There were two other aspects of the piperfile that required a bit of digging to
figure out too and would be good to include in either the ctakes-tiny-rest or
ctakes-dockhand packages. Best place might be to build them in as options in
the dockhand GUI. I will try to add them myself in the coming weeks, but don’t
have the developer chops to be sure I'm doing it well and not breaking things.
//BsvRegexSectionizer requires the path to the bsv file to be specified as the
SectionsBsv param:
add BsvRegexSectionizer SectionsBsv=path/to/file.bsv
//LookupXml is the param to specify a custom dictionary xml
//I use this to change the term consumer from Default to Precision or
SemanticCleanup
add org.apache.ctakes.dictionary.lookup2.ae.OverlapJCasTermAnnotator
LookupXml=path/to/sno_rx_16ab.xml
Tom
On 7/6/20, 12:10 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu> wrote:
> Is that the same fix you submitted?
Yep. You did some great detective work.
Thanks for the additional info.
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Monday, July 6, 2020 3:02 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL]
[SUSPICIOUS]
* External Email - Caution *
I was using the prose sentence detector (SentenceDetectorAnnotatorBIO) - I
will check the fix you submitted.
In the mean time, I WAS able to get a functioning REST server up and
running by starting a new spring project from scratch and poaching bits and
pieces from ctakes-dockhand and ctakes-tiny-rest as needed. In doing that I
came across the issue with SentenceDetectorAnnotatorBIO and address it by
adding a classifierJarPath variable in the piper file:
add SentenceDetectorAnnotatorBIO
classifierJarPath=/org/apache/ctakes/core/sentdetect/model.jar
Is that the same fix you submitted?
On 7/6/20, 10:49 AM, "Finan, Sean" <sean.fi...@childrens.harvard.edu> wrote:
Hi Tom,
Were you using the "Prose Sentences" option? If so, I think that I may
have found the problem (my fault, not the engine's). I checked in a fix but it
may take some time before it shows up on maven central.
I will test some more tonight and see what comes up.
Sean
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Wednesday, July 1, 2020 7:34 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL]
[SUSPICIOUS]
* External Email - Caution *
I hope you'll let me buy you a beer or two next time I'm in Boston -
adding the maven snapshot repo did the trick.
Followed the README.txt instructions:
4. Execute "docker build -t ctakes_tiny_rest .".
This will build an image with the tag "ctakes_tiny_rest".
5. Set the environment variable "umlsUser" to your umls username.
6. Set the environment variable "umlsPass" to your umls password.
5. Execute "docker run --name my_ctakes_rest --rm -d -p 8080:8080 -e
umlsUser -e umlsPass ctakes_tiny_rest".
This will start a container named "my_ctakes_rest" that runs the
server.
6. In a browser, visit
"https://urldefense.proofpoint.com/v2/url?u=http-3A__IP.IP.IP.IP-3A8080_ctakes-5Ftiny-5Frest&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=9qAmVa2u2__7kad06kQp3hqsj4Q6V1RfbzeZnjauUvo&s=TBQZ-y0nCfYSSP9s_iAV6NaW_MpMocKTt3FWqielDjk&e=
".
This should open a ctakes demo front page.
The demo page looks as expected but am getting an HTTP 500 error with
each attempt, and "Error processing REST call" as the output. Browser dev
console errors copied below. I'm sure I set umlsUser and umlsPass correctly and
triple checked them at the UML Terminology Services login page.
Nothing stands out to me from the trace, but I'll spend some time
looking in to it to see what I can come up with.
