Opened 8 years ago

Last modified 8 years ago

#939 closed task

Installation wizard for Relax server — at Version 11

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Relax v1.0
Component: net.sf.basedb.relax Keywords:
Cc:

Description (last modified by 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).

Change History (11)

comment:1 by Nicklas Nordborg, 8 years ago

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

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

comment:2 by Nicklas Nordborg, 8 years ago

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

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

comment:3 by Nicklas Nordborg, 8 years ago

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

Added (temporary) menu entry for the installation wizard.

comment:4 by Nicklas Nordborg, 8 years ago

Owner: set to Nicklas Nordborg
Status: new → assigned

comment:5 by Nicklas Nordborg, 8 years ago

Description: modified (diff)

comment:6 by Nicklas Nordborg, 8 years ago

(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.

comment:7 by Nicklas Nordborg, 8 years ago

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

Enhancments with inspiration from #945.

comment:8 by Nicklas Nordborg, 8 years ago

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

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

comment:9 by Nicklas Nordborg, 8 years ago

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

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

comment:10 by Nicklas Nordborg, 8 years ago

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

Added subtypes for FASTQ and raw data files.

comment:11 by Nicklas Nordborg, 8 years ago

Description: modified (diff)
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