APIS

• Java / Javascript
  • I. Architecture
    • The Java API
    • The Javascript API
  • II. API Features
    • Current Features - AS
    • Main DSS Features
    • Main AFS Features
    • Transactions
  • III. Accessing the API
    • Connecting in Java
    • Connecting in Javascript
      • AMD / RequireJS
      • AMD / RequireJS bundle
      • VAR bundle
      • ESM bundle (also available in NPM)
    • Synchronous Java vs Asynchronous Javascript
    • TypeScript support
    • React support
  • IV. AS Methods
    • Login
      • Example
    • Personal Access Tokens
    • Session Information
      • Example
    • Creating entities
      • Example
      • Properties example
      • Different ids example
      • Parent child example
    • Updating entities
      • Example
      • Properties example
      • Parents example
    • Getting authorization rights for entities
    • Freezing entities
      • Space
      • Project
      • Experiment
      • Sample
      • Data Set
    • Searching entities
      • Example
      • Example with pagination and sorting
      • Example with OR operator
      • Example with nested logical operators
      • Example with recursive fetch options
      • Global search
    • Getting entities
      • Example
    • Deleting entities
      • Example
    • Searching entity types
    • Modifications
    • Custom AS Services
      • Search for custom services
      • Execute a custom service
    • Archiving / unarchiving data sets
      • Archiving data sets
      • Unarchiving data sets
    • Executing Operations
      • Method executeOperations
      • Method getOperationExecutions / searchOperationExecutions
      • Method updateOperationExecutions / deleteOperationExecutions
      • Configuration
    • Two-phase commit transactions (AS and AFS, no DSS)
      • Protocol
      • APIs
      • Code Example
      • Configuration
    • Semantic Annotations
    • Web App Settings
    • Imports
  • V. DSS Methods
    • Search files
      • Example
    • Downloading files, folders, and datasets
    • Simple Downloading
      • Download a single file located inside a dataset
      • Download a folder located inside a dataset
      • Search for a dataset and download all its contents, file by file
      • Download a whole dataset recursively
      • Search and list all the files inside a data store
    • Fast Downloading
      • What happens under the hood?
      • Customizing Fast Downloading
    • Register Data Sets
  • VI. Web application context
  • VII. AFS Methods
    • Operations API Reference
  • For Java and Javascript
  • For Java
• Python
  • Dependencies and Requirements
  • Installation
  • General Usage
    • TAB completition and other hints in Jupyter / IPython
    • Checking input
    • Glossary
  • connect to OpenBIS
    • login
    • Verify certificate
    • Check session token, logout()
    • Authentication without user/password
    • Personal access token (PAT)
    • Caching
  • Mount openBIS dataStore server
    • Prerequisites: FUSE / SSHFS
    • Mount dataStore server with pyBIS
  • Masterdata
    • browse masterdata
    • create property types
      • Spreadsheet widget
      • Multi-value properties
    • create sample types / object types
    • assign and revoke properties to sample type / object type
      • pattern and pattern type
      • unique values
    • create a dataset type
    • create an experiment type / collection type
    • create plugins
    • Users, Groups and RoleAssignments
    • Spaces
    • Projects
    • Experiments / Collections
      • create a new experiment
      • search for experiments
      • Experiment attributes
      • Experiment properties
    • Samples / Objects
      • Deletion handling
    • create/update/delete many samples in a transaction
      • parents, children, components and container
      • sample tags
      • Sample attributes and properties
      • search for samples / objects
      • freezing samples
    • Datasets
      • working with existing dataSets
      • download dataSets
      • link dataSets
      • dataSet attributes and properties
      • search for dataSets
      • freeze dataSets
      • create a new dataset
      • create dataset with mixed content
      • create dataset container
      • get, set, add and remove parent datasets
      • get, set, add and remove child datasets
      • dataset containers
      • multi-dataset archiving
    • Semantic Annotations
    • Tags
    • Vocabulary and VocabularyTerms
    • Change ELN Settings via pyBIS
      • Main Menu
      • Storages
      • Templates
      • Custom Widgets
    • Spreadsheet API
      • Basic operations:
      • Cells
      • Columns
      • DataFrame
      • Raw data
      • Metadata
  • Things object
    • JSON response
    • DataFrame
    • Objects
  • AFS client
    • Operations
      • instance creation
      • currently implemented functionalities
  • Imaging technology
    • Operations
      • instance creation
      • creating imaging dataset
      • getting config
      • updating config
      • generating preview
      • export
  • Best practices
    • Logout
    • Iteration over tree structure
      • Iteration over raw data
• Matlab
  • Preamble
  • Setup
    • macOS
    • Windows 10
  • Usage
  • Notes
• Personal Access Tokens
  • Background
  • What are “Personal access tokens” ?
  • Who can create a “Personal access token” ?
  • Where can I use “Personal access tokens” ?
  • Where “Personal access tokens” are stored ?
  • How long should my “Personal Access Tokens” be valid ?
  • Configuration
  • Typical Application Workflow
  • V3 API
• Semantic Annotations
  • Introduction
  • Use Case 1 : Annotating a Semantic Class corresponds to Annotating an openBIS Type
  • Use Case 2 : Annotating a Semantic Class Property corresponds to Annotating an openBIS Property Assignment
  • Use Case 3 : Annotating a Semantic Property corresponds to Annotating an openBIS Property
  • Search Based on Semantic Annotations
  • Helper Class - Semantic API Extensions