Sonny Software

Just picked up Bookends after being a long time Endnote user. Looked at the other packages (Papers, Sente, Zotero, Mendeley) and blog sites plus simply experimented with the various software tools. Many people commented very positively about BE's support and community.

I have no problem importing my Endnote library...export from Endnote to xml and then import into BE.

I just started using DevonThink Pro Office, Scrivener, and Skim. I am working on my PhD dissertation, so my primary source of references are through my university's databases. I am not a distant student so not on campus.

Here are my first set of questions:

1. If I access an Ebsco or Proquest database (for example), is there any way for BE to automatically "pick up" the RIS file export (without having to save and import) the way that Endnote did?

To be honest, when I read through the documentation, I am not sure if the instructions refer to those who are on campus and are accessing their institution's journal databases through their internal system or whether they are are off campus and only logging in externally via the internet. I don't really understand what EZProxy is...

2. I have also tried to add a reference by attaching an already downloaded PDF file (to a blank reference) and then having BE find the rest of the information for me. (Love how it does this!) However, I am also finding that BE generates an additional blank reference besides the reference associated with the PDF. Not sure how to do this.

When I tried to delete the blank references, I started receiving this error (when adding new references using the same method plus when performing other BE operations...but I can't remember which ones):

Database Engine Error:

"FILE: /PARADIGMA/Developer_2/kernel/xcode/.../.../Sources/VKernal/FBL/prot/Structure/SegmentFile/FB:_SegmentFile.cpp FUNCTION: get_SegmentOffset LINE: 960" Owner name "thereference.title": segment "3" is wrong. The last segment is "2".

So in the interim, I'm not deleting any blank references...but obviously, that's not a long-term solution.

3. My use of DTPO is for document management (and basic PDF annotation), Scrivener for draft preparation, and Skim for more elaborate PDF annotation. In order for all of the software packages to have access to the PDF files, I am using a common folder for all of the references. I am having DTPO only index (link with) these files. When I annotate the file in either DTPO or Skim, the annotations are saved with the file (I think). I can view the annotations made in one program with the other program. However, I am not able to see these annotations in BE. I used the "Reveal Attachment in Finder" function in BE and it appears that the attachments are in the same common folder and have the same name (no addition document ID attached to file). Am I doing something incorrectly here? Is it a cached image of the PDF. I exited BE, restarted it and still see the unannotated file. I set my BE preferences to include the common folder as my default attachment folder. Is there something else I need to do?

Thanks in advance for any help anyone can provide!

I'm looking forward to better understanding how to use Bookends and tapping into its functionality.

pbug2020 wrote:
1. If I access an Ebsco or Proquest database (for example), is there any way for BE to automatically "pick up" the RIS file export (without having to save and import) the way that Endnote did?

Hi,

No. Safari doesn't allow helper apps, so that's not implemented. FWIW, you can drag and drop the file onto a Bookends window and in the import dialog box check "Move to Trash after import". If you do, getting rid of the file is taken care of for you.

To be honest, when I read through the documentation, I am not sure if the instructions refer to those who are on campus and are accessing their institution's journal databases through their internal system or whether they are are off campus and only logging in externally via the internet. I don't really understand what EZProxy is...

If you don't know what it is, you're not using it.

If you access your university's library via a VPN client you can do everything remotely that you can do on campus. If not, EZproxy is common mechanism many universities use (and will work with Bookends Browser, not with direct online searching).

2. I have also tried to add a reference by attaching an already downloaded PDF file (to a blank reference) and then having BE find the rest of the information for me. (Love how it does this!) However, I am also finding that BE generates an additional blank reference besides the reference associated with the PDF. Not sure how to do this.

When you attach, check the checkbox that says "attach to an empty reference and autocomplete paper" (or words to that effect). This will create a new (blank) reference for you, and offer to autocomplete.

When I tried to delete the blank references, I started receiving this error (when adding new references using the same method plus when performing other BE operations...but I can't remember which ones):

Database Engine Error:

"FILE: /PARADIGMA/Developer_2/kernel/xcode/.../.../Sources/VKernal/FBL/prot/Structure/SegmentFile/FB:_SegmentFile.cpp FUNCTION: get_SegmentOffset LINE: 960" Owner name "thereference.title": segment "3" is wrong. The last segment is "2".

So in the interim, I'm not deleting any blank references...but obviously, that's not a long-term solution.

Just Rebuild your database (File -> Database Maintenance). That will take care of this.

3. My use of DTPO is for document management (and basic PDF annotation), Scrivener for draft preparation, and Skim for more elaborate PDF annotation. In order for all of the software packages to have access to the PDF files, I am using a common folder for all of the references. I am having DTPO only index (link with) these files. When I annotate the file in either DTPO or Skim, the annotations are saved with the file (I think). I can view the annotations made in one program with the other program. However, I am not able to see these annotations in BE. I used the "Reveal Attachment in Finder" function in BE and it appears that the attachments are in the same common folder and have the same name (no addition document ID attached to file). Am I doing something incorrectly here? Is it a cached image of the PDF. I exited BE, restarted it and still see the unannotated file. I set my BE preferences to include the common folder as my default attachment folder. Is there something else I need to do?

Skim uses their own mechanism to save/view pdf markup. Bookends won't show that. Bookends will show any markup you have made in Apple's Preview, though.

I'm looking forward to better understanding how to use Bookends and tapping into its functionality.

If you haven't already, take a look at the video tutorials on our web site. Also, although it looks daunting, skimming through the TOC of the user guide and reading any interesting looking discussions are a great way to learn more about the things Bookends can do.

Jon
Sonny Software

pbug2020 wrote:1. If I access an Ebsco or Proquest database (for example), is there any way for BE to automatically "pick up" the RIS file export (without having to save and import) the way that Endnote did?

I guess you can use a folder action/automator thingy that watches a folder and triggers an action (open .ris files in BE, for example). I haven’t used folder actions since OS 9 though, so I am not sure about the details of doing this.

Thanks for the input!

I will attempt these various solutions and post my results.