Error: nid -2134436132" occurs during input of medical terms into Komet extended search

Description

Done
2019-05-06 12:24:53,634 ERROR [Startup service] sh.isaac.api.LookupService (LookupService.java:296) - Error starting isaac
org.glassfish.hk2.runlevel.CurrentlyRunningException: null
at org.glassfish.hk2.runlevel.internal.AsyncRunLevelContext.proceedTo(AsyncRunLevelContext.java:518) ~[hk2-runlevel-2.5.0-b60.jar:?]
at org.glassfish.hk2.runlevel.internal.RunLevelControllerImpl.proceedTo(RunLevelControllerImpl.java:72) ~[hk2-runlevel-2.5.0-b60.jar:?]
at sh.isaac.api.LookupService.setRunLevel(LookupService.java:594) ~[api-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.api.LookupService.startupIsaac(LookupService.java:243) [api-5.0.0-SNAPSHOT.jar:?]
at sh.komet.fx.stage.StartupAfterSelection.run(StartupAfterSelection.java:55) [application-5.0.0-SNAPSHOT.jar:?]
at java.lang.Thread.run(Thread.java:834) [?:?]
2019-05-06 12:25:01,842 WARN [JavaFX Application Thread] org.apache.shiro.realm.text.IniRealm (IniRealm.java:139) - Users or Roles are already populated. Configured Ini instance will be ignored.
2019-05-06 12:25:08,497 ERROR [JavaFX Application Thread] sh.isaac.provider.datastore.chronology.ChronologyUpdate (ChronologyUpdate.java:200) - Did not grow processing taxonomy update for SemanticChronology{Logic Graph
assemblage:EL++ stated form assemblage (SOLOR) <-2147483596>
rc:CONCEPT: IHTSDO Classifier (SOLOR) <-2147483637>
uuid: 31b49af7-8d96-52af-b7fd-516dab98b971
nid: -2147481456,
versions[
Logic Graph
Root[0]➞[3]
Necessary[3]➞[2]
And[2]➞[1]
Concept[1] Description-logic classifier (SOLOR) <-2147483407>
{Stamp≤1::Active 2019-03-18T17:03:25.897Z a:User (SOLOR) m:Core metadata module (SOLOR) p: Development path (SOLOR)≥}
]
}

[[
]]

