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 Landing Zones application title bar displays project zone status badges along with the button for creating a new zone. The status badges displayed:

Zones Badge

Amount of active zones currently in this project along with the per-project limitation of creating new active landing zones per project. If the limit has been reached, existing zones must be moved or deleted before new ones are created. If no zone creation limit is set, the badge will display as “unlimited”.

Validating Badge

The amount of currently validating landing zones in the project along with the per-project limitation of how many zones can be concurrently validated. If the limit has been reached, ongoing zone validation processes must finish before new ones can be started.

In the table, 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. In addition to the title, this column displays further landing zone information as badges:

• Assay Badge: This displays the name of the assay the landing zone is linked to, with a link to the assay in the Sample Sheets app.

• User Badge: When viewing the list as a owner or delegate, you can see zones of other users. For these zones, the user who created the zone is displayed as a badge.

• Configuration Badge: If a special configuration is used for the zone, the configuration title is presented as a badge.

• Permission Warning Badge: If you can see other users’ zones and a user has lost project permissions after creating the zone, you will see a badge warning you about the zone’s original creator being unable to access it.

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. Long status messages are truncated by default, but you can click the See more link to load the full status. 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 be able to see active zones of other users in the project. Zones created by other users are denoted by a user badge in the title column. Owners and delegates can perform the same validation, moving and deletion actions for these zones as the zone owner. Starting in SODAR v1.1, owners and delegates also gain iRODS read/write access to zones of other users.

Hint

For legacy landing zones created on SODAR versions older than 1.1, an administrator must run the syncmodifyapi administrator command to enable owner and delegate iRODS access.

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 landing zone file list modal displays collections and files within a specific landing zone.

By default, the list displays iRODS collections within the landing zone in addition to files. You can toggle the display of collections by clicking on the button in the top right corner of the modal. Your choice will be remembered the first time you open a landing zone modal.

For each item in the landing zone, the following information is displayed:

Path to Collection or File

The path below the landing zone for each collection and file is displayed. The path is a link which will open the corresponding collection or file with WebDAV.

Size

For files, the file size is displayed.

Modified

For files, the modification datetime is displayed.

MD5

This column displays an icon representing whether the expected checksum file corresponding to each actual data file is present.

iRODS

This column contains a button for copying the path to the corresponding collection or file into the clipboard.

The results may be paginated depending on the amount of collections and files in the zone as well as SODAR server settings set by admins. In case of multiple pages of results, you will find pagination controls in the bottom of the modal.

iRODS file list modal for a landing zone