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ChangeLog
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ChangeLog
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* 0.35.6
* Support 3.11
* 0.35.5
* Release automatisation moved to Earthfile.
* 0.35.4
* Release automatisation moved to Earthfile.
* 0.35.3
* Release automatisation used.
* 0.35.2
* Release automatisation added.
* 0.35.1
* New line is added on error message when setting up the Genestack user without host
* 0.35.0
* Genestack host is now mandatory when setting up the Genestack user, default host has been removed
* 0.34.0
* Initial Python 3 support
* Implement auto checking for common sub-URLs (no explicit `/frontend`
required appended to `--host`)
* Removed:
* `AffymetrixMicroarraysNormalisationApplication` and
`AgilentMicroarraysNormalisationApplication` applications
* `BioMetainfo` class
* `normalised_input` argument for ExpressionNavigator applications
* `Connection.open` method
* `DataImporter`: `create_owl_ontology` and `create_pathway_database` methods
* `FilesUtil`: `create_dataset`, `get_groups_to_share`, `share_files`,
`share_folder` methods
* `TaskLogViewer.view_log` method
* 0.33.0
* New requirement: pyrsistent
* Removed:
* `FilesUtil`: `clear_container`, `get_group_folder_info` methods
* `OrganizationUtil` class
* `StudyDesign` application
* `SudoUtils` application
* 0.32.0
* Deprecated:
* `Metainfo.add_organization`, `Metainfo.add_publication`, `Metainfo.add_person`
* `Organization`, `Publication`, `Person`
* 0.31.0
* Changed supported file types of upload dataset in `SampleLinker`
* Increased `FilesUtil.MAX_FILE_SEARCH_LIMIT` constant
* Added `jsonschema` dependency
* Changed `login` and `login_by_token` methods to handle new error codes in authentication response.
* Renamed `BioMetaKeys.EXPRESSION_LEVEL_UNIT` metainfo key, the old key will be supported
for at least 1 month
* 0.30.0
* Added new method `DataImporter.create_expression_levels`
* Added `BioMetaKeys.EXPRESSION_LEVEL_UNIT` constant
* Added `IExpressionLevels` file type
* Fixed deserialization of Unicode `MetainfoScalarValue`s
* 0.29.0
* Added `FilesUtil.replace_metainfo_value` for replacing metainfo value for several files
* Added `OrganizationUtil` class for working with organization of the current user
* Fixed error when response log printed without traceback.
* Added `MetainfoRelatedValueFilter` file filter
* Added method `FilesUtil.find_metainfo_related_terms` for loading related terms
* 0.28.0
* Added `StudyDesign` class for working with studies and managing the Study Design application.
* 0.27.0
* Added `GenestackBaseException` to the top of exception hierarchy
* Added `GenestackResponseError` and `GenestackConnectionFailure`,
extending both `urllib2.URLError` (for backward compatibility)
and `GenestackBaseException`
* Deprecated `Connection.open` method, use `Connection.perform_request` instead.
