ISA-Tab Templates Application

By default, SODAR retrieves ISA-Tab templates for the Sample Sheets application from the CUBI ISA Templates repository. These templates are static and cannot be edited or removed without upgrading to a new release of the repository in the SODAR Server repository requirements.

The ISA-Tab Templates application can be used if there is need to dynamically manage custom templates, or replace the CUBI templates altogether. It provides administrators the ability to import and export ISA-Tab templates which are compatible with the Cookiecutter templating software and the format used in the CUBI ISA Templates repository.

Note

To enable the app’s backend and access custom templates in the Sample Sheets app, make sure isatemplates_backend is included in your instance’s ENABLED_BACKEND_PLUGINS Django setting. For more information, see Enabled Backend Plugins.

User Interface

To access the graphical user interface for template management, log in with an administrator account, open the user dropdown and select ISA-Tab Templates.

Template List

The template list view is the entry point for the application. It displays the list of currently imported custom templates, with the following columns displayed for each template:

Description: Human readable description for the template. This will be displayed in the template selection view in the Sample Sheets app.
Name: Internal ID for the template, used e.g. in URLs.
User: The user who last modified the template.
Modified: The date and time of the most recent template modification.
Active: Status of the template (active/inactive).
Template Dropdown: Dropdown for updating, exporting or deleting a template.

If the CUBI templates from the separate repository are enabled, they are displayed in a second list. For controlling whether to include CUBI templates on your SODAR instance, see SODAR Settings.

_images/isatemplates_list.png — ISA-Tab Templates list view

Template Details

The template detail view can be accessed from the description column link in the template list. This view provides an overview of the template along with contents of all files included in the template. The cookiecutter.json configuration file is displayed first, followed by the ISA-Tab template files.

_images/isatemplates_detail.png — ISA-Tab Templates detail view

Template Import and Update

The template import view can be accessed by clicking the Import Template button. The following fields are included in the form:

File upload: File selector for uploading the template. The templates can be uploaded either as a Zip archive or multiple files. All files for a template must be uploaded at once. This consists of the cookiecutter.json file, the ISA-Tab investigation template file and appropriate study/assay template files.
Description: Human readable description for the template. Must be unique, also taking CUBI templates into account.
Name: Internal ID for the template. Can be left blank, in case one will be auto-generated.
Active: Select box for whether the template is active and displayed to users. This is useful if e.g. an error in the template is discovered and it should be made inactive while a fix is developed.

_images/isatemplates_form.png — ISA-Tab Templates import/update view

All of the above can be changed for existing templates by selecting Update Template from the template dropdown. The files can be replaced by new ones by providing a Zip file or individual files in the update form.

Note

All files must be included also when updating a form as this action will replace all files in the template. If no files are included, the existing files will be left unaltered.

Template File Requirements

The template files should conform to the CUBI ISA Templates way of providing sample sheets. Some important aspects to consider:

The files must include cookiecutter.json, an investigation file template and at least one study file template.
The __output_dir field is mandatory.
Files are expected to be UTF-8 encoded.
The template must be renderable to a valid ISA-Tab using the default settings provided. The import form will validate the template automatically with both Cookiecutter and the AltamISA parser upon import. The import will fail if critical errors are encountered.

Hint

We recommend looking into the cubi-isa-templates repository for examples on how to create valid templates.