BioJava - update library

[julie-sullivan]

We are on a very old (7 years?) version of the library. Specifically, I think they fixed a memory leak.

[julie-sullivan]

The current version is 3.0.4 but the legacy version is on 1.8.

The main reason for upgrading is that the FASTA doesn't process the amino acid Pyrrolysine. I think this was added in 2008 or so, after the biojava library we're using was written anyway.

http://en.wikipedia.org/wiki/FASTA_format

But if we are making this much effort to upgrade, we might as well upgrade to 3.0?

[julie-sullivan]

Fixed by 65589de, 7ee57ec, 1907ac0, ab1ee4f, 480edd8, d5f8e02

[sergiocontrino]

i think this is fixed

[julie-sullivan]

@rachellyne I've removed PDB from FlyMine temporarily until we can update the BioJava library.

This is the error I get:

[integrate] WARNING: unknown group name MSE
java.lang.OutOfMemoryError: Requested array size exceeds VM limit
Dumping heap to /tmp/java_pid19540.hprof ...
Heap dump file created [3684876297 bytes in 15.089 secs]

BUILD FAILED
/local-homes/julie/git/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/local-homes/julie/git/intermine/imbuild/source.xml:162: java.lang.OutOfMemoryError: Requested array size exceeds VM limit
    at java.util.Arrays.copyOf(Arrays.java:2367)
    at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
    at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
    at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:415)
    at java.lang.StringBuffer.append(StringBuffer.java:237)
    at org.biojava.bio.structure.PDBHeader.printTitle(PDBHeader.java:249)
    at org.biojava.bio.structure.PDBHeader.toPDB(PDBHeader.java:105)
    at org.biojava.bio.structure.io.FileConvert.toPDB(FileConvert.java:196)
    at org.biojava.bio.structure.StructureImpl.toPDB(StructureImpl.java:559)
    at org.intermine.bio.dataconversion.PdbConverter.processPDBFile(PdbConverter.java:162)
    at org.intermine.bio.dataconversion.PdbConverter.process(PdbConverter.java:104)
    at org.intermine.task.DirectoryConverterTask.execute(DirectoryConverterTask.java:104)
    at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl

This happens in Java 6 (open-jdk only), 7 and 8. FlyMine is using sun's Java 6 where this works.

I suppose BioJava is creating an array that is too big.

[julie-sullivan]

@sergiocontrino @rachellyne This is still a problem.

[julie-sullivan]

PDB won't be included in this next release of FlyMine.