Re: Fw: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi James, That code is defunct and shouldn't be used. I will take it out for the next release. From: James Masanz Sent: Wednesday, May 15, 2024 4:05 PM To: dev@ctakes.apache.org Subject: Re: Fw: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi all, To get a clean environment, I started a new Windows Sandbox (on Windows 11), installed IntelliJ, and opened the downloaded ctakes sources as a project. Not sure if this was valid to try anymore - I tried to run HelloWorldAggregatePipeline.class directly. I haven't dug into this yet, but in case someone knows offhand - although it completed with an exit code 0 and output a value for Polarity, there is also this message included. ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. The lvg.properties file does exist in that directory. The context for that message is below I will do some other testing before I take a look at HelloWorldAggregatePipeline again. - James 15 May 2024 14:44:25 INFO LvgAnnotator - URL for lvg.properties =/C:/Users/Public/cT5/ctakes-5.1.0-source-release/ctakes-5.1.0/ctakes-lvg/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties 15 May 2024 14:44:26 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/models/sentdetect/sd-med-model.zip 15 May 2024 14:44:26 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - config file absolute path = C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cwd = C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cd file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\ ** Configuration Error: file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties (The filename, directory name, or volume label syntax is incorrect) ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. ** Configuration Error: file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties (The filename, directory name, or volume label syntax is incorrect) ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cd C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0 15 May 2024 14:44:26 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 15 May 2024 14:44:26 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 15 May 2024 14:44:26 INFO SentenceDetector - Starting processing. 15 May 2024 14:44:26 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 15 May 2024 14:44:26 INFO LvgAnnotator - process(JCas) 15 May 2024 14:44:26 INFO ContextDependentTokenizerAnnotator - process(JCas) 15 May 2024 14:44:26 INFO POSTagger - process(JCas) 15 May 2024 14:44:26 INFO ConfigParameterExample - Token:Hello POS:NNP 15 May 2024 14:44:26 INFO ConfigParameterExample - Token:World POS:NNP Entity: Hello === Polarity: 0 Entity: World === Polarity: 0 Process finished with exit code 0 On Wed, May 1, 2024 at 3:55 PM Finan, Sean wrote: > Hi all, > > As you may have seen, the last 5.1.0 candidate had some issues. > > I have created a new 5.1.0 candidate, available here: > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!tLjBU3w09cUeWE4115MKOWDwD6zM9k3Nyn-PlEf6BeifISf-bW5Fe2wZs1f1X42it4dl9D0EwoYgSLc_GZjCIKOkXjw-J_TO$ > > As before, individual module jars up two levels and in associated > subdirectories. > > Hopefully this candidate fares better. Please report any findings before > next Mo
Re: Fw: Please test the Apache cTAKES 5.1.0 release candidate
Hi all, To get a clean environment, I started a new Windows Sandbox (on Windows 11), installed IntelliJ, and opened the downloaded ctakes sources as a project. Not sure if this was valid to try anymore - I tried to run HelloWorldAggregatePipeline.class directly. I haven't dug into this yet, but in case someone knows offhand - although it completed with an exit code 0 and output a value for Polarity, there is also this message included. ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. The lvg.properties file does exist in that directory. The context for that message is below I will do some other testing before I take a look at HelloWorldAggregatePipeline again. - James 15 May 2024 14:44:25 INFO LvgAnnotator - URL for lvg.properties =/C:/Users/Public/cT5/ctakes-5.1.0-source-release/ctakes-5.1.0/ctakes-lvg/target/classes/org/apache/ctakes/lvg/data/config/lvg.properties 15 May 2024 14:44:26 INFO SentenceDetector - Sentence detector model file: org/apache/ctakes/core/models/sentdetect/sd-med-model.zip 15 May 2024 14:44:26 INFO TokenizerAnnotatorPTB - Initializing org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - Loading NLM Norm and Lvg with config file = file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - config file absolute path = C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cwd = C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cd file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\ ** Configuration Error: file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties (The filename, directory name, or volume label syntax is incorrect) ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. ** Configuration Error: file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties (The filename, directory name, or volume label syntax is incorrect) ** Error: problem of opening/reading config file: 'file:\C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0\ctakes-lvg\target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x option to specify the config file path. 15 May 2024 14:44:26 INFO LvgCmdApiResourceImpl - cd C:\Users\Public\cT5\ctakes-5.1.0-source-release\ctakes-5.1.0 15 May 2024 14:44:26 INFO ContextDependentTokenizerAnnotator - Finite state machines loaded. 15 May 2024 14:44:26 INFO POSTagger - POS tagger model file: org/apache/ctakes/postagger/models/mayo-pos.zip 15 May 2024 14:44:26 INFO SentenceDetector - Starting processing. 15 May 2024 14:44:26 INFO TokenizerAnnotatorPTB - process(JCas) in org.apache.ctakes.core.ae.TokenizerAnnotatorPTB 15 May 2024 14:44:26 INFO LvgAnnotator - process(JCas) 15 May 2024 14:44:26 INFO ContextDependentTokenizerAnnotator - process(JCas) 15 May 2024 14:44:26 INFO POSTagger - process(JCas) 15 May 2024 14:44:26 INFO ConfigParameterExample - Token:Hello POS:NNP 15 May 2024 14:44:26 INFO ConfigParameterExample - Token:World POS:NNP Entity: Hello === Polarity: 0 Entity: World === Polarity: 0 Process finished with exit code 0 On Wed, May 1, 2024 at 3:55 PM Finan, Sean wrote: > Hi all, > > As you may have seen, the last 5.1.0 candidate had some issues. > > I have created a new 5.1.0 candidate, available here: > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > As before, individual module jars up two levels and in associated > subdirectories. > > Hopefully this candidate fares better. Please report any findings before > next Monday, May 6th. > > Thank you, > > Sean > > p.s. > If you test build any of the rest projects (e.g. ctakes-web-rest) or build > an installation with Dockhand, you must first run mvn install. Those > builds require ctakes module jars to exist where they can be fetched, and > as ctakes 5.1.0 will not be available through maven central before a > release, the jars must be in your .m2 directory. > > > > > >
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
+1 from me. -Dennis From: Savova, Guergana Sent: Wednesday, May 15, 2024 2:26 PM To: dev@ctakes.apache.org Subject: RE: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * +1 from me. --Guergana -Original Message- From: Finan, Sean Sent: Wednesday, May 15, 2024 1:32 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Tim! From: Miller, Timothy Sent: Wednesday, May 15, 2024 11:38 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Ah - are you just running the class within intellij? If so, you need to set the classpath in the run configuration to be ctakes-examples. Otherwise the classpath doesn't contain anything from modules outside ctakes-gui and ctakes-core. Alternatively, run the maven compile step with the "runPiperGui" profile selected. That will also run the piper file submitter gui with the correct classpath. Using a binary build, after running bin/getUmlsDictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e><https://urldefense.com/v3/_
RE: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
+1 from me. --Guergana -Original Message- From: Finan, Sean Sent: Wednesday, May 15, 2024 1:32 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Tim! From: Miller, Timothy Sent: Wednesday, May 15, 2024 11:38 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Ah - are you just running the class within intellij? If so, you need to set the classpath in the run configuration to be ctakes-examples. Otherwise the classpath doesn't contain anything from modules outside ctakes-gui and ctakes-core. Alternatively, run the maven compile step with the "runPiperGui" profile selected. That will also run the piper file submitter gui with the correct classpath. Using a binary build, after running bin/getUmlsDictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks Tim! From: Miller, Timothy Sent: Wednesday, May 15, 2024 11:38 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Ah - are you just running the class within intellij? If so, you need to set the classpath in the run configuration to be ctakes-examples. Otherwise the classpath doesn't contain anything from modules outside ctakes-gui and ctakes-core. Alternatively, run the maven compile step with the "runPiperGui" profile selected. That will also run the piper file submitter gui with the correct classpath. Using a binary build, after running bin/getUmlsDictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Thanks Sean, I was able to get it working – definitely a user/documentation issue and not an issue with the code. Looks like a great release. I’m happy to vote for release +1. Tim From: Finan, Sean Date: Tuesday, May 14, 2024 at 10:35 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * Ah - are you just running the class within intellij? If so, you need to set the classpath in the run configuration to be ctakes-examples. Otherwise the classpath doesn't contain anything from modules outside ctakes-gui and ctakes-core. Alternatively, run the maven compile step with the "runPiperGui" profile selected. That will also run the piper file submitter gui with the correct classpath. Using a binary build, after running bin/getUmlsDictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e%3e> I added a little bit to your instructions in the ctakes-web-rest README https
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Ah - are you just running the class within intellij? If so, you need to set the classpath in the run configuration to be ctakes-examples. Otherwise the classpath doesn't contain anything from modules outside ctakes-gui and ctakes-core. Alternatively, run the maven compile step with the "runPiperGui" profile selected. That will also run the piper file submitter gui with the correct classpath. Using a binary build, after running bin/getUmlsDictionary, running bin/runPiperSubmitter also works. I don't want to do it for 5.1.0, but I should make names of the class, profile and script match. I will check the wiki instructions and make sure that -exact- details are in there. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e> I added a little bit to your instructions in the ctakes-web-rest README https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e> The lines here indirectly applies to pre-release builds: https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvE
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS]
Hi Tim, Thanks for testing, I'll look into this. Sean From: Miller, Timothy Sent: Tuesday, May 14, 2024 12:55 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e> I added a little bit to your instructions in the ctakes-web-rest README https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e> The lines here indirectly applies to pre-release builds: https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3e> The 5.1.0-SNAPSHOT version
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
I can check out and build successfully with mvn from the command line. I can successfully open in intellij and run the piper file submitter. I get an error trying to run the default fast pipeline piper file: Loading Piper File DefaultTokenizerPipeline ... Error: MESSAGE LOCALIZATION FAILED: Can't find resource for bundle java.util.PropertyResourceBundle, key No Analysis Component found for ContextDependentTokenizerAnnotator It doesn’t seem to be able to find the ContextDependentTokenizerAnnotator. Tim From: Miller, Timothy Date: Tuesday, May 14, 2024 at 9:25 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS] * External Email - Caution * What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$%3e> I added a little bit to your instructions in the ctakes-web-rest README https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$%3e> The lines here indirectly applies to pre-release builds: https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$><https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3chttps:/urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$%3e> The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on the 5.1.0 version of ctakes modules (not the SNAPSHOT). https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdP
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS]
What would you recommend for testing? Download the release tag to a clean system and try to do mvn compile and run some tests? Tim From: Finan, Sean Date: Thursday, May 2, 2024 at 6:57 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] [SUSPICIOUS] * External Email - Caution * Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/pom.xml*L1074__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO4jLXZJfA$> I added a little bit to your instructions in the ctakes-web-rest README https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README__;!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7xPAX45w$> The lines here indirectly applies to pre-release builds: https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/README*L22__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO77G-Kmpw$> The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on the 5.1.0 version of ctakes modules (not the SNAPSHOT). https://urldefense.com/v3/__https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$<https://urldefense.com/v3/__https:/github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml*L14__;Iw!!NZvER7FxgEiBAiR_!qEC094V4WptTp0dDb8gSoucu-ATor3CRJ8D064AyK511nLCL-ngQkVe-b3Ci3xgtI2BMcKLF1VFuuZZ7Q0sAXaNzpr0cHK4p5MRW6FKEcjQdPO7IKyYTAw$> The pre-release basically contains an equivalent to "changed code or resources" in that the code and resources in the pre-release do not exist on maven central, which is where a maven build would normally get them. When maven builds the pre-release it will not be able to find version 5.1.0 of any jars through maven central, so it will look for them in your local .m2 directory. Maven puts the 5.1.0 jars in your .m2 directory when you run 'mvn install' on the main ctakes project. In summary, To build ctakes-web-rest to test the pre-release war, one must run 'mvn install' on the ctakes main project before they run 'mvn package' on the ctakes-web-rest project (or on the main project's web-rest-build profile). To build ctakes-web-rest once ctakes 5.1.0 has been released, the extra preliminary step of running 'mvn install' will not be necessary. * If you have some time this week, we can connect to understand what exactly is the problem. I can meet you tomorrow evening your time (4-7 pm IST) to work with you in the SQL problem. If you'd rather keep your Friday night to yourself, I can work with the same time slot any time through next Monday evening. Before the 6.0.0 release I will put some Release Manager information in the wiki. The maven release process using a GitHub repo requires a little trick that took me a long time to figure out, and the pre-release testing deserves some recorded documentation. Sean From: gandhi rajan Sent: Thursday, May 2, 2024 1:42 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi Sean, Thanks for the update. So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder you mean? Infact I was trying to build them on a machine which doesnt have a
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Thanks for the help Sean. The issue is fixed and build is working as expected. +1 for the release. On Thu, 2 May 2024 at 19:27, Finan, Sean wrote: > Hi Gandhi, > > > * So post release I would be able to run mvn clean > install on web rest module rather than relying on resources in .m2 folder > > The opposite. Pre-release there are no jars on maven central, > post-release there are. > Running 'mvn package' directly on the ctakes-web-rest project (in its > directory) > or > running 'mvn package' on the ctakes -main- project (in the main ctakes > root directory) with the web-rest-build profile enabled '-Pweb-rest-build' > will build the ctakes-web-rest.war web package. > That profile is defined in the main ctakes pom. > https://github.com/apache/ctakes/blob/main/pom.xml#L1074 > > I added a little bit to your instructions in the ctakes-web-rest README > https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README > > The lines here indirectly applies to pre-release builds: > https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README#L22 > > The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on the > 5.1.0 version of ctakes modules (not the SNAPSHOT). > https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml#L14 > > The pre-release basically contains an equivalent to "changed code or > resources" in that the code and resources in the pre-release do not exist > on maven central, which is where a maven build would normally get them. > When maven builds the pre-release it will not be able to find version > 5.1.0 of any jars through maven central, so it will look for them in your > local .m2 directory. > Maven puts the 5.1.0 jars in your .m2 directory when you run 'mvn install' > on the main ctakes project. > > In summary, > To build ctakes-web-rest to test the pre-release war, one must run 'mvn > install' on the ctakes main project before they run 'mvn package' on the > ctakes-web-rest project (or on the main project's web-rest-build profile). > To build ctakes-web-rest once ctakes 5.1.0 has been released, the extra > preliminary step of running 'mvn install' will not be necessary. > > > * If you have some time this week, we can connect to understand what > exactly is the problem. > > I can meet you tomorrow evening your time (4-7 pm IST) to work with you in > the SQL problem. If you'd rather keep your Friday night to yourself, I can > work with the same time slot any time through next Monday evening. > > Before the 6.0.0 release I will put some Release Manager information in > the wiki. The maven release process using a GitHub repo requires a little > trick that took me a long time to figure out, and the pre-release testing > deserves some recorded documentation. > > Sean > > > > > From: gandhi rajan > Sent: Thursday, May 2, 2024 1:42 AM > To: dev@ctakes.apache.org > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > [EXTERNAL] > > * External Email - Caution * > > > Hi Sean, > > Thanks for the update. So post release I would be able to run mvn clean > install on web rest module rather than relying on resources in .m2 folder > you mean? Infact I was trying to build them on a machine which doesnt have > any historic jars in the .m2 folder and thats why it was failing. > And ytex issue still remains a mystery to me. If you have some time this > week, we can connect to understand what exactly is the problem. > > On Thu, 2 May 2024 at 02:32, Finan, Sean > wrote: > > > Hi Gandhi, > > > > I can build the web-rest module. I should have mentioned that to build > > any of the rest projects you need to run mvn install. As the rest > requires > > 5.1.0 module jars and they don't exist externally (pre-release), maven > must > > be able to fetch them from your .m2 directory. > > > > I haven't been able to duplicate the ytex problems that you see and don't > > know what might be causing them. > > > > Sean > > > > > > From: gandhi rajan > > Sent: Tuesday, April 30, 2024 11:18 AM > > To: dev@ctakes.apache.org > > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > > [EXTERNAL] > > > > * External Email - Caution * > > > > > > Hi Peter, > > > > Thanks for the response. I dont think the generate test action is trying > to > > use mysql but hsql DB. Anyways, I am able to build other modules apart > from > > ytex and ytex-uima module. > > > > Sean, did you try building ctakes-web-rest module by any chance? It seems > > to be broken in
