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.
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
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…
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.
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:
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
@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.
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?
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.
Hi all, it seems this topic was solved for all those who started it. For me it is the other way round. I normally did not have problems with the DOI import for the last years. However, since some weeks (maybe some month) I cannot any longer do the DOI import and get the same error as mentioned here: “Error while fetching from DOI. Connection error.”
I also work in an institute behind a firewall. But, as I said this never made problems - with the proxy settings in the preferences. I also can do an ArXiv import, showing that it should not be the problem of reaching the www. I was running JabRev 5.0 for the last month, where I started to experience this problem. But it also exists after updating to 5.2.
All the best and thanks for ideas.
Hi all,
which URL have to be reachable for using the DOI import feature? So, in the idea which URL should be white-listed to exclude internet access issues?
Thank you for your reply. I could only have to Links in the questions, so as I reduced to 2, I am afraid that the plot got lost.
Basically I have to use JabRef behind a Firewall, where all internet access is blocked - but there is the possibility to set specific addresses on a whitelist by the IT. My question is, which addresses this would be to successfully use the DOI feature?
@arne2210
I am not sure whether I understand your question correctly or not: lets say that you want to refer this paper “Observation of Gravitational Waves from a Binary Black Hole Merger B. P. Abbott et al. (LIGO Scientific Collaboration and Virgo Collaboration), Phys. Rev. Lett. 116, 061102”. This is located in the link
Now you copy this link. Go to Jabref panel named “File” —> “New Library” —> “New Bibtex library”.
Then again go to —> “New Entry” in “Library” panel of Jabref. This will open a dialogue box “Select Entry type” —> In the “ID type”, select “DOI” and paste the copied link in “ID”
Alternatively, you may paste “10.1103/PhysRevLett.116.061102” this alone.
In almost all the cases DOI will something looks like “10.1234/******” (to my best knowledge)
JabRef queries doi.org with Accept:Application/x-bibtex header to get the bibtex information. Mostly this works. However, sometimes this query does not return anything or it redirects to the publisher site.
In addition, if the DOI is issued by the Medra (Some DOI provider) then it will query medra.org.
Some universities or institutions use a custom DOI resolver. In the latest dev version we added the option to specify a custom DOI resolution which can be used as bse.
