Project Creation and Update

The project creation and update view allows you to create a project or category, or update existing project metadata and settings.

For creating new categories or projects, you must have the role of either owner, delegate or contributor in the parent category. For updating an existing project, the role of owner or delegate is required.

_images/project_update.png

Project creation and update view

Project Metadata

The following project metadata and settings are available for updating:

Title

Update the project title. The title must be unique within the parent category.

Parent

Move the project to another category. Options only contain categories for which you have sufficient access.

Description

Set an optional longer description of the project.

ReadMe

Set an optional readme document for the project. Markdown notation can be used. Note that project guests and viewers can see the readme:s of projects and their parent categories. Providing confidential information here should be done with care.

Public access

Enable public access to the project for anyone using SODAR. Either grants full read-only access as project guest, or a partial read-only access as project viewer. For more information on the differences between these roles, see Member Roles. This feature should be used with caution and is generally intended for demonstration projects. If your SODAR server allows anonymous users, this will grant specified access to anyone browsing the site even if they have not logged in.

Enable project on {target remote site}

Enable access to project for project members on the selected target site. Target sites for which project owner/delegation modifying is enabled by an administrator are listed here. Deselecting a previously selected site will revoke access on the target site. For more information, see Remote Site Access documentation.

Notify members of landing zone uploads

Send project members email updates for file uploads using landing zones. For more information, see the Landing Zones app documentation.

Prohibited file types

If you want to prohibit uploading files of certain types to the project, add related file suffixes here as a comma-separated list. The file suffixes will be checked during landing zone validation. For more information, see Prohibited File Types.

Restrict zone contributor access

Restrict landing zone contributor access to a specific user. The user must have a contributor role in project. Owners and delegates can still access landing zones if set. For more information, see Restricting Contributor Zone Access.

Allow sample sheet editing

Enable or disable editability of sample sheets in the project.

Enable sheet synchronization

Enable sample sheet synchronization. For more information, see Remote Sheet Synchronization. Note that sheet sync settings are only visible if an administrator has enabled the sync functionality on the site via SODAR Settings.

URL for sheet synchronization

REST API URL of remote project for sample sheet synchronization.

Token for sheet synchronization

Token string for sample sheet synchronization.

IGV session genome

Genome used in generating IGV session files for the project. The name needs to be in a format accepted by IGV. Affects cancer and germline projects.

BAM and CRAM paths to omit from IGV sessions

Comma-separated list of iRODS path glob patterns for omitting BAM and CRAM files from IGV sessions and study shortcuts. Overrides site-wide setting, affects cancer and germline projects. You can input paths to subcollections under project sample data as well as file names. Using wildcards like * and ? is permitted. Providing full iRODS paths is not necessary: each pattern is assumed to start with a * wildcard. An empty setting means no files or collections are excluded. You need to run Update Sheet Cache in the Sample Sheet application for changes to take effect.

VCF paths to omit from IGV sessions

Comma-separated list of iRODS path Unix shell-style wildcard patterns for omitting BAM and CRAM files from IGV sessions and study shortcuts. Overrides site-wide setting, affects cancer and germline projects. You can input paths to subcollections under project sample data as well as file names. Using wildcards like * and ? is permitted. Paths can be relative. Empty value means no files or collections are excluded. You need to run Update Sheet Cache in the Sample Sheet application for changes to take effect.

Allowed hosts for iRODS access tickets

Comma-separated list of iRODS path Unix shell-style wildcard patterns for omitting VCF files from IGV sessions and study shortcuts. Overrides site-wide setting, affects cancer and germline projects. Behaves similarly to the related BAM/CRAM setting. You need to run Update Sheet Cache in the Sample Sheet application for changes to take effect.

IP restrict

Restrict project access to specific IP addresses if this is set.

IP allow list

List of accepted IP addresses for the IP Restrict setting.

Block project access

Temporarily block user access to project. Only available for superusers. This will block all non-superuser access to the project’s UI and REST API views in SODAR. Project iRODS collections will remain accessible.

Display public category statistics

Display top level category statistics to all users. Only available for superusers in top level categories. Toggling this enables everyone regardless of roles to see the readme and general statistics about projects under the category. The users will not gain any other rights to the category without having roles explicitly granted to them.

When creating a new project, the following fields are also included:

Type

Project type. This can either be Project or Category. The type can not be altered after the project has been created.

Owner

The user who will be set as project owner. After creation, the role can be reassigned in the Members view.

Note

After modifying any fields, make sure to click the Update button to apply the changes.

Project Archiving

From the Archive button in the top right corner of the view, it is possible to archive or unarchive a project. This will set the project data into a read-only mode for all users, including owners and delegates. The

  • Sample sheets can no longer be edited.

  • Restoring of sample sheet versions is disabled.

  • No iRODS requests for deleting sample data from iRODS can be added.

  • No new data from landing zones can be uploaded into the sample data repository.

Some editing functionality will remain active when a project is archived:

  • Project metadata such as readme and description can still be modified.

  • iRODS access tickets for sample sheets can be modified.

  • Sample sheet cache can be updated.

  • Existing landing zones can be accessed and deleted.

  • User membership can be altered, but only read-only access is granted while the project is archived.

Unarchiving the project will restore write access to data according to current member roles. Unarchive.

Note

Archiving categories is not currently supported.

Project Deletion

A category or a project can be deleted by clicking the Delete button. This takes you to a confirmation view where you must input the host name of your SODAR instance to proceed.

Cascading deletion is not supported. In order to delete a category with child categories or projects, the children need to be individually deleted. This is done to prevent accidental data loss.

Deleting a project will also delete its Timeline events. Deletion creates a summary Timeline event, which is viewable by superusers in the Site-Wide Events view.

Danger

Deleting a project will delete all of its data including sample sheets, iRODS sample data and landing zones. This operation can not be undone!