Browsing Landing Zones

This section describes how to browse your landing zones in the SODAR user interface.

Landing Zone List

The main view in the Landing Zones application displays a list of your active landing zones (also referred to as “zones” for brevity).

Landing zone list

The following details are available for each landing zone:

Zone

The title of the zone along with a tooltip for verifying to which assay the zone belongs in. The zone name also acts as its collection name in iRODS. If a special configuration is used for the zone, it is displayed here.

Status Info

Detailed status information on the most recent action performed on the zone. Successful actions are described here along with detailed information on failures. Also included is a badge displaying the zone’s current file count and size in iRODS

Status

A coloured representation of the current zone status. If the zone is currently locked for read-only access due to an ongoing operation, a lock icon is also displayed.

iRODS Links

Four buttons with iRODS links for the zone are presented here.

Zone Dropdown

For each active zone, there is a dropdown menu for zone specific operations.

Project owners and delegates will also be able to see active zones of other users in the project in a separate list within the same view. They can also perform the same validation, moving and deletion actions as the zone owner.

Status Types

The following status types can appear during the lifetime of a landing zone:

CREATING

Creation of landing zone in iRODS in process.

NOT CREATED

Creating landing zone in iRODS failed.

ACTIVE

Available with write access for the user.

PREPARING

Preparing transaction for validation and moving.

VALIDATING

Validation OK, moving files into sample data repository.

MOVED

Files moved successfully, landing zone removed.

FAILED

Validation or moving failed.

DELETING

Deletion of landing zone in process.

DELETED

Landing zone deleted.

iRODS Links

The buttons for iRODS linking for the landing zone are identical to the ones seen in the Sample Sheets application:

List Files

Opens a modal with a flat iRODS file list of the landing zone.

Copy iRODS Path into Clipboard

Copies the iRODS path of the landing zone, to be used with iRODS iCommands.

Copy WebDAV URL into Clipboard

Copies the entire WebDAV URL for the landing zone path.

Browse Files in WebDAV

Opens a new browser tab with the Davrods web interface for browsing the landing zone collection through WebDAV.

iRODS File List Modal

The iRODS file list modal is slightly different from the similar modal in the Sample Sheets app. It displays collections in addition to files to help visualize which root level collections are expected. Furthermore, a check mark is displayed on the right hand side column for files, if the expected .md5 checksum file is accompanying the actual data file.

iRODS file list modal for a landing zone