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
I'll test it today. Thanks Sean. Peter On Wed, May 1, 2024, 14:05 Finan, Sean wrote: > Hi Peter, > > I think that I have the ctakes-mastif-zoner module behavior as desired. > Let me know if you have any problems with the new candidate. > > Sean > > From: Peter Abramowitsch > Sent: Friday, April 26, 2024 11:41 PM > To: dev@ctakes.apache.org > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > [EXTERNAL] > > * External Email - Caution * > > > Hi Sean, > > It all compiles, but one of the jars is missing from the distribution. > It's the one I added: ctakes-mastif-zoner which is required if you're > going to use the Zone Annotator. > > It's in the master pom, and in the pom of ctakes-distribution, and the jar > got built in its projecte, but it's not scooped up into the distribution. > I'm not sure where else to look.Can you fix it? > > Peter > > > On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean > wrote: > > > Hi all, > > > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > > staging repository: > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZJnsDvVQ$ > > > > The code is contained within the file: > > ctakes-5.1.0-source-release.zip< > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGbgcnIf3Q$ > > > > > > > I welcome you all to test your favorite pipeline(s) and report any > issues. > > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > > Wednesday May 1. Please report any issues before that time. If any > > 'road-block' issues are found they will need to be addressed before a > > release. > > > > Thank you, > > Sean > > > > > > p.s. > > > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 > tag: > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGYS7mfi0g$ > > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZACCHJkw$ > > > > The 5.1.0 branch is a copy of the main branch: > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGaoZVS80g$ > > The version number in the 5.1.0 branch is different, but there are no > code > > differences between the two branches. > > > > > > >
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Gandhi, * So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder The opposite. Pre-release there are no jars on maven central, post-release there are. Running 'mvn package' directly on the ctakes-web-rest project (in its directory) or running 'mvn package' on the ctakes -main- project (in the main ctakes root directory) with the web-rest-build profile enabled '-Pweb-rest-build' will build the ctakes-web-rest.war web package. That profile is defined in the main ctakes pom. https://github.com/apache/ctakes/blob/main/pom.xml#L1074 I added a little bit to your instructions in the ctakes-web-rest README https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README The lines here indirectly applies to pre-release builds: https://github.com/apache/ctakes/blob/main/ctakes-web-rest/README#L22 The 5.1.0-SNAPSHOT version of ctakes-web-rest has a dependency on the 5.1.0 version of ctakes modules (not the SNAPSHOT). https://github.com/apache/ctakes/blob/main/ctakes-web-rest/pom.xml#L14 The pre-release basically contains an equivalent to "changed code or resources" in that the code and resources in the pre-release do not exist on maven central, which is where a maven build would normally get them. When maven builds the pre-release it will not be able to find version 5.1.0 of any jars through maven central, so it will look for them in your local .m2 directory. Maven puts the 5.1.0 jars in your .m2 directory when you run 'mvn install' on the main ctakes project. In summary, To build ctakes-web-rest to test the pre-release war, one must run 'mvn install' on the ctakes main project before they run 'mvn package' on the ctakes-web-rest project (or on the main project's web-rest-build profile). To build ctakes-web-rest once ctakes 5.1.0 has been released, the extra preliminary step of running 'mvn install' will not be necessary. * If you have some time this week, we can connect to understand what exactly is the problem. I can meet you tomorrow evening your time (4-7 pm IST) to work with you in the SQL problem. If you'd rather keep your Friday night to yourself, I can work with the same time slot any time through next Monday evening. Before the 6.0.0 release I will put some Release Manager information in the wiki. The maven release process using a GitHub repo requires a little trick that took me a long time to figure out, and the pre-release testing deserves some recorded documentation. Sean From: gandhi rajan Sent: Thursday, May 2, 2024 1:42 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi Sean, Thanks for the update. So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder you mean? Infact I was trying to build them on a machine which doesnt have any historic jars in the .m2 folder and thats why it was failing. And ytex issue still remains a mystery to me. If you have some time this week, we can connect to understand what exactly is the problem. On Thu, 2 May 2024 at 02:32, Finan, Sean wrote: > Hi Gandhi, > > I can build the web-rest module. I should have mentioned that to build > any of the rest projects you need to run mvn install. As the rest requires > 5.1.0 module jars and they don't exist externally (pre-release), maven must > be able to fetch them from your .m2 directory. > > I haven't been able to duplicate the ytex problems that you see and don't > know what might be causing them. > > Sean > > > From: gandhi rajan > Sent: Tuesday, April 30, 2024 11:18 AM > To: dev@ctakes.apache.org > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > [EXTERNAL] > > * External Email - Caution * > > > Hi Peter, > > Thanks for the response. I dont think the generate test action is trying to > use mysql but hsql DB. Anyways, I am able to build other modules apart from > ytex and ytex-uima module. > > Sean, did you try building ctakes-web-rest module by any chance? It seems > to be broken in my case. > > On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch > wrote: > > > Hi Gandhi, I think the email from Jeff Painter may explain your > > situation. It's a question of your version of mysql being new. The > > crucial lines in your trace are: > > > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > > [INFO] [java] Caused by: > > java.lang.reflect.InaccessibleObjectException: Unable to make protected > > final java.lang.Class > > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > > java.lang.ClassFormatError accessible: module java.base does not "opens > >
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Sean, Thanks for the update. So post release I would be able to run mvn clean install on web rest module rather than relying on resources in .m2 folder you mean? Infact I was trying to build them on a machine which doesnt have any historic jars in the .m2 folder and thats why it was failing. And ytex issue still remains a mystery to me. If you have some time this week, we can connect to understand what exactly is the problem. On Thu, 2 May 2024 at 02:32, Finan, Sean wrote: > Hi Gandhi, > > I can build the web-rest module. I should have mentioned that to build > any of the rest projects you need to run mvn install. As the rest requires > 5.1.0 module jars and they don't exist externally (pre-release), maven must > be able to fetch them from your .m2 directory. > > I haven't been able to duplicate the ytex problems that you see and don't > know what might be causing them. > > Sean > > > From: gandhi rajan > Sent: Tuesday, April 30, 2024 11:18 AM > To: dev@ctakes.apache.org > Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate > [EXTERNAL] > > * External Email - Caution * > > > Hi Peter, > > Thanks for the response. I dont think the generate test action is trying to > use mysql but hsql DB. Anyways, I am able to build other modules apart from > ytex and ytex-uima module. > > Sean, did you try building ctakes-web-rest module by any chance? It seems > to be broken in my case. > > On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch > wrote: > > > Hi Gandhi, I think the email from Jeff Painter may explain your > > situation. It's a question of your version of mysql being new. The > > crucial lines in your trace are: > > > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > > [INFO] [java] Caused by: > > java.lang.reflect.InaccessibleObjectException: Unable to make protected > > final java.lang.Class > > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > > java.lang.ClassFormatError accessible: module java.base does not "opens > > java.lang" to unnamed module @61ca2dfa > > > > And this makes it sound like it is expecting a library version where > > certain classnames or accessibility has changed. Check Jeff's pull > > requests and see if that fixes your problem. > > > > Another quick trick is maven -fae (Fail at end) It will go > > through the rest of the build and only show failures then > > Peter > > > > On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan > > wrote: > > > > > HI Peter, > > > > > > Thanks for the insights. I tried to debug from AppMain.java and it > > > eventually fails in > > > > > > > > > "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.(ObjectFactoryBind.java:43)" > > > > > > Attaching the complete stacktrace for reference: > > > > > > > > > [INFO] [java] invoking method > > > [INFO] [java] Exception in thread "main" > > > java.lang.ExceptionInInitializerError > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282) > > > [INFO] [java] at > > > > > > > > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.(SingleElementNodeProperty.java:94) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native > > > Method) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) > > > [INFO] [java] at > > > > > > > > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > > [INFO] [java] at > > > > > > > > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) > > > [INFO] [java] at > > > > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) > > > [INFO
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Peter, I think that I have the ctakes-mastif-zoner module behavior as desired. Let me know if you have any problems with the new candidate. Sean From: Peter Abramowitsch Sent: Friday, April 26, 2024 11:41 PM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi Sean, It all compiles, but one of the jars is missing from the distribution. It's the one I added: ctakes-mastif-zoner which is required if you're going to use the Zone Annotator. It's in the master pom, and in the pom of ctakes-distribution, and the jar got built in its projecte, but it's not scooped up into the distribution. I'm not sure where else to look.Can you fix it? Peter On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean wrote: > Hi all, > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > staging repository: > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZJnsDvVQ$ > > The code is contained within the file: > ctakes-5.1.0-source-release.zip< > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGbgcnIf3Q$ > > > > I welcome you all to test your favorite pipeline(s) and report any issues. > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > Wednesday May 1. Please report any issues before that time. If any > 'road-block' issues are found they will need to be addressed before a > release. > > Thank you, > Sean > > > p.s. > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: > https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGYS7mfi0g$ > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/5.1.0__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGZACCHJkw$ > > The 5.1.0 branch is a copy of the main branch: > https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!oamc_hHAvz2fBQkEZj8-lyh6rre52BxodrPgl8rcF3RzuF2yd5wK6jstb2HvAuElskKXRnpFZryui_jct7-SQsoWbGaoZVS80g$ > The version number in the 5.1.0 branch is different, but there are no code > differences between the two branches. > > >
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Gandhi, I can build the web-rest module. I should have mentioned that to build any of the rest projects you need to run mvn install. As the rest requires 5.1.0 module jars and they don't exist externally (pre-release), maven must be able to fetch them from your .m2 directory. I haven't been able to duplicate the ytex problems that you see and don't know what might be causing them. Sean From: gandhi rajan Sent: Tuesday, April 30, 2024 11:18 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi Peter, Thanks for the response. I dont think the generate test action is trying to use mysql but hsql DB. Anyways, I am able to build other modules apart from ytex and ytex-uima module. Sean, did you try building ctakes-web-rest module by any chance? It seems to be broken in my case. On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch wrote: > Hi Gandhi, I think the email from Jeff Painter may explain your > situation. It's a question of your version of mysql being new. The > crucial lines in your trace are: > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > [INFO] [java] Caused by: > java.lang.reflect.InaccessibleObjectException: Unable to make protected > final java.lang.Class > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > java.lang.ClassFormatError accessible: module java.base does not "opens > java.lang" to unnamed module @61ca2dfa > > And this makes it sound like it is expecting a library version where > certain classnames or accessibility has changed. Check Jeff's pull > requests and see if that fixes your problem. > > Another quick trick is maven -fae (Fail at end) It will go > through the rest of the build and only show failures then > Peter > > On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan > wrote: > > > HI Peter, > > > > Thanks for the insights. I tried to debug from AppMain.java and it > > eventually fails in > > > > > "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.(ObjectFactoryBind.java:43)" > > > > Attaching the complete stacktrace for reference: > > > > > > [INFO] [java] invoking method > > [INFO] [java] Exception in thread "main" > > java.lang.ExceptionInInitializerError > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.(SingleElementNodeProperty.java:94) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native > > Method) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > [INFO] [java] at > > > > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) > > [INFO] [java] at > > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:181) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:326) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:141) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1163) > > [INFO] [java] at > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145) > > [INFO] [java] at > > com.sun.xml.bind.v2.ContextFactory.createContext(Con
Fw: Please test the Apache cTAKES 5.1.0 release candidate
Hi all, As you may have seen, the last 5.1.0 candidate had some issues. I have created a new 5.1.0 candidate, available here: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ As before, individual module jars up two levels and in associated subdirectories. Hopefully this candidate fares better. Please report any findings before next Monday, May 6th. Thank you, Sean p.s. If you test build any of the rest projects (e.g. ctakes-web-rest) or build an installation with Dockhand, you must first run mvn install. Those builds require ctakes module jars to exist where they can be fetched, and as ctakes 5.1.0 will not be available through maven central before a release, the jars must be in your .m2 directory. From: Finan, Sean Sent: Friday, April 26, 2024 11:58 AM To: dev@ctakes.apache.org Subject: Please test the Apache cTAKES 5.1.0 release candidate Hi all, There is a candidate for version 5.1.0 of Apache cTAKES source code in a staging repository: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ The code is contained within the file: ctakes-5.1.0-source-release.zip<https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip> I welcome you all to test your favorite pipeline(s) and report any issues. I am calling a vote from the PMC to finish by 12:nn Eastern time, next Wednesday May 1. Please report any issues before that time. If any 'road-block' issues are found they will need to be addressed before a release. Thank you, Sean p.s. The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 The ctakes-5.1.0 tag was made from the 5.1.0 branch: https://github.com/apache/ctakes/tree/5.1.0 The 5.1.0 branch is a copy of the main branch: https://github.com/apache/ctakes/tree/main The version number in the 5.1.0 branch is different, but there are no code differences between the two branches.
