Running bin/runClinicalPipeline.sh the the bin/runctakesCVD.sh is also being used throws a jdbc connection error:
> 22 Mar 2018 22:22:40 INFO UmlsUserApprover - Checking UMLS Account at > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user myuser: > ......22 Mar 2018 22:22:42 INFO UmlsUserApprover - UMLS Account at > https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser for user myuser has > been validated > 22 Mar 2018 22:22:42 INFO JdbcConnectionFactory - Connecting to > jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab: > .................................................. 50 > ........... > 22 Mar 2018 22:23:03 ERROR JdbcConnectionFactory - Could not create > Connection with > jdbc:hsqldb:file:/home/myuser/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab > as sa > java.sql.SQLException: Database lock acquisition failure: lockFile: > org.hsqldb.persist.LockFile@87544bb[file > =/home/myuser/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab.lck, > exists=true, locked=false, valid=false, ] method: checkHeartbeat read: > 2018-03-23 08:22:52 heartbeat - read: -9441 ms. > at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) > at org.hsqldb.jdbc.JDBCUtil.sqlException(Unknown Source) > at org.hsqldb.jdbc.JDBCConnection.<init>(Unknown Source) Ending the ctakesCVD process and rerunning the runClinicalPipeline script then seems to work. Does anyone know why this is exactly? Is there perhaps a way to change this (say changing some allowed connection count value in some config file)? Thanks.
