[jira] [Commented] (CTAKES-556) Build fails with Blocked mirror for repositories

[ https://issues.apache.org/jira/browse/CTAKES-556?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649853#comment-17649853 ] Sean Finan commented on CTAKES-556: --- This (Homebrew) workflow is not supported by Apach

[jira] [Closed] (CTAKES-556) Build fails with Blocked mirror for repositories

[ https://issues.apache.org/jira/browse/CTAKES-556?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-556. - Resolution: Invalid This is not a supported workflow. > Build fails with Blocked mirror for repositories

[jira] [Closed] (CTAKES-405) Installation not possible

[ https://issues.apache.org/jira/browse/CTAKES-405?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-405. - Assignee: Sean Finan Resolution: Not A Bug >From the Reporter: UPDATE: seems that complaining abou

[jira] [Closed] (CTAKES-415) DateAnnotatorTest testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest)

[ https://issues.apache.org/jira/browse/CTAKES-415?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-415. - Assignee: Sean Finan (was: Alex Zbarcea) Resolution: Won't Do >From 9/24/2019: // Two things: 1.

[jira] [Assigned] (CTAKES-476) Nullpointer running EA with AssertionAnotator (ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml)

[ https://issues.apache.org/jira/browse/CTAKES-476?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan reassigned CTAKES-476: - Assignee: Sean Finan > Nullpointer running EA with AssertionAnotator > (ctakes-assertion/desc/A

[jira] [Closed] (CTAKES-476) Nullpointer running EA with AssertionAnotator (ctakes-assertion/desc/AssertionMiniPipelineAnalysisEngine.xml)

[ https://issues.apache.org/jira/browse/CTAKES-476?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-476. - Resolution: Workaround This is related to https://issues.apache.org/jira/browse/CTAKES-76 AssertionAnaly

[jira] [Closed] (CTAKES-548) Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.

[ https://issues.apache.org/jira/browse/CTAKES-548?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-548. - Assignee: Sean Finan Resolution: Not A Bug It seems that the user did not install the dictionary. 

[jira] [Closed] (CTAKES-449) PolarityCleartkAnalysisEngine slow for large documents

[ https://issues.apache.org/jira/browse/CTAKES-449?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-449. - Resolution: Workaround > PolarityCleartkAnalysisEngine slow for large documents > ---

[jira] [Closed] (CTAKES-446) Piper file parameter value ignored when it contains quoted equals

[ https://issues.apache.org/jira/browse/CTAKES-446?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-446. - Fix Version/s: 4.0.1 Assignee: Sean Finan Resolution: Fixed Fixed 2/26/2019. Thank you S

[jira] [Resolved] (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 ] Sean Finan resolved CTAKES-74. -- Fix Version/s: 4.0.1 Resolution: Fixed > Tokenizer PennTreeBank breaks with certain apostrophes i

[jira] [Commented] (CTAKES-72) Housekeeping - clean up eclipse launch files

[ https://issues.apache.org/jira/browse/CTAKES-72?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649925#comment-17649925 ] ASF subversion and git services commented on CTAKES-72: --- Commit f9e7

[jira] [Resolved] (CTAKES-72) Housekeeping - clean up eclipse launch files

[ https://issues.apache.org/jira/browse/CTAKES-72?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan resolved CTAKES-72. -- Assignee: Sean Finan Resolution: Fixed Removed remaining eclipse launch configurations  > Houseke

[jira] [Closed] (CTAKES-71) Housekeeping - remove multiple copies of resources in different cTAKES projects

[ https://issues.apache.org/jira/browse/CTAKES-71?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-71. Assignee: Sean Finan Resolution: Not A Problem 2 of the hyphenated lists remain, but they are not iden

[jira] [Commented] (CTAKES-106) Add component to store XMI as Lucene indexes

[ https://issues.apache.org/jira/browse/CTAKES-106?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649931#comment-17649931 ] Sean Finan commented on CTAKES-106: --- What is the intended use case for having an xmi in

[jira] [Commented] (CTAKES-555) Unable to run negation pipeline

[ https://issues.apache.org/jira/browse/CTAKES-555?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649935#comment-17649935 ] Sean Finan commented on CTAKES-555: --- Hi Joseph, Please provide some details about your

[jira] [Commented] (CTAKES-558) StrengthAnnotation,DrugchangeStatus Annotation,StrengthAnnotation,FractionStrengthAnnotation,FrequencyUnitAnnotation not coming in the ctakes-web-rest web app

[ https://issues.apache.org/jira/browse/CTAKES-558?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649939#comment-17649939 ] Sean Finan commented on CTAKES-558: --- The lack of drug-related information is not a bug.

