Mendeley Import errors ( Report ID 1926998487 )

fschuman
Hi,

i'm trying to import a Mendeley 1.18 database (last backup before updating to Mendeley 1.19) into Zotero. However it returns the errors under the above ID.


What I observed:

- a folder with many subfolders is missing from the import. Unfortunately, this is my 'projects' folder, crucial too my work, as it sorts relevant literature to projects.

- despite missing foldres, the entries/papers themselves seem to have been imported. The total number entries in Zotero that were imported from Mendeley is just 4 entries smaller than the entries in Mendeley.

- there have been a number of 'crashes' of Zotero at import when linked PDFs could not be read. Zotero asked for what action to do with the item (save, open in preview, etc.), but when doing that, Zotero stopped importing. The work around was do delete the broken PDFs in Mendeley's literature folder and start the import again.



Steps to reproduce:

- just import my Mendeley database into a new collection in Zotero. It will stop with the errors in the Report ID above.



Cheers,
Frank

  • dstillman
    - a folder with many subfolders is missing from the import. Unfortunately, this is my 'projects' folder, crucial too my work, as it sorts relevant literature to projects.
    But other folders did come through? Is there anything special about that folder in Mendeley? If you move it below another folder in Mendeley and run the importer again, does that help? (It shouldn't duplicate anything you've already imported.)
    there have been a number of 'crashes' of Zotero at import when linked PDFs could not be read. Zotero asked for what action to do with the item (save, open in preview, etc.), but when doing that, Zotero stopped importing. The work around was do delete the broken PDFs in Mendeley's literature folder and start the import again
    Did that occur with Zotero 5.0.52, or with an earlier version? This was occurring for invalid PDFs from Mendeley, but we fixed at least one cause of the hang in 5.0.52. (You'd still get the open/save popups for now, but you can cancel those.)
    [JavaScript Error: "Error(s) encountered during statement execution: Tag cannot be blank [QUERY: INSERT INTO tags (tagID, name) VALUES (?, ?)] [PARAMS: 26699, ] [ERROR: Tag cannot be blank]" {file: "chrome://zotero/content/xpcom/db.js" line: 721}]
    I'm not sure if this was during the import, but the latest Zotero beta should skip blank tags from the Mendeley database during the import. You can install that and try the import again to see if it saves additional items.
  • fschuman
    Yes, all other folders came through. Unfortunately, I've updated Mendeley to 1.19, so I can't move the folder and import again from 1.19. I could revert to 1.18 and try to re-store the last backup, and move the folder there. But didn't so far as I don't' want to loose the whole folder in the process. (It's the most important folder unfortunately).

    Yes, Zotero 5.0.52. Canceling the window didn't avoid the hang, that I've tried.

    I'll give the beta a try and import again.

  • fschuman
    This missing folder problem seems difficult. On installing Mendeley 1.18, I discovered that the restored backup doesn't preserve local links to the PDFs, but wants to download PDFs from the server. Then individuals BibText exports for each folder/subfolder are the only option, I suppose?

    The new beta version did skip blank tags during import. Thanks!
  • dstillman
    The restored 1.18 backup should have links to files — that's just a copy of your local database, which includes file links in the Files table.

    If you just reinstall 1.18 and sync to pull down data (or don't put the database in the proper place and it syncs down instead), it'll only include file links for files you synced to the server, since Mendeley (unlike Zotero) doesn't sync any attachment metadata unless you sync the actual files.

    Regardless, if you don't mind uploading the backup 1.18 database to the Zotero DB Repair Tool and you provide the Upload ID, we should be able to figure out what's going on with the main folder and fix the import. Not having the attachments wouldn't matter in that case, since they're already imported. (The repair tool won't do anything useful, so you can ignore the download link — it's just a way for you to securely upload the DB for us to inspect the folder tables. Alternatively, if you're comfortable using an SQLite browsing tool, we'd just be interested in the contents of the Folders, DocumentFolders, and RemoteFolders tables, which you could export to some format and send to support@zotero.org with a link to this thread.)

    If you export each folder and import those, you'll get duplicates for any items that exist in more than one, so you really don't want to do that.
  • fschuman
    edited June 27, 2018
    A fresh download of version 1.18 has a deprecated settings menu and will pull down from the server no matter what. As I don't have any PDFs synced, that route won't work for me. (Worse - Mendeley doesn't upload any PDFs that are modified with annotations outside of Mendeley after import)

    I've uploaded the v.1.18 database, Upload ID: 5b32a28d5af1b
    The missing folder is named "! Projects".
  • dstillman
    OK, so for some reason in your database that folder has a 'parentID' of 0, but all other top-level folders we've seen have a 'parentID' of -1. I assume that's a Mendeley bug, and we can work around it easily, but I wanted to confirm first that that is indeed a top-level folder and there's no difference from other top-level folders in your database that you're aware of.
  • dstillman
    edited June 27, 2018
    I've pushed out a new beta that should import that folder. If you're still on the beta, you can update via Help → "Check for Updates…".

    If there's something different about it, you should still let us know so that we can have the import reflect that, but this should let you get it into Zotero regardless.
  • fschuman
    Thanks so much. I've started the import again and the folder structure is imported now! (There's nothing else different about this folder that I'm aware of).
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