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medline import does not work #5645

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bernhard-kleine opened this issue Nov 19, 2019 · 12 comments · Fixed by #5752
Closed

medline import does not work #5645

bernhard-kleine opened this issue Nov 19, 2019 · 12 comments · Fixed by #5752

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@bernhard-kleine
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@bernhard-kleine bernhard-kleine commented Nov 19, 2019

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

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 tobiasdiez added the fetcher label Nov 19, 2019
@tobiasdiez tobiasdiez added this to Needs triage in Bugs via automation Nov 19, 2019
@tobiasdiez tobiasdiez added this to the v5.0 milestone Nov 19, 2019
@tobiasdiez tobiasdiez moved this from Needs triage to High priority in Bugs Nov 19, 2019
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@tobiasdiez tobiasdiez commented Dec 7, 2019

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.

@tobiasdiez tobiasdiez closed this Dec 7, 2019
Bugs automation moved this from High priority to Closed Dec 7, 2019
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@bernhard-kleine bernhard-kleine commented Dec 7, 2019

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!!!

@Siedlerchr Siedlerchr reopened this Dec 7, 2019
Bugs automation moved this from Closed to Needs triage Dec 7, 2019
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@tobiasdiez tobiasdiez commented Dec 7, 2019

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.

@tobiasdiez tobiasdiez removed this from the v5.0 milestone Dec 7, 2019
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@Siedlerchr Siedlerchr commented Dec 7, 2019

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

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@bernhard-kleine bernhard-kleine commented Dec 7, 2019

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

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@bernhard-kleine bernhard-kleine commented Dec 7, 2019

@Siedlerchr 5mins is still much to long.

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@bernhard-kleine bernhard-kleine commented Dec 7, 2019

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.

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@Siedlerchr Siedlerchr commented Dec 15, 2019

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
2. 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`]
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@tobiasdiez tobiasdiez commented Dec 15, 2019

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 #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.

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@Siedlerchr Siedlerchr commented Dec 16, 2019

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

Bugs automation moved this from Needs triage to Closed Dec 16, 2019
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@Siedlerchr Siedlerchr commented Dec 16, 2019

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.

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@bernhard-kleine bernhard-kleine commented Dec 16, 2019

works! Thank you very much.

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