Tom
javax.servlet.ServletException: Servlet.init() for servlet
[ctakes-rest-service] threw exception
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:668)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:834)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1417)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
Root Cause
org.springframework.beans.factory.BeanCreationException: Error creating
bean with name 'tinyController': Invocation of init method failed; nested
exception is java.lang.NoClassDefFoundError: Could not initialize class
org.apache.ctakes.rest.service.RestPipelineRunner
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:137)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:668)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:834)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1417)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
Root Cause
java.lang.NoClassDefFoundError: Could not initialize class
org.apache.ctakes.rest.service.RestPipelineRunner
org.apache.ctakes.rest.service.TinyController.init(TinyController.java:52)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:498)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleElement.invoke(InitDestroyAnnotationBeanPostProcessor.java:366)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor$LifecycleMetadata.invokeInitMethods(InitDestroyAnnotationBeanPostProcessor.java:311)
org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:134)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:409)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1620)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:555)
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:483)
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:761)
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:867)
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:543)
org.springframework.web.servlet.FrameworkServlet.configureAndRefreshWebApplicationContext(FrameworkServlet.java:668)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:634)
org.springframework.web.servlet.FrameworkServlet.createWebApplicationContext(FrameworkServlet.java:682)
org.springframework.web.servlet.FrameworkServlet.initWebApplicationContext(FrameworkServlet.java:553)
org.springframework.web.servlet.FrameworkServlet.initServletBean(FrameworkServlet.java:494)
org.springframework.web.servlet.HttpServletBean.init(HttpServletBean.java:171)
javax.servlet.GenericServlet.init(GenericServlet.java:158)
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:490)
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:92)
org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:668)
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:343)
org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:408)
org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)
org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:834)
org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1417)
org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
java.lang.Thread.run(Thread.java:748)
On 7/1/20, 4:06 PM, "Finan, Sean" <sean.fi...@childrens.harvard.edu>
wrote:
I had no idea that this was in the install guide:
>$ exports MAVEN_OPTS='-Xms3072m -Xmx4g -Xss128M
-XX:+CMSClassUnloadingEnabled -XX:-UseGCOverheadLimit
-Dmaven.test.failure.ignore=false'
$ mvn --fail-at-end --errors --update-snapshots clean install
sonar:sonar -DskipTests=false -Dsonar.scm.provider=svn
-Dsonar.host.url=https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_analysis&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=9qAmVa2u2__7kad06kQp3hqsj4Q6V1RfbzeZnjauUvo&s=2FoCH8QvUO_OvHjhD9TtgP30JI8ES9sohpufh8RDlgU&e=
I never do that. It is way too specific and I don't need to (or
want to) do exactly what Jenkins does unless I'm trying to fix an error on a
Jenkins build ...
All that I use is:
mvn -DskipTests=true clean package
Everything else is a default setting.
I have a thought: You may need to explicitly add the maven
snapshots repo
https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apache.org_content_groups_snapshots&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=9qAmVa2u2__7kad06kQp3hqsj4Q6V1RfbzeZnjauUvo&s=TgKg-4ASAgS0WTjSUsYmOegk9nrcEwJlYAAfAAU3wak&e=
Please:
In the pom.xml next to the Dockerfile, add the following right
above <build>..</build>
<repositories>
<repository>
<id>apache.snapshots</id>
<name>Apache Development Snapshot Repository</name>
<url>https://urldefense.proofpoint.com/v2/url?u=https-3A__repository.apache.org_content_groups_snapshots_&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=9qAmVa2u2__7kad06kQp3hqsj4Q6V1RfbzeZnjauUvo&s=bANlBnAM2tGMXMOxaQFJ8vrqnDo5vNjKl54_HAlvMHo&e=
</url>
<releases>
<enabled>false</enabled>
</releases>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
That may help. Let me know if it does then I will add it to the
pom in trunk.
Sean
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Wednesday, July 1, 2020 6:28 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL]
[SUSPICIOUS]
* External Email - Caution *
Thanks again Sean. Java8 allows the build to complete even with
Ytex - well, I should say, Ctakes built successfully, but then the sonar
portion of the build triggered by this line in the developer install guide
failed:
mvn --fail-at-end --errors --update-snapshots clean install
sonar:sonar -DskipTests=false -Dsonar.scm.provider=svn
-Dsonar.host.url=https://urldefense.proofpoint.com/v2/url?u=https-3A__builds.apache.org_analysis&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=ALGTH-Hi6voMC5fJL2YiOYyLfTucZwVZurOl-hazXwE&e=
I removed what seemed to be the offensive parts of the script and
ran again as this and it worked:
mvn --fail-at-end --errors --update-snapshots clean install
-DskipTests=false
Unfortunately, still getting the same error on docker build:
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 3.563 s
[INFO] Finished at: 2020-07-01T22:15:42Z
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal on project dockhand-rest: Could not
resolve dependencies for project
org.apache.ctakes:dockhand-rest:war:4.0.1-SNAPSHOT: The following artifacts
could not be resolved: org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT: Could not find
artifact org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT -> [Help 1]
From the stack trace here's the point where it starts throwing
warnings after successfully findings POMs for non-ctakes packages and then not
finding them for ctakes:
...
