Jabref: medline import does not work

[bernhard-kleine]

JabRef 5.0.0-dev--2019-11-19----ae02dcb46
Windows 7 6.1 amd64
Java 13.0.1

• [x] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

Steps to reproduce the behavior:

1. into the (websearch)Medline/Pubmed enter a number e.g. 29316417 and press search
2. the dialog pops up and shows "Processing 29316417"
3. nothing furthers happens, I waited 70 min.

Log File

Log file is empty. There is actually no logging.

[tobiasdiez]

This should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks! Please remember to make a backup of your library before trying-out this version.

[bernhard-kleine]

I installed this version:
JabRef 5.0-alpha--2019-12-07--d0f6c2b
Windows 7 6.1 amd64
Java 13.0.1

and jabref gets still stuck with the import dialog. The problems is not solved!!!

[tobiasdiez]

Does it only apply to the above id, or to every ID / query you try?

I tried it and it worked for me. Moreover, we have automatic tests in place which also pass. Thus I guess there is a problem with your connection or something like that.

[Siedlerchr]

Running from source code works, it takes approx 5 mins and then it's there, but running the installer I have the same effect.

[bernhard-kleine]

@tobiasdiez : This time was with an different ID, and with a third one, too.

[bernhard-kleine]

@Siedlerchr 5mins is still much to long.

[bernhard-kleine]

BTW I have in the meantime fetched a couple of entries via Zotero and that worked flawlessly. I.e, my internet connection is working very well.

[Siedlerchr]

I finally was able to debug it:

1. Remove strip-debug argument from jlink

Starting JabRef via JabRef.bat from X:\Users\CS\Downloads\JabRef-5.0-portable_windows(1)\JabRef\runtime\bin\Jabref.bat

1. Modify the bat
   Change the last line to:

pushd %DIR% & %JAVA_EXEC% -Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8000,suspend=n -p "%~dp0/../app" -m org.jabref/org.jabref.JabRefLauncher  %* & popd

Create a remote debugging connection and connect:
Setting breakpoints I saw it fails becuase of a modularity issue
@tobiasdiez Any idea how to fix this?

javax.xml.bind.JAXBException: Error while searching for service [javax.xml.bind.JAXBContextFactory]
 - with linked exception:
[java.util.ServiceConfigurationError: javax.xml.bind.JAXBContextFactory: module org.jabref.merged.module does not declare `uses`]

[tobiasdiez]

Does it help if you add uses javax.xml.bind.JAXBContextFactory; here https://github.com/JabRef/jabref/blob/master/build.gradle#L599 and/or in https://github.com/JabRef/jabref/blob/master/src/main/java/module-info.java ?

Since you manage to debug the installed version, can you please have a look at https://github.com/JabRef/jabref/issues/5475 as well (which I guess is also due to some modularity issue). And please add the above steps to the wiki so that we don't forget how to debug the installed app.

[Siedlerchr]

@tobiasdiez Thanks for the hint, the uses in the gradle worked. I also added a wiki entry

[Siedlerchr]

This issue should now be fixed in the latest master (not in the beta). It will take some time until the new binaries are uploaded.

[bernhard-kleine]

works! Thank you very much.