Lookup DOI (sometimes) freezes JabRef #2680

stefan-kolb · 2017-03-23T09:45:59Z

New in 4.0 Development version!

stefan-kolb · 2017-03-23T09:47:39Z

Maybe related to #2442 or #2645?

stefan-kolb · 2017-03-23T10:00:49Z

stefan-kolb · 2017-03-23T10:15:41Z

Looks like it has something to do with this code

    default Optional<T> findIdentifier(BibEntry entry) throws FetcherException {
        Objects.requireNonNull(entry);

        try (InputStream stream = new BufferedInputStream(getURLForEntry(entry).openStream())) {
            List<BibEntry> fetchedEntries = getParser().parseEntries(stream);

            if (fetchedEntries.isEmpty()) {
                return Optional.empty();
            }

            // Post-cleanup
            fetchedEntries.forEach(this::doPostCleanup);

            return extractIdentifier(entry, fetchedEntries);
        } catch (URISyntaxException e) {
            throw new FetcherException("Search URI is malformed", e);
        } catch (FileNotFoundException e) {
            LOGGER.debug("Id not found");
            return Optional.empty();
        } catch (IOException e) {
            // TODO: Catch HTTP Response 401 errors and report that user has no rights to access resource
            // TODO catch 503 service unavailable and alert user
            throw new FetcherException("An I/O exception occurred", e);
        } catch (ParseException e) {
            throw new FetcherException("An internal parser error occurred", e);
        }
    }

If the service is unavailable a 503 occurs and a fetcher exception is thrown.
In the course of this JabRef freezes.

stefan-kolb · 2017-03-23T10:20:45Z

After catching this error:

        doiButton.addActionListener(actionEvent -> {
            try {
                Optional<DOI> doi = WebFetchers.getIdFetcherForIdentifier(DOI.class).findIdentifier(entryEditor.getEntry());
                if (doi.isPresent()) {
                    entryEditor.getEntry().setField(FieldName.DOI, doi.get().getDOI());
                } else {
                    panel.frame().setStatus(Localization.lang("No %0 found", FieldName.getDisplayName(FieldName.DOI)));
                }
            } catch (FetcherException e) {
                LOGGER.error("Problem fetching DOI", e);
            }
        });

JabRef freezes.

stefan-kolb · 2017-03-23T12:12:06Z

Ok, we got a few problems:

Lookup DOI action for the button is not in a separate thread (ugly but present long time ago)
GUI freezes when exception from above is catched. Maybe related to the start inside the FX thread 9b28d36. Also @lynyus reported that the whole GUI stopped working for him, so maybe this also triggers the freeze problem here and we need to fix the sart in FX thread method somehow.
Error in CrossRef (500): Maybe we should report this on CrossRef's Github repo. This happens randomly!
http://api.crossref.org/works?query.title=A+break+in+the+clouds%3A+towards+a+cloud+definition&rows=20&offset=0 ->

{"status":"error","message-type":"exception","message-version":"1.0.0","message":{"name":"class java.lang.RuntimeException","description":"java.lang.RuntimeException: Solr returned a partial result set","message":"Solr returned a partial result set","cause":null}}

Error in Crossref 503 & 504
maybe log to the console and in the status bar for the user that the service is unavailable.

stefan-kolb · 2017-03-23T12:47:35Z

With reverted log addition in FX thread:
Infinite loop?!

Opening: C:\Users\stfn\Desktop\Vorlesungen\Promotion\Paper\master.bib
Opening: C:\Users\stfn\Downloads\01 - TEMP\test.bib
Problem fetching DOI
org.jabref.logic.importer.FetcherException: An I/O exception occurred
	at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:92)
	at org.jabref.gui.entryeditor.FieldExtraComponents.lambda$getDoiExtraComponent$3(FieldExtraComponents.java:186)
	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
	at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
	at java.awt.Component.processMouseEvent(Unknown Source)
	at javax.swing.JComponent.processMouseEvent(Unknown Source)
	at java.awt.Component.processEvent(Unknown Source)
	at java.awt.Container.processEvent(Unknown Source)
	at java.awt.Component.dispatchEventImpl(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
	at java.awt.Container.dispatchEventImpl(Unknown Source)
	at java.awt.Window.dispatchEventImpl(Unknown Source)
	at java.awt.Component.dispatchEvent(Unknown Source)
	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
	at java.awt.EventQueue.access$500(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.awt.EventQueue$3.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.awt.EventQueue$4.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
	at java.awt.EventQueue.dispatchEvent(Unknown Source)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
	at java.awt.EventDispatchThread.run(Unknown Source)
Caused by: java.io.IOException: Server returned HTTP response code: 500 for URL: http://api.crossref.org/works?query.title=A+break+in+the+clouds%3A+towards+a+cloud+definition&query.author=Vaquero%2C+Luis+M+and+Rodero-Merino%2C+Luis+and+Caceres%2C+Juan+and+Lindner%2C+Maik&filter=from-pub-date%3A2008&rows=20&offset=0
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.URL.openStream(Unknown Source)
	at org.jabref.logic.importer.IdParserFetcher.findIdentifier(IdParserFetcher.java:74)
	... 37 more

