Hi Sean, Thank you for the information. I'm looking through the examples and other code. CTAKES is surely an impressive work.
Don On Mon, Jan 22, 2018 at 9:55 AM, Finan, Sean < [email protected]> wrote: > Hi Don, > > To run the standard ctakes clinical pipeline you don't need the ytex > module, so indeed do not panic. If you are not getting a proper build > because of ytex then my advice (without analyzing that output) would be to > just comment out the dependency in the main ctakes pom. If you ever do > decide to play with ytex then you can tackle any build problems at that > time. > > Don't use the MultiThreadedPipeline in ctakes examples. I am 99% sure > that it doesn't work (I've run it, gotten errors, and then hunted through > the code until I found unprotected shared objects.) If you do want to try > a thread safe pipeline then I recommend that you get the trunk version of > ctakes. With that you can build using the "runPiperSubmitter" maven > profile to launch a gui. In the gui select the "TsFastClinicalPipeline" > (or something like that) in ctakes-clinical-pipeline-res. "Ts" stands for > thread-safe and you can find Ts piper files throughout the ctakes *-res > projects. > > You can check progress /comments at this jira item (ctakes-485): > https://issues.apache.org/jira/browse/CTAKES-485?jql= > project%20%3D%20CTAKES%20ORDER%20BY%20created%20DESC > > Sean > ________________________________________ > From: Don Flinn <[email protected]> > Sent: Sunday, January 21, 2018 9:41 PM > To: [email protected] > Subject: Errors in Install and examples [EXTERNAL] > > Hi, > > I'm new toctakes. I installed the system as per the cTakes 4.0 Developer > install Guide into eclipse running on Windows 10. It mostly went well. > However, there were errors in the build for the ctakes-ytexs in the pom.xml > <execution> elements. It said 'don't panic" so I'm not -:). However, due > my novice status, I don't know how to fix this. The error message is > below. Some ideas would be appreciated > > I also ran through the examples and MultiTheadedPipeline.java had an error > shown below: I would appreciate any insight into these errors. > > I still have a lot of work to do to understand all the output and > processes, but I want to first get the install correct. I've been reading > the ctakes, UMIA and NPL documents and articles. I would appreciate any > pointers to pertinent references that I should read. > > Thanks, > Don > > ========================================Build error > ============================== > > An Ant BuildException has occured: The following error occurred while > executing this line: C:\apache-ctakes-4.0.0Dev\ctakes\ctakes- > ytex\scripts\build-setup.xml:113: Problem: failed to create task or type > if Cause: the class net.sf.antcontrib.logic.IfTask was not found. Action: > Check that the component has been correctly declared and that the > implementing JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration > dialogs Do not panic, this is a common problem. It may just be a > typographical error in the build file or the task/type declaration. The > commonest > cause is a missing JAR. This is not a bug; it is a configuration problem > (org.apache.maven.plugins:maven-antrun-plugin:1.6:run:generate-test- > config:pre-integration-test) org.apache.maven.plugin. > MojoExecutionException: > An Ant BuildException has occured: The following error occurred > while executing this line: C:\apache-ctakes-4.0.0Dev\ > ctakes\ctakes-ytex\scripts\build-setup.xml:113: Problem: failed to create > task or type if Cause: > the class net.sf.antcontrib.logic.IfTask was not found. Action: Check that > the component has been correctly declared and that the implementing > JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration dialogs Do not > panic, this is a common problem. It may just be a typographical error > in the build file or the task/type declaration. The commonest cause is a > missing JAR. This is not a bug; it is a configuration problem at > org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:283) at > org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo( > DefaultBuildPluginManager.java:134) at > org.eclipse.m2e.core.internal.embedder.MavenImpl.execute( > MavenImpl.java:331) > at > org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call( > MavenImpl.java:1362) > at > org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call( > MavenImpl.java:1) > at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare( > MavenExecutionContext.java:177) at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute( > MavenExecutionContext.java:112) at > org.eclipse.m2e.core.internal.embedder.MavenImpl.execute( > MavenImpl.java:1360) > at > org.eclipse.m2e.core.project.configurator.MojoExecutionBuildParticipant. > build(MojoExecutionBuildParticipant.java:52) at > org.eclipse.m2e.core.internal.builder.MavenBuilderImpl. > build(MavenBuilderImpl.java:137) > at > org.eclipse.m2e.core.internal.builder.MavenBuilder$ > 1.method(MavenBuilder.java:172) at > org.eclipse.m2e.core.internal.builder.MavenBuilder$1.method( > MavenBuilder.java:1) > at > org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1$1.call( > MavenBuilder.java:115) > at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare( > MavenExecutionContext.java:177) at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute( > MavenExecutionContext.java:112) at > org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1.call( > MavenBuilder.java:105) > at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare( > MavenExecutionContext.java:177) at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute( > MavenExecutionContext.java:151) at > org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute( > MavenExecutionContext.java:99) > at > org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod.execute( > MavenBuilder.java:86) > at > org.eclipse.m2e.core.internal.builder.MavenBuilder.build( > MavenBuilder.java:200) > at > org.eclipse.core.internal.events.BuildManager$2.run( > BuildManager.java:735) > at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at > org.eclipse.core.internal.events.BuildManager. > basicBuild(BuildManager.java:206) > at > org.eclipse.core.internal.events.BuildManager. > basicBuild(BuildManager.java:246) > at > org.eclipse.core.internal.events.BuildManager$1.run( > BuildManager.java:301) > at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at > org.eclipse.core.internal.events.BuildManager. > basicBuild(BuildManager.java:304) > at > org.eclipse.core.internal.events.BuildManager. > basicBuildLoop(BuildManager.java:360) > at > org.eclipse.core.internal.events.BuildManager.build( > BuildManager.java:383) > at > org.eclipse.core.internal.events.AutoBuildJob.doBuild( > AutoBuildJob.java:142) > at > org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:232) > at org.eclipse.core.internal.jobs.Worker.run(Worker.java:56) Caused by: C: > \apache-ctakes-4.0.0Dev\ctakes\ctakes-ytex\target\ > antrun\build-main.xml:5: > The following error occurred while executing this line: C:\apache- > ctakes-4.0.0Dev\ctakes\ctakes-ytex\scripts\build-setup.xml:113: Problem: > failed to create task or type if Cause: the class > net.sf.antcontrib.logic.IfTask was not found. Action: Check that the > component has been correctly declared and that the implementing JAR is in > one of: -ANT_HOME\lib -the IDE Ant configuration dialogs Do not panic, > this is a common problem. It may just be a typographical error in the > build file or the task/type declaration. The commonest cause is a missing > JAR. This is not a bug; it is a configuration problem at > org.apache.tools.ant.ProjectHelper.addLocationToBuildException( > ProjectHelper.java:497) > at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java: > 444) at org.apache.tools.ant.UnknownElement.execute( > UnknownElement.java:291) > at sun.reflect.GeneratedMethodAccessor152.invoke(Unknown > Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown > Source) > at java.lang.reflect.Method.invoke(Unknown Source) at > org.apache.tools.ant.dispatch.DispatchUtils.execute( > DispatchUtils.java:106) > at org.apache.tools.ant.Task.perform(Task.java:348) at > org.apache.tools.ant.Target.execute(Target.java:390) at > org.apache.tools.ant.Target.performTasks(Target.java:411) at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397) at > org.apache.tools.ant.Project.executeTarget(Project.java:1366) at > org.apache.maven.plugin.antrun.AntRunMojo.execute(AntRunMojo.java:270) > ... > 32 more Caused by: C:\apache-ctakes-4.0.0Dev\ctakes\ctakes- > ytex\scripts\build-setup.xml:113: Problem: failed to create task or type > if Cause: the class net.sf.antcontrib.logic.IfTask was not found. Action: > Check that the component has been correctly declared and that the > implementing JAR is in one of: -ANT_HOME\lib -the IDE Ant configuration > dialogs Do not panic, this is a common problem. It may just be a > typographical error in the build file or the task/type declaration. The > commonest > cause is a missing JAR. This is not a bug; it is a configuration problem > at > org.apache.tools.ant.UnknownElement.getNotFoundException( > UnknownElement.java:487) > at > org.apache.tools.ant.UnknownElement.makeObject(UnknownElement.java:419) > at > org.apache.tools.ant.UnknownElement.maybeConfigure( > UnknownElement.java:163) > at org.apache.tools.ant.Task.perform(Task.java:347) at > org.apache.tools.ant.Target.execute(Target.java:390) at > org.apache.tools.ant.Target.performTasks(Target.java:411) at > org.apache.tools.ant.Project.executeSortedTargets(Project.java:1397) at > org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets( > SingleCheckExecutor.java:38) > at > org.apache.tools.ant.Project.executeTargets(Project.java:1249) at > org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442) ... 43 more > > ===================== MultiTheadedPipeline.java > error=================================== > ** Configuration Error: file:\C:\apache-ctakes-4.0. > 0Dev\ctakes\ctakes-lvg-res\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:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\ > target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x > option to specify the config file path. > ** Configuration Error: file:\C:\apache-ctakes-4.0. > 0Dev\ctakes\ctakes-lvg-res\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:\apache-ctakes-4.0.0Dev\ctakes\ctakes-lvg-res\ > target\classes\org\apache\ctakes\lvg\data\config\lvg.properties'. Use -x > option to specify the config file path. >
