Bibliographic Entry Manager not syncing with Zotero

[D Jacob]

I'm still really new to using Hypernomicon. I got it linked to my Zotero account, and I've associated some Work records with Zotero entries. The problem I'm having is that any entries added to Zotero after the date I originally linked it with Hypernomicon are not showing up in Hypernomicon.

These entries show up in my desktop version of Zotero, and in the web library, so they are synced from my local machine to Zotero online.

When I click on the sync button in the Bibliographic Entry Manager, nothing appears to happen. If I watch really closely, I can see that when I click it the stop button is un-greyed-out for the tiniest moment. But aside from that, I have no reason to think anything is happening when I click it.

I checked in Zotero that the access key is still active. It is, however, the Hypernomicon access key's "last used" date in Zotero is "4 months ago" which is when I originally linked it.

I updated to version 1.30.1 of Hypernomicon, but that has had no effect.

Surely I could unlink and re-link to Zotero, but it appears that would result in me losing all the current Works files associations in Hypernomincon, and that would not be ideal.

Any thoughts on what is going wrong and how to correct it?
Thank you!

[Jason Winning]

Hi,

Sorry to hear that you're having trouble. First, in Hypernomicon, could you please go to Help → About and let me know what it says next to the version number? If it says "Unable to determine latest version", then there could be a connection or firewall issue preventing synching.

If it says "You have the latest version" or "Newer version X available" then something is going wrong during synching; could be a bug with either Hypernomicon or Zotero (both have caused this type of behavior in the past). To get more information to diagnose the problem, please follow these steps:

1. Download and install the latest version (1.30.2 was just released today which has better error logging)
2. Open Hypernomicon and go to Tools → Settings → Settings applying to this computer.
3. Click ... next to the "Log file path" setting to specify a log file (the name and location don't matter).
4. Close the Settings window, open the Bibliographic Entry Manager, and click the sync button (and presumably see the same behavior as before).
5. Go back to Settings. If you click Actions next to "Log file path", there is an option to copy the log file to the clipboard. Do that, and paste the contents of the log into a response in this thread (alternatively you can attach the log file itself to a response in this thread).

Note that if you exit Hypernomicon and start Hypernomicon again, it will clear the error log, so you need to copy it to the clipboard immediately after trying to sync, without restarting Hypernomicon in between.

Hopefully I will be able to tell what's going on from the error log.

Thanks,
Jason

[D Jacob]

Thanks for taking the time to help me with this, Jason!

I updated to 1.30.2 and Hypernomicon is reporting "You have the latest version." Here is the log entry after the failed sync

java.lang.NullPointerException: Cannot invoke "org.hypernomicon.util.json.JsonArray.getObjs()" because "this.creatorsArr" is null
at org.hypernomicon.bib.zotero.ZoteroAuthors.getLists(ZoteroAuthors.java:90)
at org.hypernomicon.bib.zotero.ZoteroItem.authorsChanged(ZoteroItem.java:499)
at org.hypernomicon.bib.zotero.ZoteroItem.isSynced(ZoteroItem.java:462)
at java.base/java.util.function.Predicate.lambda$negate$1(Predicate.java:80)
at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:178)
at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133)
at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1939)
at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509)
at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499)
at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921)
at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682)
at org.hypernomicon.bib.zotero.ZoteroWrapper$1.syncChangedEntriesToServer(ZoteroWrapper.java:552)
at org.hypernomicon.bib.zotero.ZoteroWrapper$1.call(ZoteroWrapper.java:442)
at org.hypernomicon.HyperTask$InnerTask.call(HyperTask.java:89)
at org.hypernomicon.HyperTask$InnerTask.call(HyperTask.java:75)
at javafx.concurrent.Task$TaskCallable.call(Task.java:1399)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
at java.base/java.lang.Thread.run(Thread.java:1583)

[Jason Winning]

I have created a patch that I think should solve your problem. Are you running Hypernomicon in Windows? If so, please follow these instructions:
1. Close Hypernomicon if it is running.
2. Copy the attached file, Hypernomicon.jar, to your Hypernomicon installation directory (it should overwrite an existing file). The default installation directory would be something like C:\Program Files\Hypernomicon
3. Run Hypernomicon, and go to Help → About, and verify that the "Build date" is 2025-04-02
4. Try to sync Zotero again, and post the contents of the log file; hopefully it will be empty this time.
5. Verify that Zotero is now synching properly with Hypernomicon.

Hopefully this will do the trick and I can include this fix in the next release.

Let me know if you use Mac or Linux and I can post a version of the patch file for your OS.

Jason

[D Jacob]

Hi Jason,
Thank you - that did the trick!! (Obviously, yes, I'm on Windows)
The build date showed 2025-04-02, the sync with Zotero worked, and the log had no contents!
I appreciate the help and definitely appreciate all you've done to develop this super-useful software.
Thanks again
-d

[Jason Winning]

Glad to hear it solved your issue! That fix is included in version 1.30.3, which was just released.

Jason