Sonny Software

Hi,

I use DEVONthink (DT) as the basis for my work flow. As such, I always import pdfs into DT and allow it to manage the location, etc. From what I can tell (not sure, new user), BE seems to want to manage the location of the files itself. Is there anyway to tell BE to not move (nor copy) a pdf from its location, but rather use a symbolic link to the file?

Thanks,

Roger Alexander.

Bookends can attach a pdf and leave it where it is. Uncheck the copy/move option in the attach dialog.

Jon
Sonny Software

Jon wrote:Bookends can attach a pdf and leave it where it is. Uncheck the copy/move option in the attach dialog.

Jon
Sonny Software

Hi Jon,

I have the same workflow as the OP - so I am very relieved that this is possible, since it avoids another duplication of data [I now wish I had started everything in DTP with indexing, as opposed to importing - but water under the bridge!].

I am in the process of working my way through the manual - but figured I would try my luck this side as well, just to confirm things!

I am probably at 95% in terms of my literature collection - and am now writing, as opposed to still finding, resources for my PhD. I therefore have a few thousand PDFs - oh how I wish I had realised the importance of a citation/reference manager before downloading most of them - that do not necessarily contain DOI information...

I too would like to "import" without duplicating - but the question I have now - were I to do this, I presume Bookends would then not be able to do an online search to check if it can pull-down any available information, in order to autocomplete? I.e. does Bookends require the "attachment", as it were, in order to check online?

If the answer to the above is YES - then would I need to import all my pdf's (therefore duplicating), have Bookends run the searches, and find what can be found - and then effect a "global change"(??) to discard/seperate the 'newly-created' reference from its associated PDF - and then clean out/delete the PDFs in the Attachments Folder? Would this be the way to go - or am I missing/will I soon discover (in the Manual) a much simpler option to the above?

Apologies for such a lengthy first post!

I'm not sure exactly what you want to do (not exactly). Is your fear of duplication that Bookends will make a copy of each pdf? That won't happen if you tell Bookends to leave the pdfs where they are. You can attach the pdfs and have Bookends find metadata when it can, then Remove Duplicates if you have imported metadata you already have. So you don't duplicate pdfs.

Try this with dropping just 2 pdfs (on a fresh database if you like) and see what happens.

Jon
Sonny Software

Jon wrote:I'm not sure exactly what you want to do (not exactly). Is your fear of duplication that Bookends will make a copy of each pdf? That won't happen if you tell Bookends to leave the pdfs where they are. You can attach the pdfs and have Bookends find metadata when it can, then Remove Duplicates if you have imported metadata you already have. So you don't duplicate pdfs.

Try this with dropping just 2 pdfs (on a fresh database if you like) and see what happens.

Jon
Sonny Software

Thanks for the reply Jon - I will play around with a fresh database, and some pdf's - and see what happens.

I'll try and clarify what I mean though:

I have now imported a few dozen citations, that I had previously created in Endnote.
Other than that - I have no other citations/references - only PDF's on my computer - these have been duplicated into DTP, for me to manage/search/link/edit/tag etc.

My sole purpose, at this point, for using Bookends - would be to replace Endote as my citation manager.
In other words - get it to make the necessary changes to which style I set up, and work its magic after scanning my completed document in MS Word.
[I will remain using DTP as the data-manager, given the hours already invested in setting up those databases.]

The way I currently understand things, is that to create a new citation/reference, I either:-

a.) Physically type it up from scratch [i.e. have the PDF open in Skim/Preview/DTP - and transpose the relevant information into the new Citation window];
OR
b.) I drag & drop/import the PDF (from my main Data folder - i.e. not from DTP) - and Bookends attempts to "read that PDF" and auto-complete everything by creating a brand new citation, without me having to lift a finger.

Assuming the above is correct - I would obviously prefer Option B!

But again - I presume that is all dependent on their being DOI/metadata information in the existing PDF, that will allow that information to be retrieved.
The only way I can know that - is by dropping all those PDF's into Bookends, and have it find what it can find.
I can then see all the blank/no-entry citations that have been created [i.e. where no information could be located online] - and would then have to re-create those citations from scratch - i.e. by using Option A, but with the choice of simply "reading the information" off the PDF, in Bookends then.

The conclusion of the above, would see all my PDF's presumably stored in the Attachments folder, "in" Bookends.
This would then result in a duplication - which is my fear.
I would then want to remove all the PDF's back out of Bookends, so that I can clear up space, by deleting the duplication on my system.

Your suggestion to "tell Bookends to leave the pdfs where they are" is what I would prefer - BUT, does this still mean that Bookends can find/pull what information it needs to, despite not 'getting' the PDF into its database?

Cassady wrote: The way I currently understand things, is that to create a new citation/reference, I either:-

a.) Physically type it up from scratch [i.e. have the PDF open in Skim/Preview/DTP - and transpose the relevant information into the new Citation window];
OR
b.) I drag & drop/import the PDF (from my main Data folder - i.e. not from DTP) - and Bookends attempts to "read that PDF" and auto-complete everything by creating a brand new citation, without me having to lift a finger.

Assuming the above is correct - I would obviously prefer Option B!

Mostly correct. Bookends doesn't actually try to read the pdf metadata. It tries to find a doi only. If it does, it fetches the metadata from an online source.

Option c: Refs -> Autocomplete paper (for pdfs you have that don't have a doi, you can tell Bookends words to search, say, Google Scholar for, and import the metadata if found).

But again - I presume that is all dependent on their being DOI/metadata information in the existing PDF, that will allow that information to be retrieved.
The only way I can know that - is by dropping all those PDF's into Bookends, and have it find what it can find.
I can then see all the blank/no-entry citations that have been created [i.e. where no information could be located online] - and would then have to re-create those citations from scratch - i.e. by using Option A, but with the choice of simply "reading the information" off the PDF, in Bookends then.

As mentioned above, Refs -> Autocomplete paper can be very helpful in this case.

The conclusion of the above, would see all my PDF's presumably stored in the Attachments folder, "in" Bookends.
This would then result in a duplication - which is my fear.
I would then want to remove all the PDF's back out of Bookends, so that I can clear up space, by deleting the duplication on my system.

Bookends does not store pdfs internally. It only stores the attachment name. The attachment is either left on the HD where ever you had it, or moved (or copied) to the Bookends attachment folder. In your case, you want Bookends to leave it alone, which is an option in the Attachment Dialog. Please see the User Guide (Help menu) for how attachments work.

Your suggestion to "tell Bookends to leave the pdfs where they are" is what I would prefer - BUT, does this still mean that Bookends can find/pull what information it needs to, despite not 'getting' the PDF into its database?

From the above, I hope it's clear that the answer is "yes".

Jon
Sonny Software

Jon - many thanks for the reply. I have a much clearer understanding now, and know what to focus on in the manual.

Re the above - I realise now, that what I needed to get my head around, was the 'link' between the Ref in Bookends, and the actual PDF. The attachment icon/paperclip, "seeing" the pdf as a scrollable document "in" Bookends, and my deleting a reference - which saw the actual pdf pulled out of its folder, and into the Trash - confused me initially...

I never realised that Bookends was simply 'live-linking' through to the pdf in its original folder - I assumed it had duplicated the pdf. I get the distinction now. And it's obviously quite an important one to make.

No reference or pdf management app I know of actually stores pdfs in its database. That would be enormously unwieldly, not to mention wasteful.

Jon
Sonny Software