Tapis

Tapis is an open source, science-as-a-service API platform for powering your digital lab. Documentation is presented below:

Getting Started

• Introduction
  • V3 Documentation
  • Source Code
• Conventions
  • JSON Notation
  • Versioning
  • Special Character Handling
  • Secure communication
  • Requests
  • Responses
  • Formatting
  • Pagination
  • Timestamps
  • Cross Origin Resource Sharing (CORS)
  • Hypermedia
• Customizing Responses
• Status Codes
  • Success Codes
  • Error Codes
• Best Practices
  • General
  • Systems Service
  • Files Service
  • PostIts
• Tutorials
  • Prerequisites
  • Quick Start Tutorial

Guides

• Guides
• Authorization
  • Supported Authorization Flows
  • Token lifetimes
  • Authorization Code
  • Implicit Grant
  • Resource Owner Password Credentials
  • Client Credentials
• Clients and API Keys
  • Creating a new client application
  • Listing your existing client applications
  • Deleting client registrations
  • Listing current subscriptions
  • Updating client subscriptions

Systems

• Systems
  • Discovering systems
  • Filtering results
  • System details
• Storage systems
  • Supported data and authentication protocols
  • Creating a new storage system
• Execution Systems
  • Startup startupScript
  • Schedulers and system execution types
  • Defining batch queues
  • Configuring quotas
  • System login protocols
  • Scratch and work directories
  • Creating a new execution system
• Disabling
  • Enabling a system
  • Deleting systems
  • Multi-user environments
• System roles
• System scope
• Private systems
  • Public systems
  • Public Storage Systems
  • Public Execution Systems
  • Publishing a system
  • Unpublishing a system
• Default systems
  • Setting user default system
  • Unsetting user default system
  • Setting global default system

Files

• Files
  • Files service URL structure
  • Understanding file paths
• Transferring data
  • Uploading data
  • Importing data
  • Transferring data
• Basic data operations
  • Directory listing
  • Move, copy, rename, delete
• File history
  • Direct vs indirect events
  • Out of band file system changes
  • Listing file history
• File metadata management
• File permissions
  • Listing all permissions
  • List permissions for a specific user
  • Grant permissions
  • Delete single user permissions
  • Deleting all permissions
  • Recursive operations
• Publishing data
  • Publishing individual files
  • Publishing directories
  • Publishing considerations

Apps

• Apps
• Inputs and Parameters
  • Inputs
  • Input details section
  • Input semantics section
  • Input value section
  • Validating inputs
  • Parameters
  • Parameter details section
  • Parameter semantics section
  • Parameter value section
  • Validating parameters
• Wrapper Templates
  • Environment
  • Modules
  • Default job macros
  • Input data
  • Variable injection
  • Type declarations
  • Boolean values
  • Cardinality
  • Parameter Flags
  • App packaging
  • Application metadata
  • Parameter metadata
  • Output metadata
  • Tools and Utilities
• Build a samtools application bundle
• Run samtools sort locally
• Submit the job to the queue on Stampede…
• Craft a Tapis app description
• Overview
• Inputs
• Parameters
• Outputs
• Craft a shell script template
• Permissions
  • Listing permissions
  • Adding and updating permissions
  • Deleting permissions
  • App Publishing
  • Publishing an app
  • Disabling an App
  • Cloning an app

Jobs

• Jobs
• Aloe Jobs Service (now in production)
• Job submission
  • Job submission validation
• Job monitoring
  • Polling
  • Email
• Stopping
  • Deleting a job
  • Resubmitting a job
• Outputs
• Job Lifecycle Management
• Jobs Permissions and Sharing
  • Granting
  • Listing
  • Updating
  • Deleting

Notifications

• Notifications
  • Subscriptions
• URL Macros
• Creating
• Updating
• Listing
• Unsubscribing
• Retry Policies
• Failed deliveries

Postits

• PostIts
  • Creating PostIts
  • Listing PostIts
  • Listing Single PostIt
  • Updating PostIts
  • Redeeming PostIts
  • Forcing PostIt Browser Downloads
  • Expiring PostIts

Metadata

• Metadata v2
  • Metadata Structure
  • Creating Metadata
  • Updating Metadata
  • Deleting Metadata
• Metadata details
  • Metadata browsing
• Metadata Validation
• Metadata Searching
  • Search Examples
• Metadata Permissions
  • Listing all permissions
  • List permissions for a specific user
  • Grant permissions
  • Delete single user permissions
  • Deleting all permissions
• Metadata Schemata
  • Creating schemata
  • Updating schema
  • Deleting schema
  • Specifying schemata as $ref
• Metadata v3
  • Overview
  • Getting Started
  • Resources

User Profiles

• User Profiles
  • Creating
  • Extending with Metadata
  • Updating
  • Deleting
  • Registration Web Application

UUIDs

• UUID
  • Resolving a single UUID
  • Expanding a UUID query
  • Resolving multiple UUID
  • Expanding multiple UUID

Events

• Events

Search

• Search
  • Query syntax
  • Search operators
  • Multiple operators
  • Custom search result

Tooling

• Tooling
• Jupyter Hub
• Command Line Interface

Indices and tables

• Index
• Module Index
• Search Page