* Changed `Application.invoke` and `Application.upload_file` methods to raise
`GenestackConnectionFailure` or `GenestackResponseError` instead of `urllib2.URLError`
* Removed `AuthenticationErrorHandler` class
* Updated `FileType` constants to match changes in core
* 0.26.0
* New methods in the `ShareUtil` class:
* `share_files`
* `safe_share_files`
* `share_folder`
* `FilesUtil.share_folder` is deprecated
* 0.25.0
* Fixed `Metainfo.parse_metainfo_from_dict(m)` modifies `m` https://github.com/genestack/python-client/issues/269
* Added 'FilesUtil.get_metainfo_values_as_string_list' method
* Implement simple `MetainfoScalarValue.__repr__()` for its subclasses
* 0.24.0
* Added `ShareUtil` class for working with sharing-related operations
* 0.23.0
* Added `GroupsUtil.find_group_by_name` method
* Added `DatasetsUtil.add_dataset_children` and `DatasetsUtil.add_file_to_datasets` methods
for adding files to datasets
* Removed warning about missing config
* 0.22.0
* `DatasetsUtil.create_dataset` now accepts an optional `dataset_metainfo` parameter to specify
created dataset metainfo
* Added `DatasetsUtil.create_empty_dataset` method
* 0.21.0
* Changed methods `FilesUtil.share_folder` and `FilesUtil.share_files` does not require password
* 0.20.0
* Added `Connection.login_by_token` method
* Added token support to `genestack-user-setup` script
* Renamed `password` command to `change-password` (in `genestack-user-setup`)
* Added `FileUtils.share_folder` method
* Added normalization applications classes
* Deprecated:
* `AffymetrixMicroarraysNormalisationApplication`, use `AffymetrixMicroarraysNormalizationApplication` instead
* `AgilentMicroarraysNormalisationApplication`, use `AgilentMicroarraysNormalizationApplication` instead
* `normalised_input` argument of the `_BaseExpressionNavigator._create_file`, use `normalized_input` instead
* 0.19.0
* Added utility class for datasets operations
* Added additional check for argument passed as arguments and via metainfo in DataImporter methods
* 0.18.0
* Added `DataImporter.INFINIUM_ANNOTATION` constant
* 0.17.0
* Added `BelongsToDatasetFileFilter` class
* Added `SpecialFolders.MY_DATASETS` constant
* Added new method `DataImporter.create_infinium_microarray_data`
* 0.16.0
* Added support of warnings to `status` command
* Added jar loading errors and warnings output to `install` command
* Added `DataImporter.create_gene_expression_signature` method
* Added `FilesUtil.EXPRESSION_SIGNATURE` constant
* 0.15.0
* Added `status` command for getting information about application loading state
* Removed flag `-w`/`--wait` from `install` command
* Added flag `-n`/`--no-wait` to `install` command (for asynchronous loading of applications)
* Changed default behaviour of `install` command to wait applications loading
* Added `DataImporter.create_microarray_data` method
* 0.14.0
* Added `Response` class, it represents response from server and allow to access logs and traces
* Added `Application.perform_request` method
* 0.13.0
* Added flag ``-l` to `versions` command in application manager for viewing loading state of
application with specific version
* Added flag `-w` to `install` command for waiting full loading of module (including sending scripts and creating
minified resources for each application in module)
* 0.12.0
* Minor improvements
* 0.12.0
* Added wrapper classes for Expression Navigator applications (for RNA-seq counts, isoforms and microarrays)
* Added `COMPOUND_*` complex keys in `BioMetaKeys` class
* Added a method `FilesUtil.collect_metainfos` to retrieve the full metainfo of a list of files
* Added methods to convert a map sent from Java into a client `Metainfo` object
* Added getters on `MetainfoScalarValue` subclasses mimicking the Java API
* Added possibility to not supply keys to `FilesUtil.get_metainfo_values_as_strings`, in which case all non-technical keys are fetched
* Added `FileFilter` objects and `FilesUtil.find_files` method for complete file search API
* Added `MetainfoScalarValue` objects
* Added `Permissions`, `SortOrder` and `FileTypes` enumerations
* Deprecated `Metainfo.add_temperature`, `Metainfo.add_time`
* 0.10.0
* Added `term_type` to dictionary uploader
* Added ability to remove applications by specified version
* Added `FilesUtil.mark_obsolete` method
* Added `-i` flag in `install` command of application manager for setting up initial application visibility
* Added class with bio constant `genestack_client.BioMetaKeys`
