pybis 1.37.4__tar.gz

pybis-1.37.4/CHANGELOG.md

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+## Changes with pybis-1.37.4
+
+- Improvements to Spreadsheet API
+- Handling UnicodeDecodeError in spreadsheet property
+- Added revert_deletions method
+- Introduced method for getting eln url for entities
+- Improvements to ServerInformation functionalities
+- Extended supported timestamp formats to include timezones
+- Improvements to property type display information
+
+## Changes with pybis-1.37.3
+
+- Fixes to get_children/get_parents methods
+
+## Changes with pybis-1.37.2
+
+- Fixes to Fast Upload 
+
+## Changes with pybis-1.37.1
+
+- Implemented Fast download V2
+- Fixed dataset with parents creation
+- Fixed type checking for python <3.10
+- Added basic ELN Spreadsheet support
+- Added support for new OBJECT property creation with OBJECT type limitation
+- Refactored AttributeHolder class to include fetchOptions
+- Refactored get_children and get_parents methods to pull data in case of missing fetchOptions
+
+## Changes with pybis-1.37.0
+
+- Changes to new_sample method to use v3api in all cases
+- Refactored new_experiment documentation 
+- Fixed delete vocabulary term method
+- Fixed v1 dataset upload
+- Fixed PropertyAssignment data frame creation
+- Improved property data type validation 
+- Improved get_project method 
+- Added missing description parameter to new sample type method
+- Added missing DATE property type
+- Improvement to user.get_roles() method to present proper project identification
+- Improvements to property assignment display
+- Fixed clearing of vocabulary properties
+- Improved setup script
+- Fixed transaction commit function
+- Fixed mount() method to work with PAT
+- Fixed plugin updates
+- Fixed new term creation
+
+## Changes with pybis-1.36.3
+
+- Refactored metaData and multiValue properties to be backwards-compatible.
+- Refactored get_children/get_parents methods
+- Refactored property formatting functionality 
+
+
+## Changes with pybis-1.36.2
+
+- Refactoring of the set_token method.
+- Improvement to exception handling for dataset upload 
+- Improvement to PAT functionality 
+
+## Changes with pybis-1.36.1
+
+- Amended get_*_types() method to be backwards-compatible
+- Amended dataset upload functionality to support big files 
+- Added multivalued properties support for objects, collections and datasets
+
+## Changes with pybis-1.36.0
+
+- Reverted breaking changes to dataset upload functionality
+- Performance improvements to get_sample and get_samples methods 
+
+## Changes with pybis-1.35.11
+
+- Improvements to dataset upload performance
+
+## Changes with pybis-1.35.10
+
+- Fixed issue with changing properties for linked datasets 
+
+## Changes with pybis-1.35.9
+
+- Changed get_samples method to also include dataset ids depending on the params 
+
+## Changes with pybis-1.35.8
+
+- Fixed a typo in the set attribute method
+
+## Changes with pybis-1.35.7
+
+- Improvements to fast download scheme 
+
+## Changes with pybis-1.35.6
+
+- Added metaData attribute handling for sample, sampleType, experiment, experimentType, dataset, datasetType
+- Fixed property assignment to a newly created sample type.
+- Updated docs.
+- Fixed sample.del_children() method.
+- Fixed metaData attribute assignment case.
+
+## Changes with pybis-1.35.5
+
+- Implementation of array-type properties handling
+- Fixed assignment of dynamic property plugins to property types 
+
+
+## Changes with pybis-1.35.4
+
+- Changes to internal implementation of data set download/upload to use OpenBIS V3 API
+- Added TIMESTAMP property reformatting to fit formats supported by OpenBIS
+
+## Changes with pybis-1.35.3
+
+- Modified set_token() method to accept PersonalAccessToken object
+- Minor code refactoring
+
+## Changes with pybis-1.35.2
+
+- Added rising an error when re-login fails
+
+## Changes with pybis-1.35.1
+
+- fix overriding parents/children when performing update using results from get_samples call
+
+## Changes with pybis-1.35.0
+
+- removal of deprecated 'cli'
+- removal of 'click' dependency
+- update of contact information
+
+## Changes with pybis-1.34.6
+
+- new option 'permanently' in the delete method in openbis_object.py
+
+## Changes with pybis-1.34.2
+
+- fix syslog error
+
+## Changes with pybis-1.34.1
+
+- better handling of configuration
+
+## Changes with pybis-1.34.0
+
+- better error handling when connecting to openBIS server
+- add experimental support for datasets via cli
+
+## Changes with pybis-1.33.2
+
+- fix openbis.support.email key error
+- raise error if invalid token is passed to constructor
+- show more attributes for spaces and projects
+
+## Changes with pybis-1.33.0
+
+- add support for personal access tokens (PAT)
+- fix default dataset kind (was PHYSICAL_DATA instead of PHYSICAL)