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Peter, Thanks for the response. I dont think the generate test action is trying to use mysql but hsql DB. Anyways, I am able to build other modules apart from ytex and ytex-uima module. Sean, did you try building ctakes-web-rest module by any chance? It seems to be broken in my case. On Tue, 30 Apr 2024 at 01:28, Peter Abramowitsch wrote: > Hi Gandhi, I think the email from Jeff Painter may explain your > situation. It's a question of your version of mysql being new. The > crucial lines in your trace are: > > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > [INFO] [java] Caused by: > java.lang.reflect.InaccessibleObjectException: Unable to make protected > final java.lang.Class > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > java.lang.ClassFormatError accessible: module java.base does not "opens > java.lang" to unnamed module @61ca2dfa > > And this makes it sound like it is expecting a library version where > certain classnames or accessibility has changed. Check Jeff's pull > requests and see if that fixes your problem. > > Another quick trick is maven -fae (Fail at end) It will go > through the rest of the build and only show failures then > Peter > > On Mon, Apr 29, 2024 at 12:29 PM gandhi rajan > wrote: > > > HI Peter, > > > > Thanks for the insights. I tried to debug from AppMain.java and it > > eventually fails in > > > > > "org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryBind.(ObjectFactoryBind.java:43)" > > > > Attaching the complete stacktrace for reference: > > > > > > [INFO] [java] invoking method > > [INFO] [java] Exception in thread "main" > > java.lang.ExceptionInInitializerError > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.AccessorInjector.prepare(AccessorInjector.java:83) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.opt.OptimizedAccessorFactory.get(OptimizedAccessorFactory.java:176) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.reflect.Accessor$FieldReflection.optimize(Accessor.java:282) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.property.SingleElementNodeProperty.(SingleElementNodeProperty.java:94) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native > > Method) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) > > [INFO] [java] at > > > > > java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) > > [INFO] [java] at > > java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.property.PropertyFactory.create(PropertyFactory.java:128) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.(ClassBeanInfoImpl.java:181) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.getOrCreate(JAXBContextImpl.java:509) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:326) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl.(JAXBContextImpl.java:141) > > [INFO] [java] at > > > > > com.sun.xml.bind.v2.runtime.JAXBContextImpl$JAXBContextBuilder.build(JAXBContextImpl.java:1163) > > [INFO] [java] at > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:145) > > [INFO] [java] at > > com.sun.xml.bind.v2.ContextFactory.createContext(ContextFactory.java:236) > > [INFO] [java] at > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native > > Method) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) > > [INFO] [java] at > > > > > java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > > [INFO] [java] at > > java.base/java.lang.reflect.Method.invoke(Method.java:568) > > [INF
Re: Please test the Apache cTAKES 5.1.0 release candidate
axb.ObjectFactoryUtil.getJAXBElementBySrcXml(ObjectFactoryUtil.java:49) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getConnTypeBySrcXml(ObjectFactoryUtil.java:86) > [INFO] [java] at > > org.apache.ctakes.jdl.data.xml.jaxb.ObjectFactoryUtil.getJdbcTypeBySrcXml(ObjectFactoryUtil.java:64) > [INFO] [java] at > org.apache.ctakes.jdl.AppJdl.execute(AppJdl.java:80) > [INFO] [java] at > org.apache.ctakes.jdl.AppMain.main(AppMain.java:84) > [INFO] [java] Caused by: > java.lang.reflect.InaccessibleObjectException: Unable to make protected > final java.lang.Class > java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int) throws > java.lang.ClassFormatError accessible: module java.base does not "opens > java.lang" to unnamed module @61ca2dfa > [INFO] [java] at > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:354) > [INFO] [java] at > > java.base/java.lang.reflect.AccessibleObject.checkCanSetAccessible(AccessibleObject.java:297) > [INFO] [java] at > java.base/java.lang.reflect.Method.checkCanSetAccessible(Method.java:199) > [INFO] [java] at > java.base/java.lang.reflect.Method.setAccessible(Method.java:193) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:177) > [INFO] [java] at > com.sun.xml.bind.v2.runtime.reflect.opt.Injector$1.run(Injector.java:172) > [INFO] [java] at > > java.base/java.security.AccessController.doPrivileged(AccessController.java:318) > [INFO] [java] at > > com.sun.xml.bind.v2.runtime.reflect.opt.Injector.(Injector.java:172) > [INFO] [java] ... 34 more > > On Mon, 29 Apr 2024 at 21:21, Peter Abramowitsch > wrote: > > > I think this is the class where Java is exiting with 1 > > /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java > > > > btw my environment is MacOS and I notice yours is Windows, so the root > > cause why this class is giving you trouble is something I wouldn't be > able > > to help you with. But some debug statements rather than asserts would > tell > > you, I think. > > > > Peter > > > > On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch < > > pabramowit...@gmail.com> > > wrote: > > > > > Hi Gandhi > > > This project is an odd one in the sense that when you tell it to skip > the > > > tests, it still goes through the effort in building up the db > environment > > > that the tests would use. But in any case, for me it does build either > > > way. In the attached log, I've run a maven clean before doing the > build > > > without tests. > > > > > > However, check my previous email about your issue. Whereas you'd > > narrowed > > > it down to a script, I found a line in your email which showed the > error > > > within that script's execution: A java program: jdl running as > App.Main > > > threw an assertion on one of the tasks connected with the mysql > database > > it > > > was trying to configure. You could put some debugging statements in > > there > > > to see which one. > > > > > > Peter > > > > > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan > > > wrote: > > > > > >> Thanks for the insights Peter. I dint make it clear that I did ran the > > >> install on ytex module with test case execution toggled off. I used > the > > >> following command - "mvn -e clean install -Dmaven.test.skip=true" and > I > > >> still hit the same error. > > >> > > >> On digging deep, I could find that the build process is trying to > > execute > > >> "" in > > >> build-main.xml which in turn is trying to invoke the following target > in > > >> build.setup.xml: > > >> > > >> > >> depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > >> > > >> > > >> > > >> Did you try running this on a fresh setup Peter? > > >> > > >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch < > > pabramowit...@gmail.com > > >> > > > >> wrote: > > >> > > >> > Hi Gandhi > > >> > Your error appears to be at this line > > >> > > > >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > >> Java > > >> >
Re: Please test the Apache cTAKES 5.1.0 release candidate
ime.reflect.opt.Injector$1.run(Injector.java:172) [INFO] [java] at java.base/java.security.AccessController.doPrivileged(AccessController.java:318) [INFO] [java] at com.sun.xml.bind.v2.runtime.reflect.opt.Injector.(Injector.java:172) [INFO] [java] ... 34 more On Mon, 29 Apr 2024 at 21:21, Peter Abramowitsch wrote: > I think this is the class where Java is exiting with 1 > /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java > > btw my environment is MacOS and I notice yours is Windows, so the root > cause why this class is giving you trouble is something I wouldn't be able > to help you with. But some debug statements rather than asserts would tell > you, I think. > > Peter > > On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch < > pabramowit...@gmail.com> > wrote: > > > Hi Gandhi > > This project is an odd one in the sense that when you tell it to skip the > > tests, it still goes through the effort in building up the db environment > > that the tests would use. But in any case, for me it does build either > > way. In the attached log, I've run a maven clean before doing the build > > without tests. > > > > However, check my previous email about your issue. Whereas you'd > narrowed > > it down to a script, I found a line in your email which showed the error > > within that script's execution: A java program: jdl running as App.Main > > threw an assertion on one of the tasks connected with the mysql database > it > > was trying to configure. You could put some debugging statements in > there > > to see which one. > > > > Peter > > > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan > > wrote: > > > >> Thanks for the insights Peter. I dint make it clear that I did ran the > >> install on ytex module with test case execution toggled off. I used the > >> following command - "mvn -e clean install -Dmaven.test.skip=true" and I > >> still hit the same error. > >> > >> On digging deep, I could find that the build process is trying to > execute > >> "" in > >> build-main.xml which in turn is trying to invoke the following target in > >> build.setup.xml: > >> > >> >> depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > >> > >> > >> > >> Did you try running this on a fresh setup Peter? > >> > >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch < > pabramowit...@gmail.com > >> > > >> wrote: > >> > >> > Hi Gandhi > >> > Your error appears to be at this line > >> > > >> > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > >> Java > >> > returned: 1 > >> > > >> > A test application being run here: AppMain is in charge of loading a > >> > temporary mysqldb that is used to test that part of ytex. For me it > is > >> > working, but if you can find a way to run that surefire test in the > >> > debugger, you can find out why it's failing on one of the assertions. > >> > Otherwise you can take this shortcut > >> > > >> > mvn -Dmaven.test.skip=true > >> > > >> > To build the project without running any tests. > >> > > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan > > >> > wrote: > >> > > >> > > Hi Sean, > >> > > > >> > > When I tried to build the complete ctakes suite, i get build failure > >> for > >> > > ctakes-ytex module with the following error: > >> > > > >> > > [ERROR] Failed to execute goal > >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > >> > > (generate-test-config) on project ctakes-ytex: An Ant BuildException > >> has > >> > > occured: The following error occurred while executing this line: > >> > > [ERROR] > >> > > > >> C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > >> > The > >> > > following error occurred while executing this line: > >> > > [ERROR] > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > >> > The > >> > > following error occurred while executing this line: > >> > > [ERROR] > >> > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > >> > The > &g
Re: Please test the Apache cTAKES 5.1.0 release candidate
Also, depending on your setup, newer versions of MySQL will break with current code until my PRs are incorporated :-) https://github.com/apache/ctakes/pull/10 https://github.com/apache/ctakes/pull/13 https://github.com/apache/ctakes/pull/14 https://github.com/apache/ctakes/pull/16 #10 adds support for more modern versions of MySQL - Sean indicated that they wanted to get the release out before they merge these PRs, but you can try them out if you want to test on Windows setup - I've only tested under Linux. I'm not using anything other than ytex from the ctakes project in my current work, so not sure I can add much to the convo otherwise. Thanks, Jeff On 4/29/24 11:50, Peter Abramowitsch wrote: I think this is the class where Java is exiting with 1 /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java btw my environment is MacOS and I notice yours is Windows, so the root cause why this class is giving you trouble is something I wouldn't be able to help you with. But some debug statements rather than asserts would tell you, I think. Peter On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch wrote: Hi Gandhi This project is an odd one in the sense that when you tell it to skip the tests, it still goes through the effort in building up the db environment that the tests would use. But in any case, for me it does build either way. In the attached log, I've run a maven clean before doing the build without tests. However, check my previous email about your issue. Whereas you'd narrowed it down to a script, I found a line in your email which showed the error within that script's execution: A java program: jdl running as App.Main threw an assertion on one of the tasks connected with the mysql database it was trying to configure. You could put some debugging statements in there to see which one. Peter On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan wrote: Thanks for the insights Peter. I dint make it clear that I did ran the install on ytex module with test case execution toggled off. I used the following command - "mvn -e clean install -Dmaven.test.skip=true" and I still hit the same error. On digging deep, I could find that the build process is trying to execute "" in build-main.xml which in turn is trying to invoke the following target in build.setup.xml: Did you try running this on a fresh setup Peter? On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch Hi Gandhi Your error appears to be at this line C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java returned: 1 A test application being run here: AppMain is in charge of loading a temporary mysqldb that is used to test that part of ytex. For me it is working, but if you can find a way to run that surefire test in the debugger, you can find out why it's failing on one of the assertions. Otherwise you can take this shortcut mvn -Dmaven.test.skip=true To build the project without running any tests. On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan wrote: Hi Sean, When I tried to build the complete ctakes suite, i get build failure for ctakes-ytex module with the following error: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run (generate-test-config) on project ctakes-ytex: An Ant BuildException has occured: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java returned: 1 [ERROR] around Ant part ... dir="scripts" target="test.setup">... @ 5:70 in C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml Is this expected Sean? On Fri, 26 Apr 2024 at 21:30, Finan, Sean wrote: Hi all, There is a candidate for version 5.1.0 of Apache cTAKES source code in a staging repository: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ The code is contained within the file: ctakes-5.1.0-source-release.zip< https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip I welcome you all to test your favorite pipeline(s) and report any issues. I am calling a vote from the PMC to finish by 12:nn Eastern time, next Wednesday May 1. Please report any issues before that time. If any 'road-block' issues are found they will need to be addressed before a release. Thank you, Sean p.s. The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: https://github.com/apach
