[jira] [Created] (CTAKES-194) InvalidXMLException: An import could not be resolved. org.apache.ctakes.drugner.types.Typesystem DrugCNP2LookupWindow.xml

James Joseph Masanz created CTAKES-194: -- Summary: InvalidXMLException: An import could not be resolved. org.apache.ctakes.drugner.types.Typesystem DrugCNP2LookupWindow.xml Key: CTAKES-194 URL:

[jira] [Commented] (CTAKES-211) Remove special test models used for Unit Tests?

[ https://issues.apache.org/jira/browse/CTAKES-211?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13683671#comment-13683671 ] James Joseph Masanz commented on CTAKES-211: Agree about getting rid of the

[jira] [Created] (CTAKES-218) java.io.FileNotFoundException: at java.io.FileInputStream.open(Native Method)

James Joseph Masanz created CTAKES-218: -- Summary: java.io.FileNotFoundException: at java.io.FileInputStream.open(Native Method) Key: CTAKES-218 URL: https://issues.apache.org/jira/browse/CTAKES-218

[jira] [Created] (CTAKES-221) java.io.FileNotFoundException: org\apache\ctakes\dependency\parser\models\lemmatizer\dictionary-1.3.1.jar

James Joseph Masanz created CTAKES-221: -- Summary: java.io.FileNotFoundException: org\apache\ctakes\dependency\parser\models\lemmatizer\dictionary-1.3.1.jar Key: CTAKES-221 URL:

[jira] [Commented] (CTAKES-226) CEM Templates- In the xxxMentions locations/severity store Annotation instead of the BinaryTextRelation

[ https://issues.apache.org/jira/browse/CTAKES-226?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13747605#comment-13747605 ] James Joseph Masanz commented on CTAKES-226: I was thinking more for demo

[jira] [Created] (CTAKES-227) Broca's - PunctuationToken instead of ContractionToken - caused by apostrophe seen as sentence ending

James Joseph Masanz created CTAKES-227: -- Summary: Broca's - PunctuationToken instead of ContractionToken - caused by apostrophe seen as sentence ending Key: CTAKES-227 URL:

[jira] [Updated] (CTAKES-74) Tokenizer PennTreeBank breaks with certain apostrophes in tokens.

[ https://issues.apache.org/jira/browse/CTAKES-74?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-74: -- Fix Version/s: (was: 3.1) 3.2 Tokenizer PennTreeBank breaks

[jira] [Commented] (CTAKES-74) Tokenizer PennTreeBank breaks with certain apostrophes in tokens.

[ https://issues.apache.org/jira/browse/CTAKES-74?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13750435#comment-13750435 ] James Joseph Masanz commented on CTAKES-74: --- moving to 3.2

[jira] [Updated] (CTAKES-178) parsing of medication strength does not verify a number was discovered (strength value includes both the dosage and strength value in some cases)

[ https://issues.apache.org/jira/browse/CTAKES-178?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-178: --- Fix Version/s: (was: 3.1) 3.2 parsing of medication

[jira] [Resolved] (CTAKES-139) FileNotFoundException: .... SideEffectTypeSystem.xml (The system cannot find the path specified)

[ https://issues.apache.org/jira/browse/CTAKES-139?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-139. Resolution: Duplicate Fix Version/s: (was: 3.0-incubating) fixed under

[jira] [Updated] (CTAKES-155) SimpleSegmentWithTagsAnnotator assumes all section names are 5 characters

[ https://issues.apache.org/jira/browse/CTAKES-155?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-155: --- Fix Version/s: (was: 3.1) 3.2

[jira] [Updated] (CTAKES-161) Take advantage of Java 1.5+ functionality

[ https://issues.apache.org/jira/browse/CTAKES-161?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-161: --- Summary: Take advantage of Java 1.5+ functionality (was: Java 1.5+) Take

[jira] [Resolved] (CTAKES-69) Add the code for reading Knowtator XML annotations into the UIMA type system.

