i2b2 term search never returns when more than one word is used (1.8.1)

[Dale Johnson]

Hello.  I am still looking for guidance on this problem.

i2b2 version 1.8.1

If a user searches for a single word in the term search, the search quickly returns an answer.  But if the search contains two or more words, the search never returns and times out, no matter how we limit the search to specific categories.

The Wildfly server log shows the error below for a 2+word search.  (There is no such error in the log for a single-word search.)  Where should we be looking for the 'stopword' entry?  

Thank you!

Dale Johnson

University of Alabama at Birmingham

2026-02-03 06:41:45,219 ERROR [stderr] (Thread-7983) edu.harvard.i2b2.common.exception.I2B2Exception: Application property file(edu.harvard.i2b2.ontology.stopword entry
2026-02-03 06:41:45,220 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.util.OntologyUtil.getPropertyValue(OntologyUtil.java:303)
2026-02-03 06:41:45,220 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.util.OntologyUtil.getStopWord(OntologyUtil.java:185)
2026-02-03 06:41:45,220 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.dao.ConceptDao.getStopWords(ConceptDao.java:1097)
2026-02-03 06:41:45,220 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.dao.ConceptDao.parseMatchString(ConceptDao.java:1071)
2026-02-03 06:41:45,221 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.dao.ConceptDao.findNameInfo(ConceptDao.java:671)
2026-02-03 06:41:45,221 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.delegate.GetNameInfoHandler.execute(GetNameInfoHandler.java:86)
2026-02-03 06:41:45,221 ERROR [stderr] (Thread-7983)  at edu.harvard.i2b2.ontology.ws.ExecutorRunnable.run(ExecutorRunnable.java:76)
2026-02-03 06:41:45,221 ERROR [stderr] (Thread-7983)  at java.base/java.lang.Thread.run(Thread.java:829)
2026-02-03 06:44:45,217 ERROR [edu.harvard.i2b2.ontology.ws.OntologyService] (default task-64) er.jobException is null

[mabaj...@mac.com]

Hello,

I am unable to reproduce the error you are seeing. I am using i2b2 v1.8.2.

In my copy of i2b2, the default value for 'edu.harvard.i2b2.ontology.stopword' is 

'a,able,about,across,after,all,almost,also,am,among,an,and,any,are,as,at,be,because,been,but,by,can,cannot,could,dear,did,do,does,either,else,ever,every,for,from,get,got,had,has,have,he,her,hers,him,his,how,however,i,if,in,into,is,it,its,just,least,let,like,likely,may,me,might,most,must,my,neither,no,nor,not,of,off,often,on,only,or,other,our,own,rather,said,say,says,she,should,since,so,some,than,that,the,their,them,then,there,these,they,this,tis,to,too,twas,us,wants,was,we,were,what,when,where,which,while,who,whom,why,will,with,would,yet,you,your'

That's all one line, no newlines, no carriage returns, and the single quotes are there only to set it off, they are not part of the value.

This item is set in the HIVE_CELL_PARAMS table. You should probably check your HIVE_CELL_PARAMS table. My table (i2b2 1.8.2) has 87 rows. And that 'edu.harvard.i2b2.ontology.stopword' entry is one of them. Does this entry exist in your HIVE_CELL_PARAMS table?

Kind regards,

Mark Abajian

Abajian Consulting, LLC
P.O. Box 8017, Glendale, CA  91224

[mabaj...@mac.com]

Hello, Dale Johnson,

I offered a suggestion about a week ago. Was this helpful?

Mark Abajian

Abajian Consulting, LLC
P.O. Box 8017, Glendale, CA  91224

[Dale Johnson]

Mark, thank you for your response, and I apologize for not responding sooner.

That entry was completely missing from our hive params, so I added it and, unfortunately, it did not fix the problem or remove the error from the error log.

But it did give us something to look into further - did we miss something important during the upgrade or is something else not 'turned on' in our local i2b2?

Take care.

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[maba...@mac.com]

Hello, Dale,

Reminder: changes to Hive Params take effect only after restarting WildFly. They are not instantaneous like some other aspects of the database.

Maybe you have restarted already, but I hope this helps.

Kind regards,

Mark

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[Dale Johnson]

Mark, you are a hero!!!  After the weekly server reboot, the search is finally working for multiple words.

I cannot thank you enough.

Take care!

Dale Johnson