how to use visualize

[jeanphilippegoldman]

Hi,
thanks for your work.
Am I the only one to have difficulties to use -visualize option ?
I'm using it like this:
-Dexec.args="-bratfile1 file1 -bratfile2 file2.ann -visualize=Trigger_EI"

with Trigger_EI being one possibile entity
I'm having this Exception below. (The other options greedyMatching and WeightedTypeMatching don't throw this)

Thanks for your help.

jean-philippe

java.lang.NullPointerException
at gemini.Visualization.display (Visualization.java:79)
at gemini.Main.main (Main.java:273)
at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke (Method.java:498)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run (ExecJavaMojo.java:282)
at java.lang.Thread.run (Thread.java:748)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 1.934 s
[INFO] Finished at: 2019-10-17T15:51:52+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:java (default-cli) on project gemini: An exception occured while executing the Java class. null: NullPointerException -> [Help 1]
org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.6.0:java (default-cli) on project gemini: An exception occured while executing the Java class. null

[fyh828]

Hello Jean-Philippe,

To use visualization option, the first file has to be XML format. Because the visualization function requires the origin text, otherwise with two annotation files there will be nothing to visualize. You could try this:
-Dexec.args="-xmlfile1 file1.xml -bratfile2 file2.ann -visualize=Trigger_EI"

[jeanphilippegoldman]

thanks for your reply. I understand. but how do you get xml files ?

…

On Fri, Oct 18, 2019 at 12:49 AM Yuheng FENG ***@***.***> wrote: Hello Jean-Philippe, To use visualization option, the first file has to be XML format. Because the visualization function requires the origin text, otherwise with two annotation files there will be nothing to visualize. You could try this: -Dexec.args="*-xmlfile1 file1.xml* -bratfile2 file2.ann -visualize=Trigger_EI" — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1?email_source=notifications&email_token=ADQ5ZKYGX37NYPWHFKKFOQ3QPDTWVA5CNFSM4JB2IPUKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBRYSKQ#issuecomment-543394090>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADQ5ZK6VLKMF7JUEJ3INAIDQPDTWVANCNFSM4JB2IPUA> .

[fyh828]

If you want to use text file as input, you could simply change the extension name from *.txt to *.xml, then add at the beginning of the document, add at the end of the document.