From WikiPathways
Unable to convert to /var/www/wikipathways/images/c/c8/WP176_35277.owl:
<BR>Status:1
<BR>Message:[ 0.005] Info: Preferences file /var/www/.PathVisio/.PathVisio doesn't exist, using defaults
[ 1.036] Info: Recognized format [Namespace: prefix "" is mapped to URI "http://genmapp.org/GPML/2008a"]
[ 1.561] Info: Document is valid according to the xml schema definition 'GPML2008a.xsd'
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
INFO [main] (EditorMapAdapter.java:172) - skipping restricted participant property
Saving from GPML to Biopax
HMDB
HMDB
HMDB
HMDB
HMDB
Entrez Gene
HMDB
HMDB
Entrez Gene
HMDB
Entrez Gene
HMDB
HMDB
HMDB
HMDB
HMDB
Entrez Gene
Entrez Gene
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
PubChem
HMDB
Entrez Gene
HMDB
HMDB
HMDB
Entrez Gene
Entrez Gene
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
HMDB
Exception in thread "main" java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:48)
at java.lang.Integer.parseInt(Integer.java:470)
at java.lang.Integer.parseInt(Integer.java:499)
at org.pathvisio.biopax3.exporter.ExportHelper.transferPublicationXref(ExportHelper.java:94)
at org.pathvisio.biopax3.exporter.ExportHelper.createOrGetPhysicalEntity(ExportHelper.java:406)
at org.pathvisio.biopax3.exporter.ExportHelper.mapPathway(ExportHelper.java:502)
at org.pathvisio.biopax3.exporter.ExportHelper.<init>(ExportHelper.java:131)
at org.pathvisio.biopax3.BiopaxFormat.doExport(BiopaxFormat.java:36)
at org.pathvisio.Engine.exportPathway(Engine.java:116)
at org.pathvisio.util.Converter.main(Converter.java:148)
<BR>Command:java -Xmx512M -jar /var/www/wikipathways/wpi/bin/pathvisio_core.jar "/var/www/wikipathways/images/f/f1/WP176_35277.gpml" "/var/www/wikipathways/images/c/c8/WP176_35277.owl" 2>&1<BR>