2019-05-06 12:30:25,969 ERROR [ISAAC-Q-work-thread 180] sh.isaac.provider.query.search.SearchHandler (SearchHandler.java:247) - Unexpected error during lucene search
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:615) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at sh.isaac.provider.query.lucene.LuceneIndexer.searchInternal(LuceneIndexer.java:743) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.LuceneIndexer.search(LuceneIndexer.java:697) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.indexers.DescriptionIndexer.query(DescriptionIndexer.java:304) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.api.index.IndexDescriptionQueryService.query(IndexDescriptionQueryService.java:134) ~[api-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.ExtendedSearchViewController.lambda$search$10(ExtendedSearchViewController.java:764) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.search.SearchHandler.lambda$search$1(SearchHandler.java:241) ~[query-5.0.0-SNAPSHOT.jar:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) [?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) [?:?]
at java.lang.Thread.run(Thread.java:834) [?:?]
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:?]
at java.util.concurrent.FutureTask.get(FutureTask.java:191) ~[?:?]
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:611) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
... 9 more
Caused by: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at sh.isaac.api.externalizable.IsaacObjectType.readAndValidateHeader(IsaacObjectType.java:190) ~[api-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyProvider.getSemanticChronology(ChronologyProvider.java:532) ~[chronology-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.TimeStatusRestriction$1.test(TimeStatusRestriction.java:71) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.TimeStatusRestriction$1.test(TimeStatusRestriction.java:65) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.IsaacFilteredCollectorManager$IsaacFilteredCollector$1.collect(IsaacFilteredCollectorManager.java:119) ~[query-5.0.0-SNAPSHOT.jar:?]
at org.apache.lucene.search.BooleanScorer.scoreDocument(BooleanScorer.java:188) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreMatches(BooleanScorer.java:201) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindowIntoBitSetAndReplay(BooleanScorer.java:215) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindowMultipleScorers(BooleanScorer.java:259) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindow(BooleanScorer.java:304) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.score(BooleanScorer.java:316) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BulkScorer.score(BulkScorer.java:39) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:660) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher$5.call(IndexSearcher.java:602) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher$5.call(IndexSearcher.java:599) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
... 3 more
2019-05-06 12:30:25,973 ERROR [JavaFX Application Thread] sh.komet.gui.search.extended.ExtendedSearchViewController (ExtendedSearchViewController.java:691) - Unexpected Search Error
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:615) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at sh.isaac.provider.query.lucene.LuceneIndexer.searchInternal(LuceneIndexer.java:743) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.LuceneIndexer.search(LuceneIndexer.java:697) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.indexers.DescriptionIndexer.query(DescriptionIndexer.java:304) ~[query-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.api.index.IndexDescriptionQueryService.query(IndexDescriptionQueryService.java:134) ~[api-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.ExtendedSearchViewController.lambda$search$10(ExtendedSearchViewController.java:764) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.search.SearchHandler.lambda$search$1(SearchHandler.java:241) ~[query-5.0.0-SNAPSHOT.jar:?]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128) ~[?:?]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628) ~[?:?]
at java.lang.Thread.run(Thread.java:834) ~[?:?]
Caused by: java.util.concurrent.ExecutionException: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[?:?]
at java.util.concurrent.FutureTask.get(FutureTask.java:191) ~[?:?]
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:611) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
... 9 more
Caused by: java.lang.IllegalStateException: Expecting token for: Semantic found: Concept(token: 1)
at sh.isaac.api.externalizable.IsaacObjectType.readAndValidateHeader(IsaacObjectType.java:190) ~[api-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.datastore.chronology.ChronologyProvider.getSemanticChronology(ChronologyProvider.java:532) ~[chronology-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.TimeStatusRestriction$1.test(TimeStatusRestriction.java:71) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.komet.gui.search.extended.TimeStatusRestriction$1.test(TimeStatusRestriction.java:65) ~[search-view-5.0.0-SNAPSHOT.jar:?]
at sh.isaac.provider.query.lucene.IsaacFilteredCollectorManager$IsaacFilteredCollector$1.collect(IsaacFilteredCollectorManager.java:119) ~[query-5.0.0-SNAPSHOT.jar:?]
at org.apache.lucene.search.BooleanScorer.scoreDocument(BooleanScorer.java:188) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreMatches(BooleanScorer.java:201) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindowIntoBitSetAndReplay(BooleanScorer.java:215) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindowMultipleScorers(BooleanScorer.java:259) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.scoreWindow(BooleanScorer.java:304) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BooleanScorer.score(BooleanScorer.java:316) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.BulkScorer.score(BulkScorer.java:39) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher.search(IndexSearcher.java:660) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher$5.call(IndexSearcher.java:602) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at org.apache.lucene.search.IndexSearcher$5.call(IndexSearcher.java:599) ~[lucene-core-7.2.1.jar:7.2.1 b2b6438b37073bee1fca40374e85bf91aa457c0b - ubuntu - 2018-01-10 00:48:43]
at java.util.concurrent.FutureTask.run(FutureTask.java:264) ~[?:?]
... 3 more
2019-05-06 12:32:40,544 WARN [JavaFX Application Thread] org.apache.shiro.realm.text.IniRealm (IniRealm.java:139) - Users or Roles are already populated. Configured Ini instance will be ignored.
2019-05-06 12:32:46,399 ERROR [JavaFX Application Thread] sh.isaac.provider.datastore.chronology.ChronologyUpdate (ChronologyUpdate.java:200) - Did not grow processing taxonomy update for SemanticChronology{Logic Graph
assemblage:EL++ stated form assemblage (SOLOR) <-2147483596>
rc:CONCEPT: IHTSDO Classifier (SOLOR) <-2147483637>
uuid: 31b49af7-8d96-52af-b7fd-516dab98b971
nid: -2147481456,
versions[
Logic Graph
Root[0]➞[3]
Necessary[3]➞[2]
And[2]➞[1]
Concept[1] Description-logic classifier (SOLOR) <-2147483407>
{Stamp≤1::Active 2019-03-18T17:03:25.897Z a:User (SOLOR) m:Core metadata module (SOLOR) p: Development path (SOLOR)≥}
]
}

[[
]]

Environment

None

Activity

Show:
Saif Baig
May 8, 2019, 8:33 PM

Changeset with error zip file

Keith Campbell
May 10, 2019, 7:57 PM

Modified error handling to query will succeed with other matches, while error is logged.

Assignee

Keith Campbell

Reporter

Saif Baig

Labels

None

Priority

Major
Configure