+- refactor existing pyBIS code
+
+## Changes with pybis-1.32.1
+
+- fixing the issue with incorrectly named reference to DataSetKind.PHYSICAL
+
+## Changes with pybis-1.32.0
+
+- throw error when invalid token is assigned
+- to not show an error message if stored token is invalid (just do not use it)
+- fixed a bug which led to missing parents and children
+
+## Changes with pybis-1.31.6
+
+- automatically setting the project if only experiment was set
+
+## Changes with pybis-1.31.5
+
+- optimised error generation without assert
+
+## Changes with pybis-1.31.4
+
+- fix another exception when saving a sample with custom code
+
+## Changes with pybis-1.31.3
+
+- fix exception in sample.save
+
+## Changes with pybis-1.31.1
+
+- fixed a file download problem when filename contained special characters (e.g. #)
+
+## Changes with pybis-1.31.0
+
+- new entity-type methods: get_next_code() and get_next_sequence()
+- allow to set code manually for samples of sampleType with autoGeneratedCode=True
+
+## Changes with pybis-1.30.4
+
+- fixed and optimised (deprecated) download_attachments()
+
+## Changes with pybis-1.30.3
+
+- Another code fix for create_data_frame() in pybis.py to make group ID and user ID separate
+
+## Changes with pybis-1.30.2
+
+- Possible issue fixes with data frame in create_data_frame() in entity_type.py
+- Code fix for create_data_frame() in pybis.py to make group ID and user ID separate
+
+## Changes with pybis-1.30.1
+
+- fixed KeyError when creating an empty data frame
+
+## Changes with pybis-1.30.0
+
+- session management reworked
+
+## Changes with pybis-1.20.5
+
+- fixed same problems as 1.20.5
+- wrong version published
+
+## Changes with pybis-1.20.4
+
+- fixed parents/children problem when get_samples(), get_datasets()
+- sorted imports
+
+## Changes with pybis-1.20.3
+
+- deactivated debugging logs
+- creation of property type accets vocabulary object
+
+## Changes with pybis-1.20.2
+
+- fixed omitted function parameter which could cause issues
+
+## Changes with pybis-1.20.1
+
+- improved search performance
+- introduced lazy loading for Things.df and Things.objects, so all necessary, and potentially
+  costly, computation takes place only when the user requests those properties
+
+## Changes with pybis-1.20.0
+
+- metadata for property_types can now be changed to:
+    - {'custom_widget' : 'Word Processor'}
+    - {'custom_widget' : 'Spreadsheet'}
+- added documentation how to change the ELN settings
+- removed deprecated update_sample()
+- removed deprecated update_experiment()
+
+## Changes with pybis-1.19.1
+
+- add set_token() method to set a token and also store it locally
+
+## Changes with pybis-1.19.0
+
+- added caching for get_experiment
+- included OR when providing codes/permIds for samples and datasets
+- improved documentation
+- fixed property assigning problem with newly created entity types
+
+## Changes with pybis-1.18.12
+
+- fixed rel_file_links, prepended /
+
+## Changes with pybis-1.18.11
+
+- added rel_file_links to datasets for embedding in ELN-LIMS
+
+## Changes with pybis-1.18.10
+
+- added deprecation warnings for components/containers and attachments
+- added download_path and file_links to datasets
+
+## Changes with pybis-1.18.9
+
+- fixed problem when searching for experiments
+
+## Changes with pybis-1.18.8
+
+- fixed problem with 20.10 releases where samples could not be found using the permId
+
+## Changes with pybis-1.18.7
+
+- fixed entity_type caching problem
+
+## Changes with pybis-1.18.6
+
+- fixed create samples bug
+- fixed zip upload bug
+
+## Changes with pybis-1.18.5
+
+- fixed deref bug for container
+- added set and get methods for properties
+
+## Changes with pybis-1.18.4
+
+- fixed bug in returning identifiers (thanks, Fabian!)
+
+## Changes with pybis-1.18.3
+
+- prevent other users to read the saved token (chmod 600)
+- fixed various pylint issues
+- fixed «session no longer valid» message
+- fixed search issues
+
+## Changes with pybis-1.18.2
+
+- added deletion to transaction
+
+## Changes with pybis-1.18.1
+
+- fixed del_parents() bug accidentally introduced in 1.18.0
+
+## Changes with pybis-1.18.0
+
+- speed improvement when searching for samples and dataSets and then cycling through the results
+- implemented search for number comparison, date comparison, string comparison (<, >, <=, >=)
+- implemented search for parents identities and properties
+- fixed minor bugs when connecting
+
+## Changes with pybis-1.17.4
+
+- fixed another vocabularies update bug
+- extended tests
+- extended documentation
+
+## Changes with pybis-1.17.3
+
+- fixed vocabularies bug
+- fixed updating vocabularies
+
+## Changes with pybis-1.17.1
+
+- fixed datastore bug
+
+## Changes with pybis-1.17.0
+
+- added caching for often used but rarely updated openBIS objects.