[ https://issues.apache.org/jira/browse/CTAKES-69?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-69. --- Resolution: Fixed marking as fixed, as the Description section indicates

[jira] [Resolved] (CTAKES-218) java.io.FileNotFoundException: at java.io.FileInputStream.open(Native Method)

[ https://issues.apache.org/jira/browse/CTAKES-218?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-218. Resolution: Fixed java.io.FileNotFoundException: at

[jira] [Resolved] (CTAKES-211) Remove special test models used for Unit Tests?

[ https://issues.apache.org/jira/browse/CTAKES-211?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-211. Resolution: Fixed Remove special test models used for Unit Tests?

[jira] [Resolved] (CTAKES-82) Add ctakes-temporal module

[ https://issues.apache.org/jira/browse/CTAKES-82?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-82. --- Resolution: Fixed marking as fixed to get the reports updated since it was written

[jira] [Resolved] (CTAKES-7) Pre-Migration- Update/Migrate current cTAKES documentation

[ https://issues.apache.org/jira/browse/CTAKES-7?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-7. -- Resolution: Fixed we are using the apache wiki for install and use documentation

[jira] [Updated] (CTAKES-98) update our OpenNLP wrappers- write to the cTAKES TypeSystem types just via configuration

[ https://issues.apache.org/jira/browse/CTAKES-98?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-98: -- Fix Version/s: (was: 3.1) 3.2 update our OpenNLP wrappers-

[jira] [Updated] (CTAKES-50) Remove UIMA Deprecated references in Annotators

[ https://issues.apache.org/jira/browse/CTAKES-50?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-50: -- Fix Version/s: (was: 3.1) future enhancement Remove UIMA

[jira] [Updated] (CTAKES-172) relation-extractor is using StatusAnnotator and NegationAnnotator instead of AssertionAnnotator

[ https://issues.apache.org/jira/browse/CTAKES-172?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-172: --- Fix Version/s: (was: 3.1) 3.2 relation-extractor is

[jira] [Commented] (CTAKES-122) include LVG with 3.1

[ https://issues.apache.org/jira/browse/CTAKES-122?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13750511#comment-13750511 ] James Joseph Masanz commented on CTAKES-122: moved this to 3.2 since it's late

[jira] [Updated] (CTAKES-122) include LVG with 3.1

[ https://issues.apache.org/jira/browse/CTAKES-122?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-122: --- Fix Version/s: (was: 3.1) 3.2 include LVG with 3.1

[jira] [Resolved] (CTAKES-148) java.io.FileNotFoundException: C:\cTAKES\xxxx\desc\Constituency Parser\desc\ConstituencyParserAnnotator.xml

[ https://issues.apache.org/jira/browse/CTAKES-148?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-148. Resolution: Fixed r1517852 for 3.1, already fixed in 3.0.0-incubating branch

[jira] [Resolved] (CTAKES-141) side effect descriptors referencing old package names - edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator

[ https://issues.apache.org/jira/browse/CTAKES-141?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-141. Resolution: Fixed side effect descriptors referencing old package names -

[jira] [Resolved] (CTAKES-220) some named entities not found, e.g.coronary artery disease (chunker not labeling chunks correctly)

[ https://issues.apache.org/jira/browse/CTAKES-220?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-220. Resolution: Fixed some named entities not found, e.g.coronary artery disease

[jira] [Resolved] (CTAKES-32) dictionary lookup creates new LookupTokens many times

[ https://issues.apache.org/jira/browse/CTAKES-32?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-32. --- Resolution: Fixed This was fixed as part of r1442975 - see CTAKES-143

[jira] [Resolved] (CTAKES-190) dictionary lookup should create specific XxxxMention annotations instead of more generic EntityMention

[ https://issues.apache.org/jira/browse/CTAKES-190?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-190. Resolution: Fixed dictionary lookup should create specific XxxxMention

[jira] [Commented] (CTAKES-94) refactoring assertion module to use a cleartk-based analysis engine (and include evaluation)

[ https://issues.apache.org/jira/browse/CTAKES-94?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13751402#comment-13751402 ] James Joseph Masanz commented on CTAKES-94: --- moving to 3.2 - use of cleartk-based

