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Commit 181b2150 authored by Swen Vermeul's avatar Swen Vermeul
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Merge branch 'release/1.30.4'

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pybis/src/python/CHANGELOG.md
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## 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
- 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'}
- {'custom_widget' : 'Word Processor'}
- {'custom_widget' : 'Spreadsheet'}
- added documentation how to change the ELN settings
- removed deprecated update_sample()
- removed deprecated update_experiment()
......@@ -35,6 +55,7 @@
## 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
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## 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
......@@ -156,14 +179,13 @@
- 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
- no automagic detection of mountpoint, because of Windows incompatibilities
## Changes with pybis-1.14.4
......@@ -184,7 +206,7 @@
## Changes with pybis-1.14.0
- use props="*" to get all properties of all samples or datasets
- use props="\*" to get all properties of all samples or datasets
## Changes with pybis-1.13.0
......@@ -208,218 +230,195 @@
## Changes with pybis-1.11.1
- added automatically accepting host key, otherwise mount() will hang the first time
- 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
- 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
- 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
- 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
- added possibility to download files without /original/DEFAULT folders
## Changes with pybis-1.10.5
* bugfix: creating projects
- bugfix: creating projects
## Changes with pybis-1.10.4
* better error messages when downloading files from datastore server
- 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.
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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)
- 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`
- 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
- 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
- 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()
- 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
- 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)
- 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
- 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
- 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
- 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!
- 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!
pybis/src/python/README.md
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pybis/src/python/pybis/__init__.py
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name = "pybis"
__author__ = "Swen Vermeul"
__email__ = "swen@ethz.ch"
__version__ = "1.30.3"
__version__ = "1.30.4"
from . import pybis
from .pybis import DataSet
......
pybis/src/python/setup.py
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......@@ -13,7 +13,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setup(
name="PyBIS",
version="1.30.3",
version="1.30.4",
author="Swen Vermeul • ID SIS • ETH Zürich",
author_email="swen@ethz.ch",
description="openBIS connection and interaction, optimized for using with Jupyter",
......
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