Newer
Older
## 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
Swen Vermeul
committed
- 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
## Changes with pybis-1.14.10
- bugfix when deleting dataSets
- some improvements with the documentation
- 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
- 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
Swen Vermeul
committed
## 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
Swen Vermeul
committed
## 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
## Changes with pybis-1.8.5
* changed to v3 API when fetching datastores
Swen Vermeul
committed
* 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)
* 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
## 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()
* 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
Swen Vermeul
committed
## 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
Swen Vermeul
committed
## 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!