Error while fetching from DOI

Help
#1

I am facing an issue in Jabref.

Usually I used to add bib entries by just pasting DOI, like e.g. 10.1029/2017GL076880 . When I do now, I am getting error “Error while fetching from DOI. Connection error”. So, now I go to the article site/google scholar and copy the bib entry. As you might be aware this is a tedious one.

One thing I notices is that if you click the icon in the black box as shown in the screenshot, it takes me to the article file. But if I paste the doi, it is giving me the error.

Jabref
Jabref1920×1080 191 KB

I am not sure this information will be useful or not. If I click the red box, I am getting message “Unhandled exception occured.”
“An I/O exception occured”
“The exception stacktrace was:”

org.jabref.logic.importer.FetcherException: An I/O exception occurred
at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:93)
at org.jabref.gui.fieldeditors.IdentifierEditorViewModel.lambda$lookupIdentifier$3(IdentifierEditorViewModel.java:96)
at org.jabref.gui.util.BackgroundTask$1.call(BackgroundTask.java:39)
at org.jabref.gui.util.DefaultTaskExecutor$1.call(DefaultTaskExecutor.java:98)
at javafx.concurrent.Task$TaskCallable.call(Task.java:1423)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
Caused by: java.net.ConnectException: Connection timed out: connect
at java.net.DualStackPlainSocketImpl.connect0(Native Method)
at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source)
at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source)
at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source)
at java.net.AbstractPlainSocketImpl.connect(Unknown Source)
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.security.ssl.SSLSocketImpl.connect(Unknown Source)
at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.(Unknown Source)
at sun.net.www.protocol.https.HttpsClient.New(Unknown Source)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source)
at java.net.URL.openStream(Unknown Source)
at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:74)
… 10

Jabref details:

JabRef 4.3.1

Windows 10 10.0 amd64

Java 1.8.0_172

#2

Hi,

this issue should be fixed int eh 5.0 Release:

Please make a backup of your library before trying out the new versions.

Regards

#3

Thanks you for the reply. But I am getting the same message even if i installed the latest version. See the screenshot:

Jabref
Jabref2508×799 176 KB

The black one is Jabref 4.3, the red one is the latest one.

Another thing which i noticed is that while installing Jabref 5, it did not ask to create a start folder in start menu and hence I cannot search it in the start menu. Why is it behaving in this fashion? Am I doing anything wrong?
Thanks in advance…

#4

Works fine for me in the latest master version. Maybe a temporary issue.

Regarding the installer, I noticed that as well.
The reason is that with version 5 we switched to the new jpackage tool for creating native installers. We probably need to add that options somewhere in our installer template.

Regards

#5

The issue with the missing startmenu entry is fixed in the latest master:
https://builds.jabref.org/master/

#6

Thank you.

Thanks again for looking into this issue. I think, as i am using windows I have to download “JabRef-5.1-portable_windows.zip” file. I did so and when I extracted it shows many files:

Jabref
Jabref1636×941 306 KB

Still I did not find Jabref in start now also.

#7

@sreerajt90 For Windows installer, you need to use the JabRef-5.1.msi file

#8

Thanks one again. It worked, though it is not making any start menu folder, at-least it can be searched in start menu.
It is not seen @ https://www.fosshub.com/JabRef.html. So, is this a developer version? If yes, I hope in the next release this will be included- including creating folder in start menu, as in Jabref-4.3

1 Like
#9

@sreerajt90 Yes, you are right, this is the current development version which will become the new release version 5.1. (We don’t have a plan for release of 5.1 yet)
We will see if it will be possible to create a StartMenu folder as well. Maybe needs some additional tweaks. Thanks for reporting back.

Regards

1 Like
#10

Hello, I’m new here and I have the same problem.

I installed Jabref 5.1 (Version windows) and everything works fine. The only thing that does not work is the reference import via doi and the search option. Could it be, that the problem is a firewall? I am working at the university.

Can anyone help me, what for settings could resolve this problem?

Thanks a lot.

Christoph

#11

You are right: it may be the problem with the firewall. In my case, some settings done in wifi was creating this issue. I figured out very lately. Change the network and check it.

#12

Good morning sreerajt90,

thanks a lot for your support. I will ask the IT-administration. I hope it will than works fine.

#13

Yeah, with wifi it works brilliant. Both, the search option and the data import via doi, pubmendID etc.

Thanks.

#14

Pleasure to help… :smile: