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: 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
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 [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. >> >> >>
