search

LHNCBC / metamaplite

A near real-time named-entity recognizer
https://metamap.nlm.nih.gov/MetaMapLite.shtml
Other
55 stars 14 forks source link

FileNotFoundException when opening default gv.words.temp.filename on Windows #22

Open dcronkite opened 1 year ago

dcronkite commented 1 year ago

The default bin/create_indexes.bat runs into a FileNotFoundException when running GenerateVariants (see https://github.com/lhncbc/metamaplite/blob/827a5c1f7a0174247ea499117d82745af827c628/bin/create_indexes.bat#L58-L60) as the default value for wordsFilename is /tmp/words.txt.tmp: https://github.com/lhncbc/metamaplite/blob/8aae39319a4a4b40a013180bf6cde09b172c78a8/src/main/java/gov/nih/nlm/nls/metamap/dfbuilder/GenerateVariants.java#L226-L227. It appears Java on Windows is unable to resolve the /tmp directory.

I was able to workaround the issue by adding the system property gv.words.temp.filename to the command line as just words.txt.tmp:

java -Xmx4g "-Dgv.words.temp.filename=words.txt.tmp" -cp %projectdir%\target\metamaplite-%MML_VERSION%-standalone.jar ^
     gov.nih.nlm.nls.metamap.dfbuilder.GenerateVariants ^
     %MRCONSO% %IVFDIR%\tables\vars.txt

Can this be added the create_indexes.bat script? Or, /tmp be replaced by something like System.getProperty("java.io.tmpdir")?