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Article Database: TBX -> VoodooPad Integration (Read 11724 times)
Peter Pawelek
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Article Database: TBX -> VoodooPad Integration
Sep 04th, 2007, 5:32pm
 
Hi everyone,

One of my (many) uses for Tinderbox is to manage my ever-burgeoning collection of scientific papers in PDF format. I've also been using VoodooPad/Flysketch combo to take notes on these articles. Each article is represented as a page in a monolithic VoodooPad file (this VoodooPad approach predates my usage of Tinderbox, although I'll probably continue using VP for making article notes along with TBX and Skim -- I find that the choice of note-taking tool is dependent on the kind of note I want to make).

So, I'm now building a TBX database file in which each article is a note (the note title reflects the prefix portion of my naming scheme for PDF articles; for example: 'lastname_year_startingpagenumber.pdf'). The file slot of this note points directly to the PDF file itself (although this might change to point to the marked up Skim file instead). The text area of the note contains the abstract of the article. This note will then be a container for other notes relevant to that article that I may want to make in TBX. I intend on using this TBX file as my central reference site,  such that it could hook into whatever other applications that I'm using for note taking (i.e., VoodooPad), data mining (i.e. DevonThink Pro), etc.

So far I've been trying to get TBX to hook into VoodooPad. What I've been wrestling with has been trying to get TBX to link to a particular *page* within my monolithic VoodooPad file. At first I naively tried to drag the file icon from within the article-specific VP page to the file slot in TBX. Of course that didn't work since this only would point to the VP file itself, not the page of interest within VP. Then, to my delight, I came across something on the VoodooPad forum that solved my problem. Within VoodooPad, click on the 'Information' button that opens the information sheet for that particular page. This sheet will give you the UUID for that page (it will look something like '48c231d7-5334-4158-9c22-3de1e6193cf3'). Copy this UUID to your clipboard. In the TBX note corresponding to the article, add an 'URL' Key Attribute. In the 'URL' field, type in the following:

x-voodoopad-item://{uuid}

where {uuid} is replaced by the UUID string that you copied from VP.

This will now cause the file URL pointing to the desired VP page to appear in the URL slot to the left of the note's text field. You can now click on this button and it will fire up VoodooPad and open it to the page corresponding to the desired article. Beautiful!

I've now added this Key Attribute to my article prototype, so each newly created article will now have a slot to allow linkage to my VoodooPad notes database.

I find this UUID approach to be quite powerful, and it opens up a number of questions: I wonder if it can it be generalized to allow TBX to hook into other applications in a similar manner? Conversely, does each Tinderbox note have a UUID value that would allow me to, for example, have a link in a VoodooPad page that will fire up TBX such that it's opened up the right TBX file at the appropriate note?  If so, where would I find this value?




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Talal
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Re: Article Database: TBX -> VoodooPad Integration
Reply #1 - Oct 21st, 2007, 7:42pm
 
Sorry that I'm not answering your question, but rather adding another: why don't you do all of your note-taking right in TBX? I ask, because I currently manage my PDFs using Bookends (with the bibliographic info there), index their contents in DEVONthink Pro, take notes in DT Pro as well, and then use TBX for particular research projects. However, I have thought of doing all three-four things in TBX. My only hangup has been the lack of unicode, which is necessary for each of those stages for me. If unicode is not a problem for you, why would you just do it all in TBX, considering it has metadata flexibility like no other?
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RobertW
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Re: Article Database: TBX -> VoodooPad Integration
Reply #2 - Oct 22nd, 2007, 6:10am
 
I wonder if it can it be generalized to allow TBX to hook into other applications in a similar manner?

In a Yojimbo note, the menu choice "copy item link" will put an address to that specific note onto the clipboard that works in TB and other apps. I cannot find anything similar in OmniOutliner or Devonthink. Maybe there could be a page on the TB wiki to collect such tricks from a variety of apps.

Conversely, does each Tinderbox note have a UUID value that would allow me to, for example, have a link in a VoodooPad page that will fire up TBX such that it's opened up the right TBX file at the appropriate note?

Not that I know of, but that's a great suggestion. It may a structural issue, though. In the apps where there are links to individual notes, it is also possible to find individual notes by Spotlight. In the apps where there are no links to individual notes, there is also no Spotlight to individual notes.
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Willem Smelik
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Re: Article Database: TBX -> VoodooPad Integration
Reply #3 - Oct 22nd, 2007, 9:25am
 
If you use Skim, why not take notes in BibDesk - which can link to PDF's and works with Skim (same authors)?

(Having said this, I'm still wavering myself between apps. For certain projects I use Tbx, but general notetaking goes to BibDesk, and my PDF's end up in Devonthink - which I open in Skim. What I always fear with external links is that these do get broken; importing in Devonthink solves that issue.)

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« Last Edit: Oct 22nd, 2007, 9:35am by Willem Smelik »  
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Mark Bernstein
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Re: Article Database: TBX -> VoodooPad Integration
Reply #4 - Oct 24th, 2007, 8:00am
 
Tinderbox doesn't currently have a scheme for opening a specific note from an outside program.  But much of the necessary infrastructure for such a facility does already exist; I'd like to hear more about applications that this would facilitate.
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Talal
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Re: Article Database: TBX -> VoodooPad Integration
Reply #5 - Oct 24th, 2007, 8:15am
 
Hi Mark, I could give you one application that I'd want to use it for. My PDF's of academic articles reside in a single folder in the Finder, simply filed by [AuthorLastName, Title]. I have their context indexed by Devonthink Pro so that DTP can suggest related articles for me using its "See Also" feature. I then have the same PDF's (in the Finder) linked to their bibliographic information in Bookends, which also serves as my organiser by topic for the PDF's.

What about my research notes *on* these articles, or from books whose bibliographic information I have in Bookends? What I'd like to do in the long run (once TBX has unicode, for my purposes) is take all my notes in TBX in order to avail myself of all TBX's analysis and organisational goodness. Then, I would link the notes of a given article/book to its bibliographic entry in Bookends. To say it differently: all my reading/research notes (for my dissertation, for example) would reside in one great TBX file, and each subset of multiple notes related to journal article X, or book Y, would be linked to the Bookends entry, which has recently become possible in BE in the attachments section of its preview pane.
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Peter Pawelek
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Re: Article Database: TBX -> VoodooPad Integration
Reply #6 - Nov 10th, 2007, 1:57pm
 
Thanks all for your replies. I'm glad to see a nice discussion about this has developed.

As for why I don't do all my notetaking in Tinderbox, I prefer to jot down 'on the fly' notes in Skim so that these are associated by proximity with relevant text in the PDF. I then export all Skim notes as a text file that is read into the VoodooPad entry associated with that particular article. VoodoPad is also used to make more extensive notes on figures and tables, which are embedded into the VP entry via FlySketch captures. I then use Tinderbox to compose more 'refined', secondary notes based on these raw, primary notes. As it stands now, everything is linked together and that makes me happy.
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