bio4j/Bio4j — Issue #2: Problem with ImportNCBITaxonomy program
Author: pablopareja
Created: 2012-02-03 17:52:56+00:00
State: open
Labels: bug

There seems to be a bug with the program ImportNCBITaxonomy in the last version (0.7) getting the following stacktrace:

```javascript
java -d64 -Xmx32G -jar CreateWholeBio4j.jar executionsBio4j.xml
Feb 3, 2012 3:55:25 PM
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy main
INFO: creating manager...
Feb 3, 2012 3:55:25 PM
org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool logWarn
WARNING: [/home/bio4j_db/
neostore.propertystore.db.index] Unable to memory map
Feb 3, 2012 3:55:25 PM
org.neo4j.kernel.impl.nioneo.store.PersistenceWindowPool logWarn
WARNING: [/home/bio4j_db/
neostore.propertystore.db.index.keys] Unable to memory map
graphservice hashcode: 1680266759
Feb 3, 2012 3:55:25 PM
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy main
INFO: reading nodes file...
Feb 3, 2012 3:55:25 PM
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy main
SEVERE: null
org.neo4j.kernel.impl.core.ReadOnlyDbException: This is a read only
embedded Neo4j instance
at
org.neo4j.kernel.impl.core.ReadOnlyNodeManager.createNode(ReadOnlyNodeManag er.java:
50)
at
org.neo4j.kernel.EmbeddedGraphDbImpl.createNode(EmbeddedGraphDbImpl.java:
316)
at
org.neo4j.kernel.EmbeddedReadOnlyGraphDatabase.createNode(EmbeddedReadOnlyG raphDatabase.java:
104)
at
com.era7.bioinfo.bioinfoneo4j.Neo4jManager.createNode(Neo4jManager.java:
37)
at
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy.main(ImportNCBITaxonomy. java:
95)
at
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy.execute(ImportNCBITaxono my.java:
45)
at
com.era7.lib.bioinfo.bioinfoutil.ExecuteFromFile.main(ExecuteFromFile.java:
66)
at
com.era7.bioinfo.bio4j.programs.CreateWholeBio4j.main(CreateWholeBio4j.java :
28)
Feb 3, 2012 3:55:25 PM
com.era7.bioinfo.bio4j.programs.ImportNCBITaxonomy main
INFO: Closing up inserter and index service....
```

I'm working on it and think already found the problem.

Pablo