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Old 08-18-2008, 02:52 AM   #1
IanHelgesen
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Device: Irex Iliad
Referencer plugin

Referencer (http://icculus.org/referencer/) is a rather nice reference manager for Linux. I figure it would be even nicer if it integrated well with my Iliad, so I've started working on a plugin to do exactly that. This plugin is still in very early developement, so bugs are likely and there is little error handling. However, it should be useable, so I'm uploading an initial release. Currently, it supports sending documents to your shared Iliad directory, complete with metadata from your referencer library.

Installation:
Unzip the attached files in you referencer plugin directory (~/.referencer/plugins). Start referencer, and enable the Iliad plugin. Click configure to open a settings window where you can set the output directory, and if you want documents to open fullscreen.
You should have an Iliad icon on you toolbar, and a "Send to Iliad" entry in your documents menu and the context menu for your documents. Click on any of these to send the selected document to your sync directory.

Limitations:
This does not check file type, so it will happily send PS files which the Iliad can't open. I plan to add transparent conversion of these files in the next few days.
If you try to send a file that is already in the outbox, that file will be silently skipped. I should probably give the option of overriding.
This uses local paths for files. Files accessed through the VFS (such as ones on a windows share on a different computer) will not work.
I have done only very basic testing, and there is very little error handling logic. This means that there are likely bugs. If you encounter problems not mentioned here, please let me know.

Future Plans:
Transparent conversion of PS files (should be done in the next few days).

Automatic cropping of PDFs, using the pdfcrop tool packaged with LaTeX (also in the next few days).
Done.

Icons. While I could easily add thumbnails, it seems rather pointless (pretty much all academic papers will look the same). I'd like to use a thumbnail of the journal cover, but I'm not sure where I can pull these from. Suggestions would be appreciated.

Support USB connections. Currently, this is written with wireless sync in mind. At some point, I'd like to add an option of sending files to a connected drive. I'm not really sure when I'll manage this, though.

VFS support (windows shares, etc). Ubuntu does not have python binding for gio, and I am not interested in learning a depreciated vfs system, so this will likely not be in the near future.

More metadata and organisation. I can't do much here without more features being added to Referencer's plugin system.

Manage snippets/annotationed version. This is currently stalled due to bugs in Referencer's plugin system, but willl be a high priority once those are fixed.
Attached Files
File Type: zip referencer.zip (6.7 KB, 198 views)

Last edited by IanHelgesen; 08-28-2008 at 01:41 AM.
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Old 08-18-2008, 03:30 AM   #2
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Looks interesting. I'll take a closer look soon.
Quote:
Originally Posted by IanHelgesen View Post
[...] Icons. While I could easily add thumbnails, it seems rather pointless (pretty much all academic papers will look the same). I'd like to use a thumbnail of the journal cover, but I'm not sure where I can pull these from. Suggestions would be appreciated.
Most journals I read seem to have a website with cover images that can be snarfed. For some of them a little imagemagick processing is helpful.

BTW, thumbnails can be useful even for academic journals, either I have a mental image of a paper, or I can recognise a paper by its broad layout.

If you are processing with latex you can also make the thumbnails into hyperlinks so you can, for example, have add a 3x4 grid of thumbnails at the front of a paper and make each one a hyperclickable (is that really a word?) to go the page. I have a script to do this that is almost useful, but it doesn't handle longer papers where the thumbnails go onto a second page (I need to deal with the fact that the first real page of the paper will start on page 3 instead of page 2: not much to fix, just not time to do it).

EDIT: Ah, I've now looked at referencer and see that you probably mean thumbnails of the first page only of articles to display them file manager-style.

Last edited by daudi; 08-18-2008 at 03:34 AM.
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Old 08-18-2008, 01:13 PM   #3
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Yes, I just mean thumbnails of the first page (for the content-lister). Being able to select a page by thumbnail would be nice, but that's something that should be handled by ipdf. Currently, I don't alter the paper at all, although I may add that in the future (inserting blank pages for notes, etc).
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Old 08-21-2008, 02:16 PM   #4
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Quote:
Originally Posted by IanHelgesen View Post
Manage snippets/annotationed version. This is currently stalled due to bugs in Referencer's plugin system, but willl be a high priority once those are fixed.
This would really be outstanding. If annotating or selecting a snippet of a PDF would result in an entry in a reference system, along with the metadata needed to generate a valid reference I'd... actually, I don't know what I'd do. Do you like cookies?
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Old 08-28-2008, 01:39 AM   #5
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Quote:
Originally Posted by nekokami View Post
This would really be outstanding. If annotating or selecting a snippet of a PDF would result in an entry in a reference system, along with the metadata needed to generate a valid reference I'd... actually, I don't know what I'd do. Do you like cookies?
I was thinking it would be linked to the original document, so that you would right-click on the entry and select 'view snippets' or 'view annotations'. It wouldn't be hard to create a separate entry, though, as long as Referencer's plug-in supports this (I'm not certain if it does at the moment though). And yes, I do like cookes.

Also, I'm uploading a new version which includes autmatic margin cropping. You'll need the pdfcrop util (packaged with LaTeX) in your path for this to work. I've also been working on conversion of ps files, but this isn't working yet, and the bug disappears when I open my debugger. Hopefully I can fix this soon, but I've just started grad school and am not certain how much time I'll have to work on this.
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Old 12-16-2008, 07:49 PM   #6
RahulG
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Hi Ian
I am so happy to see your post as I have been searching for a perfect solution to my PDF problems. The appearance of Iliad type of devices to store and reqad PDF was one part of the solution and the other is a Reference (or Quosa or Endnote) type of a program. But since these two are not available together, I havent yet ventured into buying the Iliad or the EReader and was asking some bioinformatics friends to help me in designing a custom program for Iliad. Thanks to you, it will no longer be necessary.

Please do tell me how is the Referencer running for you on the Iliad (issues about small memory of the iliad if any) and if you are still refining it further by attempting to add features like full text search in allfiles inside a folder.
I am sure it will be a great service to the researcher community who needs to handle PDF files...as and when they switch to an Iliad like device that is (as opposed to taking prints of a paper and losing it and printing it again half a dozen times!).
regards
Rahul Gaur
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Old 12-22-2008, 09:24 PM   #7
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Referencer doesn't actually run on the Iliad (would be great if it did, but that would require someone who knows C to port it). This plugin is for the copy running on your computer, and lets you send files to your outbox fold (to be synced with the Iliad over wifi), and writes out title and author information so it will be shown properly on the Iliad. I never had issues with the memory limitations, since I only had a few articles on the device at a time (my to-read list and current lab reading).

Unfortunately, I probably won't be developing this further in the near future (if at all). I was intending to work on it over the holidays, as my programming time has been turned towards research lately. However, my Iliad's screen broke about a month ago, and I've decided to wait for the 9" models from Astek and Jinke to come out before I get a replacement.
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