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 "${project.repositories}" when prompted.
My default repository is:
<repositories>
<repository>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
</repositories>
Yours should be the same.
Sean
________________________________________
From: Finan, Sean <[email protected]>
Sent: Wednesday, July 1, 2020 3:58 PM
To: [email protected]
Subject: Re: ctakes-tiny-rest - any guidance on running? [EXTERNAL] [SUSPICIOUS]
* External Email - Caution *
Hi Tom,
ctakes requires java 8. So the first thing that needs to be done is putting
java 8 on your system and starting the whole process from scratch. You may end
up commenting out the ytex stuff, but the rest of the experience should be
different.
I am also not a maven expert. I will have to look at my settings.xml and get
back to you (after a meeting).
!! If anybody else out there has a quick answer, please speak up.
Sean
________________________________________
From: Thomas W Loehfelm <[email protected]>
Sent: Wednesday, July 1, 2020 3:14 PM
To: [email protected]
Subject: RE: ctakes-tiny-rest - any guidance on running? [EXTERNAL]
* External Email - Caution *
Not behind any firewalls or weird port issues - home internet and personal
computer, no VPN.
javac -version: 14.0.1
If I understand maven correctly (spoiler alert: I don't) - it will look for
artifacts in repos that are listed in the settings.xml file. I'm noticing my
settings.xml file doesn't have ANY repos listed. Would you mind sharing the
relevant sections of yours if you think that might be part of the problem?
On macos if installed with homebrew the maven settings are in:
/usr/local/Cellar/maven/{maven version; mine is
3.6.3_1}/libexec/conf/settings.xml
My settings.xml is pretty much all commented out (it came that way!), but I've
added the following localRepository:
<localRepository>${user.name}/.m2/repository</localRepository>
It seems like I should have some other public repos listed here...
-----Original Message-----
From: Finan, Sean <[email protected]>
Sent: Wednesday, July 01, 2020 5:25 AM
To: [email protected]
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 <[email protected]>
Sent: Tuesday, June 30, 2020 7:06 PM
To: [email protected]
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" <[email protected]> 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 <[email protected]>
Sent: Friday, June 26, 2020 5:04 PM
To: [email protected]
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
