CHANGELOG.md

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: can't 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!