Opened 12 years ago

Closed 12 years ago

Last modified 12 years ago

#1446 closed enhancement (fixed)

Use the core "Reporter importer" without a file format configuration

Reported by: Jari Häkkinen Owned by: Nicklas Nordborg
Priority: minor Milestone: BASE 2.15
Component: coreplugins Version: 2.14.1
Keywords: Cc:

Description

Can the reporter importer interface be improved with the nice "Test with file" feature available for other imports like the batch importers.

Change History (11)

comment:1 Changed 12 years ago by Nicklas Nordborg

The "Test with file" button is there when I try it. Browser issue?

comment:2 Changed 12 years ago by Jari Häkkinen

I see the test with file functionality in many places. Are we talking about the same dialogue? I am talking about the dialogue appearing when pressing 'Import' in the reporter list view. Creating plug-in configurations features 'Test with file' functionality.

I use Firefox 3.5.5 on OS X 10.6.2, but the dialogue does not show in Safari either.

comment:3 Changed 12 years ago by Nicklas Nordborg

No we are probably not talking about the same dialogue. The reporter importer needs to be configured before it can be used. The "Test with file" is available in the configuration phase. When using the importer an existing configuration must be selected or auto-detected.

comment:4 Changed 12 years ago by Jari Häkkinen

Is it possible to add the 'Test with file' to reporter importer. The functionality is available for batch importers (even in cases where a configuration is available).

comment:5 Changed 12 years ago by Nicklas Nordborg

The "Test with file" button only appears i plug-ins that doesn't require a configuration, so what you really want to do is to change the reporter importer so that it can be used without a configuration. If a configuration is selected it is only used as a suggestion which the user can change before actually running the importer.

The only issue I can think of is that this change will also affect the Illumina BGX reporter importer since it is a subclass of the core reporter importer. We'll have to check if there are any consequences for the Illumina plug-in as well and maybe update the Illumina package also.

comment:6 Changed 12 years ago by Nicklas Nordborg

Priority: majorminor
Summary: Importing/updating reporter annotations/extended properties interface improvement requestUse the core "Reporter importer" without a file format configuration

I have investigated what a change like this would mean for the Illumina BGX reporter importer. The current implementation will fail with importing the reporters in the [Controls] section if the file parsing options is specified in the job parameters instead of in the plug-in configuration. So, the Illumina package must be updated and the release should be synchronized with the release of BASE 2.15.

comment:8 Changed 12 years ago by Nicklas Nordborg

Owner: changed from everyone to Nicklas Nordborg
Status: newassigned

comment:9 Changed 12 years ago by Nicklas Nordborg

(In [5241]) References #1446: Use the core "Reporter importer" without a file format configuration

This should fix the issue, though I have not yet tested it with the web client. I'll also keep this ticket open until the Illumina importer ticket has been fixed: http://baseplugins.thep.lu.se/ticket/257

comment:10 Changed 12 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed

(In [5242]) Fixes #1446: Use the core "Reporter importer" without a file format configuration

Fixed some remaining issues (NullPointerException?) when running without a configuration and when used to import reporter lists.

comment:11 Changed 12 years ago by Nicklas Nordborg

(In [5243]) References #1446: Use the core "Reporter importer" without a file format configuration

This should make the plug-in less sensitive to programs that use it with file parsing parameters in the configuration instead of in the job.

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