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Gandhi, Peter, I am on Windows and the tests work fine. They must all run for the release phases. Peter, I found the problem. In the candidate the -distribution bin definition was missing mastif-zoner. I added it and all looks good except that the xml files aren't there. I am putting them in a src/user/resources/ directory to match other projects and adding all of the requisites for that paradigm. That will copy them to resources/ in a source compile / package and binary distribution zip(s). It will place them in the ctakes-user-resources.jar for use as a dependency in maven projects. --> If you would rather they be in the mastif-zoner jar then that isn't a problem, just let me know and I'll do it that way. Sean From: Peter Abramowitsch Sent: Monday, April 29, 2024 11:50 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * I think this is the class where Java is exiting with 1 /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java btw my environment is MacOS and I notice yours is Windows, so the root cause why this class is giving you trouble is something I wouldn't be able to help you with. But some debug statements rather than asserts would tell you, I think. Peter On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch wrote: > Hi Gandhi > This project is an odd one in the sense that when you tell it to skip the > tests, it still goes through the effort in building up the db environment > that the tests would use. But in any case, for me it does build either > way. In the attached log, I've run a maven clean before doing the build > without tests. > > However, check my previous email about your issue. Whereas you'd narrowed > it down to a script, I found a line in your email which showed the error > within that script's execution: A java program: jdl running as App.Main > threw an assertion on one of the tasks connected with the mysql database it > was trying to configure. You could put some debugging statements in there > to see which one. > > Peter > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan > wrote: > >> Thanks for the insights Peter. I dint make it clear that I did ran the >> install on ytex module with test case execution toggled off. I used the >> following command - "mvn -e clean install -Dmaven.test.skip=true" and I >> still hit the same error. >> >> On digging deep, I could find that the build process is trying to execute >> "" in >> build-main.xml which in turn is trying to invoke the following target in >> build.setup.xml: >> >> > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> >> >> >> >> Did you try running this on a fresh setup Peter? >> >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch > > >> wrote: >> >> > Hi Gandhi >> > Your error appears to be at this line >> > >> > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: >> Java >> > returned: 1 >> > >> > A test application being run here: AppMain is in charge of loading a >> > temporary mysqldb that is used to test that part of ytex. For me it is >> > working, but if you can find a way to run that surefire test in the >> > debugger, you can find out why it's failing on one of the assertions. >> > Otherwise you can take this shortcut >> > >> > mvn -Dmaven.test.skip=true >> > >> > To build the project without running any tests. >> > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan >> > wrote: >> > >> > > Hi Sean, >> > > >> > > When I tried to build the complete ctakes suite, i get build failure >> for >> > > ctakes-ytex module with the following error: >> > > >> > > [ERROR] Failed to execute goal >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run >> > > (generate-test-config) on project ctakes-ytex: An Ant BuildException >> has >> > > occured: The following error occurred while executing this line: >> > > [ERROR] >> > > >> C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scrip
Re: Please test the Apache cTAKES 5.1.0 release candidate
I think this is the class where Java is exiting with 1 /ctakes-ytex/src/test/java/org/apache/ctakes/jdl/AppMainTest.java btw my environment is MacOS and I notice yours is Windows, so the root cause why this class is giving you trouble is something I wouldn't be able to help you with. But some debug statements rather than asserts would tell you, I think. Peter On Mon, Apr 29, 2024 at 8:43 AM Peter Abramowitsch wrote: > Hi Gandhi > This project is an odd one in the sense that when you tell it to skip the > tests, it still goes through the effort in building up the db environment > that the tests would use. But in any case, for me it does build either > way. In the attached log, I've run a maven clean before doing the build > without tests. > > However, check my previous email about your issue. Whereas you'd narrowed > it down to a script, I found a line in your email which showed the error > within that script's execution: A java program: jdl running as App.Main > threw an assertion on one of the tasks connected with the mysql database it > was trying to configure. You could put some debugging statements in there > to see which one. > > Peter > > On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan > wrote: > >> Thanks for the insights Peter. I dint make it clear that I did ran the >> install on ytex module with test case execution toggled off. I used the >> following command - "mvn -e clean install -Dmaven.test.skip=true" and I >> still hit the same error. >> >> On digging deep, I could find that the build process is trying to execute >> "" in >> build-main.xml which in turn is trying to invoke the following target in >> build.setup.xml: >> >> > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> >> >> >> >> Did you try running this on a fresh setup Peter? >> >> On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch > > >> wrote: >> >> > Hi Gandhi >> > Your error appears to be at this line >> > >> > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: >> Java >> > returned: 1 >> > >> > A test application being run here: AppMain is in charge of loading a >> > temporary mysqldb that is used to test that part of ytex. For me it is >> > working, but if you can find a way to run that surefire test in the >> > debugger, you can find out why it's failing on one of the assertions. >> > Otherwise you can take this shortcut >> > >> > mvn -Dmaven.test.skip=true >> > >> > To build the project without running any tests. >> > >> > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan >> > wrote: >> > >> > > Hi Sean, >> > > >> > > When I tried to build the complete ctakes suite, i get build failure >> for >> > > ctakes-ytex module with the following error: >> > > >> > > [ERROR] Failed to execute goal >> > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run >> > > (generate-test-config) on project ctakes-ytex: An Ant BuildException >> has >> > > occured: The following error occurred while executing this line: >> > > [ERROR] >> > > >> C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: >> > The >> > > following error occurred while executing this line: >> > > [ERROR] >> > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: >> > Java >> > > returned: 1 >> > > [ERROR] around Ant part ...> dir="scripts" >> > > target="test.setup">... @ 5:70 in >> > > >> C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml >> > > >> > > Is this expected Sean? >> > > >> > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean >> > > wrote: >> > > >> > > > Hi all, >> > > > >> > > > There is a candidate for version 5.1.0 of Apache cTAKES source code >> in >> > a >> > > > staging repository: >> > > > >> > > > >> &
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Gandhi This project is an odd one in the sense that when you tell it to skip the tests, it still goes through the effort in building up the db environment that the tests would use. But in any case, for me it does build either way. In the attached log, I've run a maven clean before doing the build without tests. However, check my previous email about your issue. Whereas you'd narrowed it down to a script, I found a line in your email which showed the error within that script's execution: A java program: jdl running as App.Main threw an assertion on one of the tasks connected with the mysql database it was trying to configure. You could put some debugging statements in there to see which one. Peter On Mon, Apr 29, 2024 at 4:55 AM gandhi rajan wrote: > Thanks for the insights Peter. I dint make it clear that I did ran the > install on ytex module with test case execution toggled off. I used the > following command - "mvn -e clean install -Dmaven.test.skip=true" and I > still hit the same error. > > On digging deep, I could find that the build process is trying to execute > "" in > build-main.xml which in turn is trying to invoke the following target in > build.setup.xml: > > depends="generateTestYtexProperties,templateToConfig,deleteTestDb"> > > > > Did you try running this on a fresh setup Peter? > > On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch > wrote: > > > Hi Gandhi > > Your error appears to be at this line > > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > Java > > returned: 1 > > > > A test application being run here: AppMain is in charge of loading a > > temporary mysqldb that is used to test that part of ytex. For me it is > > working, but if you can find a way to run that surefire test in the > > debugger, you can find out why it's failing on one of the assertions. > > Otherwise you can take this shortcut > > > > mvn -Dmaven.test.skip=true > > > > To build the project without running any tests. > > > > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan > > wrote: > > > > > Hi Sean, > > > > > > When I tried to build the complete ctakes suite, i get build failure > for > > > ctakes-ytex module with the following error: > > > > > > [ERROR] Failed to execute goal > > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > > (generate-test-config) on project ctakes-ytex: An Ant BuildException > has > > > occured: The following error occurred while executing this line: > > > [ERROR] > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > > The > > > following error occurred while executing this line: > > > [ERROR] > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > > The > > > following error occurred while executing this line: > > > [ERROR] > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > > The > > > following error occurred while executing this line: > > > [ERROR] > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > > Java > > > returned: 1 > > > [ERROR] around Ant part ... > > target="test.setup">... @ 5:70 in > > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > > > > > Is this expected Sean? > > > > > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > > wrote: > > > > > > > Hi all, > > > > > > > > There is a candidate for version 5.1.0 of Apache cTAKES source code > in > > a > > > > staging repository: > > > > > > > > > > > > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > > > > > > > The code is contained within the file: > > > > ctakes-5.1.0-source-release.zip< > > > > > > > > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > > > > > > > > > > I welcome you all to test your favorite pipeline(s) and report any > > > issues. > > > > I am calling a vote from the PMC to finish by 12:nn Eastern time, > next > > > > Wednesday May 1. Please report any issues before that time. If any > > > > 'road-block' issues are found they will need to be addressed before a > > > > release. > > > > > > > &g
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Gandhi, Thank you for testing. I have not seen this error but will try to see if I can reproduce it or otherwise diagnose it. Before I build the release candidate I make sure that my build area, maven cache, temp directories, etc. are empty, but maybe I still have something left from a previous build. Sean From: gandhi rajan Sent: Monday, April 29, 2024 7:54 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Thanks for the insights Peter. I dint make it clear that I did ran the install on ytex module with test case execution toggled off. I used the following command - "mvn -e clean install -Dmaven.test.skip=true" and I still hit the same error. On digging deep, I could find that the build process is trying to execute "" in build-main.xml which in turn is trying to invoke the following target in build.setup.xml: Did you try running this on a fresh setup Peter? On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch wrote: > Hi Gandhi > Your error appears to be at this line > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java > returned: 1 > > A test application being run here: AppMain is in charge of loading a > temporary mysqldb that is used to test that part of ytex. For me it is > working, but if you can find a way to run that surefire test in the > debugger, you can find out why it's failing on one of the assertions. > Otherwise you can take this shortcut > > mvn -Dmaven.test.skip=true > > To build the project without running any tests. > > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan > wrote: > > > Hi Sean, > > > > When I tried to build the complete ctakes suite, i get build failure for > > ctakes-ytex module with the following error: > > > > [ERROR] Failed to execute goal > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > (generate-test-config) on project ctakes-ytex: An Ant BuildException has > > occured: The following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > Java > > returned: 1 > > [ERROR] around Ant part ... > target="test.setup">... @ 5:70 in > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > > > Is this expected Sean? > > > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > wrote: > > > > > Hi all, > > > > > > There is a candidate for version 5.1.0 of Apache cTAKES source code in > a > > > staging repository: > > > > > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!o1HhLIOtrhbcq3eWO7A8MyQs9yWveCrI0nWVqT7mgYPonu6AeAo8EI3Jpj0RSGZ-cVwLwf44oOtMoJQCtSuifMhxRi5BTyzwGA$ > > > > > > The code is contained within the file: > > > ctakes-5.1.0-source-release.zip< > > > > > > https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!o1HhLIOtrhbcq3eWO7A8MyQs9yWveCrI0nWVqT7mgYPonu6AeAo8EI3Jpj0RSGZ-cVwLwf44oOtMoJQCtSuifMhxRi48T86umQ$ > > > > > > > > > > I welcome you all to test your favorite pipeline(s) and report any > > issues. > > > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > > > Wednesday May 1. Please report any issues before that time. If any > > > 'road-block' issues are found they will need to be addressed before a > > > release. > > > > > > Thank you, > > > Sean > > > > > > > > > p.s. > > > > > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 > > tag: > > > https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!o1HhLIOtrhbcq3eWO7A8MyQs9yWveCrI0nWVqT7mgYPonu6AeAo8EI3Jpj0RSGZ-cVwLwf44oOtMoJQCtSuifMhxRi7ofZf95w$ > > > > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > >
Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL]