[jira] [Updated] (CTAKES-94) refactoring assertion module to use a cleartk-based analysis engine (and include evaluation)

[ https://issues.apache.org/jira/browse/CTAKES-94?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-94: -- Fix Version/s: (was: 3.1) 3.2 refactoring assertion module

[jira] [Updated] (CTAKES-76) get third party dependencies into Maven Central

[ https://issues.apache.org/jira/browse/CTAKES-76?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-76: -- Fix Version/s: (was: 3.1) 3.2 get third party dependencies

[jira] [Updated] (CTAKES-138) Remove 3rd party jars from our SVN

[ https://issues.apache.org/jira/browse/CTAKES-138?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-138: --- Fix Version/s: (was: 3.1) 3.2 Remove 3rd party jars from

[jira] [Updated] (CTAKES-197) Upgrade cTAKES to Java 7

[ https://issues.apache.org/jira/browse/CTAKES-197?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-197: --- Fix Version/s: (was: 3.1) 3.2 Upgrade cTAKES to Java 7

[jira] [Resolved] (CTAKES-156) java.io.FileNotFoundException: lookup/rxnorm_index when using DictionaryLookupAnnotator_sideEffectUMLS.xml

[ https://issues.apache.org/jira/browse/CTAKES-156?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-156. Resolution: Fixed java.io.FileNotFoundException: lookup/rxnorm_index when

[jira] [Created] (CTAKES-229) SvmVectorCreator reference within MipacqSvmVectorCreator.xml uses old package naming

James Joseph Masanz created CTAKES-229: -- Summary: SvmVectorCreator reference within MipacqSvmVectorCreator.xml uses old package naming Key: CTAKES-229 URL: https://issues.apache.org/jira/browse/CTAKES-229

[jira] [Resolved] (CTAKES-142) can't find lookup/snomed-like_codes_sample Side effect descriptors need relative path updates

[ https://issues.apache.org/jira/browse/CTAKES-142?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-142. Resolution: Duplicate Fix Version/s: (was: 3.0-incubating) fixed under

[jira] [Resolved] (CTAKES-228) SideEffect import type system

[ https://issues.apache.org/jira/browse/CTAKES-228?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-228. Resolution: Fixed SideEffect import type system

[jira] [Updated] (CTAKES-77) Update POSTagger Unit Tests

[ https://issues.apache.org/jira/browse/CTAKES-77?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-77: -- Fix Version/s: (was: 3.1) 3.2 Update POSTagger Unit Tests

[jira] [Commented] (CTAKES-215) create a 3.1release of Apache cTAKES

[ https://issues.apache.org/jira/browse/CTAKES-215?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13752489#comment-13752489 ] James Joseph Masanz commented on CTAKES-215: - 4096 bit RSA KEY created -

[jira] [Commented] (CTAKES-95) Add MedER module

[ https://issues.apache.org/jira/browse/CTAKES-95?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13752571#comment-13752571 ] James Joseph Masanz commented on CTAKES-95: --- FYI, planning to call it MedXN.

[jira] [Updated] (CTAKES-231) missing NEs because of inconsistent chunking for parallel sentence constructions

[ https://issues.apache.org/jira/browse/CTAKES-231?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-231: --- Attachment: liver.cancer.chunking.issue.xmi.xml missing NEs because of

[jira] [Created] (CTAKES-231) missing NEs because of inconsistent chunking for parallel sentence constructions

James Joseph Masanz created CTAKES-231: -- Summary: missing NEs because of inconsistent chunking for parallel sentence constructions Key: CTAKES-231 URL: https://issues.apache.org/jira/browse/CTAKES-231

[jira] [Commented] (CTAKES-240) Download page must have link to KEYS file

[ https://issues.apache.org/jira/browse/CTAKES-240?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13760224#comment-13760224 ] James Joseph Masanz commented on CTAKES-240: Thanks Sebb and Pei. I have

[jira] [Created] (CTAKES-242) XCasWriterCasConsumer issues with Apache cTAKES 3.1

James Joseph Masanz created CTAKES-242: -- Summary: XCasWriterCasConsumer issues with Apache cTAKES 3.1 Key: CTAKES-242 URL: https://issues.apache.org/jira/browse/CTAKES-242 Project: cTAKES

[jira] [Created] (CTAKES-244) error using relation extractor launch (see also CTAKES-72)

James Joseph Masanz created CTAKES-244: -- Summary: error using relation extractor launch (see also CTAKES-72) Key: CTAKES-244 URL: https://issues.apache.org/jira/browse/CTAKES-244 Project: cTAKES

[jira] [Closed] (CTAKES-227) Broca's - PunctuationToken instead of ContractionToken - caused by apostrophe seen as sentence ending

[ https://issues.apache.org/jira/browse/CTAKES-227?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-227. -- Broca's - PunctuationToken instead of ContractionToken - caused by apostrophe seen

[jira] [Closed] (CTAKES-215) Create a 3.1 release of Apache cTAKES

[ https://issues.apache.org/jira/browse/CTAKES-215?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-215. -- Create a 3.1 release of Apache cTAKES -

[jira] [Resolved] (CTAKES-215) Create a 3.1 release of Apache cTAKES

[ https://issues.apache.org/jira/browse/CTAKES-215?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-215. Resolution: Implemented Create a 3.1 release of Apache cTAKES

[jira] [Resolved] (CTAKES-240) Download page must have link to KEYS file

[ https://issues.apache.org/jira/browse/CTAKES-240?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-240. Resolution: Fixed Download page must have link to KEYS file

[jira] [Closed] (CTAKES-45) opennlp-tools-1.4.3 for medKAT/p

[ https://issues.apache.org/jira/browse/CTAKES-45?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-45. - opennlp-tools-1.4.3 for medKAT/p

[jira] [Updated] (CTAKES-150) Apostrophe parsing is not thread safe because of global variable

[ https://issues.apache.org/jira/browse/CTAKES-150?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-150: --- Fix Version/s: 3.1.1 Apostrophe parsing is not thread safe because of global

[jira] [Created] (CTAKES-248) include original covered text of NEs which can't be recovered post if NE is from a disjoint span

James Joseph Masanz created CTAKES-248: -- Summary: include original covered text of NEs which can't be recovered post if NE is from a disjoint span Key: CTAKES-248 URL:

[jira] [Updated] (CTAKES-262) Create VM distribution for evaluation

[ https://issues.apache.org/jira/browse/CTAKES-262?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-262: --- Fix Version/s: (was: 3.1.1) future enhancement Create VM

[jira] [Commented] (CTAKES-262) Create VM distribution for evaluation

[ https://issues.apache.org/jira/browse/CTAKES-262?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13822959#comment-13822959 ] James Joseph Masanz commented on CTAKES-262: changed fix version to future

[jira] [Updated] (CTAKES-162) Command line scripts leave the user back one directory

[ https://issues.apache.org/jira/browse/CTAKES-162?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-162: --- Fix Version/s: (was: 3.1.1) 3.2 Command line scripts leave

[jira] [Created] (CTAKES-270) ctakes-assertion-zoner missing from trunk's bin.xml in ctakes-distribution

James Joseph Masanz created CTAKES-270: -- Summary: ctakes-assertion-zoner missing from trunk's bin.xml in ctakes-distribution Key: CTAKES-270 URL: https://issues.apache.org/jira/browse/CTAKES-270

[jira] [Resolved] (CTAKES-270) ctakes-assertion-zoner missing from trunk's bin.xml in ctakes-distribution

[ https://issues.apache.org/jira/browse/CTAKES-270?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-270. Resolution: Implemented ctakes-assertion-zoner missing from trunk's bin.xml in

[jira] [Created] (CTAKES-271) build fails due to mismatches within expectedoutput directory - e.g Sentence model was changed in 3.1.0

James Joseph Masanz created CTAKES-271: -- Summary: build fails due to mismatches within expectedoutput directory - e.g Sentence model was changed in 3.1.0 Key: CTAKES-271 URL:

[jira] [Closed] (CTAKES-271) build fails due to mismatches within expectedoutput directory - e.g Sentence model was changed in 3.1.0

