How to export indexed database

Hello everyone! Here’s my very first question…

Although I have the licence for some years, I’m only starting just now to actually use it; because I didn’t know what to do with it, or how to do something I wanted to do with it. Now that I’ve learned and implemented the wonderful ways of GTD with OmniFocus, I also reopened the case with DT.

Here’s my case…

I have a huge archive, with lots of organised and unorganised folder structures, collected from various drives I have been using since the beginning of time. I want to use DT to organise them.

At the moment, I don’t have enough empty storage space to import all these to DT’s own library. I can only index them now, organise the structure, and hope to be able to export that structure as a real file/folder structure output to a new hard drive I’ll get in the future. Is that possible? I know that it’s not possible to sync an indexed database (DT can only sync indexed databases one way: actual files to its index, whereas I need the exact opposite kind of syncing). I was wondering if it is possible to export an indexed and organised structure later to an external space.

Thank you.

PS: I’ll also very much appreciate if anyone can point me to a good place to see helpful tutorials, as I haven’t seen any helpful ones by simply googling.

The way I read this is that you have a structure of folders in your filesystem, that you want to index that structure in DEVONthink, then move the documents around in a new, improved set of groups, and then export that new structure onto a different drive. Your existing folder and document structure on your drive is to remain unchanged throughout. Is that the scenario?

If my description of the steps you want to is correct, it’s a workable scenario. Try it on a small scale, say with one or two folders, and you’ll see in practice how it goes. If while reorganizing the structure in DEVONthink you delete something, but don’t want to delete the original in your filesystem, then be careful when emptying the trash to use the “only in database” option so that you don’t inadvertently destroy a file you really want to keep.

Thanks for the help.

So, I can just index my folders, reorganise them, and then when I export them, DT will make a copy of the whole reorganised database to another place I desire? Index, organise, export… Right?

Is there another way? I wouldn’t mind if it just reorganised my existing folders in where they are now; without creating a new database. I would actually prefer that option. In the end, I would like to have all my reference files organised and kept under DT’s own library. If I had the available space, I would do that. However, I don’t want to wait until I get another hard drive.

Then perhaps the easier way is to index your existing folder(s). After they are indexed, used the “Move Into Database” command. At that point, the files all exist in DT’s own library and no longer exist in their external location – so you have only a minimal increase in disk space used - for some overhead files that DT creates in the database. After moving into the database, you can rearrange and will not need to export to a new drive.


once imported how might these files be exported again for indexing, say after moving to a new computer? My more detailed senario is ( … -indexing/) :

I am in the process of moving to a new Mac. I use an indexed folder for my 3 GB pdf library that lives my reference manager (currently Zotero but it might be Papers, Sente, Bookends, ReadCube, etc). My question is what’s the best way to make the DT database and indexed library portable for migration? I’m looking for a method short of cloning the system, which is not an option because I want to start with a fresh install. In addition would like to move the indexed folder back out of the database in the new setup since I my library changes over time. Another point is that Zotero renames the library folder on a fresh install, so the index link breaks in the process. This tip offers some advice about how to backup up the database, but does not discuss unpacking to a new computer: … -database/

Peter, how integrated with other documents are the files that are indexed in DEVONthink? Do you have other documents in the database that link to those indexed documents, lots of tags, flags, or anything else that would be broken if the index links were severed?

Actually yes, I have used a notes script to link annotations living inside DTP to the ref mgr library outside DTP.

You mentioned that “Zotero renames the library folder on a fresh install” – is there anyway to prevent that, or to let Zotero name the Library on the new machine and then change it back to the older name manually?

If so, then the first thing I would do is an experiment. Let’s say the folder hierarchy on your old machine is something like

…PDF Library …

and it is “PDF Library” that is indexed in DEVONthink. In other words, they are indexed at ~/Documents/Zotero/PDF Library/…

If you can manage to get the same names on the new machine, then the index links should also work because on the new machine the files will be at ~/Documents/Zotero/PDF Library/… The documents are are the same position relative to the root of the new machine as they are on the old machine. The experiment here is to set up Zotero and its library, then zip an archival copy of the database on the old machine (File > Export > Database Archive), unzip it on the new machine and test the indexing. One hopes it will work without a problem. I’ve done this several times moving databases among machines and by keeping folder names intact you should be successful.

But…if you cannot keep the names intact, there will be a problem.

That worked perfectly!

It did take a little tinkering with Zotero. To “bundle” the Zotero app + the old profile (with original random string), I used a tip I found here (look for Appcleaner): … nother-mac. This involves using Appcleaner to collect Zotero ands its associated files/folders into the trash. Here’s an image of what it found:

Untitled.tiff (60.3 KB)
From the trash I copied and moved the Zotero items to the new machine’s respective locations:
~/Library/Preferences/Application Support/Zotero (where the library lives)
~/Library/Saved Application State/org.zotero.zotero.savedState

Keeping my fingers crossed I restarted the new machine, unzipped the database, and ran the verify & repair command… no issues! All the links are intact!

Thank you very much!