[jira] [Commented] (CTAKES-542) Error : Initialization of annotator class "org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator" failed.

[ https://issues.apache.org/jira/browse/CTAKES-542?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649942#comment-17649942 ] Sean Finan commented on CTAKES-542: --- There is no further information on the error from

[jira] [Commented] (CTAKES-557) remove log4jv1 dependency

[ https://issues.apache.org/jira/browse/CTAKES-557?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649944#comment-17649944 ] Sean Finan commented on CTAKES-557: --- An upgrade to log4j 2 is being discussed. > remov

[jira] [Commented] (CTAKES-551) cTAKES Download link is not working

[ https://issues.apache.org/jira/browse/CTAKES-551?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649948#comment-17649948 ] Sean Finan commented on CTAKES-551: --- This appears to be an intermittent problem, my apo

[jira] [Commented] (CTAKES-544) Smoking Status Annotator Question

[ https://issues.apache.org/jira/browse/CTAKES-544?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649950#comment-17649950 ] Sean Finan commented on CTAKES-544: --- Hi Aishwarya, You can run piper files using this

[jira] [Commented] (CTAKES-536) test program info

[ https://issues.apache.org/jira/browse/CTAKES-536?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649951#comment-17649951 ] Sean Finan commented on CTAKES-536: --- Hi Piero, There have been efforts using ctakes in

[jira] [Closed] (CTAKES-536) test program info

[ https://issues.apache.org/jira/browse/CTAKES-536?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-536. - Resolution: Information Provided Pointed to user, dev lists for posting questions. > test program info >

[jira] [Closed] (CTAKES-534) Error while creating custom dictionary

[ https://issues.apache.org/jira/browse/CTAKES-534?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-534. - Resolution: Not A Bug The UMLS source must be obtained from the NIH.   [https://www.nlm.nih.gov/research/

[jira] [Commented] (CTAKES-533) Cannot create custom words with "." in the custom BSV file

[ https://issues.apache.org/jira/browse/CTAKES-533?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649956#comment-17649956 ] Sean Finan commented on CTAKES-533: --- There are a couple of things that might be going o

[jira] [Commented] (CTAKES-385) URI is not hierarchical when attempting to obtain lvg.properties within JAR

[ https://issues.apache.org/jira/browse/CTAKES-385?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649962#comment-17649962 ] Sean Finan commented on CTAKES-385: --- A kludge was added 10/1/2017.  It may not be in th

[jira] [Closed] (CTAKES-532) ctakes-assertion throws NullPointerException

[ https://issues.apache.org/jira/browse/CTAKES-532?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-532. - Fix Version/s: future enhancement Assignee: Sean Finan Resolution: Information Provided A

[jira] [Commented] (CTAKES-531) String.replaceAll() has bad performance against replace() if not regex.

[ https://issues.apache.org/jira/browse/CTAKES-531?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649967#comment-17649967 ] ASF subversion and git services commented on CTAKES-531: Commit 4

[jira] [Commented] (CTAKES-532) ctakes-assertion throws NullPointerException

[ https://issues.apache.org/jira/browse/CTAKES-532?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649966#comment-17649966 ] ASF subversion and git services commented on CTAKES-532: Commit 4

[jira] [Resolved] (CTAKES-531) String.replaceAll() has bad performance against replace() if not regex.