Hi Peter, Thank you for testing! I will see if I can get the mastif-zoner in the distribution and push a 5.1.1 candidate. From: Peter Abramowitsch Sent: Saturday, April 27, 2024 1:48 AM To: dev@ctakes.apache.org Subject: Re: Please test the Apache cTAKES 5.1.0 release candidate [EXTERNAL] * External Email - Caution * Hi again Sean Perfect Compile Within our context and our pipeline, it runs well. Tried with simple and complex pipelines. I have not used most of the piperRunner/Creator/ scripts. I haven't exercised any of the PBJ stuff yet. I don't use the REST projects or the YTEX DB stuff - we have our own Apart from the missing project I mentioned in the previous email that does need to be fixed, I would give 5.1.0 a plus for release. Peter On Fri, Apr 26, 2024 at 8:41 PM Peter Abramowitsch wrote: > Hi Sean, > > It all compiles, but one of the jars is missing from the distribution. > It's the one I added: ctakes-mastif-zoner which is required if you're > going to use the Zone Annotator. > > It's in the master pom, and in the pom of ctakes-distribution, and the jar > got built in its projecte, but it's not scooped up into the distribution. > I'm not sure where else to look.Can you fix it? > > Peter > > > On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean > wrote: > >> Hi all, >> >> There is a candidate for version 5.1.0 of Apache cTAKES source code in a >> staging repository: >> >> https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/__;!!NZvER7FxgEiBAiR_!otrJcgURLIeDrSgLjElYcfJXYPS7d0mMiE8_4tzF072l9casDyG4p1GpjTe3piQ4w3ONCm1ycaUtHLQ5jhEQ3wLwVFpBqoBA6Q$ >> >> The code is contained within the file: >> ctakes-5.1.0-source-release.zip< >> https://urldefense.com/v3/__https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip__;!!NZvER7FxgEiBAiR_!otrJcgURLIeDrSgLjElYcfJXYPS7d0mMiE8_4tzF072l9casDyG4p1GpjTe3piQ4w3ONCm1ycaUtHLQ5jhEQ3wLwVFpmZx3omA$ >> > >> >> I welcome you all to test your favorite pipeline(s) and report any issues. >> I am calling a vote from the PMC to finish by 12:nn Eastern time, next >> Wednesday May 1. Please report any issues before that time. If any >> 'road-block' issues are found they will need to be addressed before a >> release. >> >> Thank you, >> Sean >> >> >> p.s. >> >> The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: >> https://urldefense.com/v3/__https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0__;!!NZvER7FxgEiBAiR_!otrJcgURLIeDrSgLjElYcfJXYPS7d0mMiE8_4tzF072l9casDyG4p1GpjTe3piQ4w3ONCm1ycaUtHLQ5jhEQ3wLwVFqRzUqi_A$ >> >> The ctakes-5.1.0 tag was made from the 5.1.0 branch: >> https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/5.1.0__;!!NZvER7FxgEiBAiR_!otrJcgURLIeDrSgLjElYcfJXYPS7d0mMiE8_4tzF072l9casDyG4p1GpjTe3piQ4w3ONCm1ycaUtHLQ5jhEQ3wLwVFqL1XNqbA$ >> >> The 5.1.0 branch is a copy of the main branch: >> https://urldefense.com/v3/__https://github.com/apache/ctakes/tree/main__;!!NZvER7FxgEiBAiR_!otrJcgURLIeDrSgLjElYcfJXYPS7d0mMiE8_4tzF072l9casDyG4p1GpjTe3piQ4w3ONCm1ycaUtHLQ5jhEQ3wLwVFrvD9mPJw$ >> The version number in the 5.1.0 branch is different, but there are no >> code differences between the two branches. >> >> >>
Re: Please test the Apache cTAKES 5.1.0 release candidate
Thanks for the insights Peter. I dint make it clear that I did ran the install on ytex module with test case execution toggled off. I used the following command - "mvn -e clean install -Dmaven.test.skip=true" and I still hit the same error. On digging deep, I could find that the build process is trying to execute "" in build-main.xml which in turn is trying to invoke the following target in build.setup.xml: Did you try running this on a fresh setup Peter? On Sun, 28 Apr 2024 at 01:17, Peter Abramowitsch wrote: > Hi Gandhi > Your error appears to be at this line > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java > returned: 1 > > A test application being run here: AppMain is in charge of loading a > temporary mysqldb that is used to test that part of ytex. For me it is > working, but if you can find a way to run that surefire test in the > debugger, you can find out why it's failing on one of the assertions. > Otherwise you can take this shortcut > > mvn -Dmaven.test.skip=true > > To build the project without running any tests. > > On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan > wrote: > > > Hi Sean, > > > > When I tried to build the complete ctakes suite, i get build failure for > > ctakes-ytex module with the following error: > > > > [ERROR] Failed to execute goal > > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > > (generate-test-config) on project ctakes-ytex: An Ant BuildException has > > occured: The following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: > The > > following error occurred while executing this line: > > [ERROR] > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: > Java > > returned: 1 > > [ERROR] around Ant part ... > target="test.setup">... @ 5:70 in > > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > > > Is this expected Sean? > > > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > > wrote: > > > > > Hi all, > > > > > > There is a candidate for version 5.1.0 of Apache cTAKES source code in > a > > > staging repository: > > > > > > > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > > > > > The code is contained within the file: > > > ctakes-5.1.0-source-release.zip< > > > > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > > > > > > > I welcome you all to test your favorite pipeline(s) and report any > > issues. > > > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > > > Wednesday May 1. Please report any issues before that time. If any > > > 'road-block' issues are found they will need to be addressed before a > > > release. > > > > > > Thank you, > > > Sean > > > > > > > > > p.s. > > > > > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 > > tag: > > > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > > > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > > https://github.com/apache/ctakes/tree/5.1.0 > > > > > > The 5.1.0 branch is a copy of the main branch: > > > https://github.com/apache/ctakes/tree/main > > > The version number in the 5.1.0 branch is different, but there are no > > code > > > differences between the two branches. > > > > > > > > > > > > > -- > > Regards, > > Gandhi > > > > "The best way to find urself is to lose urself in the service of others > > !!!" > > > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Gandhi Your error appears to be at this line C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java returned: 1 A test application being run here: AppMain is in charge of loading a temporary mysqldb that is used to test that part of ytex. For me it is working, but if you can find a way to run that surefire test in the debugger, you can find out why it's failing on one of the assertions. Otherwise you can take this shortcut mvn -Dmaven.test.skip=true To build the project without running any tests. On Sat, Apr 27, 2024 at 7:35 AM gandhi rajan wrote: > Hi Sean, > > When I tried to build the complete ctakes suite, i get build failure for > ctakes-ytex module with the following error: > > [ERROR] Failed to execute goal > org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run > (generate-test-config) on project ctakes-ytex: An Ant BuildException has > occured: The following error occurred while executing this line: > [ERROR] > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: The > following error occurred while executing this line: > [ERROR] > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: The > following error occurred while executing this line: > [ERROR] > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: The > following error occurred while executing this line: > [ERROR] > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java > returned: 1 > [ERROR] around Ant part ... target="test.setup">... @ 5:70 in > C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml > > Is this expected Sean? > > On Fri, 26 Apr 2024 at 21:30, Finan, Sean > wrote: > > > Hi all, > > > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > > staging repository: > > > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > > > The code is contained within the file: > > ctakes-5.1.0-source-release.zip< > > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > > > > I welcome you all to test your favorite pipeline(s) and report any > issues. > > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > > Wednesday May 1. Please report any issues before that time. If any > > 'road-block' issues are found they will need to be addressed before a > > release. > > > > Thank you, > > Sean > > > > > > p.s. > > > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 > tag: > > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > > https://github.com/apache/ctakes/tree/5.1.0 > > > > The 5.1.0 branch is a copy of the main branch: > > https://github.com/apache/ctakes/tree/main > > The version number in the 5.1.0 branch is different, but there are no > code > > differences between the two branches. > > > > > > > > -- > Regards, > Gandhi > > "The best way to find urself is to lose urself in the service of others > !!!" >
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Sean, When I tried to build the complete ctakes suite, i get build failure for ctakes-ytex module with the following error: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-antrun-plugin:3.1.0:run (generate-test-config) on project ctakes-ytex: An Ant BuildException has occured: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\build-setup.xml:149: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:148: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:295: The following error occurred while executing this line: [ERROR] C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\scripts\data\build.xml:456: Java returned: 1 [ERROR] around Ant part .. @ 5:70 in C:\Gandhi\Project\ctakes-5.1.0\ctakes-ytex\target\antrun\build-main.xml Is this expected Sean? On Fri, 26 Apr 2024 at 21:30, Finan, Sean wrote: > Hi all, > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > staging repository: > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > The code is contained within the file: > ctakes-5.1.0-source-release.zip< > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > I welcome you all to test your favorite pipeline(s) and report any issues. > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > Wednesday May 1. Please report any issues before that time. If any > 'road-block' issues are found they will need to be addressed before a > release. > > Thank you, > Sean > > > p.s. > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > https://github.com/apache/ctakes/tree/5.1.0 > > The 5.1.0 branch is a copy of the main branch: > https://github.com/apache/ctakes/tree/main > The version number in the 5.1.0 branch is different, but there are no code > differences between the two branches. > > > -- Regards, Gandhi "The best way to find urself is to lose urself in the service of others !!!"
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi again Sean Perfect Compile Within our context and our pipeline, it runs well. Tried with simple and complex pipelines. I have not used most of the piperRunner/Creator/ scripts. I haven't exercised any of the PBJ stuff yet. I don't use the REST projects or the YTEX DB stuff - we have our own Apart from the missing project I mentioned in the previous email that does need to be fixed, I would give 5.1.0 a plus for release. Peter On Fri, Apr 26, 2024 at 8:41 PM Peter Abramowitsch wrote: > Hi Sean, > > It all compiles, but one of the jars is missing from the distribution. > It's the one I added: ctakes-mastif-zoner which is required if you're > going to use the Zone Annotator. > > It's in the master pom, and in the pom of ctakes-distribution, and the jar > got built in its projecte, but it's not scooped up into the distribution. > I'm not sure where else to look.Can you fix it? > > Peter > > > On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean > wrote: > >> Hi all, >> >> There is a candidate for version 5.1.0 of Apache cTAKES source code in a >> staging repository: >> >> https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ >> >> The code is contained within the file: >> ctakes-5.1.0-source-release.zip< >> https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip >> > >> >> I welcome you all to test your favorite pipeline(s) and report any issues. >> I am calling a vote from the PMC to finish by 12:nn Eastern time, next >> Wednesday May 1. Please report any issues before that time. If any >> 'road-block' issues are found they will need to be addressed before a >> release. >> >> Thank you, >> Sean >> >> >> p.s. >> >> The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: >> https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 >> >> The ctakes-5.1.0 tag was made from the 5.1.0 branch: >> https://github.com/apache/ctakes/tree/5.1.0 >> >> The 5.1.0 branch is a copy of the main branch: >> https://github.com/apache/ctakes/tree/main >> The version number in the 5.1.0 branch is different, but there are no >> code differences between the two branches. >> >> >>
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Sean, It all compiles, but one of the jars is missing from the distribution. It's the one I added: ctakes-mastif-zoner which is required if you're going to use the Zone Annotator. It's in the master pom, and in the pom of ctakes-distribution, and the jar got built in its projecte, but it's not scooped up into the distribution. I'm not sure where else to look.Can you fix it? Peter On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean wrote: > Hi all, > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > staging repository: > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > The code is contained within the file: > ctakes-5.1.0-source-release.zip< > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > I welcome you all to test your favorite pipeline(s) and report any issues. > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > Wednesday May 1. Please report any issues before that time. If any > 'road-block' issues are found they will need to be addressed before a > release. > > Thank you, > Sean > > > p.s. > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > https://github.com/apache/ctakes/tree/5.1.0 > > The 5.1.0 branch is a copy of the main branch: > https://github.com/apache/ctakes/tree/main > The version number in the 5.1.0 branch is different, but there are no code > differences between the two branches. > > >
Re: Please test the Apache cTAKES 5.1.0 release candidate
Hi Sean I'll do a runthrough. But looking through the commits, except for label changes, it looks as if most of the last code additions & changes were mine from a couple of months ago. I'm planning to put this release (wrapped in our webservice framework) into production in a month or so. Peter On Fri, Apr 26, 2024 at 8:59 AM Finan, Sean wrote: > Hi all, > > There is a candidate for version 5.1.0 of Apache cTAKES source code in a > staging repository: > > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ > > The code is contained within the file: > ctakes-5.1.0-source-release.zip< > https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip > > > > I welcome you all to test your favorite pipeline(s) and report any issues. > I am calling a vote from the PMC to finish by 12:nn Eastern time, next > Wednesday May 1. Please report any issues before that time. If any > 'road-block' issues are found they will need to be addressed before a > release. > > Thank you, > Sean > > > p.s. > > The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: > https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 > > The ctakes-5.1.0 tag was made from the 5.1.0 branch: > https://github.com/apache/ctakes/tree/5.1.0 > > The 5.1.0 branch is a copy of the main branch: > https://github.com/apache/ctakes/tree/main > The version number in the 5.1.0 branch is different, but there are no code > differences between the two branches. > > >
Please test the Apache cTAKES 5.1.0 release candidate
Hi all, There is a candidate for version 5.1.0 of Apache cTAKES source code in a staging repository: https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ The code is contained within the file: ctakes-5.1.0-source-release.zip<https://repository.apache.org/content/repositories/staging/org/apache/ctakes/ctakes/5.1.0/ctakes-5.1.0-source-release.zip> I welcome you all to test your favorite pipeline(s) and report any issues. I am calling a vote from the PMC to finish by 12:nn Eastern time, next Wednesday May 1. Please report any issues before that time. If any 'road-block' issues are found they will need to be addressed before a release. Thank you, Sean p.s. The 5.1.0 candidate is based upon the source code in the ctakes-5.1.0 tag: https://github.com/apache/ctakes/releases/tag/ctakes-5.1.0 The ctakes-5.1.0 tag was made from the 5.1.0 branch: https://github.com/apache/ctakes/tree/5.1.0 The 5.1.0 branch is a copy of the main branch: https://github.com/apache/ctakes/tree/main The version number in the 5.1.0 branch is different, but there are no code differences between the two branches.
