalaxyClient object is initialised with email and password on Python 3 (thanks to Marius van den Beek).

  • Documentation improvements.

BioBlend v0.9.0 - 2017-05-25

  • Dropped support for Galaxy releases 14.02, 14.04, 14.06 and 14.08. Added support for Python 3.5 and 3.6, and Galaxy releases 16.07, 16.10, 17.01 and 17.05.

  • Deprecated import_workflow_json() and export_workflow_json() methods of WorkflowClient in favor of import_workflow_dict() and export_workflow_dict() (reported by @manabuishii).

  • Deprecated show_stderr() and show_stdout() methods of DatasetClient in favour of JobsClient.show_job() with full_details=True.

  • Added install_dependencies() method to ToolClient (thanks to Marius van den Beek).

  • Added reload_data_table() method to ToolDataClient (thanks to Marius van den Beek).

  • Added create_folder(), update_folder(), get_permissions(), set_permissions() methods to FoldersClient (thanks to Eric Rasche).

  • Added get_version() method to ConfigClient (thanks to Eric Rasche).

  • Added get_user_apikey() method to UserClient (thanks to Eric Rasche).

  • Added create_quota(), update_quota(), delete_quota() and undelete_quota() methods to QuotaClient (thanks to Eric Rasche).

  • Added purge parameter to HistoryClient.delete_dataset() method.

  • Added f_email, f_name, and f_any parameters to UserClient.get_users() method (thanks to Eric Rasche).

  • Updated WorkflowClient.import_shared_workflow() method to use the newer Galaxy API request (thanks to @DamCorreia).

  • Fixed HistoryClient.update_history() and History.update() methods when name parameter is not specified.

  • Added warning if content size differs from content-length header in DatasetClient.download_dataset().

  • BioBlend.objects: added purge parameter to HistoryDatasetAssociation.delete() method.

  • BioBlend.objects: added purged attribute to Dataset objects.

  • BioBlend.objects: added published attribute to History objects.

  • Code refactoring, added tests and documentation improvements.

BioBlend v0.8.0 - 2016-08-11

  • Removed deprecated create_user() method of UserClient.

  • Deprecated HistoryClient.download_dataset() in favor of DatasetClient.download_dataset().

  • Modified update_dataset(), update_dataset_collection() and update_history() methods of HistoryClient to return the details instead of the status code.

  • Modified update_dataset(), update_dataset_collection() and update_history() methods of HistoryClient to return the details instead of the status code.

  • Modified GalaxyClient.make_put_request() to return the decoded response content.

  • Added install_resolver_dependencies parameter to ToolShedClient.install_repository_revision(), applicable for Galaxy release_16.07 and later (thanks to Marius van den Beek).

  • Improve DatasetClient.download_dataset() by downloading the dataset in chunks when saving to file (thanks to Jorrit Boekel).

  • Added bioblend.toolshed.categories.ToolShedCategoryClient; renamed bioblend.toolshed.repositories.ToolShedClient class to bioblend.toolshed.repositories.ToolShedRepositoryClient; renamed bioblend.toolshed.tools.ToolShedClient class to bioblend.toolshed.tools.ToolShedToolClient.

  • Added delete_user() method to UserClient.

  • BioBlend.objects: added update() method to HistoryDatasetAssociation.

  • BioBlend.objects: added annotation and genome_build attributes to HistoryDatasetAssociation objects.

  • BioBlend.objects: added update() method to HistoryDatasetAssociation.

  • BioBlend.objects: added ability to create and delete dataset collections (thanks to Alex MacLean).

  • BioBlend.objects: added dataset collections to the outputs of Workflow.run().

  • Added ability to launch Galaxy CloudMan instances into AWS VPC.

  • A number of testing tweaks, documentation improvements and minor fixes.

BioBlend v0.7.0 - 2015-11-02

  • BioBlend.objects: enabled import of workflows containing dataset collection inputs.

  • Implemented APIs for a modern Galaxy workflow APIs (i.e. delayed scheduling).

  • Implemented APIs to search Tool Shed repositories and tools.

  • Added support for uploading (importing) from FTP (thanks to Eric Rasche).

  • Added to_posix_lines and space_to_tab params to upload_file(), upload_from_ftp() and paste_content() methods of ToolClient.

  • BioBlend.objects: added upload_from_ftp() method to History.

  • Updated the testing framework to work with Galaxy wheels; use TravisCI's container infrastructure; test Galaxy release 15.07.

  • Updated CloudmanLauncher's launch method to accept subnet_id parameter, for VPC support (thanks to Matthew Ralston).

  • Properly pass extra parameters to cloud instance userdata.

  • Updated placement finding methods and get_clusters_pd method to return a dict vs. lists so error messages can be included.

  • A numer of documentation improvements and minor updates/fixes (see individual commits).

BioBlend v0.6.1 - 2015-07-27

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

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

  • BioBlend.objects: added 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 - 2015-06-30

  • Added support for Python >= 3.3.

  • Added get_library_permissions() method to LibraryClient.

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

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

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

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

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

  • Verify SSL certificates by default.

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

  • Solidified automated testing by using tox and flake8.

BioBlend v0.5.3 - 2015-03-18

  • 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).

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

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

  • Added get_state() method to JobsClient.

  • Added copy_from_dataset() method to LibraryClient.

  • Added create_repository() method to ToolShedRepositoryClient (thanks to Eric Rasche).

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

  • Made 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: added method to fetch instance types.

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

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

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

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

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

  • BioBlend.objects: the parent property of a Folder object is now set to its parent folder object (thanks to John M. Eppley).

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

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

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

  • BioBlend.objects: renamed 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 - 2014-10-17

  • BioBlend.objects: enabled email&password auth

  • Enabled Tool Shed tar ball uploads

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

  • BioBlend.objects: fixed library dataset downloads

  • Fixed the Tool Shed tool installation method

  • Added '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 - 2014-08-19

  • 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.

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