# Problems with Medline fetcher

**URL:** <https://discourse.jabref.org/t/problems-with-medline-fetcher/343>\
**Category:** Help\
**Created:** [November 23, 2016, 10:47am UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343 "2016-11-23T10:47:23Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![GwJO](https://avatars.discourse-cdn.com/v4/letter/g/8e8cbc/32.png) [@GwJO](https://discourse.jabref.org/u/GwJO)\
**Post date:** [November 23, 2016, 10:47am UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/1 "2016-11-23T10:47:23Z")

</div>

Hello,

JabRef is very great, but I have the same issue with MEDLINE. I downloaded the 3.7 version and it doesn’t work, whereas some other searching sites work.  
Thank you for the help

Error is :  
Error while fetching from Medline  
Please try again later…  
unable to get PUBMED IDs

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<div class="post-metadata">

**Author:** ![matthiasgeiger](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.jabref.org/matthiasgeiger/32/7_2.png) [@matthiasgeiger](https://discourse.jabref.org/u/matthiasgeiger)\
**Post date:** [November 23, 2016, 11:47am UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/2 "2016-11-23T11:47:53Z")

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Hi!  
I just tested it locally and it works fine for me.

Can you please check whether the Error Console (accessible using “Help -\> Show error console”) provides some more information?

What was the search term you entered?

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<div class="post-metadata">

**Author:** ![GwJO](https://avatars.discourse-cdn.com/v4/letter/g/8e8cbc/32.png) [@GwJO](https://discourse.jabref.org/u/GwJO)\
**Post date:** [November 23, 2016, 2:06pm UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/3 "2016-11-23T14:06:11Z")

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I tried very large search, like : skin ultrasound oct imaging  
and also very precised one like PMID number : 23189155.  
Could it be that the delay is too long and it stops the connection ?

The error is :

```auto
15:05:04.810 [JabRef CachedThreadPool] ERROR net.sf.jabref.gui.importer.fetcher.SearchBasedEntryFetcher - Error while fetching from Medline
net.sf.jabref.logic.importer.FetcherException: Unable to get PubMed IDs
	at net.sf.jabref.logic.importer.fetcher.MedlineFetcher.getPubMedIdsFromQuery(MedlineFetcher.java:114) ~[JabRef-3.7.jar:?]
	at net.sf.jabref.logic.importer.fetcher.MedlineFetcher.performSearch(MedlineFetcher.java:162) ~[JabRef-3.7.jar:?]
	at net.sf.jabref.gui.importer.fetcher.SearchBasedEntryFetcher.processQuery(SearchBasedEntryFetcher.java:37) ~[JabRef-3.7.jar:?]
	at net.sf.jabref.gui.importer.fetcher.GeneralFetcher.lambda$actionPerformed$5(GeneralFetcher.java:217) ~[JabRef-3.7.jar:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [?:1.8.0_77]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [?:1.8.0_77]
	at java.lang.Thread.run(Unknown Source) [?:1.8.0_77]
Caused by: java.net.ConnectException: Connection timed out: connect
	at java.net.DualStackPlainSocketImpl.connect0(Native Method) ~[?:1.8.0_77]
	at java.net.DualStackPlainSocketImpl.socketConnect(Unknown Source) ~[?:1.8.0_77]
	at java.net.AbstractPlainSocketImpl.doConnect(Unknown Source) ~[?:1.8.0_77]
	at java.net.AbstractPlainSocketImpl.connectToAddress(Unknown Source) ~[?:1.8.0_77]
	at java.net.AbstractPlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_77]
	at java.net.PlainSocketImpl.connect(Unknown Source) ~[?:1.8.0_77]
	at java.net.SocksSocketImpl.connect(Unknown Source) ~[?:1.8.0_77]
	at java.net.Socket.connect(Unknown Source) ~[?:1.8.0_77]
	at sun.security.ssl.SSLSocketImpl.connect(Unknown Source) ~[?:1.8.0_77]
	at sun.security.ssl.BaseSSLSocketImpl.connect(Unknown Source) ~[?:1.8.0_77]
	at sun.net.NetworkClient.doConnect(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.http.HttpClient.openServer(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.http.HttpClient.openServer(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.https.HttpsClient.<init>(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.https.HttpsClient.New(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) ~[?:1.8.0_77]
	at sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(Unknown Source) ~[?:1.8.0_77]
	at java.net.URL.openStream(Unknown Source) ~[?:1.8.0_77]
	at net.sf.jabref.logic.importer.fetcher.MedlineFetcher.getPubMedIdsFromQuery(MedlineFetcher.java:76) ~[JabRef-3.7.jar:?]
	... 6 more

```

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<div class="post-metadata">

**Author:** ![matthiasgeiger](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.jabref.org/matthiasgeiger/32/7_2.png) [@matthiasgeiger](https://discourse.jabref.org/u/matthiasgeiger)\
**Post date:** [November 23, 2016, 2:37pm UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/4 "2016-11-23T14:37:49Z")

</div>

Hmm…

Both of your queries work for me.  
The error `java.net.ConnectException: Connection timed out: connect` either indicates that the accessed server is down (which is at least at the moment not the case) or that the connection is somehow blocked - most likely by a firewall.

You have already tested other web searches within JabRef? E.g., Google Scholar or Springer? And they are working?

Can you please check whether you can directly access the URL [https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&sort=relevance&retmax=50&term=skin+ultrasound+oct+imaging](https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&sort=relevance&retmax=50&term=skin+ultrasound+oct+imaging) in your browser. Does this work? (an XML-Dokument is loaded beginning with `<eSearchResult><Count>221</Count><RetMax>50</RetMax><RetStart>0</RetStart><IdList> ...`)

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<div class="post-metadata">

**Author:** ![GwJO](https://avatars.discourse-cdn.com/v4/letter/g/8e8cbc/32.png) [@GwJO](https://discourse.jabref.org/u/GwJO)\
**Post date:** [November 23, 2016, 3:08pm UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/5 "2016-11-23T15:08:46Z")

</div>

Not all the search data base work, CiteSeerX works quickly and only for simple search.

The direct search of the URL seems to work :  
It sends :

\<?xml version="1.0" encoding="UTF-8"?\>

-

221

50

0

-

22766121

19566334

20202160

25253828  
…

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<div class="post-metadata">

**Author:** ![matthiasgeiger](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.jabref.org/matthiasgeiger/32/7_2.png) [@matthiasgeiger](https://discourse.jabref.org/u/matthiasgeiger)\
**Post date:** [November 24, 2016, 8:28am UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/6 "2016-11-24T08:28:19Z")

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Okay. Then I can’t really help you, as a) JabRef is generally not blocked and b) the medline URL is not generally blocked and medline is up and running I don’t really understand what is wrong here. 😟

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<div class="post-metadata">

**Author:** ![GwJO](https://avatars.discourse-cdn.com/v4/letter/g/8e8cbc/32.png) [@GwJO](https://discourse.jabref.org/u/GwJO)\
**Post date:** [November 25, 2016, 1:10pm UTC](https://discourse.jabref.org/t/problems-with-medline-fetcher/343/7 "2016-11-25T13:10:58Z")

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Thanks for helping. Just eventually, would it possible that Jabref tries a longer time to stay connected?