Clicking 'Get fulltext' triggers a 'null pointer exception' when a databse is opened in a current directory.

[sauliusg]

JabRef version JabRef 3.8.2 and JabRef 4.0.0-dev (master commit e7fc94c), running on 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux, LinuxMin 18.1, openjdk version "1.8.0_121", triggers "Null pointer exception" when database is opened in the current directory, with no explicit path.

Steps to reproduce (using stock 'bash' on LinuxMint):

mkdir -p ~/tmp/jabref/pdf; cd ~/tmp/jabref

touch pdf/Feringa1983.pdf

jabref &

# Options|Preferences|File: remove the tick from "Open last edited databases at startup"
4a. Set "Main file directory" to "/home/saulius/tmp/jabref" (replace "saulius" with your login name)

Exit from Jabref

unpack the attached "bibliography.bib" (from the attached "bibliography.zip", contains just one entry) to the working directory;

jabref bibliography.bib

Edit the entry; go to "General"; remove the file; click "Get fulltext"
=> the java.lang.NullPointerException: null is thrown (see the log below)

bibliography.zip

the GUI can be closed normally.

If a database is opened using menus, "File|Open Database|...", the current master works as expected.

An excerpt of the log file here:
saulius@kolibris Feringa/ $ JabRef bibliography.bib &
[3] 16038
saulius@kolibris Feringa/ $ AI: INFO 14-04-2017 22:45, 11: Configuration file has been successfully found as resource
AI: INFO 14-04-2017 22:45, 11: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 14-04-2017 22:45, 11: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: TRACE 14-04-2017 22:45, 11: Using Http Client version 4.3+
AI: INFO 14-04-2017 22:45, 11: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: INFO 14-04-2017 22:45, 11: Configuration file has been successfully found as resource
AI: INFO 14-04-2017 22:45, 11: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 14-04-2017 22:45, 11: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: INFO 14-04-2017 22:45, 11: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: TRACE 14-04-2017 22:45, 23: Telemetry Configuration: instrumentation key 'null' is not in UUID format
AI: TRACE 14-04-2017 22:45, 23: Telemetry Configuration: illegal instrumentation key: null
22:45:30.349 [AWT-EventQueue-0] INFO  org.jabref.logic.importer.OpenDatabase - Opening: bibliography.bib
22:45:30.406 [AWT-EventQueue-0] WARN  org.jabref.JabRefGUI - There seem to be problems with OpenJDK and the default GTK Look&Feel. Using Metal L&F instead. Change to another L&F with caution.
File: grouptree.fxml not found, attempting with camel case
Apr 14, 2017 10:45:31 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
File: grouptree.css not found, attempting with camel case
22:45:37.539 [AWT-EventQueue-0] WARN  org.jabref.gui.date.DatePickerButton - Unable to parse stored date for field 'date' with current settings. Clear button in calender popup will not work.
22:45:42.125 [JabRef CachedThreadPool] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception Occurred in Thread[JabRef CachedThreadPool,6,main]
java.lang.NullPointerException: null
	at org.jabref.model.database.BibDatabaseContext.lambda$getFileDirectories$4(BibDatabaseContext.java:201) ~[JabRef-4.0.0-dev.jar:?]
	at java.util.Optional.ifPresent(Optional.java:159) ~[?:1.8.0_121]
	at org.jabref.model.database.BibDatabaseContext.getFileDirectories(BibDatabaseContext.java:200) ~[JabRef-4.0.0-dev.jar:?]
	at org.jabref.model.database.BibDatabaseContext.getFileDirectories(BibDatabaseContext.java:148) ~[JabRef-4.0.0-dev.jar:?]
	at org.jabref.gui.externalfiles.AutoSetLinks$1.run(AutoSetLinks.java:103) ~[JabRef-4.0.0-dev.jar:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[?:1.8.0_121]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[?:1.8.0_121]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]
AI: TRACE 14-04-2017 22:45, 42: Telemetry Configuration: illegal instrumentation key: null

