Skip to content
Snippets Groups Projects
Select Git revision
  • BIS-1397-remove-log4j-AS-DSS
  • bis-738-afs-archiving
  • master default
  • bis-1715-rebuild-schema-from-ro-crate
  • bis-1715-ro-crate-import
  • 20.10.x
  • BIS-1611-spectra-locator
  • BIS-1032-RC-Zenodo-exports
  • BIS-1779-enable-ontologies-info
  • bis-1797-afs-api-chunking-mechanism
  • BIS-1789-new-widget-integrate--eln-ui-IV
  • 6.7.x
  • BIS-1789-new-widget-integrate--eln-ui-IV-copy
  • bis-1767-fix-tests-again
  • bis-1767-fix-tests
  • bis-1767-import-multiple-semantic-annotations
  • bis-1802-shared-identifi
  • BIS-1789-new-widget-integrate--eln-ui-III
  • BIS-1789-new-widget-integrate--eln-ui-III-copy
  • BIS-1789-new-widget-integrate--eln-ui-II
  • 6.7.0
  • 443.0
  • 442.0
  • 441.0
  • 440.0
  • 20.10.11.1
  • 20.10.11
  • 435.0
  • 434.0
  • 6.6.0
  • 20.10.10
  • 433.0
  • 432.0
  • 20.10.9.1
  • 429.0
  • 20.10.9
  • 428.0
  • 425.0
  • 423.0
  • test
40 results
Compare
Name Last commit Last update
.obis
docs
src
.gitignore
README.md
README.rst
README.md

Welcome to pyBIS!

pyBIS is a Python module for interacting with openBIS, designed to be used in Jupyter. It offers a sort of IDE for openBIS, supporting TAB completition and input checks, making the life of a researcher hopefully easier.

PyBIS Documentation

Requirements and organization

Dependencies and Requirements

  • pyBIS relies the openBIS API v3; openBIS version 16.05.2 or newer
  • pyBIS uses Python 3.3 and pandas

Installation

  • locate the jupyter-api folder found in pybis/src/coreplugins
  • copy this folder to openbis/servers/core-plugins in your openBIS installation
  • register the plugin by editing openbis/servers/core-plugins/core-plugins.properties :
  • enabled-modules = jupyter-api (separate multiple plugins with comma)
  • restart your DSS to activate the plugin

Project Organization

This project is devided in several parts:

  • src/python/PyBis Python module which holds all the method to interact with OpenBIS
  • src/python/OBis a command-line tool to register large datasets in OpenBIS without actually copying the data. Uses git annex for version control and OpenBIS linkedDataSet objects to register the metadata.
  • src/python/JupyterBis a JupyterHub authenticator module which uses pyBIS for authenticating against openBIS, validating and storing the session token
  • src/core-plugins/jupyter-api, an ingestion plug-in for openBIS, allowing people to upload new datasets
  • src/vagrant/jupyter-bis/Vagrantfile to set up JupyterHub on a virtual machine (CentOS 7), which uses the JupyterBis authenticator module
  • src/vagrant/obis/Vagrantfile to set up a complete OpenBIS instance on a virtual machine (CentOS 7)