= Updating to Relax 1.4 =

The following steps should be done after installing Relax 1.4.

=== Create Lysate items between RNA and Specimen ===

The data model has been updated with a `Lysate` item type that sits between the `Specimen` and `RNA` items in the old model (see #1072). `Lysate` items need to be created and properly linked with the existing `Specimen` and `RNA` items. Some annotations also need to be moved from the existing `RNA` items to the `Lysate` items. 

The '''Relax installation wizard''' contains a function for doing this. When you enter the installation wizard it will most likely complain about some missing subtypes and annotation type, etc. After fixing this the installation wizard should display a note about the number of `RNA` items that are linked to `Specimen` items and a button '''Create Lysate and re-link RNA'''. Click on this button and wait for the installation wizard to finish. It will take some time for it to finish but it will save the results at regular intervals so if there is a problem it should be possible to re-start and try again.

=== Add annotation types to the Cufflinks and !StringTie categories ===

The Cohort exporter and Level 3 exporter plug-ins has been updated to only export annotations and data that is correctly shared and matched against raw data types (#1099). To make sure that the proper annotations are included when exporting the following steps need to be done:

Go to the '''Administrate - Types - Annotation type categories''' page and locate the `Cufflinks` and `StringTie` categories. Open the edit dialog for each one, switch to the '''Annotation types''' tab. The only annotation type so far should be the `FirstReleasedIn` annotation type. Add more annotation types:

 * For `Cufflinks`: All annotation types for raw bioassays except the `QC_GenoTypeHET_PCT` annotation.
 * For `StringTie`: All annotation types for raw bioassays except those starting with `PILOT_`.

The categories also need to be shared to the releases (=projects) that they are used in. For the `Cufflinks` category this typically means that it should be shared with READ permission to all existing projects and for the `StringTie` category that is should be shared to the 4.0 project.


=== Populate the !FirstReleasedIn annotation ===

This step is optional. The `FirstReleasedIn` is not critical for any functionality in Relax.

The `FirstReleasedIn` annotation type was introduced by #1090. The release importer plug-in will automatically set a value for new items that are created. Existing items will not get a value unless it is added manually. It should be possible to do with the help of a batch export and import process. Exporting a tab-separated file with at least the "ID" (internal) and "Shared to" columns should be enough. From the data in the "Shared to" column it should be possible to determine the value of the `FirstReleasedIn` annotation using, for example, a smart script or a spreadsheet program. The resulting file can then be uploaded to BASE and imported with the "Annotation importer" plug-in. The process need to be repeated once for each main item type: BIOSOURCE, SAMPLE, EXTRACT, DERIVEDBIOASSAY and RAWBIOASSAY.