[sauliusg]

The reason seems to be in the public List getFileDirectories(String fieldName, FileDirectoryPreferences preferences) method (BibDatabaseContext.java:171), line 'String parentDir = dbPath.getParent().toAbsolutePath().toString();' -- when a database is opened as 'bibliography.bib', the dbPath.getParent() is null. Below is the output from my branch ([email protected]:sauliusg/jabref.git, fix-2700-null-pointer-exception-on-Get-fulltext fa84e4e Adding a bunch of debug prints...) with debug prints. I think I can pin down the reason and offer a fix tomorrow... vis.:

saulius@kolibris Feringa/ $ JAVA_OPTS=-ea JabRef bibliography.bib &
[3] 17726
saulius@kolibris Feringa/ $ AI: INFO 14-04-2017 22:53, 11: Configuration file has been successfully found as resource
AI: INFO 14-04-2017 22:53, 11: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 14-04-2017 22:53, 11: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: TRACE 14-04-2017 22:53, 11: Using Http Client version 4.3+
AI: INFO 14-04-2017 22:53, 11: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: INFO 14-04-2017 22:53, 11: Configuration file has been successfully found as resource
AI: INFO 14-04-2017 22:53, 11: 'MaxTelemetryBufferCapacity': null value is replaced with '500'
AI: INFO 14-04-2017 22:53, 11: 'FlushIntervalInSeconds': null value is replaced with '5'
AI: INFO 14-04-2017 22:53, 11: 'Channel.MaxTransmissionStorageCapacityInMB': null value is replaced with '10'
AI: TRACE 14-04-2017 22:53, 23: Telemetry Configuration: instrumentation key 'null' is not in UUID format
AI: TRACE 14-04-2017 22:53, 23: Telemetry Configuration: illegal instrumentation key: null
22:53:04.223 [AWT-EventQueue-0] INFO  org.jabref.logic.importer.OpenDatabase - Opening: bibliography.bib
22:53:04.300 [AWT-EventQueue-0] WARN  org.jabref.JabRefGUI - There seem to be problems with OpenJDK and the default GTK Look&Feel. Using Metal L&F instead. Change to another L&F with caution.
File: grouptree.fxml not found, attempting with camel case
Apr 14, 2017 10:53:05 PM javafx.fxml.FXMLLoader$ValueElement processValue
WARNING: Loading FXML document with JavaFX API of version 8.0.112 by JavaFX runtime of version 8.0.60
File: grouptree.css not found, attempting with camel case
22:53:09.957 [AWT-EventQueue-0] WARN  org.jabref.gui.date.DatePickerButton - Unable to parse stored date for field 'date' with current settings. Clear button in calender popup will not work.
>>> HERE!
EEE>>> dbPath is NOT null: bibliography.bib
22:53:14.596 [JabRef CachedThreadPool] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception Occurred in Thread[JabRef CachedThreadPool,6,main]
java.lang.AssertionError: dbPath.getParent() is null
	at org.jabref.model.database.BibDatabaseContext.lambda$getFileDirectories$4(BibDatabaseContext.java:209) ~[JabRef-4.0.0-dev.jar:?]
	at java.util.Optional.ifPresent(Optional.java:159) ~[?:1.8.0_121]
	at org.jabref.model.database.BibDatabaseContext.getFileDirectories(BibDatabaseContext.java:202) ~[JabRef-4.0.0-dev.jar:?]
	at org.jabref.model.database.BibDatabaseContext.getFileDirectories(BibDatabaseContext.java:148) ~[JabRef-4.0.0-dev.jar:?]
	at org.jabref.gui.externalfiles.AutoSetLinks$1.run(AutoSetLinks.java:103) ~[JabRef-4.0.0-dev.jar:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[?:1.8.0_121]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[?:1.8.0_121]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]
AI: TRACE 14-04-2017 22:53, 42: Telemetry Configuration: illegal instrumentation key: null

[sauliusg]

Was closed by mistake, reopening.