+- if you need to create a lot of Samples, this will improve your speed a lot
+- by default, caching is enabled
+
+## Changes with pybis-1.16.2
+
+- transaction.commit() now updates all added samples with their respective permIds
+
+## Changes with pybis-1.16.1
+
+- new_dataset bugfix
+
+## Changes with pybis-1.16.0
+
+- added support for batch creation of samples
+- changed Python minimum requirement to Python 3.6
+- new vocabulary and new property_type: internalNameSpace was removed
+- this will cause possible incompatibilities with older versions of openBIS (< 20.10.x)
+
+## Changes with pybis-1.15.1
+
+- added support for date-searching
+- bugfix in property-searching
+
+## Changes with pybis-1.14.10
+
+- bugfix when deleting dataSets
+- some improvements with the documentation
+
+## Changes with pybis-1.14.9
+
+- quick fix of parse_jackson error in special circumstances
+
+## Changes with pybis-1.14.7
+
+- bugfix: no longer any error in get_samples(), get_datasets() and get_experiments() when
+  properties are provided but no data was found
+
+## Changes with pybis-1.14.6
+
+- bugfix duplicate property-columns in get_samples() and get_datasets()
+
+## Changes with pybis-1.14.5
+
+- no automagic detection of mountpoint, because of Windows incompatibilities
+
+## Changes with pybis-1.14.4
+
+- added new convenience methods: get_experiments, get_projects etc.
+
+## Changes with pybis-1.14.3
+
+- small bugfix: prevent error
+
+## Changes with pybis-1.14.2
+
+- properties can be provided with either upper or lowercase
+- bugfix of duplicate property columns
+
+## Changes with pybis-1.14.1
+
+- small bugfix
+
+## Changes with pybis-1.14.0
+
+- use props="\*" to get all properties of all samples or datasets
+
+## Changes with pybis-1.13.0
+
+- added symlink() method for datasets to automatically create symlinks
+- added `is_symlink()` and `is_physical()` methods for dataSets
+- new `o.download_prefix` attribute for `download()` and `symlink()`
+- `download_prefix` defaults to `data/openbis-hostname`
+
+## Changes with pybis-1.12.4
+
+- fixed a bug which occured on some opeBIS instances when retrieving samples
+
+## Changes with pybis-1.12.3
+
+- datasets, samples and experiments now successfully return project and space attributes
+
+## Changes with pybis-1.12.0
+
+- added possibility to get any additional attributes in the get_samples() method
+- added possibility to get any additional attributes in the get_dataSets() method
+
+## Changes with pybis-1.11.1
+
+- added automatically accepting host key, otherwise mount() will hang the first time
+
+## Changes with pybis-1.11.0
+
+- implemented mount() and unmount() methods to mount openBIS dataStore server via SSHFS and FUSE
+- implemented is_mounted() and get_mountpoint() methods
+- added instructions how to install FUSE/SSHFS on Unix systems
+
+## Changes with pybis-1.10.8
+
+- dataSets of kind CONTAINER now also allow download of files
+
+## Changes with pybis-1.10.7
+
+- made download work, even downloadUrl attribute is missing in dataSets
+
+## Changes with pybis-1.10.6
+
+- added possibility to download files without /original/DEFAULT folders
+
+## Changes with pybis-1.10.5
+
+- bugfix: creating projects
+
+## Changes with pybis-1.10.4
+
+- better error messages when downloading files from datastore server
+
+## Changes with pybis-1.10.3
+
+- print warning message when downloaded file-size does not match with promised file-size. Do not
+  die.