* Removed `DictionaryUtil`
* Removed `-r` flag in `install` command of application manager
* Deprecated `genestack_client.BioMetainfo`
* Methods `add_ethnic_group` and `add_organism` replaced by `Metainfo.add_string`
* Constants with metainfo keys moved to `bio_meta_keys.BioMetaKeys`
* 0.9.0
* Added `DataImporter.create_microarray_annotation`
* Renamed `DataImporter.create_owl_ontology` to `DataImporter.create_dictionary`
* 0.8.1a1
* Added support of 'group' and 'organization' visibilities
* 0.6.2
* Added waiting of application loading to `release`, `visibility`, and `markAsStable` (for SYSTEM scope only) commands
* Removed backward compatibility hack for `release` command
(use `ApplicationManagerApplication.releaseApplication(string, string, string)` method only)
* 0.6.1
* `Connection.login` raises GenestackAuthenticationException is authentication is failed
* `Connection.check_version` version argument removed, module version always used
* fix infinite ask password loop in case of use of old version
* version 0.5.2
* Fix GenestackServerException constructor to correctly pass exceptions
thrown in pool processes
* `release_applications` fixed according to last changes in application-manager application
(removed `override` argument)
* version 0.5.1
* Fix error on print exception in shell
* version 0.5.0
* Added `visibility` and `release` commands to `genestack-application-manager`
* Added `release` flag to `install` command in `genestack-application-manager`
* Added `create_owl_ontology` to `DataImporter`
* Added support for retrieving application logs
* Deprecated `genestack.bio:strain/breed/cultivar`, use `genestack.bio:strainBreedCultivar` instead
* version 0.4.1
* Fixed genestack-uploader crash
* version 0.4.0
* Added `add_publication`, `add_memory_size`, and `add_temperature` methods to Metainfo
* Changed confirmation dialog
* version 0.3.0
* Added `DictionaryUtil`
* Added new methods `get_metainfo_values_as_strings`, `link_files` and `unlink_files` to `FilesUtil`
* Moved `rename_file` method form `CLAplication` to `FilesUtil`, return type changed to `None`
* version 0.2.1
* Allow to run `genestack-user-setup` init with ``-H/--host argument`
* version 0.2.0
* Compatibility fixes according to the upcoming changes in the genestack platform
* new core returns JSON with application response stored in 'result' field
* chunked upload completion is marked as 'lastChunkUploaded' : true
* Updated documentation
* version 0.1.9
* Percent encode incoming urls for s3 in `DataImporter`
* Renamed `GenestackShell` module to `genestack_shell`
* Renamed `UnalignedReads` to `unaligned_reads`
* Added new method `create_mapped_reads_count` to `DataImporter`
* version 0.1.8
* Renamed pythonSDK to Python Client Library, `genestack` -> 'genestack-client'
* version 0.1.7
* Added TaskLogViewer application binding
* Renamed arguments with `link` in name to `url` in DataImporter fro
consistency (old arguments still present, for compatibility, will be removed
on next release.)
* Removed extension from all installable scripts
`genestack-application-manager.py` -> `genestack-application-manager`
* Server version checked at login. If version is not compatible raise exception
* version 0.1.6
* Added more classes for CLA
* Added `get_infos` and `get_complete_infos` methods to `FilesUtils`.
* Application ID without vendor is not supported by Connection
* Changed signature of add_external_link, now text argument is optional. Order
of arguments changed need to update all files.
* Droped support for short application ID
* version 0.1.2
* Improved console output for shell based scripts
* Added chunked upload feature
* new dependency `requests` was added
* upload speed improved for files more then 5mb
* upload can be resumed in case of interrupt
* Added warning if vendor is not specified in application ID
* Added constant SECONDARY_ACCESSION to BioMetainfo
* Removed Admin application (move it to core scripts)
* Removed optional accession param from FileUtils.create_folder()
* Made parent optional for DataImporter, use Imported folder as default.
* Replaced PRIVATE and PUBLIC constants in FilesUtils with methods.
* version 0.1.1
* Removed login and logout from Admin
* Removed get_string_value from Metainfo
* Removed link_name argument form create_dbnsfp
* version 0.1.0
* Added `remove` command to genestack-user-setup.py
* Added version.py, use same version in github releases and documentation
* version 0
* Added python sdk