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Old 01-11-2008, 05:21 AM   #31
Matt
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Originally Posted by daudi View Post
...
I just take notes in the "Review" window in jabref, so they are relatively easy to search, including specifying fields and are all in one place.
...
Daudi, are you running Jabref on the iLiad? I assume from jharker's description of his process that he is running lyx on the actual device. If either is true, how do you switch back and forth between note-taking and PDF reading?

Or do you both (or either) scribble on the pdf and then transpose on the computer?
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Old 01-11-2008, 06:03 AM   #32
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Hi Matt,

No, I don't run jabref on the iliad I'm afraid (now that would be cool). I'm still refining my work flow, but for now I am reading on the iliad and writing on my PC. I read an article and underline or markup parts that are interesting or important as I go, and then once I have finished the paper I make a quick summary in the review section of jabref using the marks I have made as prompts. Having read the paper, skipping through and taking notes is quite quick.

I am very close to being able to use jabref (running on my PC) to open pdfs on the iliad. I have one little issue to sort out, that I think is a jabref issue that I can work around. I'll try to get time to play with finalising it this weekend.
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Old 01-11-2008, 04:45 PM   #33
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Thanks for the input Daudi, I will see if I can get something like this to work on my new mac and with my new Iliad.
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Old 01-11-2008, 08:15 PM   #34
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See, I was thinking if I had the iPDF with comments patch, I could write a script to suck the comments from the XML that creates into a bib utility.
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Old 01-13-2008, 06:53 AM   #35
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Well, I have this mostly working now. I can use jabref to manage my refs, I have a filter that makes it easy to create a manifest file that contains the author(s) in the title, paper title in the first line of the description and journal name and pages in the second line of the description so they look good and are easy to identify on the iliad.

I also have another export filter that creates symlinks, so I can select a group of refs, export to symlinks and move the symlinks to some work folder on the iliad. That way I can keep all my refs in one folder and have collections for particular projects in another that point to the original articles.

But when you have hundreds of articles and no bibliography manager on the iliad using the iliad search becomes a pain. So, I have installed samba as shown recently (thanks ajnorth!) on the iliad and access it from my PCs. I have setup some scripts and registered these as external file handlers in jabref (this is much simpler than it might sound, it's like setting up file associations in Windows 98 or something) and the scripts themselves are quite simple. I then network my PC to my iliad and setup an article entry to do different things depending on which option is chosen. The choices are:

i) open and view the PDF on the PC
ii) Merge the PDF and scribbles and view on the PC
iii) Make a symlink in an easily accessible folder on the iliad so I don't have to search for it
iv) open the PDF directly on the iliad (via ssh)

(The last option works in that it opens the PDF and was what I was after in the first place, but I have trouble closing it afterwards and might have to give up on this approach.)

Here's a screenshot showing the choices. I might even try to make a video and put it on youtube if people are interested and if I can figure out how to do it (never tried youtube before).

Jabref is really nice. I am really getting to like it. At the moment I am liking the static and dynamic groups. And it looks like there will be a plugin for OpenOffice soon (it is already in the dev version).
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Old 01-14-2008, 11:20 AM   #36
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I have started to work with this and JabRef seems very nice. One thing I do not get is whether I can export several manifest files at the same time. I have a bunch of old articles that I'm starting to sort out and I want to create separate
<bibtexkey>.manifest.xml files in one go and then batch-run daudis container script on all of them. Does anyone know if this is possible?

/ SP
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Old 01-14-2008, 12:00 PM   #37
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Try registering this attached file as an export filter. Using this to export refs will produce a bash script that will create each manifest file. So, if you make the default extension for this filter to be .sh, and then you select a load of refs and export them using this filter and save it as myrefs.sh you can do:
Code:
sh myrefs.sh
to create all the manifest files in the current directory.
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Old 01-14-2008, 12:28 PM   #38
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Even if jabref would run on the iLiad, you'd have the problem of switching between it and the text you are reading, wouldn't you? We need a window switcher (or a split screen) to be able to do reading and note-taking directly on the iLiad.
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Old 01-14-2008, 12:43 PM   #39
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Quote:
Originally Posted by nekokami View Post
Even if jabref would run on the iLiad, you'd have the problem of switching between it and the text you are reading, wouldn't you? We need a window switcher (or a split screen) to be able to do reading and note-taking directly on the iLiad.
Agreed. And it would need to be fast otherwise I think it would interrupt my flow too much. I'm not sure that things refreshes will get too much faster with the current hardware, unless it really is a software issue. I have startd using ssh to login to and poke around the iliad and was surprised how fast it was. I now have a feel for the lag caused by the E-ink.

So, for now, I am focussing on making a PC-based bib manager work *with* the iliad rather than *on* the iliad.

