Opened 9 years ago

Closed 9 years ago

#112 closed defect (fixed)

Illumina plug-in installer script fails (in some cases)

Reported by: jari Owned by: martin
Priority: major Milestone: Illumina package v1.2
Component: net.sf.basedb.illumina Keywords:
Cc:

Description

The plug-in installer fails when I try to rerun it with the below stack trace. I have set the error option to 'skip' for already existing items.

net.sf.basedb.core.ItemAlreadyExistsException: Item already exists: nullBGX file has invalid jar path.
This datafiletype can not be used.
at net.sf.basedb.illumina.install.Install.createDataFileType(Install.java:780)
at net.sf.basedb.illumina.install.Install.installIlluminaItems(Install.java:469)
at net.sf.basedb.illumina.install.Install.run(Install.java:266)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:108)
at net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:487)
at java.lang.Thread.run(Thread.java:619)

Change History (7)

comment:1 Changed 9 years ago by jari

I should maybe mention that on my 2.7.0pre I have no problems but on a 2.6.2 I get the stacktrace.

comment:2 Changed 9 years ago by jari

  • Component changed from net.sf.basedb.examples.extensions to net.sf.basedb.illumina

comment:3 Changed 9 years ago by jari

  • Summary changed from Illumina plug-in installer script fails to Illumina plug-in installer script fails (in some cases)

comment:4 Changed 9 years ago by martin

  • Owner changed from nicklas to martin
  • Status changed from new to assigned

comment:5 Changed 9 years ago by martin

In some way the jar path of the validator and the meta-data reader is different compare to the jar path used by the installation plug-in.
The message is a bit cryptic and should be changed.
Perhaps a 'use'-option should be added to alternatives of how existing items should be handled?

comment:6 Changed 9 years ago by martin

(In [732]) References #112 Changed the exception message.

comment:7 Changed 9 years ago by martin

  • Resolution set to fixed
  • Status changed from assigned to closed

(In [736]) Fixes #112. Changed the property validation when installing a data file-type which already exists.

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