No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().

stefan-kolb · 2017-03-23T13:02:42Z

Also happens for get BibTeX data from DOI:

Could not copy input
java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:152)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:169)
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:55)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:47)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:22)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.HttpURLConnection.getResponseCode(Unknown Source)
	at org.jabref.logic.net.URLDownload.openConnection(URLDownload.java:297)
	... 11 more

Info cannot be found
org.jabref.logic.importer.FetcherException: Invalid URL
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:65)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:47)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:22)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:152)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:169)
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:55)
	... 8 more
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.HttpURLConnection.getResponseCode(Unknown Source)
	at org.jabref.logic.net.URLDownload.openConnection(URLDownload.java:297)
	... 11 more

Could not copy input
java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:152)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:169)
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:55)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:47)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:22)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.HttpURLConnection.getResponseCode(Unknown Source)
	at org.jabref.logic.net.URLDownload.openConnection(URLDownload.java:297)
	... 11 more

Info cannot be found
org.jabref.logic.importer.FetcherException: Invalid URL
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:65)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:47)
	at org.jabref.gui.mergeentries.FetchAndMergeWorker.doInBackground(FetchAndMergeWorker.java:22)
	at javax.swing.SwingWorker$1.call(Unknown Source)
	at java.util.concurrent.FutureTask.run(Unknown Source)
	at javax.swing.SwingWorker.run(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.lang.Thread.run(Unknown Source)
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection$10.run(Unknown Source)
	at java.security.AccessController.doPrivileged(Native Method)
	at sun.net.www.protocol.http.HttpURLConnection.getChainedException(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:152)
	at org.jabref.logic.net.URLDownload.asString(URLDownload.java:169)
	at org.jabref.logic.importer.fetcher.DoiFetcher.performSearchById(DoiFetcher.java:55)
	... 8 more
Caused by: java.io.IOException: Server returned HTTP response code: 503 for URL: http://data.crossref.org/10.1145%2F1496091.1496100
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
	at java.net.HttpURLConnection.getResponseCode(Unknown Source)
	at org.jabref.logic.net.URLDownload.openConnection(URLDownload.java:297)
	... 11 more

No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().
No localized message exception message defined. Falling back to getMessage().

…t freezing

tobiasdiez · 2017-03-24T09:54:33Z

Closed as the other DOI related problems are tracked at #2682.

* upstream/master: Localization: General: French: Translation of new entries Localization: Menu: French: Translation of an entry (#2685) Fix #2680 and fix #2667: Swing errors are catched properly and without freezing (#2681) Do not log AND throw Replace misleading error message for fetcher connection error Document CrossRef test Fix subtitle detection for CrossRef fetcher Revert "Invoke LogMessages.add in JavaFX thread" Use global user agent Update mockito from 2.7.17 to 2.7.18 Move GuiAppender to GUI package Invoke LogMessages.add in JavaFX thread [WIP] Put the PDFAnnotationImporter under Test, enhance FileAnnotationTab (#2640) Fix for "Paying off technical debt: almost all utility classes have a private constructor now." (#2672) Revert "Paying off technical debt: almost all utility classes have a private constructor now. (#2649)" (#2670) Paying off technical debt: almost all utility classes have a private constructor now. (#2649) Changed codeformatting for better fxml annotation (#2668) Disalbe Google Scholar tests on all CI environments (#2654) Fix JSONException in Crossref fetcher as mentioned in #2442

stefan-kolb added the bug Confirmed bugs or reports that are very likely to be bugs label Mar 23, 2017

stefan-kolb changed the title ~~Lookup DOI sometimes freezes JabRef~~ Lookup DOI (sometimes) freezes JabRef Mar 23, 2017

stefan-kolb added this to the v4.0 milestone Mar 23, 2017

tobiasdiez added a commit that referenced this issue Mar 23, 2017

Fix #2680 and fix #2667: Swing errors are catched properly and withou…

ee2afd9

…t freezing

tobiasdiez mentioned this issue Mar 23, 2017

Fix #2680 and fix #2667: Swing errors are catched properly and without freezing #2681

Merged

6 tasks

This was referenced Mar 23, 2017

Bibtex code errors freeze JabRef #2678

Closed

Look up DOI improvements #2682

Closed

tobiasdiez closed this as completed in 2c7ea60 Mar 24, 2017

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Lookup DOI (sometimes) freezes JabRef #2680

Lookup DOI (sometimes) freezes JabRef #2680

stefan-kolb commented Mar 23, 2017

stefan-kolb commented Mar 23, 2017 •

edited

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stefan-kolb commented Mar 23, 2017

stefan-kolb commented Mar 23, 2017

stefan-kolb commented Mar 23, 2017 •

edited

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stefan-kolb commented Mar 23, 2017

stefan-kolb commented Mar 23, 2017

tobiasdiez commented Mar 24, 2017

Lookup DOI (sometimes) freezes JabRef #2680

Lookup DOI (sometimes) freezes JabRef #2680

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edited

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edited

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