[ https://issues.apache.org/jira/browse/CTAKES-271?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-271. -- Resolution: Fixed Assignee: James Joseph Masanz another difference was caused by

[jira] [Updated] (CTAKES-275) some of the older junit tests don't have the right Project name in the run configurations

[ https://issues.apache.org/jira/browse/CTAKES-275?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-275: --- Component/s: ctakes-ne-contexts ctakes-chunker

[jira] [Created] (CTAKES-275) some of the older junit tests don't have the right Project name in the run configurations

James Joseph Masanz created CTAKES-275: -- Summary: some of the older junit tests don't have the right Project name in the run configurations Key: CTAKES-275 URL:

[jira] [Resolved] (CTAKES-267) create a 3.1.1 patch release

[ https://issues.apache.org/jira/browse/CTAKES-267?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-267. Resolution: Done VOTE for rc2 passed. Will send announce after waiting for

[jira] [Closed] (CTAKES-272) regression test run during build of 3.1.1 fails with NoClassDefFoundError: CharacterOffsetToLineTokenConverter

[ https://issues.apache.org/jira/browse/CTAKES-272?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-272. -- regression test run during build of 3.1.1 fails with NoClassDefFoundError:

[jira] [Created] (CTAKES-276) Error grabbing Grapes -- [unresolved dependency: jwnl#jwnl;1.3.3: not found] from parser.groovy script

James Joseph Masanz created CTAKES-276: -- Summary: Error grabbing Grapes -- [unresolved dependency: jwnl#jwnl;1.3.3: not found] from parser.groovy script Key: CTAKES-276 URL:

[jira] [Resolved] (CTAKES-276) Error grabbing Grapes -- [unresolved dependency: jwnl#jwnl;1.3.3: not found] from parser.groovy script

[ https://issues.apache.org/jira/browse/CTAKES-276?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-276. Resolution: Fixed Error grabbing Grapes -- [unresolved dependency:

[jira] [Commented] (CTAKES-191) Update Apache OpenNLP dependency to 1.5.3

[ https://issues.apache.org/jira/browse/CTAKES-191?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13841690#comment-13841690 ] James Joseph Masanz commented on CTAKES-191:

[jira] [Commented] (CTAKES-82) Add ctakes-temporal module

[ https://issues.apache.org/jira/browse/CTAKES-82?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13850568#comment-13850568 ] James Joseph Masanz commented on CTAKES-82: --- I'm out until Tuesday 12/17. For

[jira] [Commented] (CTAKES-278) UMLS user and password should be validated

[ https://issues.apache.org/jira/browse/CTAKES-278?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13855748#comment-13855748 ] James Joseph Masanz commented on CTAKES-278: Hi Chen, Which version of

[jira] [Commented] (CTAKES-278) UMLS user and password should be validated

[ https://issues.apache.org/jira/browse/CTAKES-278?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13855771#comment-13855771 ] James Joseph Masanz commented on CTAKES-278: Since you are using trunk, it

[jira] [Created] (CTAKES-279) ArrayIndexOutOfBoundsException: 7 generateFeatures(SingleDocumentProcessor.java:274)

James Joseph Masanz created CTAKES-279: -- Summary: ArrayIndexOutOfBoundsException: 7 generateFeatures(SingleDocumentProcessor.java:274) Key: CTAKES-279 URL: https://issues.apache.org/jira/browse/CTAKES-279

[jira] [Updated] (CTAKES-279) ArrayIndexOutOfBoundsException: 7 generateFeatures(SingleDocumentProcessor.java:274)

[ https://issues.apache.org/jira/browse/CTAKES-279?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-279: --- Priority: Minor (was: Major) ArrayIndexOutOfBoundsException: 7

[jira] [Resolved] (CTAKES-288) Severity not set for DiseaseDisorderMention

[ https://issues.apache.org/jira/browse/CTAKES-288?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-288. Resolution: Fixed Fix Version/s: (was: 3.1.2) 3.2

[jira] [Created] (CTAKES-290) bodyLocation not being set for diseases or signs/symptoms from LocationOfTextRelation

