wiki:net.sf.basedb.relax/notes14

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.

Last modified 13 months ago Last modified on Jan 17, 2019, 11:41:40 AM