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* Re: Org Mode and PDF Notes!
@ 2015-11-11 15:15 Peter Davis
  0 siblings, 0 replies; 28+ messages in thread
From: Peter Davis @ 2015-11-11 15:15 UTC (permalink / raw)
  To: Matt Price; +Cc: Org Mode

Matt Price <moptop99@gmail.com> writes:

> I've just written up a post on my workflow for PDF's Since my blog
> has, I think, a readership of 0 (surely there's a way to get emacsers
> to follow me? ah well), I will post a link here in the hopes that
> someone will be interested:
>
> http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/

Thanks, Matt. This looks interesting. I've run into poppler before, but was not familiar with pdf-tools. I'll have to take a closer
look.

-pd

^ permalink raw reply	[flat|nested] 28+ messages in thread

[parent not found: <20@gmane.emacs.orgmode.nnrss>]

• * Re: Org Mode and PDF Notes!
         [not found] <20@gmane.emacs.orgmode.nnrss>
  @ 2015-11-13  8:04 ` Matti Minkkinen
    2015-11-16 10:07   ` Ramon Diaz-Uriarte
    0 siblings, 1 reply; 28+ messages in thread
  From: Matti Minkkinen @ 2015-11-13  8:04 UTC (permalink / raw)
    To: emacs-orgmode
  
  Ramon Diaz-Uriarte writes:
  
  > On Thu, 12-11-2015, at 14:11, Matt Price gmail.com> wrote:
  > It works! I get the highlighted text (I have just tried with a pdf I
  > highlighted with EzPDF, the one that, above, was giving just the location
  > and properties). And it still does the correct thing in your pdf (the one
  > from repligo).
  > Awesome! Thanks.
  > R.
  >
  > link
  
  I also have a strong interest in getting PDF annotations from Android to
  org-mode notes easily, so I've been following this thread with great
  interest.
  
  Very recently, on 11 November, there were a couple of commits to this
  pdf-tools fork which also let you export highlighted text:
  https://github.com/pinguim06/pdf-tools
  
  Matt Price already referred to the pull request from that fork, but
  those commits are more recent than the original pull request. I think it
  uses the same principle as the solution mentioned here but maybe it's
  more elaborate. I don't know enough elisp to confirm that.
  
  --
  Matti
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• • * Re: Org Mode and PDF Notes!
      2015-11-13  8:04 ` Matti Minkkinen
    @ 2015-11-16 10:07   ` Ramon Diaz-Uriarte
      0 siblings, 0 replies; 28+ messages in thread
    From: Ramon Diaz-Uriarte @ 2015-11-16 10:07 UTC (permalink / raw)
      To: Matti Minkkinen; +Cc: emacs-orgmode
    
    Thanks for the pointer.
    
    
    On Fri, 13-11-2015, at 09:04, Matti Minkkinen <matti.minkkinen@iki.fi> wrote:
    > Ramon Diaz-Uriarte writes:
    >
    >> On Thu, 12-11-2015, at 14:11, Matt Price gmail.com> wrote:
    >> It works! I get the highlighted text (I have just tried with a pdf I
    >> highlighted with EzPDF, the one that, above, was giving just the location
    >> and properties). And it still does the correct thing in your pdf (the one
    >> from repligo).
    >> Awesome! Thanks.
    >> R.
    >>
    >> link
    >
    > I also have a strong interest in getting PDF annotations from Android to
    > org-mode notes easily, so I've been following this thread with great
    > interest.
    >
    > Very recently, on 11 November, there were a couple of commits to this
    > pdf-tools fork which also let you export highlighted text:
    > https://github.com/pinguim06/pdf-tools
    >
    > Matt Price already referred to the pull request from that fork, but
    > those commits are more recent than the original pull request. I think it
    > uses the same principle as the solution mentioned here but maybe it's
    > more elaborate. I don't know enough elisp to confirm that.
    
    
    -- 
    Ramon Diaz-Uriarte
    Department of Biochemistry, Lab B-25
    Facultad de Medicina
    Universidad Autónoma de Madrid 
    Arzobispo Morcillo, 4
    28029 Madrid
    Spain
    
    Phone: +34-91-497-2412
    
    Email: rdiaz02@gmail.com
           ramon.diaz@iib.uam.es
    
    http://ligarto.org/rdiaz
    
    ^ permalink raw reply	[flat|nested] 28+ messages in thread

* Org Mode and PDF Notes!
@ 2015-11-11 14:42 Matt Price
  2015-11-11 14:59 ` Kaushal Modi
                   ` (6 more replies)
  0 siblings, 7 replies; 28+ messages in thread
From: Matt Price @ 2015-11-11 14:42 UTC (permalink / raw)
  To: Org Mode

[-- Attachment #1: Type: text/plain, Size: 317 bytes --]

I've just written up a post on my workflow for PDF's Since my blog has, I
think, a readership of 0 (surely there's a way to get emacsers to follow
me? ah well), I will post a link here in the hopes that someone will be
interested:

http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/

All best!
Matt

[-- Attachment #2: Type: text/html, Size: 475 bytes --]

