Skip to content

Latest commit

 

History

History
551 lines (363 loc) · 20.5 KB

CHANGELOG.md

File metadata and controls

551 lines (363 loc) · 20.5 KB

BioBlend v - unreleased

  • BioBlend.objects: Removed deprecated container_id property of Dataset and Folder objects.
  • Pass the API key for all requests as the x-api-key header instead of as a parameter (thanks to rikeshi).
  • Added get_invocation_biocompute_object, get_invocation_report_pdf, get_invocation_step_jobs_summary methods to InvocationClient (thanks to rikeshi).
  • Improvements to tests and documentation (thanks to rikeshi).

BioBlend v0.15.0 - 2021-02-10

  • Dropped support for Python 3.5. Added support for Python 3.9. Added support for Galaxy releases 20.09 and 21.01.

  • Changed the return value of RolesClient.create_role() method from a 1-element list containing a dict to a dict.

  • Removed deprecated download_dataset() and get_current_history methods of HistoryClient.

  • Removed deprecated export_workflow_json() and import_workflow_json methods of WorkflowClient.

  • Added copy_content(), get_published_histories() and open_history() methods to HistoryClient.

  • Added rerun_job() method to JobsClient.

  • Added requirements() method to ToolClient (thanks to cat-bro).

  • Added published and slug parameters to HistoryClient.get_histories().

  • Added require_state_ok parameter to DatasetClient.download_dataset().

  • Added input_format parameter to ToolClient.run_tool().

  • Deprecated history_id parameter of HistoryClient.get_histories() method.

  • BioBlend.objects: Added owner property to Workflow objects. Added annotation, published and purged properties to HistoryPreview objects.

  • Fixed issue where specifying the Galaxy URL with "http://" instead of "https://" when creating a GalaxyInstance made the subsequent non-GET requests to silently fail.

  • Moved the Continuous Integration (CI) from TravisCI to GitHub workflows (thanks to Oleg Zharkov).

  • Improvements to tests and documentation (thanks to Gianmauro Cuccuru).

BioBlend v0.14.0 - 2020-07-04

  • Dropped support for Python 2.7. Dropped support for Galaxy releases 14.10-17.05. Added support for Python 3.8. Added support for Galaxy releases 19.09, 20.01 and 20.05.

  • Added a new invocations attribute to GalaxyInstance objects, which is an instance of the new InvocationClient class. This new module can be used to get all workflow invocations, show or cancel an invocation, show or pause an invocation step, get a summary or a report for an invocation (thanks to Simon Bray).

  • Added get_datasets() method to DatasetClient (thanks to Simon Bray).

  • Added import_history() method to HistoryClient (thanks to David Christiany and Marius van den Beek).

  • Added copy_dataset() method to HistoryClient (thanks to Simon Bray).

  • Added get_metrics() method to JobsClient (thanks to Andreas Skorczyk).

  • Added report_error() method to JobsClient (thanks to Peter Selten).

  • Added get_dataset_permissions() and set_dataset_permissions() methods to LibraryClient (thanks to Frederic Sapet).

  • Added update_user() method to UserClient (thanks to Anthony Bretaudeau).

  • Added update_workflow() method to WorkflowClient.

  • Added tags parameter to upload_file_from_url(), upload_file_contents(), upload_file_from_local_path(), upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient (thanks to Anthony Bretaudeau).

  • Changed the default for the tag_using_filenames parameter of upload_file_from_server() and upload_from_galaxy_filesystem() methods of LibraryClient from True to False (thanks to Anthony Bretaudeau).

  • Added version parameter to show_workflow() and export_workflow_dict() methods of WorkflowClient.

  • Added inputs_by option to invoke_workflow() method of WorkflowClient (thanks to Marius van den Beek).

  • Removed deprecated show_stderr() and show_stdout methods of DatasetClient.

  • BioBlend.objects: Allowed workflow steps of type parameter_input and subworkflow. Added parameter_input_ids property to Workflow objects (reported by Nolan Woods).

  • Fixed HistoryClient.export_history(..., wait=False, maxwait=None) (reported by David Christiany).

  • Moved internal _make_url() method from GalaxyClient to Client class.

BioBlend v0.13.0 - 2019-08-09

  • Dropped support for Python 3.4. Added support for Galaxy releases 19.01 and 19.05.

  • Updated requests-toolbelt requirement to >=0.5.1 to prevent failing of uploads to Galaxy (reported by m93).

  • Added toolshed attribute to GalaxyInstance and made toolShed an alias to it (reported by Miriam Payá).

  • Added uninstall_repository_revision() method to ToolShedClient (thanks to Helena Rasche, reported by Alexander Lenail).

  • Added maxwait parameter to HistoryClient.export_history() and History.export() methods.

  • Fixed handling of type parameter in HistoryClient.show_history() (thanks to Marius van den Beek).

  • Fixed handling of deleted parameter in LibraryClient.get_libraries() (thanks to Luke Sargent, reported by Katie).

  • Fixed LibraryClient.wait_for_dataset() when maxwait or interval parameters are of type float.

  • Unify JSON-encoding of non-file parameters of POST requests inside GalaxyClient.make_post_request().

  • Improvements to tests and documentation (thanks to Helena Rasche, Peter Selten and Pablo Moreno).

BioBlend v0.12.0 - 2018-12-17

  • Added support 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 support 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 Helena 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 Helena 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 Helena 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 Helena Rasche).

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

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

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