test
Please ignore. Tim
Re: YTEX Assistance required RE: Test case failure [EXTERNAL]
Hi Gandhi, I suggest you remove /tmp/ctakes-*. No I did not change anything, as Jenkins is starting with clean environment every single time. Alex On Sat, Nov 18, 2017 at 4:51 PM, Gandhi Rajan Natarajan < gandhi.natara...@arisglobal.com> wrote: > Hi Alex, > > I tried out a fresh checkout from SVN and git. Tried a full build in both > setups and DateAnnotatorTest fails consistently for me. Did you changed > build order or something in pom to fix it? > > Regards, > Gandhi > > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Sunday, November 19, 2017 2:47 AM > To: dev@ctakes.apache.org > Subject: RE: YTEX Assistance required RE: Test case failure [EXTERNAL] > > Thanks for the info Alex. Will check and keep you posted. > > Regards, > Gandhi > > > -Original Message- > From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] > Sent: Sunday, November 19, 2017 2:29 AM > To: Apache cTAKES Dev <dev@ctakes.apache.org> > Subject: Re: YTEX Assistance required RE: Test case failure [EXTERNAL] > > Hi Gandhi, > > I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also > encountered the issue few times, and is very inconsistent, without being > able to track it down. > > It seems that ytexDates.iterator() is empty in certain conditions. I think > is related to the order of executions and how resources are generated. On > the last builds I couldn't reproduce it. > > So I suggest a full: > mvn clean install > > Alex > > [1] - > https://builds.apache.org/view/C/view/Apache%20cTAKES/ > job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex- > uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/ > testParseDate/ > > > On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > Is anybody that was involved with ytex still out there? > > > > -Original Message- > > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > > Sent: Saturday, November 18, 2017 9:53 AM > > To: dev@ctakes.apache.org > > Subject: Test case failure [EXTERNAL] > > > > Hi All, > > > > I did a fresh check out of cTAKES code from SVN to work on Spring > > upgrade patch. But I have one failed test case in ctakes-ytex-uima > > module. The error trace is as follows, > > > > > > --- > > Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > > > > --- > > Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 > > sec <<< FAILURE! > > testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > > ) > > Time elapsed: 0.547 sec <<< FAILURE! > > java.lang.AssertionError > > at org.junit.Assert.fail(Assert.java:86) > > at org.junit.Assert.assertTrue(Assert.java:41) > > at org.junit.Assert.assertTrue(Assert.java:52) > > at org.apache.ctakes.ytex.uima. > > annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > > Method) > > at sun.reflect.NativeMethodAccessorImpl.invoke( > > NativeMethodAccessorImpl.java:62) > > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > > DelegatingMethodAccessorImpl.java:43) > > at java.lang.reflect.Method.invoke(Method.java:498) > > at org.junit.runners.model.FrameworkMethod$1. > > runReflectiveCall(FrameworkMethod.java:47) > > at org.junit.internal.runners. > > model.ReflectiveCallable.run(ReflectiveCallable.java:12) > > at org.junit.runners.model.FrameworkMethod. > > invokeExplosively(FrameworkMethod.java:44) > > at org.junit.internal.runners.statements.InvokeMethod. > > evaluate(InvokeMethod.java:17) > > at org.junit.runners.ParentRunner.runLeaf( > > ParentRunner.java:271) > > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > > BlockJUnit4ClassRunner.java:70) > > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > > BlockJUnit4ClassRunner.java:50) > > at org.junit.runners.ParentRunner$3.run( > > ParentRunner.java:238) > > at org.junit.runners.ParentRunner$1.schedule( > > ParentRunner.java:63) >
RE: YTEX Assistance required RE: Test case failure [EXTERNAL]
Hi Alex, I tried out a fresh checkout from SVN and git. Tried a full build in both setups and DateAnnotatorTest fails consistently for me. Did you changed build order or something in pom to fix it? Regards, Gandhi -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Sunday, November 19, 2017 2:47 AM To: dev@ctakes.apache.org Subject: RE: YTEX Assistance required RE: Test case failure [EXTERNAL] Thanks for the info Alex. Will check and keep you posted. Regards, Gandhi -Original Message- From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] Sent: Sunday, November 19, 2017 2:29 AM To: Apache cTAKES Dev <dev@ctakes.apache.org> Subject: Re: YTEX Assistance required RE: Test case failure [EXTERNAL] Hi Gandhi, I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also encountered the issue few times, and is very inconsistent, without being able to track it down. It seems that ytexDates.iterator() is empty in certain conditions. I think is related to the order of executions and how resources are generated. On the last builds I couldn't reproduce it. So I suggest a full: mvn clean install Alex [1] - https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex-uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/testParseDate/ On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Is anybody that was involved with ytex still out there? > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Saturday, November 18, 2017 9:53 AM > To: dev@ctakes.apache.org > Subject: Test case failure [EXTERNAL] > > Hi All, > > I did a fresh check out of cTAKES code from SVN to work on Spring > upgrade patch. But I have one failed test case in ctakes-ytex-uima > module. The error trace is as follows, > > > --- > Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > > --- > Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 > sec <<< FAILURE! > testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > ) > Time elapsed: 0.547 sec <<< FAILURE! > java.lang.AssertionError > at org.junit.Assert.fail(Assert.java:86) > at org.junit.Assert.assertTrue(Assert.java:41) > at org.junit.Assert.assertTrue(Assert.java:52) > at org.apache.ctakes.ytex.uima. > annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > at sun.reflect.NativeMethodAccessorImpl.invoke( > NativeMethodAccessorImpl.java:62) > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at org.junit.runners.model.FrameworkMethod$1. > runReflectiveCall(FrameworkMethod.java:47) > at org.junit.internal.runners. > model.ReflectiveCallable.run(ReflectiveCallable.java:12) > at org.junit.runners.model.FrameworkMethod. > invokeExplosively(FrameworkMethod.java:44) > at org.junit.internal.runners.statements.InvokeMethod. > evaluate(InvokeMethod.java:17) > at org.junit.runners.ParentRunner.runLeaf( > ParentRunner.java:271) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:70) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:50) > at org.junit.runners.ParentRunner$3.run( > ParentRunner.java:238) > at org.junit.runners.ParentRunner$1.schedule( > ParentRunner.java:63) > at org.junit.runners.ParentRunner.runChildren( > ParentRunner.java:236) > at org.junit.runners.ParentRunner.access$000( > ParentRunner.java:53) > at org.junit.runners.ParentRunner$2.evaluate( > ParentRunner.java:229) > at org.junit.runners.ParentRunner.run(ParentRunner. > java:309) > at org.apache.maven.surefire. > junit4.JUnit4Provider.execute(JUnit4Provider.java:249) > at org.apache.maven.surefire.junit4.JUnit4Provider. > executeTestSet(JUnit4Provider.java:142) > at > org.apache.maven.surefire.junit4.JUnit4Provider.invoke( > JUnit4Provider.java:113) > at sun.reflect.NativeMethodAcces
RE: YTEX Assistance required RE: Test case failure [EXTERNAL]
Thanks for the info Alex. Will check and keep you posted. Regards, Gandhi -Original Message- From: Alexandru Zbarcea [mailto:zbarce...@gmail.com] Sent: Sunday, November 19, 2017 2:29 AM To: Apache cTAKES Dev <dev@ctakes.apache.org> Subject: Re: YTEX Assistance required RE: Test case failure [EXTERNAL] Hi Gandhi, I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also encountered the issue few times, and is very inconsistent, without being able to track it down. It seems that ytexDates.iterator() is empty in certain conditions. I think is related to the order of executions and how resources are generated. On the last builds I couldn't reproduce it. So I suggest a full: mvn clean install Alex [1] - https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex-uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/testParseDate/ On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Is anybody that was involved with ytex still out there? > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Saturday, November 18, 2017 9:53 AM > To: dev@ctakes.apache.org > Subject: Test case failure [EXTERNAL] > > Hi All, > > I did a fresh check out of cTAKES code from SVN to work on Spring > upgrade patch. But I have one failed test case in ctakes-ytex-uima > module. The error trace is as follows, > > > --- > Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > > --- > Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 > sec <<< FAILURE! > testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > ) > Time elapsed: 0.547 sec <<< FAILURE! > java.lang.AssertionError > at org.junit.Assert.fail(Assert.java:86) > at org.junit.Assert.assertTrue(Assert.java:41) > at org.junit.Assert.assertTrue(Assert.java:52) > at org.apache.ctakes.ytex.uima. > annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > at sun.reflect.NativeMethodAccessorImpl.invoke( > NativeMethodAccessorImpl.java:62) > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at org.junit.runners.model.FrameworkMethod$1. > runReflectiveCall(FrameworkMethod.java:47) > at org.junit.internal.runners. > model.ReflectiveCallable.run(ReflectiveCallable.java:12) > at org.junit.runners.model.FrameworkMethod. > invokeExplosively(FrameworkMethod.java:44) > at org.junit.internal.runners.statements.InvokeMethod. > evaluate(InvokeMethod.java:17) > at org.junit.runners.ParentRunner.runLeaf( > ParentRunner.java:271) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:70) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:50) > at org.junit.runners.ParentRunner$3.run( > ParentRunner.java:238) > at org.junit.runners.ParentRunner$1.schedule( > ParentRunner.java:63) > at org.junit.runners.ParentRunner.runChildren( > ParentRunner.java:236) > at org.junit.runners.ParentRunner.access$000( > ParentRunner.java:53) > at org.junit.runners.ParentRunner$2.evaluate( > ParentRunner.java:229) > at org.junit.runners.ParentRunner.run(ParentRunner. > java:309) > at org.apache.maven.surefire. > junit4.JUnit4Provider.execute(JUnit4Provider.java:249) > at org.apache.maven.surefire.junit4.JUnit4Provider. > executeTestSet(JUnit4Provider.java:142) > at > org.apache.maven.surefire.junit4.JUnit4Provider.invoke( > JUnit4Provider.java:113) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > at sun.reflect.NativeMethodAccessorImpl.invoke( > NativeMethodAccessorImpl.java:62) > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at org.apache.maven.surefire.util.ReflectionUtils. > invokeMethod
Re: YTEX Assistance required RE: Test case failure [EXTERNAL]
Hi Gandhi, I saw the same thing on the cTAKES-trunk-Java-1.8 build #38 [1]. I also encountered the issue few times, and is very inconsistent, without being able to track it down. It seems that ytexDates.iterator() is empty in certain conditions. I think is related to the order of executions and how resources are generated. On the last builds I couldn't reproduce it. So I suggest a full: mvn clean install Alex [1] - https://builds.apache.org/view/C/view/Apache%20cTAKES/job/cTAKES-trunk-Java-1.8/38/org.apache.ctakes$ctakes-ytex-uima/testReport/org.apache.ctakes.ytex.uima.annotators/DateAnnotatorTest/testParseDate/ On Sat, Nov 18, 2017 at 12:11 PM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Is anybody that was involved with ytex still out there? > > -Original Message- > From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] > Sent: Saturday, November 18, 2017 9:53 AM > To: dev@ctakes.apache.org > Subject: Test case failure [EXTERNAL] > > Hi All, > > I did a fresh check out of cTAKES code from SVN to work on Spring upgrade > patch. But I have one failed test case in ctakes-ytex-uima module. The > error trace is as follows, > > ---- > --- > Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest > > --- > Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec > <<< FAILURE! > testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest) > Time elapsed: 0.547 sec <<< FAILURE! > java.lang.AssertionError > at org.junit.Assert.fail(Assert.java:86) > at org.junit.Assert.assertTrue(Assert.java:41) > at org.junit.Assert.assertTrue(Assert.java:52) > at org.apache.ctakes.ytex.uima. > annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > at sun.reflect.NativeMethodAccessorImpl.invoke( > NativeMethodAccessorImpl.java:62) > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at org.junit.runners.model.FrameworkMethod$1. > runReflectiveCall(FrameworkMethod.java:47) > at org.junit.internal.runners. > model.ReflectiveCallable.run(ReflectiveCallable.java:12) > at org.junit.runners.model.FrameworkMethod. > invokeExplosively(FrameworkMethod.java:44) > at org.junit.internal.runners.statements.InvokeMethod. > evaluate(InvokeMethod.java:17) > at org.junit.runners.ParentRunner.runLeaf( > ParentRunner.java:271) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:70) > at org.junit.runners.BlockJUnit4ClassRunner.runChild( > BlockJUnit4ClassRunner.java:50) > at org.junit.runners.ParentRunner$3.run( > ParentRunner.java:238) > at org.junit.runners.ParentRunner$1.schedule( > ParentRunner.java:63) > at org.junit.runners.ParentRunner.runChildren( > ParentRunner.java:236) > at org.junit.runners.ParentRunner.access$000( > ParentRunner.java:53) > at org.junit.runners.ParentRunner$2.evaluate( > ParentRunner.java:229) > at org.junit.runners.ParentRunner.run(ParentRunner. > java:309) > at org.apache.maven.surefire. > junit4.JUnit4Provider.execute(JUnit4Provider.java:249) > at org.apache.maven.surefire.junit4.JUnit4Provider. > executeTestSet(JUnit4Provider.java:142) > at org.apache.maven.surefire.junit4.JUnit4Provider.invoke( > JUnit4Provider.java:113) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native > Method) > at sun.reflect.NativeMethodAccessorImpl.invoke( > NativeMethodAccessorImpl.java:62) > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:498) > at org.apache.maven.surefire.util.ReflectionUtils. > invokeMethodWithArray(ReflectionUtils.java:189) > at org.apache.maven.surefire.booter.ProviderFactory$ > ProviderProxy.invoke(ProviderFactory.java:165) > at org.apache.maven.surefire.booter.ProviderFactory. > invokeProvider(ProviderFactory.java:85) > at org.apache.maven.surefire.booter.ForkedBooter. > runSuitesInProcess(ForkedBoo
YTEX Assistance required RE: Test case failure [EXTERNAL]
Is anybody that was involved with ytex still out there? -Original Message- From: Gandhi Rajan Natarajan [mailto:gandhi.natara...@arisglobal.com] Sent: Saturday, November 18, 2017 9:53 AM To: dev@ctakes.apache.org Subject: Test case failure [EXTERNAL] Hi All, I did a fresh check out of cTAKES code from SVN to work on Spring upgrade patch. But I have one failed test case in ctakes-ytex-uima module. The error trace is as follows, --- Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest --- Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec <<< FAILURE! testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest) Time elapsed: 0.547 sec <<< FAILURE! java.lang.AssertionError at org.junit.Assert.fail(Assert.java:86) at org.junit.Assert.assertTrue(Assert.java:41) at org.junit.Assert.assertTrue(Assert.java:52) at org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47) at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12) at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44) at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50) at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238) at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63) at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236) at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53) at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229) at org.junit.runners.ParentRunner.run(ParentRunner.java:309) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189) at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165) at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75) Am I missing something or is it broken recently? Regards, Gandhi This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Test case failure
