RELATED: HSQLDB out of memory with custom dictionary

[MatthewVita]

Hi Sean, Tim, cTAKES Community,

I have put together what I am considering a pretty standard dictionary with sources from the following:

• MEDLINEPLUS
• MSH
• NCI
• NDFRT
• CHV
• CSP
• ICPC2P
• MEDCIN
• SNOMED
• RXNORM
• ICD10

However, when copied over to cTAKES (handled by the handy Dictionary Creator GUI) HSQLDB runs out of memory.

This is my first experience with HSQLDB so you’ll have to excuse my limited knowledge here. I do understand that it can run either in-memory and on disk, but I’m not sure how to configure this.

Here is how I am connecting to it:

 <dictionary>
  <name>sno_rx_16abTerms</name>
  <implementationName>org.apache.ctakes.dictionary.lookup2.dictionary.UmlsJdbcRareWordDictionary</implementationName>
  <properties>
    <property key="jdbcDriver" value="org.hsqldb.jdbcDriver" />
    <property key="jdbcUrl" value="jdbc:hsqldb:file:resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab" />
    <property key="jdbcUser" value="sa" />
    <property key="jdbcPass" value="" />
    <property key="rareWordTable" value="cui_terms" />
    <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser" />
    <property key="umlsVendor" value="NLM-6515182895" />
    <property key="umlsUser" value="CHANGE_ME" />
    <property key="umlsPass" value="CHANGE_ME" />
  </properties>
</dictionary>
<dictionary>

Can I configure HSQLDB to be used on disk? If this is not a good approach, can I spin up MySQL in its place?

Sorry if this has asked before.

Thanks,

Matthew Vita www.matthewvita.com

[MatthewVita]

Maybe we can bring in a MySQL container if this is a good fit. Maybe this won't be appropriate as a default, but I am happy to provide documentation in the README.

[MatthewVita]

working on this: https://github.com/GoTeamEpsilon/cTAKES-HSQLDB-to-MySQL-Dictionary :)