Downloading from central:
https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2_org_apache_apache_13_apache-2D13.pom&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=C0m12_VckGoFGqAwADXB1DaLyIdK0I_Par3nQ_4ULxE&e=
Downloaded from central:
https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2_org_apache_apache_13_apache-2D13.pom&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=C0m12_VckGoFGqAwADXB1DaLyIdK0I_Par3nQ_4ULxE&e=
(14 kB at 285 kB/s)
Downloading from central:
https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2_org_apache_maven_plugins_maven-2Dcompiler-2Dplugin_3.1_maven-2Dcompiler-2Dplugin-2D3.1.jar&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=DifUiCkszwnyoA2NvmPd31RmtsOh4rOLS5hOQKwiKPk&e=
Downloaded from central:
https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2_org_apache_maven_plugins_maven-2Dcompiler-2Dplugin_3.1_maven-2Dcompiler-2Dplugin-2D3.1.jar&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=DifUiCkszwnyoA2NvmPd31RmtsOh4rOLS5hOQKwiKPk&e=
(43 kB at 401 kB/s)
[WARNING] The POM for
org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT is missing, no dependency
information available
[WARNING] The POM for
org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT is missing, no dependency
information available
[WARNING] The POM for
org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT is missing, no
dependency information available
...
I ran the same "mvn help:evaluate" on my computer and get the same
result as you. I commented out the ctakes-related commands from Dockerfile so
that I could at least build the container with tomcat, maven, and openjdk8, and
ran mvn help:evaluate from the container as well and got the same output.
In case the issue was that I was building ALL of ctakes and not
just dockhand, I tried that too from a fresh svn checkout of ctakes, cd
{ctakes-dockhand} > mvn package and run the jar, but same issue.
Ah well - I just don't have enough understanding of maven and java
devops to get to the bottom of this. I really appreciate you taking the time to
respond Sean, and apologize for the java version issue - rookie mistake!
Tom
On 7/1/20, 2:02 PM, "Finan, Sean"
<sean.fi...@childrens.harvard.edu> wrote:
Hi Tom,
My settings.xml is completely commented. It looks like
defaults are used when nothing specific is provided.
I ran "mvn help:evaluate" and entered "${project.repositories}"
when prompted. My default repository is:
<repositories>
<repository>
<id>central</id>
<name>Central Repository</name>
<url>https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=tQsd4rvmkg8PlC7NV-oGCVoBJU8lW8hWcVj4oCX74l0&s=LbWH-d8QbjhFJh3OOL0NpLt0T8QGO9LFTuGv1EyVGB4&e=
</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
Yours should be the same.
Sean
________________________________________
From: Finan, Sean <sean.fi...@childrens.harvard.edu>
Sent: Wednesday, July 1, 2020 3:58 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running?
[EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Tom,
ctakes requires java 8. So the first thing that needs to be
done is putting java 8 on your system and starting the whole process from
scratch. You may end up commenting out the ytex stuff, but the rest of the
experience should be different.
I am also not a maven expert. I will have to look at my
settings.xml and get back to you (after a meeting).
!! If anybody else out there has a quick answer, please speak
up.
Sean
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Wednesday, July 1, 2020 3:14 PM
To: dev@ctakes.apache.org
Subject: RE: ctakes-tiny-rest - any guidance on running?
[EXTERNAL]
* External Email - Caution *
Not behind any firewalls or weird port issues - home internet
and personal computer, no VPN.
javac -version: 14.0.1
If I understand maven correctly (spoiler alert: I don't) - it
will look for artifacts in repos that are listed in the settings.xml file. I'm
noticing my settings.xml file doesn't have ANY repos listed. Would you mind
sharing the relevant sections of yours if you think that might be part of the
problem?
