Recent changes to maltcms-bugs

#15 MzXML Data Source causes too many open files

Nils Hoffmann — Tue, 04 Feb 2014 10:41:22 -0000

MzXML Data Source causes too many open files

Nils Hoffmann — Tue, 04 Feb 2014 10:40:16 -0000

The mzXML data source causes an issue with too many open files. The root cause has been investigated and was located in the mzXML StaX API library. There, for each read operation, two file handles are opened, but only one is closed properly, leading to the too many open files error.

MzXML Data Source causes too many open files

Nils Hoffmann — Tue, 04 Feb 2014 10:40:16 -0000

Ticket 15 has been modified: MzXML Data Source causes too many open files
Edited By: Nils Hoffmann (nilshoffmann)

Ehcache interferes with FileFragment via key serialization

Nils Hoffmann — Thu, 31 Oct 2013 09:27:39 -0000

In release 1.3, the ehcache library was updated. Through a change in caching behaviour, FileFragments were accidentally serialized when used as cache keys, while still being actively changed, which is not advisable.

This has been fixed in 1.3.1 by using the Fragment URI as key, which is safely serializable.

#13 Wrap all external non-osgi dependencies as osgi bundles

Nils Hoffmann — Thu, 31 Oct 2013 09:22:32 -0000

Group: 1.3 --> Future

#11 Investigate Launch4J

Nils Hoffmann — Thu, 31 Oct 2013 09:22:14 -0000

Group: 1.3 --> Future

#12 Exception in TICPeakFinder

Nils Hoffmann — Thu, 31 Oct 2013 09:21:16 -0000

status: open --> closed
Group: 1.3 --> 1.3.1

Wrap all external non-osgi dependencies as osgi bundles

Nils Hoffmann — Thu, 31 Oct 2013 09:19:50 -0000

Currently, around 10 dependencies of Maltcms do not expose OSGI information directly. Those have been manually updated and deployed to the artifactory repository. It would be beneficial to pull the original versions from public sources and wrap them as osgi bundles from within the cross / maltcms maven project.

Wrap all external non-osgi dependencies as osgi bundles

Nils Hoffmann — Thu, 31 Oct 2013 09:19:50 -0000

Ticket 13 has been modified: Wrap all external non-osgi dependencies as osgi bundles
Edited By: Nils Hoffmann (nilshoffmann)
_milestone updated: u'1.3' => u'Future'

Exception in TICPeakFinder

Nils Hoffmann — Sun, 29 Sep 2013 17:12:11 -0000

An exception is thrown when TICPeakFinder area normalization is enabled:

Caught exception while executing pipeline:
cross.exception.ConstraintViolationException: Called from maltcms.io.andims.NetcdfDataSource@7b63daaf: Called from maltcms.io.andims.NetcdfDataSource@7b63daaf: Argument was null!
at cross.datastructures.tools.EvalTools.notNull(EvalTools.java:386)
at cross.datastructures.tools.EvalTools.notNull(EvalTools.java:379)
at maltcms.io.andims.NetcdfDataSource.write(NetcdfDataSource.java:939)
at cross.datastructures.fragments.FileFragment.save(FileFragment.java:1022)
at maltcms.commands.fragments.peakfinding.TICPeakFinder.findPeaks(TICPeakFinder.java:357)