Hi All, I did a fresh check out of cTAKES code from SVN to work on Spring upgrade patch. But I have one failed test case in ctakes-ytex-uima module. The error trace is as follows, --- Test set: org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest --- Tests run: 1, Failures: 1, Errors: 0, Skipped: 0, Time elapsed: 0.583 sec <<< FAILURE! testParseDate(org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest) Time elapsed: 0.547 sec <<< FAILURE! java.lang.AssertionError at org.junit.Assert.fail(Assert.java:86) at org.junit.Assert.assertTrue(Assert.java:41) at org.junit.Assert.assertTrue(Assert.java:52) at org.apache.ctakes.ytex.uima.annotators.DateAnnotatorTest.testParseDate(DateAnnotatorTest.java:54) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47) at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12) at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44) at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17) at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70) at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50) at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238) at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63) at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236) at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53) at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229) at org.junit.runners.ParentRunner.run(ParentRunner.java:309) at org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:249) at org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:142) at org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:113) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.maven.surefire.util.ReflectionUtils.invokeMethodWithArray(ReflectionUtils.java:189) at org.apache.maven.surefire.booter.ProviderFactory$ProviderProxy.invoke(ProviderFactory.java:165) at org.apache.maven.surefire.booter.ProviderFactory.invokeProvider(ProviderFactory.java:85) at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:104) at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:75) Am I missing something or is it broken recently? Regards, Gandhi This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
Re: CTAKES-460: coreference Test should not be part of main [EXTERNAL]
Thank you Tim Alex On Oct 2, 2017 10:43, "Miller, Timothy" < timothy.mil...@childrens.harvard.edu> wrote: Thanks Alex, I've committed this patch. I unfortunately looked at the wrong tab when typing my commit message and committed it with the wrong issue number (459). Tim On Mon, 2017-10-02 at 08:17 -0400, Alexandru Zbarcea wrote: > Hi, > > I have refactor a main class that should have been a UTest. > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.or > g_jira_browse_CTAKES- > 2D460=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup- > IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=T0fckwyf1n_TXQgdwCR5YlQItLlxMx > 9nU_S5EUx1Iu0=f5ZcQqm3Dbk91cdhymh20-kg5cyZGoHPFjK0x9ZH32k= > > This moves the test code from src/main to src/test and also added > some > refactoring. > > No impact. Can easily be merged. > > Alex
Re: CTAKES-460: coreference Test should not be part of main [EXTERNAL]
Thanks Alex, I've committed this patch. I unfortunately looked at the wrong tab when typing my commit message and committed it with the wrong issue number (459). Tim On Mon, 2017-10-02 at 08:17 -0400, Alexandru Zbarcea wrote: > Hi, > > I have refactor a main class that should have been a UTest. > https://urldefense.proofpoint.com/v2/url?u=https-3A__issues.apache.or > g_jira_browse_CTAKES- > 2D460=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=Heup- > IbsIg9Q1TPOylpP9FE4GTK- > OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h=T0fckwyf1n_TXQgdwCR5YlQItLlxMx > 9nU_S5EUx1Iu0=f5ZcQqm3Dbk91cdhymh20-kg5cyZGoHPFjK0x9ZH32k= > > This moves the test code from src/main to src/test and also added > some > refactoring. > > No impact. Can easily be merged. > > Alex
CTAKES-460: coreference Test should not be part of main
Hi, I have refactor a main class that should have been a UTest. https://issues.apache.org/jira/browse/CTAKES-460 This moves the test code from src/main to src/test and also added some refactoring. No impact. Can easily be merged. Alex
Re: Builds are now clean [was: Travis has one test failed [EXTERNAL]]
That's excellent! My preference would be for you to continue to submit attachments to JIRA issues. James On Sep 10, 2017 7:48 PM, "Hadrian Zbarcea" <hzbar...@gmail.com> wrote: Hi all, I had issues with the tests as well. We need clean tests if we were to do any incremental refactoring. I added to patches to #334 [1] and #445 [2]. One of my comments for #334 is incorrect in that I thought there was one more test failing, but the issue was not properly escaping my umls password in the env var (not the best practice, but I'll leave this for another time). That said with the 2 patches above, now I get clean builds and tests with java 8 on linux. I do not use windows, but I strongly suspect that it'll be a clean build on windows as well. Because of the delay in applying patches, I am not sure if best would be for me to fork on github and start working on a branch and submit PRs or continue with attachments to JIRA. Please let me know what the committers/community preference is and I'll adapt. Cheers, Hadrian [1] https://issues.apache.org/jira/browse/CTAKES-334 [2] https://issues.apache.org/jira/browse/CTAKES-445 On 09/03/2017 05:59 PM, Finan, Sean wrote: > Hi Steve, > > I have gotten a couple that were my fault because I hadn't yet checked in > all of the required changes / classes. Terribly poor form on my part. > Those were the CC: emails. Other than that I haven't gotten any. I will > double-check to make sure that I'm on notifications@ ... though if it > fills my mailbox then maybe I don't want to ... > > Thanks, > Sean > > From: Steven Bethard <steven.beth...@gmail.com> > Sent: Sunday, September 3, 2017 5:45 PM > To: dev@ctakes.apache.org > Subject: Re: Travis has one test failed [EXTERNAL] > > Sean, aren't you subscribed to > notificati...@ctakes.apache.org? I've been getting failed test messages > from the official cTakes build for weeks now. You've even been CC'd on some > of them. Maybe check your junk mail? I haven't said anything about these > emails because 1) I assumed everyone else was getting them and 2) I don't > have the time now to look into a fix. > > Steve > > On Sun, Sep 3, 2017, 14:16 Finan, Sean <sean.fi...@childrens.harvard.edu> > wrote: > > Hi Andrey, >> >> So you did set up a travis test for ctakes? Cool. >> >> In my opinion that test should be disabled for automated builds. In >> addition to requiring credentials that should not be on a public system, >> it >> is basically a partial integration test that assures that a single >> workflow >> runs to completion. As far as I know there is no check on generated >> output >> values, it just depends upon thrown exceptions or an absence of output >> files to reveal problems. It also takes a long time to set up and run. >> It >> produces a lot of output that has little to do with any actual testing. >> There are names for these testing antipatterns: >> the liar, the giant, the loudmouth, the slowpoke, and most of all, the >> secret catcher. >> >> Please don't read into this; I am not trying to be mean or stating that >> the test doesn't have its place. It can be a valuable sanity check for >> anybody making changes to the specific functionality that it covers. >> People are welcome to disagree with me on this, but I think that this >> test is better done as-needed on an individual's system with their umls >> credentials. This may create a "Local Hero" (another antipattern), but so >> what, you have to start somewhere. A few people have slowly added unit >> tests to ctakes, and I hope that such valuable contributions continue. >> >> That was probably more than you care to read; in summary I think that that >> particular test can be disabled for automation regression. I can turn it >> off but will refrain for now in case others want to take another route. >> >> Thanks again, >> Sean >> >> From: Andrey Kurdumov <kant2...@googlemail.com> >> Sent: Sunday, September 3, 2017 3:33 PM >> To: cTakes developers list >> Subject: Travis has one test failed [EXTERNAL] >> >> The travis for cTakes has one test[1] failed due to missing UMLS license. >> Maybe somebody could configure Travis to provide valid UMLS license, or >> disable this test. >> >> I would like to volunteer to help with this, but looks like this change is >> for contributors only. >> >> [1] >> >> https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. >> apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org.ap >> ache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apac >> he.ctakes.regression.test_RegressionPipelineTest_testCPE_= >> DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs6 >> 7GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_z10X >> o1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs-BC >> VF3i-mvJgUeZ4= >> >>
Builds are now clean [was: Travis has one test failed [EXTERNAL]]
Hi all, I had issues with the tests as well. We need clean tests if we were to do any incremental refactoring. I added to patches to #334 [1] and #445 [2]. One of my comments for #334 is incorrect in that I thought there was one more test failing, but the issue was not properly escaping my umls password in the env var (not the best practice, but I'll leave this for another time). That said with the 2 patches above, now I get clean builds and tests with java 8 on linux. I do not use windows, but I strongly suspect that it'll be a clean build on windows as well. Because of the delay in applying patches, I am not sure if best would be for me to fork on github and start working on a branch and submit PRs or continue with attachments to JIRA. Please let me know what the committers/community preference is and I'll adapt. Cheers, Hadrian [1] https://issues.apache.org/jira/browse/CTAKES-334 [2] https://issues.apache.org/jira/browse/CTAKES-445 On 09/03/2017 05:59 PM, Finan, Sean wrote: Hi Steve, I have gotten a couple that were my fault because I hadn't yet checked in all of the required changes / classes. Terribly poor form on my part. Those were the CC: emails. Other than that I haven't gotten any. I will double-check to make sure that I'm on notifications@ ... though if it fills my mailbox then maybe I don't want to ... Thanks, Sean From: Steven Bethard <steven.beth...@gmail.com> Sent: Sunday, September 3, 2017 5:45 PM To: dev@ctakes.apache.org Subject: Re: Travis has one test failed [EXTERNAL] Sean, aren't you subscribed to notificati...@ctakes.apache.org? I've been getting failed test messages from the official cTakes build for weeks now. You've even been CC'd on some of them. Maybe check your junk mail? I haven't said anything about these emails because 1) I assumed everyone else was getting them and 2) I don't have the time now to look into a fix. Steve On Sun, Sep 3, 2017, 14:16 Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: Hi Andrey, So you did set up a travis test for ctakes? Cool. In my opinion that test should be disabled for automated builds. In addition to requiring credentials that should not be on a public system, it is basically a partial integration test that assures that a single workflow runs to completion. As far as I know there is no check on generated output values, it just depends upon thrown exceptions or an absence of output files to reveal problems. It also takes a long time to set up and run. It produces a lot of output that has little to do with any actual testing. There are names for these testing antipatterns: the liar, the giant, the loudmouth, the slowpoke, and most of all, the secret catcher. Please don't read into this; I am not trying to be mean or stating that the test doesn't have its place. It can be a valuable sanity check for anybody making changes to the specific functionality that it covers. People are welcome to disagree with me on this, but I think that this test is better done as-needed on an individual's system with their umls credentials. This may create a "Local Hero" (another antipattern), but so what, you have to start somewhere. A few people have slowly added unit tests to ctakes, and I hope that such valuable contributions continue. That was probably more than you care to read; in summary I think that that particular test can be disabled for automation regression. I can turn it off but will refrain for now in case others want to take another route. Thanks again, Sean From: Andrey Kurdumov <kant2...@googlemail.com> Sent: Sunday, September 3, 2017 3:33 PM To: cTakes developers list Subject: Travis has one test failed [EXTERNAL] The travis for cTakes has one test[1] failed due to missing UMLS license. Maybe somebody could configure Travis to provide valid UMLS license, or disable this test. I would like to volunteer to help with this, but looks like this change is for contributors only. [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org.apache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apache.ctakes.regression.test_RegressionPipelineTest_testCPE_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_z10Xo1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs-BCVF3i-mvJgUeZ4=
Re: Travis has one test failed [EXTERNAL]
Hi Steve, I have gotten a couple that were my fault because I hadn't yet checked in all of the required changes / classes. Terribly poor form on my part. Those were the CC: emails. Other than that I haven't gotten any. I will double-check to make sure that I'm on notifications@ ... though if it fills my mailbox then maybe I don't want to ... Thanks, Sean From: Steven Bethard <steven.beth...@gmail.com> Sent: Sunday, September 3, 2017 5:45 PM To: dev@ctakes.apache.org Subject: Re: Travis has one test failed [EXTERNAL] Sean, aren't you subscribed to notificati...@ctakes.apache.org? I've been getting failed test messages from the official cTakes build for weeks now. You've even been CC'd on some of them. Maybe check your junk mail? I haven't said anything about these emails because 1) I assumed everyone else was getting them and 2) I don't have the time now to look into a fix. Steve On Sun, Sep 3, 2017, 14:16 Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Andrey, > > So you did set up a travis test for ctakes? Cool. > > In my opinion that test should be disabled for automated builds. In > addition to requiring credentials that should not be on a public system, it > is basically a partial integration test that assures that a single workflow > runs to completion. As far as I know there is no check on generated output > values, it just depends upon thrown exceptions or an absence of output > files to reveal problems. It also takes a long time to set up and run. It > produces a lot of output that has little to do with any actual testing. > There are names for these testing antipatterns: > the liar, the giant, the loudmouth, the slowpoke, and most of all, the > secret catcher. > > Please don't read into this; I am not trying to be mean or stating that > the test doesn't have its place. It can be a valuable sanity check for > anybody making changes to the specific functionality that it covers. > People are welcome to disagree with me on this, but I think that this > test is better done as-needed on an individual's system with their umls > credentials. This may create a "Local Hero" (another antipattern), but so > what, you have to start somewhere. A few people have slowly added unit > tests to ctakes, and I hope that such valuable contributions continue. > > That was probably more than you care to read; in summary I think that that > particular test can be disabled for automation regression. I can turn it > off but will refrain for now in case others want to take another route. > > Thanks again, > Sean > > From: Andrey Kurdumov <kant2...@googlemail.com> > Sent: Sunday, September 3, 2017 3:33 PM > To: cTakes developers list > Subject: Travis has one test failed [EXTERNAL] > > The travis for cTakes has one test[1] failed due to missing UMLS license. > Maybe somebody could configure Travis to provide valid UMLS license, or > disable this test. > > I would like to volunteer to help with this, but looks like this change is > for contributors only. > > [1] > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org.apache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apache.ctakes.regression.test_RegressionPipelineTest_testCPE_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_z10Xo1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs-BCVF3i-mvJgUeZ4= >