On macos if installed with homebrew the maven settings are in:
/usr/local/Cellar/maven/{maven version; mine is
3.6.3_1}/libexec/conf/settings.xml
My settings.xml is pretty much all commented out (it came that
way!), but I've added the following localRepository:
<localRepository>${user.name}/.m2/repository</localRepository>
It seems like I should have some other public repos listed
here...
-----Original Message-----
From: Finan, Sean <sean.fi...@childrens.harvard.edu>
Sent: Wednesday, July 01, 2020 5:25 AM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running?
[EXTERNAL]
Hi Tom,
first, let me offer my commiseration regarding the ytex
failure. I think that at some point I will write the community for objections
and then make it a separate build from (primary) ctakes. I think that your
solution of removing ytex from the main project on your system is absolutely
the correct thing to do since you don't want it anyway.
After that, I have only guesses as to what might be going on.
I haven't personally had any of the build problems that you are facing.
One thing that I didn't make clear: You only need to build the
ctakes-dockhand.jar, not all of ctakes. But the errors you see are still
troublesome (especially in docker).
> [ERROR] Failed to execute goal on project dockhand-rest:
Could not resolve dependencies for project
org.apache.ctakes:dockhand-rest:war:4.0.1-SNAPSHOT: The following artifacts
could not be resolved: org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT: Could not find
artifact org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT -> [Help 1]
I don't understand the above error at all. All of those
artifacts do exist. I use them on a (practically) daily basis. Is it possible
that you don't have a port open or that your docker machine is behind a
firewall of some sort?
There is one question that I have for you about the error
>ERROR]
/Users/thomas/projects/ctakes/trunk/ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/TinyController.java:[28,23]
error: cannot find symbol
[ERROR] symbol: class PostConstruct
[ERROR] location: package javax.annotation
What version of java are you using? ctakes requires version 8.
javax.annotation -should- be standard in java 8. You can try running "javac
-version".
Sean
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Tuesday, June 30, 2020 7:06 PM
To: dev@ctakes.apache.org
Subject: Re: ctakes-tiny-rest - any guidance on running?
[EXTERNAL]
* External Email - Caution *
Thank you for the direction, Sean. I ran in to build issues,
some addressed on prior threads (YTEX related), some that I couldn’t find
references to in the mailing list archives. I am still stuck not able to
complete the docker build due to an unresolved dependency. Including the info
below in case it is helpful to anyone, and in case anyone can help with what
(hopefully!) is the final error.
Working through Dev install
guide<https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_cTAKES-2B4.0-2BDeveloper-2BInstall-2BGuide&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=pUTbexmiZnykTq7rQgTwZdj0cSAzpWfjzJzMSmD_07c&s=V7soEGQAN0_YigZAyAX_xHg6I72rT0_sx5ggS9ojp2A&e=
>:
1. I get a FAILURE on building cTAKES YTEX
…
[INFO] ctakes-examples-res ................................
SUCCESS [ 0.363 s]
[INFO] ctakes-examples ....................................
SUCCESS [ 1.311 s]
[INFO] Apache cTAKES Resources ctakes-ytex-res ............
SUCCESS [ 0.308 s]
[INFO] Apache cTAKES YTEX .................................
FAILURE [ 0.717 s]
[INFO] Apache cTAKES YTEX UIMA ............................
SKIPPED
[INFO] Apache cTAKES Tiny Rest Service ....................
SKIPPED
[INFO] Apache cTAKES Distribution .........................
SKIPPED
[INFO] Apache cTAKES Regression-test ......................
SKIPPED
[INFO] Apache cTAKES template filler ......................
SKIPPED
[INFO] Apache cTAKES Dockhand .............................