James Joseph Masanz created CTAKES-290: -- Summary: bodyLocation not being set for diseases or signs/symptoms from LocationOfTextRelation Key: CTAKES-290 URL: https://issues.apache.org/jira/browse/CTAKES-290

[jira] [Resolved] (CTAKES-290) bodyLocation not being set for diseases or signs/symptoms from LocationOfTextRelation

[ https://issues.apache.org/jira/browse/CTAKES-290?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-290. Resolution: Fixed Fix Version/s: 3.1.2 updated TemplateFillerAnnotator.java

[jira] [Commented] (CTAKES-82) Add ctakes-temporal module

[ https://issues.apache.org/jira/browse/CTAKES-82?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=13964179#comment-13964179 ] James Joseph Masanz commented on CTAKES-82: ---  I'm out of the office until

[jira] [Issue Comment Deleted] (CTAKES-82) Add ctakes-temporal module

[ https://issues.apache.org/jira/browse/CTAKES-82?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-82: -- Comment: was deleted (was:   I'm out of the office this morning, back this

[jira] [Created] (CTAKES-302) Element type hibernate-mapping must be followed by either attribute specifications, or /.

James Joseph Masanz created CTAKES-302: -- Summary: Element type hibernate-mapping must be followed by either attribute specifications, or /. Key: CTAKES-302 URL:

[jira] [Updated] (CTAKES-302) Element type hibernate-mapping must be followed by either attribute specifications, or /.

[ https://issues.apache.org/jira/browse/CTAKES-302?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-302: --- Component/s: ctakes-ytex-res Element type hibernate-mapping must be followed by

[jira] [Assigned] (CTAKES-305) Broken link to Maven binary in documentation

[ https://issues.apache.org/jira/browse/CTAKES-305?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz reassigned CTAKES-305: -- Assignee: James Joseph Masanz Broken link to Maven binary in documentation

[jira] [Resolved] (CTAKES-305) Broken link to Maven binary in documentation

[ https://issues.apache.org/jira/browse/CTAKES-305?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-305. Resolution: Fixed Fix Version/s: 3.1.1 updated URLs on wiki page to the

[jira] [Commented] (CTAKES-338) Download/Unpack full LVG by default

[ https://issues.apache.org/jira/browse/CTAKES-338?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanelfocusedCommentId=14230002#comment-14230002 ] James Joseph Masanz commented on CTAKES-338: I should have said the size kept

[jira] [Resolved] (CTAKES-418) Exception: java.io.FileNotFoundException: ctakes-temporal/data/misc/{various}

[ https://issues.apache.org/jira/browse/CTAKES-418?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-418. Resolution: Fixed > Exception: java.io.FileNotFoundException:

[jira] [Created] (CTAKES-419) ctakes-trunk-compiletest fails Caused by: org.apache.uima.cas.CASRuntimeException: No sofaFS with name UriView found.

James Joseph Masanz created CTAKES-419: -- Summary: ctakes-trunk-compiletest fails Caused by: org.apache.uima.cas.CASRuntimeException: No sofaFS with name UriView found. Key: CTAKES-419 URL:

[jira] [Commented] (CTAKES-418) Exception: java.io.FileNotFoundException: ctakes-temporal/data/misc/{various}

[ https://issues.apache.org/jira/browse/CTAKES-418?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15876445#comment-15876445 ] James Joseph Masanz commented on CTAKES-418: Looks like the problem is that in

[jira] [Closed] (CTAKES-282) Dirty on check-out in Eclipse

[ https://issues.apache.org/jira/browse/CTAKES-282?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-282. -- > Dirty on check-out in Eclipse > - > > Key:

[jira] [Resolved] (CTAKES-355) Upgrade to UIMA 2.7.x

[ https://issues.apache.org/jira/browse/CTAKES-355?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-355. Resolution: Fixed Updated UIMA to 2.9 (including update of Uimafit to latest which

[jira] [Closed] (CTAKES-191) Update Apache OpenNLP dependency to 1.5.3

[ https://issues.apache.org/jira/browse/CTAKES-191?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-191. -- Resolution: Won't Fix I checked in r1788492 referencing this JIRA by mistake. this one

