Landing Zone Creation and Update

This section describes the creation and updating of landing zones.

Landing Zone Creation

Creating a landing zone and uploading data into a project has the following preqrequisites:

Sample sheets have been set up for your project. For more information, see Metadata Recording and Importing and Creating Sheets.
iRODS collections have been created for your project. For more information, see Create iRODS Collections.

Creating landing zones and uploading files is permitted to users with the project contributor access level or higher. Multiple simultaneous landing zones for a single assay are allowed.

Initially navigating to the Landing Zones app presents you a notification on no zones being available, with a Create Zone button on the right hand side.

_images/zone_list_empty.png — Landing zone list with no zones

Clicking the button opens up the landing zone creation form, which allows you to set up and configure your new landing zone.

_images/zone_form.png — Landing zone creation form

The form contains the following fields:

Assay

The assay under which the files in this landing zone will be uploaded.

Title suffix

Optional suffix for the landing zone title, mostly usable for differentiating between multiple zones.

Description

Optional description for e.g. notes regarding the landing zone.

User message

Optional message displayed to project users upon successful validation and upload of this zone. This can contain e.g. a description of the files uploaded.

Collection creation

Select the method of automatic creation of iRODS collections. If enabled, this will create expected root level collections under the zone. This helps to e.g. assure the expected collection names corresponding to the sample sheets, avoiding errors such as typos. When moving files from the landing zone, empty collections will not be created in the sample repository.

By default this is set to RESTRICT, where user write access is restricted to created collections. Subcollections can be freely created, but the user can not create new root collections in the landing zone. This default mode is recommended. If there is need to e.g. upload data corresponding to samples not yet in the sampl sheets, you can select CREATE to create expected collections and enable creation of new ones, or NONE for manual collection creation.

Configuration

Selection for special configurations of landing zones with extra features. In most use cases this should be left blank.

Once you have filled out the form, clicking Create will start the zone creation process and redirect you to the landing zone list, where you can see the zone status and move further with file uploads.

The next sections will provide instructions on browsing your landing zones and how to proceed with your file uploads.

Attention

The administrators of your SODAR instance may limit the amount of active landing zones that can be created per project. If a limit is active and reached, you will be notified about this in the UI and the REST API. In this case, existing zones in the project will have to be moved or deleted before new ones are created.

Landing Zone Update

Landing zones can be updated by following the Update Zone link on the dropdown menu on the right hand side of the zone list. This opens up the same form as in the creation process, with the fields pre-filled with the current values. Currently the only fields that can be updated are description and user message. Once you have made your changes, click Update to save them.

Restricting Contributor Zone Access

It is possible to restrict contributor access to a specific user in cases where it is desirable to only have one user, such as an automated service account, uploading files into a project.

To enable the restriction, an owner or a delegate must set the Restrict zone contributor access setting in the project creation and update form to the user name of the desired user. This user must have the role of contributor in the project.

Once set, only the specified contributor user has access for creating, updating and moving landing zones. Other contributors retain contributor level functionality regarding e.g. sample sheets, but are denied access to landing zones. Note that project owners and delegates will retain zone access in the project even with this restriction in place.

Hint

If you want to set similar restricted landing zone access to multiple projects inside a category, you can grant the desired user contributor access to the parent category. This way you don’t need to separately assign them as contributor to each project.