SKIPPED
…
Caused by: java.lang.ClassNotFoundException:
javax.activation.MimeTypeParseException
at
org.codehaus.plexus.classworlds.strategy.SelfFirstStrategy.loadClass(SelfFirstStrategy.java:50)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.unsynchronizedLoadClass(ClassRealm.java:271)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:247)
at
org.codehaus.plexus.classworlds.realm.ClassRealm.loadClass(ClassRealm.java:239)
... 51 more
* From this
thread<https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201907.mbox_-253cCALfEtMvGzE9TppFCuLTNdgqzSU5ew5RVkVjUgq19WF3pwNTyRQ-40mail.gmail.com-253e&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=pUTbexmiZnykTq7rQgTwZdj0cSAzpWfjzJzMSmD_07c&s=1UdlzWnTMDEq7f2ix9ZemrMBvsS4TAo2Kl0i7jOLq_g&e=
> I tried:
i. mvn clean install -Dmaven.test.skip=true
* I get the same FAILURE and stack trace
* From your comment in that same thread (“Wouldn't it be
better to remove [YTEX] dependency from the cTAKES core pom.xml…”) I thought
I’d try removing all references to YTEX from {ctakes_trunk}/pom.xml:
i. Comment out lines 201-204, 789-807, and 1023
* Rerun mvn clean install -Dmaven.test.skip=true
i. Immediate ERROR due to YTEX dependencies in
ctakes/trunk/ctakes-distribution/pom.xml
* Remove references to YTEX from
ctakes-distribution/pom.xml
i. Comment out lines 123-130
* Rerun mvn clean install -Dmaven.test.skip=true
1. Now I get a FAILURE on cTAKES Tiny Rest Service:
…
[INFO] ctakes-examples-res ................................
SUCCESS [ 0.231 s]
[INFO] ctakes-examples ....................................
SUCCESS [ 0.680 s]
[INFO] Apache cTAKES Tiny Rest Service ....................
FAILURE [ 0.275 s]
[INFO] Apache cTAKES Distribution .........................
SKIPPED
[INFO] Apache cTAKES Regression-test ......................
SKIPPED
[INFO] Apache cTAKES template filler ......................
SKIPPED
[INFO] Apache cTAKES Dockhand .............................
SKIPPED
[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-compiler-plugin:2.4:compile (default-compile) on
project ctakes-tiny-rest: Compilation failure: Compilation failure:
[ERROR]
/Users/thomas/projects/ctakes/trunk/ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/TinyController.java:[28,23]
error: cannot find symbol
[ERROR] symbol: class PostConstruct
[ERROR] location: package javax.annotation
[ERROR]
/Users/thomas/projects/ctakes/trunk/ctakes-tiny-rest/src/main/java/org/apache/ctakes/rest/service/TinyController.java:[43,4]
error: cannot find symbol
1. I added the following dependency to
ctakes/trunk/ctakes-tiny-rest/pom.xml:
<dependency>
<groupId>javax.annotation</groupId>
<artifactId>javax.annotation-api</artifactId>
<version>1.3.2</version>
</dependency>
1. …and commented out the <scope>provided</scope> attribute
of the <groupId>javax.servlet</groupId> dependency in the same file
* I did this first, before adding the
javax.annotation-api dependency mentioned above, and build still failed. I
forgot to revert it before applying adding that dependency, so don’t know if it
helped or not.
1. [INFO]
------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO]
------------------------------------------------------------------------
1. I then went through the steps you outlined:
* Run the ctakes-dockhand jar
* Choose: Rest Server Docker Bundle
* Add description
* Select pipeline features: [Multiple Sections, Prose
Sentences, Tokens, Entities, Attributes, Locations, Severities]
* Select pipeline outputs: [FHIR, Text, Properties, XMI,
CUI List]
* Finish -> Add Save To location
* cd {save-to location}/repos
* docker build -t dockhandtest .