BTW, I made a terrible movie on youtube showing the integrated iliad and jabref-on-PC. It's so bad I'll have to explain what I am doing:

SETUP:
i) PDFs are on the iliad (in fact on the USB in the iliad)
ii) jabref is running on the PC
iii) I have the USB shared using samba (i.e. a windows share)
iv) I have custom file handlers

MOVIE:
i) I select a ref, then right-click to open it on the PC for viewing
ii) I then merge scribbles and open it on the PC for viewing
iii) I then show that there is nothing in the "readnow" directory on the iliad
iv) Next I choose the "make symlink in readnow" menu option in jabref
v) then I show that there is now a link in readnow and open the PDF on the iliad.
vi) I fumble around trying to get the pen out then write "Hi" on the the screen
vii) I go back to the PC and merge and view again and show that "Hi" is now there.

http://www.youtube.com/watch?v=GM-34CA6Cg4
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Old 01-14-2008, 03:23 PM   #40
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This looks really interesting! When you are done, could you share your scripts with us? Maybe a little howto for the not so experienced users?

Thanks
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Old 01-14-2008, 04:24 PM   #41
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Sure, will do. I think it should be possible to do this on a windows PC and Mac as well because there's not much to it. Jabref is a java app, so no worries there. I use the scribble merging tool posted elsewhere on mobileread for the merges (java again). jabref makes it easy to specify "associations" and I have just created some very simple scripts that could be rewritten as batch files.

The thing that makes it all so simple now is samba which was contributed recently on mobileread. For (windows?) users who don't know what this is, it setups up linux directories as windows shares. So this should also work fine with a windows PC.

I might not have time for a full howto until next weekend.

Last edited by daudi; 01-14-2008 at 04:26 PM.
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Old 01-14-2008, 05:32 PM   #42
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Daudi, I tried the batch export from JabRef, but Im stuck. How to do it?

Where do I have to apply the code (sh myrefs.sh) ?? Is this only for linux? (I run Windows).

Thanks
Gogolo

Edit: I dont understand this prodcedure:
Quote:
Try registering this attached file as an export filter. Using this to export refs will produce a bash script that will create each manifest file. So, if you make the default extension for this filter to be .sh, and then you select a load of refs and export them using this filter and save it as myrefs.sh you can do:

Last edited by Gogolo; 01-14-2008 at 05:35 PM.
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Old 01-14-2008, 06:07 PM   #43
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Gogolo,

Ah, sorry, for some reason I thought you were using linux. The export layout file creates the shell script when you use jabref export. The shell script is really just a load of "heredocs" but I don't know what the equivalent would be in windows, or as a dos batch file. An alternative would be to write it as a python script (or other language). That would be platform independent (I think) but then would mean you would have to install python.

If you just want to do this once, you could send me the shell file that you create, I could run it and send back the manifest files in a zip file. It might be sensible to try a small number (say 50) refs first before the whole lot to make sure it works.

One other idea: I used to use jython a while back. This is python implemented in java. Presumably you have java already (to run jabref) so perhaps all that is needed is a small change to the export filter to create a python/jython script and then the jython jar file. It's a bit too late for me to get my head around this now. Another thing to add to my list for the weekend.
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Old 01-15-2008, 03:53 AM   #44
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Thanks for your nice help Daudi. Im still updating my Library - so maybe in a while I will come back to your offer, thanks!

Programming phyton etc... I once programmed games in basic on commodore 64. uuhhhmm seems to be a pretty long time ago

Greetings
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Old 01-15-2008, 04:28 AM   #45
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Doh! It's amazing what a good night's sleep and really big cup of tea can do.
Gogolo, take a look at the batch layout file (posted above), I think you should be able to see what it does. It uses the cat command to write the template to a file name specified at the end of the cat line. You should be able to modify this layout file to produce a DOS bat file that writes the lines out using echo. Something like this:
Code:
echo "<?xml version="1.0" encoding="utf-8"?>"  > \format{\bibtexkey}.manifest.xml
echo "<package>"  >>  \format{\bibtexkey}.manifest.xml                                                                        
echo "<metadata>"  >>  \format{\bibtexkey}.manifest.xml
etc. Note the single > to redirect output to a new file and subsequent >> to append to that file. This assumes that echo will happily echo everything between the quotes. You might need to escape the quotes in the first line or use single quotes, but hopefully the idea is clear. If echo does agree to play nicely, then once you've done this for each line and then used it to export several refs, you'll end up with a DOS bat file that should create each manifest file.

If there are problems with echoing (e.g. the < or other characters) then it's back to python/jython. I think the layout file would be really simple, something like:

Code:
f = open('\format{\bibtextkey.manifest.xml}', 'w')
bib = """
<?xml version="1.0" encoding="utf-8"?>
<package><metadata><dc-metadata>
<Title>\format[Replace("&",and),AuthorLastFirst,AuthorLastFirstAbbreviator,AuthorAndsCommaReplacer]{\author}</Title>
***etc. rest of manifest here***
"""
f.write(bib)
f.close()
So you'd use this layout file to create a python script (e.g. myrefs.py) that you'd run with something like:

Code:
java -jar jython.jar myrefs.py
I think I'll play with using jython again a little more it was fun, and it allows access to the java libraries so it could then be possible to create guis and things if necessary.

And for those wondering why I don't just use java in the first place: i) I find it takes too long to write quick code to do simple tasks; and ii) I'm not very good at it.
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