Installation wizard for Relax server

[Nicklas Nordborg]

The installation wizard should be similar to the Reggie installation wizard. It must check and create items that are needed for the Relax server to work as intended.

Item subtypes:

• Patient (biosource)
• Case (Sample)
• Specimen (Sample)
• RNA (Extract)
• Library (Extract)
• MergedSequences (Derived bioassay)

From the derived bioassay we go directly to raw bioassay with a relevant raw data type (most likely a file-only data type since we want to avoid importing data to the database).

Raw data types:

• Cufflinks (we need to support 2.x releases)
• Kallisto (for the new pipeline)
• ... and other raw data type in the future

On each level we also need to define annotation types. Annotation types and data file types are defined as part of the import and created/updated by the importer (#940).

The installation wizard should also disabled the "Packed file exporter" plug-in for regular users. It could for example just make sure that this plug-in is not shared to the "Everyone" group anymore. It may have to check the configurations as well.

Some more things that are needed:

• Directory for creating file items referencing data files (/home/Releases)
• A file server that is storing released data files and the JSON files that the importer needs for importing a release (ReleaseArchive)

[Nicklas Nordborg]

(In [4350]) References #939: Installation wizard for Relax server

Created the installation servlet but it is only an empty template so far.

[Nicklas Nordborg]

(In [4353]) References #939: Installation wizard for Relax server

Added some substypes and implemented installation code for checking/installing them.

[Nicklas Nordborg]

(In [4354]) References #939: Installation wizard for Relax server

Added (temporary) menu entry for the installation wizard.

[Nicklas Nordborg]

(In [4360]) References #939: Installation wizard for Relax server

Re-designed the installation wizard to display all items in a (filterable) table instead of multiple columns. I think the same approach may be better in Reggie as well.

[Nicklas Nordborg]

(In [4362]) References #939: Installation wizard for Relax server

Enhancments with inspiration from #945.

[Nicklas Nordborg]

(In [4363]) References #939: Installation wizard for Relax server

Updated the menu entry so that it is only visible for administrators.

[Nicklas Nordborg]

(In [4406]) References #939: Installation wizard for Relax server

Added check/installation for file server and directory for released files.

[Nicklas Nordborg]

(In [4409]) References #939: Installation wizard for Relax server

Added subtypes for FASTQ and raw data files.

[Nicklas Nordborg]

(In [4514]) References #939: Installation wizard for Relax server

Checking that the "Packed file exporter" plug-in is disabled and not shared to the "Everyone" group.

[Nicklas Nordborg]

(In [4515]) References #939: Installation wizard for Relax server

Added a raw data type check that simply checks if a definition with a given name (eg. cufflinks) exists.