[ https://issues.apache.org/jira/browse/CTAKES-531?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan resolved CTAKES-531. --- Fix Version/s: future enhancement Resolution: Fixed replaced > String.replaceAll() has bad pe

[jira] [Closed] (CTAKES-519) Polarity not working with Piper files

[ https://issues.apache.org/jira/browse/CTAKES-519?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-519. - Assignee: Sean Finan Resolution: Information Provided > Polarity not working with Piper files > ---

[jira] [Commented] (CTAKES-528) annotation confidence is always 0

[ https://issues.apache.org/jira/browse/CTAKES-528?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649972#comment-17649972 ] Sean Finan commented on CTAKES-528: --- There is currently no confidence calculated by the

[jira] [Closed] (CTAKES-471) i cant load the Apache Ctakes AggregatePlaintextFastUMLSProcessor.xml file

[ https://issues.apache.org/jira/browse/CTAKES-471?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-471. - Assignee: Sean Finan Resolution: Information Provided > i cant load the Apache Ctakes AggregatePlai

[jira] [Closed] (CTAKES-474) CTakes help getting sign /symptoms

[ https://issues.apache.org/jira/browse/CTAKES-474?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-474. - Assignee: Sean Finan Resolution: Information Provided > CTakes help getting sign /symptoms > --

[jira] [Closed] (CTAKES-512) Initialization of Annotator Class Failed

[ https://issues.apache.org/jira/browse/CTAKES-512?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-512. - Resolution: Information Provided > Initialization of Annotator Class Failed > ---

[jira] [Closed] (CTAKES-515) Failing to compile runPiperGui profile in Intellij

[ https://issues.apache.org/jira/browse/CTAKES-515?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-515. - Resolution: Information Provided Assumed java version error, no futher information from reporter 4 years

[jira] [Resolved] (CTAKES-525) Can't create custom dictionaries for resources with a dash in their names

[ https://issues.apache.org/jira/browse/CTAKES-525?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan resolved CTAKES-525. --- Fix Version/s: 4.0.1 Resolution: Fixed Fixed 12/19/18 > Can't create custom dictionaries for

[jira] [Closed] (CTAKES-521) Please specify PARAM_IS_TRAINING - unable to infer it from context

[ https://issues.apache.org/jira/browse/CTAKES-521?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-521. - Assignee: Sean Finan Resolution: Information Provided > Please specify PARAM_IS_TRAINING - unable

[jira] [Closed] (CTAKES-514) Running cTakes on Eclipse

[ https://issues.apache.org/jira/browse/CTAKES-514?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-514. - Resolution: Information Provided > Running cTakes on Eclipse > - > >

[jira] [Commented] (CTAKES-517) Running command line interface for development version throws error

[ https://issues.apache.org/jira/browse/CTAKES-517?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649992#comment-17649992 ] Sean Finan commented on CTAKES-517: --- Please run the runPiperFile script from the ctakes

[jira] [Closed] (CTAKES-517) Running command line interface for development version throws error

[ https://issues.apache.org/jira/browse/CTAKES-517?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-517. - Resolution: Information Provided > Running command line interface for development version throws error >

[jira] [Commented] (CTAKES-509) Build Error

[ https://issues.apache.org/jira/browse/CTAKES-509?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17649998#comment-17649998 ] Sean Finan commented on CTAKES-509: --- Just build with "{{{}mvn clean package -DskipTests

[jira] [Closed] (CTAKES-492) New cTAKES user question

[ https://issues.apache.org/jira/browse/CTAKES-492?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-492. - Resolution: Information Provided > New cTAKES user question > > >

[jira] [Commented] (CTAKES-352) Performance Report

[ https://issues.apache.org/jira/browse/CTAKES-352?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17650005#comment-17650005 ] Sean Finan commented on CTAKES-352: --- As far as I know it is useful for profiling annota

[jira] [Closed] (CTAKES-352) Performance Report

[ https://issues.apache.org/jira/browse/CTAKES-352?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan closed CTAKES-352. - Resolution: Information Provided > Performance Report > -- > > Key: CTAKE

[jira] [Resolved] (CTAKES-246) DrugMentionAnnotator falls to infinite loop for some expression

[ https://issues.apache.org/jira/browse/CTAKES-246?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ] Sean Finan resolved CTAKES-246. --- Resolution: Fixed Fixed several years ago and used by Chen. > DrugMentionAnnotator falls to infinite