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 3.076 s
[INFO] Finished at: 2020-06-30T22:54:45Z
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal on project dockhand-rest: Could
not resolve dependencies for project
org.apache.ctakes:dockhand-rest:war:4.0.1-SNAPSHOT: The following artifacts
could not be resolved: org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-utils:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-relation-extractor:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-chunker:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dictionary-lookup-fast:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-constituency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-dependency-parser:jar:4.0.1-SNAPSHOT,
org.apache.ctakes:ctakes-context-tokenizer:jar:4.0.1-SNAPSHOT: Could not find
artifact org.apache.ctakes:ctakes-tiny-rest:jar:4.0.1-SNAPSHOT -> [Help 1]
1. From {save-to location}/repos
* Edit pom.xml – change ctakes.version from
4.0.1-SNAPSHOT to 4.0.1 (same error) then to 4.0.0:
<properties>
<ctakes.version>4.0.0</ctakes.version>
</properties>
* Rerun docker build -t dockhandtest .: error message
improved – only one missing dependency now:
[INFO]
------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO]
------------------------------------------------------------------------
[INFO] Total time: 43.040 s
[INFO] Finished at: 2020-06-30T23:00:38Z
[INFO]
------------------------------------------------------------------------
[ERROR] Failed to execute goal on project dockhand-rest: Could
not resolve dependencies for project
org.apache.ctakes:dockhand-rest:war:4.0.1-SNAPSHOT: Could not find artifact
org.apache.ctakes:ctakes-tiny-rest:jar:4.0.0 in central
(https://urldefense.proofpoint.com/v2/url?u=https-3A__repo.maven.apache.org_maven2&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=pUTbexmiZnykTq7rQgTwZdj0cSAzpWfjzJzMSmD_07c&s=pcCpMxdVbxWvYPBx912AgjRUbL5FuLW8RCXHafDNpuM&e=
) -> [Help 1]
1. And this is where I am stuck. I understand that
ctakes-tiny-rest:jar must not exist in 4.0.0 or 4.0.1 repositories, but am not
sure how to get beyond this point.
On 6/26/20, 2:33 PM, "Finan, Sean"
<sean.fi...@childrens.harvard.edu> wrote:
Hi Tom,
Tiny Rest is not really a standalone deal, but utilization
is pretty simple once you know what it is for.
What you can try is:
Create the jar for ctakes-dockhand using "mvn package".
You can put that jar file anywhere, even a system that doesn't have ctakes.
Run that jar in a graphical environment (ms windows, gnome,
etc.). Double-click should start it.
ctakes-dockhand is an installation tool that looks pretty
much like any "wizard" style installer. Make selections on each screen, click
next, etc.
Your selection on the first panel should be "docker rest" -
or "rest docker" or something like that. I can't remember.
Then give it some description, create the pipeline that you
want, etc.
After you finish the last panel and click "Finish" a small
number of files will be created in your chosen directory. *Note, the tool
will not exit by iteself.
If you are familiar with docker, you can use the Dockerfile
that is in that directory to create an image of a ctakes rest service.
The docker image contains everything you need and when you
run it will start a rest service.
I haven't tried it, but you should also be able to just
maven package using the pom in that same output directory without docker. It
will create a war file.
If you go without docker then you will need to have a web
server (tomcat, etc.) and move the war file into the webapps directory or
whatever is required for that server.
There is a little demo page that you can launch on a
browser. Just http to the ip address (of a VM, docker VM, localhost) with the
port 8080 and ctakes_tiny_rest.
For instance:
https://urldefense.proofpoint.com/v2/url?u=http-3A__192.168.99.101-3A8080_ctakes-5Ftiny-5Frest&d=DwIGaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=pUTbexmiZnykTq7rQgTwZdj0cSAzpWfjzJzMSmD_07c&s=genox1Kxui9FMmo5ZeAVCeHiwiELuEeSO-y0RqpUYaM&e=
You can curl or use some other rest client, but you should
probably use the demo page just to see what it can do.
To get different output formats you can send with "fhir",
"umls", "cui", or "xmi". "pretty" and "property" are works in progress. The
default is fhir json.
Sean
________________________________________
From: Thomas W Loehfelm <twloehf...@ucdavis.edu.INVALID>
Sent: Friday, June 26, 2020 5:04 PM
To: dev@ctakes.apache.org
Subject: ctakes-tiny-rest - any guidance on running?
[EXTERNAL]
* External Email - Caution *
I was very excited to find the ctakes-tiny-rest package in
the svn repo, but have not been able to get it stood up.
What I have tried:
1. Cloning the svn repo
2. mvn package
3. java -cp target/ctakes-tiny-rest-4.0.1-SNAPSHOT.jar
org.apache.ctakes.rest.service.TinyController
* Error: Unable to initialize main class
org.apache.ctakes.rest.service.TinyController
Caused by: java.lang.NoClassDefFoundError:
org/apache/uima/resource/ResourceInitializationException
I am not very familiar with mvn or with the Spring
framework so I suspect I am missing something fundamental.
Is anyone making use of this component and can point me in
the right direction?
Thanks for your time and consideration!
Tom
Thomas Loehfelm, MD
UC Davis Medical Center
Abdominal Radiology
