Package index • LimsaR

Configuration

Functions for configuring SODAR and iRODS

sodar_config(): Set the SODAR configuration.

sodar_whoami(): Returns information about the user making the request

sodar_irods_configuration(): Retrieve the iRODS configuration

Project management

Functions for managing projects

sodar_project_create(): Create a new project in SODAR

sodar_project_list(): Get the SODAR project list table.

sodar_project_update(): Update a project or category in SODAR

sodar_project_retrieve(): Retrieve details of a project or category

sodar_category_list(): Returns a list of all projects and categories belonging to a category

sodar_user_list(): List all SODAR users

sodar_user_role_create() sodar_user_role_update(): Create or modify a new user in a project

Sample sheets & co.

Functions for managing sample sheets and investigations

sodar_investigation_retrieve(): Retrieve details of an investigation from a project

sodar_sheet_import(): Import an ISAtab sample sheet from a file

sodar_sheet_export_zip() sodar_sheet_export_json(): Export an ISAtab sample sheet from a project

Functions related to iRODS and iRODS paths

sodar_irods_configuration(): Retrieve the iRODS configuration

sodar_create_irods(): Create an iRODS collection for a project

sodar_file_exists(): Check if a file exists in iRODS using md5 checksum

sodar_file_list(): List files present in a project sample data repository

sodar_assay_irods_path() sodar_study_irods_path(): Retrieve the iRODS path of an assay or study

Landing Zone management

Functions for managing the landing zones

sodar_lz_create(): Create a landing zone for a project

sodar_lz_list(): List landing zones for a project

sodar_lz_retrieve() sodar_lz_status() sodar_lz_delete() sodar_lz_move() sodar_lz_validate(): Handling existing landing zones

Deletion requests

Functions for managing deletion requests

sodar_delete_request() sodar_request_list() sodar_request_cancel() sodar_request_reject() sodar_request_accept(): Create and process iRODS data requests

Tickets

Functions for managing tickets

sodar_ticket_create() sodar_ticket_list() sodar_ticket_retrieve() sodar_ticket_delete(): Manage SODAR iRODS tickets