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LHNCBC / metamaplite

A near real-time named-entity recognizer
https://metamap.nlm.nih.gov/MetaMapLite.shtml
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FileNotFoundException when building Indices #21

Open dcronkite opened 1 year ago

dcronkite commented 1 year ago

I built a custom UMLS and then attempted to index the output using bin/create_indexes.bat, but ran into an issue:

Exception in thread "main" java.io.FileNotFoundException: C:\path\to\indices\meshtcrelaxed\postings (The system cannot find the path specified)
        at java.io.RandomAccessFile.open0(Native Method)
        at java.io.RandomAccessFile.open(RandomAccessFile.java:316)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:243)
        at java.io.RandomAccessFile.<init>(RandomAccessFile.java:124)
        at irutils.MappedMultiKeyIndexDiskBasedGeneration.writeFinalIndex(MappedMultiKeyIndexDiskBasedGeneration.java:265)
        at gov.nih.nlm.nls.metamap.dfbuilder.BuildIndex.createIndex(BuildIndex.java:120)
        at gov.nih.nlm.nls.metamap.dfbuilder.BuildIndex.main(BuildIndex.java:155)

This seems to be caused by the containing directory (in my case, 'meshtcrelaxed') not existing when instantiating a new RandomAccessFile class here: https://github.com/lhncbc/metamaplite/blob/8aae39319a4a4b40a013180bf6cde09b172c78a8/src/main/java/irutils/MappedMultiKeyIndexDiskBasedGeneration.java#L265

If I manually create the containing directory C:\path\to\indices\meshtcrelaxed and then re-run, I don't encounter this error.