Raw bioassays are available for inclusion in root bioassay creation even if there is no raw data

[Jari Häkkinen]

Creating a new root bioassay from raw bioassays in some cases fail because not all raw bioassays have their data stored as the root bioassay importer expects it to be stored. Take Illumina IBS as a example where data can be stored in a file associated with a raw bioassay, but when creating a root bioassay data must be in the raw tables. In my case I have severa raw bioassays with raw data in tables and a few with data in files only. The dialog for creating a root bioassay allows me to select the non-table raw bioassay.

Anticipating future use where mixed storage of raw bioassays will occur, we need to specify how the raw bioassay dialogue should treat different cases.

1) No raw bioassay has data in raw tables nor files associated then the new root button should be disabled.

2) If either data is stored in raw tables or in files and there is at least one plug-in that can create a root bioassay set the new root button should be available.

3) If data is in a "mixed" mode of raw tables and data in files and missing data the plug-in dialogue should highlight the raw bioassay. They should still be presented so that the user can take action.

[Nicklas Nordborg]

Just to clarify, this ticket is about the "Formula intensity calculator" plug-in that is used to create a root bioassay set from raw data stored in the database.

1) and 2) requires #376 to be solved. This is unfortunately a BASE 3.0 feature.

3) is possible if a custom JSP is created for parameter input.

In any case, the first thing to fix is that the plug-in should validate that all selected raw bioassays has data before the job parameters are saved to the database. Then, 3) may be implemented if needed.

[Jari Häkkinen]

Replying to nicklas:

Just to clarify, this ticket is about the "Formula intensity calculator" plug-in that is used to create a root bioassay set from raw data stored in the database.

1) and 2) requires #376 to be solved. This is unfortunately a BASE 3.0 feature.

Ah, this has been discussed before. Is the new root button always available as soon as a there is at least one raw bioassay? I'll check .... no, it is available even if there is no raw bioassay in the experiment.

3) is possible if a custom JSP is created for parameter input.

In any case, the first thing to fix is that the plug-in should validate that all selected raw bioassays has data before the job parameters are saved to the database. Then, 3) may be implemented if needed.

Does this mean that only raw bioassays that have data in the raw tables will be visible in the dialog?

[Nicklas Nordborg]

Replying to jari:

Replying to nicklas:

Just to clarify, this ticket is about the "Formula intensity calculator" plug-in that is used to create a root bioassay set from raw data stored in the database.

1) and 2) requires #376 to be solved. This is unfortunately a BASE 3.0 feature.

Ah, this has been discussed before. Is the new root button always available as soon as a there is at least one raw bioassay? I'll check .... no, it is available even if there is no raw bioassay in the experiment.

No, the button is displayed when there is at least one intensity calculator plug-in installed on the system that the currently logged in user has permission to use.

3) is possible if a custom JSP is created for parameter input.

In any case, the first thing to fix is that the plug-in should validate that all selected raw bioassays has data before the job parameters are saved to the database. Then, 3) may be implemented if needed.

Does this mean that only raw bioassays that have data in the raw tables will be visible in the dialog?

A custom JSP is needed for highlighting raw bioassays without raw data. An alternative and easier solution is to only list raw bioassays that has data. This can be done with the generic parameter form.

[Jari Häkkinen]

The easy solution seems to be enough if we add a note in the raw bioassay selection dialogue saying something like

Select the raw bioassays to use when creating the root bioassay set.

Missing raw bioassays? Maybe you have not imported data for some raw bioassays.

or something like that to give a confused user a hint of what may be wrong.

[Nicklas Nordborg]

If a note about the "missing raw bioassays" is enough, then it should not be very hard to fix this ticket.

[Jari Häkkinen]

I see no reason to go for a more complicated solution now, just add a note and go for the straightforward fix.

[Nicklas Nordborg]

(In [4569]) Fixes #1134: Raw bioassays are available for inclusion in root bioassay creation even if there is no raw data