+
+## Changes with pybis-1.10.2
+
+- typo bugfix
+
+## Changes with pybis-1.10.1
+
+- fixed a nasty threading bug: open threads are now closed when downloading or uploading datasets
+- this bugfix avoids this RuntimeError: cannot start new thread
+
+## Changes with pybis-1.10.0
+
+- dataSet upload now supports zipfiles
+- dataSet upload now supports files and folders
+- different behaviour when providing a folder: files are no longer flattened out, structure is kept
+  intact
+
+## Changes with pybis-1.9.8
+
+- new: create and update Dateset Types
+- new: create and update Experiment Types
+- new: create and update Material Types
+- many bugfixes
+- extended documentation about creating these entity types
+
+## Changes with pybis-1.9.7
+
+- bugfix for creating propertyTypes of type controlled vocabulary and material
+
+## Changes with pybis-1.9.6
+
+- bugfix when vocabulary attribute was not identical to the code of the aassigned property type
+
+## Changes with pybis-1.9.5
+
+- bugfixes: get_property_assignments() method fixed for dataSet-, experiment- and materialTypes
+
+## Changes with pybis-1.9.4
+
+- bugfix when searching for experiments or datasets of a given type
+
+## Changes with pybis-1.9.3
+
+- fixed documentation: add_members (not add_persons)
+- bugfix role assignments of groups
+
+## Changes with pybis-1.9.2
+
+- searches for datasets and samples are highly improved
+- search parameters can accept a code, an identifier or an openbis entity
+- searching for all datasets in a project now works
+- bugfixes
+
+## Changes with pybis-1.9.1
+
+- bugfix: controlled vocabulary
+
+## Changes with pybis-1.9.0
+
+- new: search, create, update and delete Property Types
+- new: search, create, update and delete Plugins
+- new: create and update Sample Types
+- freeze entities to prevent changes
+- added more tests
+
+## Changes with pybis-1.8.5
+
+- changed to v3 API when fetching datastores
+- gen_permId to generate unique permIds used for dataSets
+- support ELN-LIMS style identifiers: /SPACE/PROJECT/COLLECTION/OBJECT_CODE
+- terms now can be moved either to the top or after another term
+
+## Changes with pybis-1.8.4
+
+- totalCount attribute added in every Things object
+- totalCount will return the total number of elements matching a search
+- bugfix in get_semantic_annotation method
+
+## Changes with pybis-1.8.3
+
+- new method for attributes: .attrs.all() will return a dict, much like .props.all()
+- attributes like registrator and modifier are now returned by default
+
+## Changes with pybis-1.8.2
+
+- added key-lookup and setting for properties that contain either dots or dashes
+- sample.props['some-weird.property-name'] = "some value"
+- check for mandatory properties in samples (objects), datasets and experiments (collections)
+
+## Changes with pybis-1.8.1
+
+- revised documentation
+- improved DataSet creation
+- added missing delete function for DataSets
+- wrong entity attributes will now immediately throw an error
+- more DataSet creation tests
+- paging tests added
+- `collection` is now alias for `experiment`
+- `object` is alias for `sample`
+
+## Changes with pybis-1.8.0
+
+- better support for fetching entity-types (dataSetTypes, sampleTypes)
+- separation of propertyAssignments from entity-types
+- added .get_propertyAssignments() method to all entity-types
+
+## Changes with pybis-1.7.6
+
+- bugfix dataset upload for relative files (e.g. ../../file or /User/username/file)
+- always only the filename is added to the dataset, not the folder containing it
+- corrected License file
+
+## Changes with pybis-1.7.5
+
+- added paging support for all search functions by providing start_with and count arguments
+- make search more robust: allow get_sample('SPACE/CODE') instead of get_sample('/SPACE/CODE')
+- make search more robust: allow get_sample(' 20160706001644827-208 ')
+- make interface more robust (allow sample.permid instead of sample.permId)
+- make properties more robust: allow get_samples(props='name') instead of get_samples(
+  props=['name'])
+- fixed bug when parent/children of more than one element was searched: o.get_experiments()
+  .get_samples().get_parents()
+
+## Changes with pybis-1.7.4
+
+- pyBIS now allows to create dataset-containers that contain no data themselves
+- datasets now show a «kind» attribute, which can be either PHYSICAL, LINK or CONTAINER
+- PropertyAssignments and other internal data are now finally nicely presented in Jupyter
+- various bugfixes
+- README.md is now correctly displayed
+- setup.py is fixed, installation should no longer fail because of some utf-8 problems on certain
+  machines
+
+## Changes with pybis-1.7.3
+
+- improved packaging information
+- LICENSE included (Apache License v.2)
+
+## Changes with pybis-1.7.2
+
+- added server_information to openBIS connection
+- bugfix: project samples are only fetched when instance supports them
+
+## Changes with pybis-1.7.1
+
+- fixed bug in controlled vocabulary when property name did not match the vocabulary name
+- added `xxx_contained()` methods to Samples and DataSets
+- updated documentation
+
+## Changes with pybis-1.7.0
+
+- added components and containers functionality to both datasets and samples
+- `set_attributes()` no longer automatically saves the object
+- tags now have to be created (and saved) before they can be assigned
+- `get_tag()` now can search for more than one tag at once and supports both code and permId
+- `get_tags()` now available for almost all objects, returns a dataframe
+- improved and enhanced documentation
+
+## Changes with pybis-1.6.8
+
+- fixed bugs with parents and children of both samples and datasets
+- new samples can be defined with parents / children
+- `get_parents()` and `get_children()` methods now also work on new, not yet saved objects
+- `get_sample()` and `get_dataset()` now also accept arrays of permIds / identifiers
+- pybis now has a CHANGELOG!