Re: Travis has one test failed [EXTERNAL]
Sean, aren't you subscribed to notificati...@ctakes.apache.org? I've been getting failed test messages from the official cTakes build for weeks now. You've even been CC'd on some of them. Maybe check your junk mail? I haven't said anything about these emails because 1) I assumed everyone else was getting them and 2) I don't have the time now to look into a fix. Steve On Sun, Sep 3, 2017, 14:16 Finan, Sean <sean.fi...@childrens.harvard.edu> wrote: > Hi Andrey, > > So you did set up a travis test for ctakes? Cool. > > In my opinion that test should be disabled for automated builds. In > addition to requiring credentials that should not be on a public system, it > is basically a partial integration test that assures that a single workflow > runs to completion. As far as I know there is no check on generated output > values, it just depends upon thrown exceptions or an absence of output > files to reveal problems. It also takes a long time to set up and run. It > produces a lot of output that has little to do with any actual testing. > There are names for these testing antipatterns: > the liar, the giant, the loudmouth, the slowpoke, and most of all, the > secret catcher. > > Please don't read into this; I am not trying to be mean or stating that > the test doesn't have its place. It can be a valuable sanity check for > anybody making changes to the specific functionality that it covers. > People are welcome to disagree with me on this, but I think that this > test is better done as-needed on an individual's system with their umls > credentials. This may create a "Local Hero" (another antipattern), but so > what, you have to start somewhere. A few people have slowly added unit > tests to ctakes, and I hope that such valuable contributions continue. > > That was probably more than you care to read; in summary I think that that > particular test can be disabled for automation regression. I can turn it > off but will refrain for now in case others want to take another route. > > Thanks again, > Sean > > From: Andrey Kurdumov <kant2...@googlemail.com> > Sent: Sunday, September 3, 2017 3:33 PM > To: cTakes developers list > Subject: Travis has one test failed [EXTERNAL] > > The travis for cTakes has one test[1] failed due to missing UMLS license. > Maybe somebody could configure Travis to provide valid UMLS license, or > disable this test. > > I would like to volunteer to help with this, but looks like this change is > for contributors only. > > [1] > > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org.apache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apache.ctakes.regression.test_RegressionPipelineTest_testCPE_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_z10Xo1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs-BCVF3i-mvJgUeZ4= >
Re: Travis has one test failed [EXTERNAL]
Sorry, CI was on Jenkins which is part of Apache Infra. My bad that I confuse this. Somebody from contributors setup this 2 jobs. One completely green - https://builds.apache.org/job/ctakes-trunk-package/ One has single test failed - https://builds.apache.org/job/ctakes-trunk-compiletest/ Since this is cTakes test suite which running automatically, so it is not for me to decide what is better :) 2017-09-04 3:16 GMT+06:00 Finan, Sean <sean.fi...@childrens.harvard.edu>: > Hi Andrey, > > So you did set up a travis test for ctakes? Cool. > > In my opinion that test should be disabled for automated builds. In > addition to requiring credentials that should not be on a public system, it > is basically a partial integration test that assures that a single workflow > runs to completion. As far as I know there is no check on generated output > values, it just depends upon thrown exceptions or an absence of output > files to reveal problems. It also takes a long time to set up and run. It > produces a lot of output that has little to do with any actual testing. > There are names for these testing antipatterns: > the liar, the giant, the loudmouth, the slowpoke, and most of all, the > secret catcher. > > Please don't read into this; I am not trying to be mean or stating that > the test doesn't have its place. It can be a valuable sanity check for > anybody making changes to the specific functionality that it covers. > People are welcome to disagree with me on this, but I think that this > test is better done as-needed on an individual's system with their umls > credentials. This may create a "Local Hero" (another antipattern), but so > what, you have to start somewhere. A few people have slowly added unit > tests to ctakes, and I hope that such valuable contributions continue. > > That was probably more than you care to read; in summary I think that that > particular test can be disabled for automation regression. I can turn it > off but will refrain for now in case others want to take another route. > > Thanks again, > Sean > > From: Andrey Kurdumov <kant2...@googlemail.com> > Sent: Sunday, September 3, 2017 3:33 PM > To: cTakes developers list > Subject: Travis has one test failed [EXTERNAL] > > The travis for cTakes has one test[1] failed due to missing UMLS license. > Maybe somebody could configure Travis to provide valid UMLS license, or > disable this test. > > I would like to volunteer to help with this, but looks like this change is > for contributors only. > > [1] > https://urldefense.proofpoint.com/v2/url?u=https-3A__builds. > apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org. > apache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apache.ctakes. > regression.test_RegressionPipelineTest_testCPE_=DwIBaQ= > qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU= > fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_ > z10Xo1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs- > BCVF3i-mvJgUeZ4= >
Re: Travis has one test failed [EXTERNAL]
Hi Andrey, So you did set up a travis test for ctakes? Cool. In my opinion that test should be disabled for automated builds. In addition to requiring credentials that should not be on a public system, it is basically a partial integration test that assures that a single workflow runs to completion. As far as I know there is no check on generated output values, it just depends upon thrown exceptions or an absence of output files to reveal problems. It also takes a long time to set up and run. It produces a lot of output that has little to do with any actual testing. There are names for these testing antipatterns: the liar, the giant, the loudmouth, the slowpoke, and most of all, the secret catcher. Please don't read into this; I am not trying to be mean or stating that the test doesn't have its place. It can be a valuable sanity check for anybody making changes to the specific functionality that it covers. People are welcome to disagree with me on this, but I think that this test is better done as-needed on an individual's system with their umls credentials. This may create a "Local Hero" (another antipattern), but so what, you have to start somewhere. A few people have slowly added unit tests to ctakes, and I hope that such valuable contributions continue. That was probably more than you care to read; in summary I think that that particular test can be disabled for automation regression. I can turn it off but will refrain for now in case others want to take another route. Thanks again, Sean From: Andrey Kurdumov <kant2...@googlemail.com> Sent: Sunday, September 3, 2017 3:33 PM To: cTakes developers list Subject: Travis has one test failed [EXTERNAL] The travis for cTakes has one test[1] failed due to missing UMLS license. Maybe somebody could configure Travis to provide valid UMLS license, or disable this test. I would like to volunteer to help with this, but looks like this change is for contributors only. [1] https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_job_ctakes-2Dtrunk-2Dcompiletest_lastBuild_org.apache.ctakes-24ctakes-2Dregression-2Dtest_testReport_org.apache.ctakes.regression.test_RegressionPipelineTest_testCPE_=DwIBaQ=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao=4yTefwCxCfgP_z10Xo1oqK-A1NyZxXXt-2AvIvd6D7A=P3h16k70ouJKAOji8P5Wc8NRuLs-BCVF3i-mvJgUeZ4=
Re: mvn install error on ctakes-temporal module test
You may be getting the same “URI is not hierarchical error” I was experiencing
last month. This is a known problem. While it’s getting fixed, there’s a
temporary fix. Please take a look at the message archive and look for the
messages with title: “URI is not hierarchical”. Here’s the gist of what you
need to do:
"I checked out lvg from
svn.code.sf.net/p/ctakesresources/code/trunk/ctakes-resources-lvg2008/src/main/resources/org/apache/ctakes/lvg/
and put it in target/classes/org/apache/ctakes/."
Dima
> On May 18, 2017, at 13:55, Mullane, Sean *HS <sp...@hscmail.mcc.virginia.edu>
> wrote:
>
> I have so far been unable to build and install ctakes 4.0.0 or
> 4.0.1-snapshot. With both versions, the mvn clean install fails on the
> ctakes-temporal module test. Environment info and test results below. Has
> anyone else encountered this? This seems similar to the "URI is not
> hierarchical" thread from last month but it's not clear to me whether that
> thread applies here.
>
> Environment:
> Windows 7 Pro
> Eclipse 4.5 Mars
> jdk1.8.0_131
>
> I followed the step by step install instructions here exactly:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
> Then in Eclipse I right-clicked the top-level package -> Run As -> Maven
> Build... -> mvn clean install
>
> The results are below:
>
>
> ---
> T E S T S
> ---
> Running org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest
> log4j: reset attribute= "false".
> log4j: Threshold ="null".
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressAppender] additivity to [false].
> log4j: Level value for ProgressAppender is [INFO].
> log4j: ProgressAppender level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m].
> log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
> log4j: Retreiving an instance of org.apache.log4j.Logger.
> log4j: Setting [ProgressDone] additivity to [false].
> log4j: Level value for ProgressDone is [INFO].
> log4j: ProgressDone level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%m%n].
> log4j: Adding appender named [eolAppender] to category [ProgressDone].
> log4j: Level value for root is [INFO].
> log4j: root level set to INFO
> log4j: Class name: [org.apache.log4j.ConsoleAppender]
> log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
> log4j: Setting property [conversionPattern] to [%d{dd MMM HH:mm:ss} %5p
> %c{1} - %m%n].
> log4j: Adding appender named [consoleAppender] to category [root].
> 18 May 2017 14:09:40 INFO LvgAnnotator - URL for lvg.properties
> =file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> 18 May 2017 14:09:41 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 18 May 2017 14:09:42 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.311 sec <<<
> FAILURE!
> Running org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest
> 18 May 2017 14:09:42 INFO LvgAnnotator - URL for lvg.properties
> =file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> 18 May 2017 14:09:44 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 18 May 2017 14:09:44 INFO TokenizerAnnotatorPTB - Initializing
> org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
> Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 2.355 sec <<<
> FAILURE!
> Running org.apache.ctakes.temporal.ae.EventAnnotatorTest
> 18 May 2017 14:09:45 INFO LvgAnnotator - URL for lvg.properties
> =file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
> 18 May 2017 14:09:46 INFO SentenceDetector - Sentence detector model file:
> org/apache/ctakes/core/sentdetect/sd-med-model.zip
> 18 May 2017 14:09:46 INFO Tokenizer
mvn install error on ctakes-temporal module test
I have so far been unable to build and install ctakes 4.0.0 or 4.0.1-snapshot.
With both versions, the mvn clean install fails on the ctakes-temporal module
test. Environment info and test results below. Has anyone else encountered
this? This seems similar to the "URI is not hierarchical" thread from last
month but it's not clear to me whether that thread applies here.
Environment:
Windows 7 Pro
Eclipse 4.5 Mars
jdk1.8.0_131
I followed the step by step install instructions here exactly:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide
Then in Eclipse I right-clicked the top-level package -> Run As -> Maven
Build... -> mvn clean install
The results are below:
---
T E S T S
---
Running org.apache.ctakes.temporal.ae.BackwardsTimeAnnotatorTest
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressAppender] additivity to [false].
log4j: Level value for ProgressAppender is [INFO].
log4j: ProgressAppender level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m].
log4j: Adding appender named [noEolAppender] to category [ProgressAppender].
log4j: Retreiving an instance of org.apache.log4j.Logger.
log4j: Setting [ProgressDone] additivity to [false].
log4j: Level value for ProgressDone is [INFO].
log4j: ProgressDone level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%m%n].
log4j: Adding appender named [eolAppender] to category [ProgressDone].
log4j: Level value for root is [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM HH:mm:ss} %5p
%c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
18 May 2017 14:09:40 INFO LvgAnnotator - URL for lvg.properties
=file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
18 May 2017 14:09:41 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
18 May 2017 14:09:42 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 3.311 sec <<<
FAILURE!
Running org.apache.ctakes.temporal.ae.ContextualModalityAnnotatorTest
18 May 2017 14:09:42 INFO LvgAnnotator - URL for lvg.properties
=file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
18 May 2017 14:09:44 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
18 May 2017 14:09:44 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 2.355 sec <<<
FAILURE!
Running org.apache.ctakes.temporal.ae.EventAnnotatorTest
18 May 2017 14:09:45 INFO LvgAnnotator - URL for lvg.properties
=file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
18 May 2017 14:09:46 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
18 May 2017 14:09:46 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 1.653 sec <<<
FAILURE!
Running org.apache.ctakes.temporal.ae.EventEventRelationAnnotatorTest
18 May 2017 14:09:46 INFO LvgAnnotator - URL for lvg.properties
=file:/C:/Users/*/.m2/repository/net/sourceforge/ctakesresources/ctakes-resources-lvg2008/4.0.0/ctakes-resources-lvg2008-4.0.0.jar!/org/apache/ctakes/lvg/data/config/lvg.properties
18 May 2017 14:09:48 INFO SentenceDetector - Sentence detector model file:
org/apache/ctakes/core/sentdetect/sd-med-model.zip
18 May 2017 14:09:48 INFO TokenizerAnnotatorPTB - Initializing
org.apache.ctakes.core.ae.TokenizerAnnotatorPTB
Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 2.01 sec <<<
FAILURE!
Running org.apache.ctakes.temporal.ae.EventTimeRelationAnnotatorTest
18 May 2017 14:09:48 INFO LvgAnnotator - URL for lvg.properties
=file:/C:/Users/*/.m2/rep
Time to test rc3 ...
Murali, You are the man! When everything is done do you want to send out a new copy of Pei's original vote: email? Thanks, Sean