[jira] [Assigned] (CTAKES-355) Upgrade to UIMA 2.9

[ https://issues.apache.org/jira/browse/CTAKES-355?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz reassigned CTAKES-355: -- Assignee: James Joseph Masanz > Upgrade to UIMA 2.9 > --- > >

[jira] [Updated] (CTAKES-355) Upgrade to UIMA 2.9

[ https://issues.apache.org/jira/browse/CTAKES-355?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-355: --- Summary: Upgrade to UIMA 2.9 (was: Upgrade to UIMA 2.7.x) > Upgrade to UIMA 2.9 >

[jira] [Reopened] (CTAKES-191) Update Apache OpenNLP dependency to 1.5.3

[ https://issues.apache.org/jira/browse/CTAKES-191?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz reopened CTAKES-191: Assignee: James Joseph Masanz > Update Apache OpenNLP dependency to 1.5.3 >

[jira] [Updated] (CTAKES-417) Update OpenNLP to 1.7.2

[ https://issues.apache.org/jira/browse/CTAKES-417?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-417: --- Summary: Update OpenNLP to 1.7.2 (was: Update OpenNLP to 1.7.1 ) > Update OpenNLP

[jira] [Commented] (CTAKES-417) Update OpenNLP to 1.7.1

[ https://issues.apache.org/jira/browse/CTAKES-417?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15941062#comment-15941062 ] James Joseph Masanz commented on CTAKES-417: Commit 1788492 [ https://svn.apache.org/r1788492

[jira] [Resolved] (CTAKES-282) Dirty on check-out in Eclipse

[ https://issues.apache.org/jira/browse/CTAKES-282?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-282. Resolution: Fixed Fix Version/s: 4.0.0 I do not see any .project,

[jira] [Updated] (CTAKES-39) Upgrade LVG to a later version

[ https://issues.apache.org/jira/browse/CTAKES-39?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-39: -- Fix Version/s: 4.0.0 > Upgrade LVG to a later version > -- >

[jira] [Resolved] (CTAKES-417) Update OpenNLP to 1.7.2

[ https://issues.apache.org/jira/browse/CTAKES-417?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-417. Resolution: Fixed > Update OpenNLP to 1.7.2 > > >

[jira] [Closed] (CTAKES-421) Incorporate dictionary builder GUI into cTAKES

[ https://issues.apache.org/jira/browse/CTAKES-421?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-421. -- Resolution: Duplicate Sean is doing this as part of the more generic GUI Jira item

[jira] [Commented] (CTAKES-165) no maven profiles for running via maven other than mvn -PrunCPE and mvn -RrunCVD which are in ctakes-clinical-pipeline

[ https://issues.apache.org/jira/browse/CTAKES-165?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=15947600#comment-15947600 ] James Joseph Masanz commented on CTAKES-165: I think this is low, low priority since there

[jira] [Closed] (CTAKES-122) include LVG with a future version of cTAKES?

[ https://issues.apache.org/jira/browse/CTAKES-122?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz closed CTAKES-122. -- Resolution: Won't Fix Fix Version/s: (was: 3.2.3) At nearly a GB, not going

[jira] [Resolved] (CTAKES-423) Remove redundant entries from pom.xml

[ https://issues.apache.org/jira/browse/CTAKES-423?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz resolved CTAKES-423. Resolution: Fixed > Remove redundant entries from pom.xml >

[jira] [Assigned] (CTAKES-39) Upgrade LVG to a later version

[ https://issues.apache.org/jira/browse/CTAKES-39?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz reassigned CTAKES-39: - Assignee: James Joseph Masanz > Upgrade LVG to a later version >

[jira] [Updated] (CTAKES-411) Fix Unit tests with LVG (URI is not hierarchal in mvn package) test

[ https://issues.apache.org/jira/browse/CTAKES-411?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] James Joseph Masanz updated CTAKES-411: --- Fix Version/s: (was: 3.2.3) 4.0.0 > Fix Unit tests with LVG

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