I now have two Zotero directories

cjpoor

I recently had to repair my database. It seems that afterwards Zotero pointed to the default data directory and perhaps switched off sync. Unfortunately I didn't notice this for over a week. Now I have two different Zotero directories: The default one with the (somewhat complete) sqlite file and the custom one with about 1,000 more items in storage (but last modified on 25th Feb - the same as the web library - and with a much smaller sqlite - 5.1 MB versus 1.8 GB). The problem is that, over the last week, I have added very many items and annotated many too. Is there some way I can merge the data directories without overwriting the annotated files etc?

So - I think the database in the default location is probably complete and up to date. I think I just need to merge the storage directories.
Should I use the linux command

cp -a -u "custom storage directory" "default storage directory"
and to be sure also run
cp -a -u "default storage directory" "custom storage directory"

I am using Zotero 6 on Linux Mint.

adamsmith

You shouldn't need the -a flag (but it won't hurt, either) but otherwise that should work.

Alternatively, you could make sure the current directory is fully synced, then point back at the custom one and sync there.

dstillman

@cjpoor: While it might not make a difference here, this is a job for rsync, not cp:

rsync -a custom_storage_dir/ default_storage_dir/

(Note the trailing slashes.)

cjpoor

Although quite a few pdfs are missing from both directories

Most of the files missing from default directory are:

.zotero-ft-unprocessed (there are over 4k in cust. dir. but only 10 in default dir.)
and
detail.htm (these seem to be snapshots so I guess they can't do any harm)

Most of those missing from custom directory are:

.zotero-ft-cache

Should I exclude these files when using rsync with --exclude '.zotero-ft-unprocessed'?

Perhaps
"Alternatively, you could make sure the current directory is fully synced, then point back at the custom one and sync there."
Will avoid the dilemma.