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Posted to dev@uima.apache.org by GitBox <gi...@apache.org> on 2023/01/09 06:55:44 UTC
[GitHub] [uima-ruta] Baytars opened a new issue, #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
Baytars opened a new issue, #116:
URL: https://github.com/apache/uima-ruta/issues/116
**Describe the bug**
[SimpleServer](https://uima.apache.org/d/uima-addons-current/SimpleServer/simpleServerUserGuide.html) does not recognize relation annotation as mentioned in [Apache UIMA Ruta™ Guide and Reference](https://uima.apache.org/d/ruta-current/tools.ruta.book.html). It will throw error when recognizing any such annotation.
```
HTTP Status 500 - XML output failed
type Exception report
message XML output failed
description The server encountered an internal error that prevented it from fulfilling this request.
exception
java.lang.RuntimeException: XML output failed
org.apache.uima.simpleserver.output.ResultConverter.getXMLString(ResultConverter.java:88)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.transformResult(SimpleServerServlet.java:296)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.analyze(SimpleServerServlet.java:213)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.doPost(SimpleServerServlet.java:190)
javax.servlet.http.HttpServlet.service(HttpServlet.java:643)
javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
root cause
java.lang.NullPointerException: Cannot invoke "org.apache.uima.simpleserver.output.Result.getResultEntries()" because "result" is null
org.apache.uima.simpleserver.output.ResultConverter.getXMLString(ResultConverter.java:60)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.transformResult(SimpleServerServlet.java:296)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.analyze(SimpleServerServlet.java:213)
org.apache.uima.simpleserver.servlet.SimpleServerServlet.doPost(SimpleServerServlet.java:190)
javax.servlet.http.HttpServlet.service(HttpServlet.java:643)
javax.servlet.http.HttpServlet.service(HttpServlet.java:723)
```
**To Reproduce**
Steps to reproduce the behavior:
1. Clone the repo `https://e.coding.net/cvd-bioinformatics/transdifferentiation/reprogramming-uima-tomcat.git` in Eclipse
2. In Eclipse, right click on `pom.xml > Run as > maven install` (Make sure you have installed `M2Eclipse`)
3. Right click on the project root, `Run As > Run on Server` (Make sure you have installed `Eclipse Java EE Developer Tools`,`Eclipse Java Web Developer Tools`,`Eclipse Web Developer Tools`,`Eclipse XML Editors and Tools`,`JST Server Adapters Extensions` and `JST Server Adapters Extensions (Apache Tomcat)`, configured at least one available Tomcat server in Eclipse and add the server runtime into the project classpath.)
4. In the browser, visit `http://localhost:8080/UIMADemo/?mode=form` and enter `Neurog2 is downstream of Pax6`. Click "Submit Query".
**Expected behavior**
The server should return an xml response about the text analysis result instead of error messages.
**Please complete the following information:**
Versions:
- OS: Windows 10 Professional (version: 21H2)
- Eclipse: 2022-06 (4.24.0) (Build id: 20220609-1112)
- Java: Eclipse Adoptium jdk-17.0.1.12-hotspot
- Maven: Eclipse Embedded 3.8.4/1.18.3.20220227-1319
- Apache Tomcat: 6.0.37
- org.apache.uima.uimaj-core: 3.3.1
- org.apache.uima.SimpleServer: 2.3.1
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[GitHub] [uima-ruta] reckart commented on issue #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
Posted by GitBox <gi...@apache.org>.
reckart commented on issue #116:
URL: https://github.com/apache/uima-ruta/issues/116#issuecomment-1375402545
Thanks. Unfortunately, it appears that the simple server is swallowing the root exception. In the debugger, I can unearth it:
```
java.lang.IllegalArgumentException: Not able to resolve type: Sentence in script SoMeRutaPear
```
Indeed, I do not find a type `...Sentence` in the type system that is contained in the PEAR.
Note that I had to install a Tomcat 9 to test this. When trying with Tomcat 10, I got a different set of exceptions indicating that the simple server is not compatible with the Servlet API version of Tomcat 10.
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[GitHub] [uima-ruta] Baytars closed issue #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
Posted by GitBox <gi...@apache.org>.
Baytars closed issue #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
URL: https://github.com/apache/uima-ruta/issues/116
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[GitHub] [uima-ruta] Baytars commented on issue #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
Posted by GitBox <gi...@apache.org>.
Baytars commented on issue #116:
URL: https://github.com/apache/uima-ruta/issues/116#issuecomment-1375181354
@reckart The issue is the replicate of that on [UIMA Jira](https://issues.apache.org/jira/browse/UIMA-6483).
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[GitHub] [uima-ruta] Baytars commented on issue #116: UIMA SimpleServer is not compatible with the latest Ruta feature (relation annotation)
Posted by GitBox <gi...@apache.org>.
Baytars commented on issue #116:
URL: https://github.com/apache/uima-ruta/issues/116#issuecomment-1375659896
> Thanks. Unfortunately, it appears that the simple server is swallowing the root exception. In the debugger, I can unearth it:
>
> ```
> java.lang.IllegalArgumentException: Not able to resolve type: Sentence in script SoMeRutaPear
> ```
>
> Indeed, I do not find a type `...Sentence` in the type system that is contained in the PEAR.
>
> Note that I had to install a Tomcat 9 to test this. When trying with Tomcat 10, I got a different set of exceptions indicating that the simple server is not compatible with the Servlet API version of Tomcat 10.
@reckart Yeah, you are right! My negligence caused this error! After deleting the undefined `Sentence`, the server works fine now! You are so helpful! Thank you!
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