Hypernomicon beginner

[Cristina Andreea]

Hello Hypernomicon Community,

I just installed this awesome software last night and I already started arranging all my resources/topics of interest in a nice structure. I created the database folder in the Mega cloud folder on my computer. I also managed to sync my Zotero so I went to bed pretty excited by my work. But this morning when I opened Hypernomicon there was nothing there, except for my Zotero database. I tried to upload the database.hdb file from the database folder when asked to open an existing database, but everything is still empty. I have re-watched all the tutorials and can't actually realize what I did wrong. Did I actually lose all my work?

Could anyone help?

Thanx!

[Jason Winning]

Hi Cristina,

I'm sorry to hear about that. Using Hypernomicon version 1.24.3, I just tried to recreate your workflow. I created a Mega account, downloaded the desktop application, and synched to a folder on my computer. I then created a database in that folder, created some debate, position, argument, and note records, and then synched to a Zotero database. I then created some Hypernomicon work records from the Zotero entries, and exited Hypernomicon. I was then able to open Hypernomicon, and my records were still there. I am using Windows 10; please let me know if anything was different (Hypernomicon version, OS, etc.) from what you did. It might help if you send a screenshot of what it shows when you go to Help -> About (and General tab of the About menu).

Some questions to clarify. If there was no Hypernomicon database at all (like all the files in your database folder were somehow deleted), then when you start Hypernomicon, it should show a Welcome window with buttons to "Start a new database", etc. Is that what you saw? Or did it at least recognize an existing database (maybe an empty one missing the records you created) and load it, in which case the "Save to XML" button is activated, etc.? In that case, the problem would be not that the database itself no longer exists, but possibly that some records you created no longer exist. If you can load the database at least (but records are missing), what do you see when you go to the Tree tab? Can you go to the other tabs and confirm that they each list no more than 1 existing record (i.e., it says "1 of 1" in the Record field at the bottom)? Also, was Hypernomicon still synched to Zotero (so that the Bib Mgr button is activated)? If you created folders and/or moved outside files under the database folder, are those still there? If you were successfully able to sync to Zotero, then it should have saved the database at least once (it always saves when synching to your reference manager) so the problem shouldn't be that it never saved anything to the XML files.

Unfortunately I don't have any experience with Mega but I would expect it to work reliably for something like Hypernomicon that is mostly just saving/modifying a bunch of XML files. Another possibility could be some kind of conflict resolution that happened if you downloaded the Mega desktop application to multiple computers, and Mega got confused and thought the computer without your newest changes had the most recent version of files. But you didn't mention anything about synching on multiple computers. I have also see issues with desktop synching applications (I remember Dropbox, and maybe Google Drive years ago) not synching properly if you shut down your computer while it is in the middle of synching, so it is important not to do that. If you had files or folders deleted that were under the Hypernomicon folder, I've never encountered anything like that and I don't know of any way that can possibly happen unless something went wrong with the Mega synching like I suggested. Saving/exiting Hypernomicon never affects any files except the ones in the XML folder.

[Jason Winning]

Another thing to add is that I also recommend people to use something like Dropbox (or Mega, etc.) because they often have the ability to restore previous versions. I just noticed that file versioning was on by default in the Mega account I just created. Assuming it is the same for you, you should be able to restore the XML files (all the files in the XML folder; also the Bib.json file which is for Zotero) as they were when you saved them last night; you will know because the previous version file sizes will be larger. See this on the Mega website and this reddit thread.

You may need to restore each file individually. It looks like Mega, unlike Dropbox, cannot restore previous versions of an entire folder at once.

[Cristina Andreea]

Hi Jason,

Thank you for the very detailed answer, I really appreciate it. When I open Hypernomicon it recognizes an existing database, but an empty one missing the records I created - the "Save to XML" button is activated. There are no records in none of the tabs. Weirdly enough, it is still linked with Zotero, I have all the bibliography there. Also, I didn't sync on multiple computers, so that shouldn't be a problem.

Most probably it is a sync problem, the thing is that I don't know how to restore the XML files. Whenever I try to restore the Poistions.xml file, I get the message> What file should be imported as? and I only get the Work, Misc and Bib. details options. And when I click on one of them, I get an error message.

[Jason Winning]

Restoring the files has to be done when you are logged into Mega on a web browser (see the links in my last post). It shouldn't be done when Hypernomicon is open. You need to log into Mega in a web browser and navigate to the XML folder directly under your database folder. Then you will see the XML files and Bib.json file. It should look like the attached picture. Then you can right-click each file, choose "Previous versions", and choose the version to restore to. Or you can click the 3 dots that appear when you select one of the files and choose "Previous versions". Then select the version you want to go back to and choose the "Revert" option. The date/time for each file when you are restoring should be the same; otherwise there could be data corruption. Look for the date/time that has the largest file size. Once you've reverted all the files and it is synched to your computer, you should just be able to open Hypernomicon and the records will hopefully be there.

[Jason Winning]

One other thing. I think I mentioned this in the Introductory tutorial but the changes you make in Hypernomicon are not permanent until you do one of two things:
1. Click "Save to XML"
2. Exit the application
If you make changes in Hypernomicon, and then shut down your computer without exiting Hypernomiconor or clicking "Save to XML" first, the changes will be lost. I wonder if that is what happened in your case.

Actually, this would explain why it is linked to Zotero but there are no records. When you first created the database, I assume you immediately linked to Zotero, and the database saved to XML as part of that process. If you then created a bunch of records but then shut down your computer without saving/exiting, then the result would be what you're seeing. Unfortunately in that scenario you won't be able to restore the files because your changes were never saved. There will likely only be 2 versions of the XML files: before and after synching to Zotero.

Nobody has asked for this yet but maybe it is time to implement a feature to autosave a backup version of the database every few minutes. A feature like that would prevent the scenerio of losing data when a shutdown occurs without saving.