^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
  @ 2015-11-11 14:59 ` Kaushal Modi
    2015-11-11 20:38   ` Matt Price
    2015-11-11 15:06 ` Xebar Saram
                     ` (5 subsequent siblings)
    6 siblings, 1 reply; 28+ messages in thread
  From: Kaushal Modi @ 2015-11-11 14:59 UTC (permalink / raw)
    To: Matt Price; +Cc: Org Mode
  
  Have you had a look at https://github.com/rudolfochrist/interleave
  
  The interleave package works great for me: taking notes in an org-mode
  buffer in one side (buffer) corresponding to the pdf page open in
  pdf-tools on the other side (buffer).
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• • * Re: Org Mode and PDF Notes!
      2015-11-11 14:59 ` Kaushal Modi
    @ 2015-11-11 20:38   ` Matt Price
      2015-11-11 20:48     ` Kaushal Modi
      0 siblings, 1 reply; 28+ messages in thread
    From: Matt Price @ 2015-11-11 20:38 UTC (permalink / raw)
      Cc: Org Mode
    
    [-- Attachment #1: Type: text/plain, Size: 834 bytes --]
    
    On Wed, Nov 11, 2015 at 9:59 AM, Kaushal Modi <kaushal.modi@gmail.com>
    wrote:
    
    > Have you had a look at https://github.com/rudolfochrist/interleave
    
    
    not till now!
    
    >
    >
    > The interleave package works great for me: taking notes in an org-mode
    > buffer in one side (buffer) corresponding to the pdf page open in
    > pdf-tools on the other side (buffer).
    >
    Huh.  Looks pretty neat.  Doesn't seem to work with pdfview yet, and I'm
    sort of addicted now. But it seems like a great idea.  I can think of some
    changes, e.g., would be nice to keep all my notes for all
    books/articles/etc. in a single file; if the interleave options could be
    set on a per-heading basis that owuld be really cool. And if it worked with
    pdfview, one could add highlights to the pdf text while writing notes in
    the org window. Huh. Interesting. Thanks for sharing.
    
    [-- Attachment #2: Type: text/html, Size: 1392 bytes --]
    
    ^ permalink raw reply	[flat|nested] 28+ messages in thread

  • • * Re: Org Mode and PDF Notes!
        2015-11-11 20:38   ` Matt Price
      @ 2015-11-11 20:48     ` Kaushal Modi
        2015-11-11 20:58       ` Matt Price
        2015-11-12 11:58       ` Sebastian Christ
        0 siblings, 2 replies; 28+ messages in thread
      From: Kaushal Modi @ 2015-11-11 20:48 UTC (permalink / raw)
        To: Matt Price; +Cc: Org Mode
      
      >  Doesn't seem to work with pdfview yet, and I'm sort of addicted now.
      
      I use pdf-view too (the major mode for viewing PDF files that comes
      with pdf-tools, right?) and interleave works great!
      
      > I can think of some changes, e.g., would be nice to keep all my notes for all books/articles/etc. in a single file
      
      Yeah, right now it is one org file per pdf.
      
      > if the interleave options could be set on a per-heading basis that would be really cool.
      
      What sort of options are you thinking about? Right now it creates one
      org heading for each set of notes corresponding to a page.
      
      May be you can work with the interleave.el dev to add in your ideas
      and code. I had worked with him to make interleave support pdf-tools
      and it was a pleasure to work with him.
      
      ^ permalink raw reply	[flat|nested] 28+ messages in thread

    • • * Re: Org Mode and PDF Notes!
          2015-11-11 20:48     ` Kaushal Modi
        @ 2015-11-11 20:58       ` Matt Price
          2015-11-12 12:02         ` Sebastian Christ
          2015-11-12 11:58       ` Sebastian Christ
          1 sibling, 1 reply; 28+ messages in thread
        From: Matt Price @ 2015-11-11 20:58 UTC (permalink / raw)
          Cc: Org Mode
        
        [-- Attachment #1: Type: text/plain, Size: 1028 bytes --]
        
        On Wed, Nov 11, 2015 at 3:48 PM, Kaushal Modi <kaushal.modi@gmail.com>
        wrote:
        
        > >  Doesn't seem to work with pdfview yet, and I'm sort of addicted now.
        >
        > I use pdf-view too (the major mode for viewing PDF files that comes
        > with pdf-tools, right?) and interleave works great!
        >
        ah cool, i didn't know that.
        
        >
        > > I can think of some changes, e.g., would be nice to keep all my notes
        > for all books/articles/etc. in a single file
        >
        > Yeah, right now it is one org file per pdf.
        >
        > > if the interleave options could be set on a per-heading basis that would
        > be really cool.
        >
        > What sort of options are you thinking about? Right now it creates one
        > org heading for each set of notes corresponding to a page.
        >
        
        > May be you can work with the interleave.el dev to add in your ideas
        > and code. I had worked with him to make interleave support pdf-tools
        > and it was a pleasure to work with him.
        >
        I meant INTERLEAVE_PDF. I just opened an issue:
        https://github.com/rudolfochrist/interleave/issues/13  so who knows,
        maybe...
        
        [-- Attachment #2: Type: text/html, Size: 1832 bytes --]
        
        ^ permalink raw reply	[flat|nested] 28+ messages in thread

      • • * Re: Org Mode and PDF Notes!
            2015-11-11 20:58       ` Matt Price
          @ 2015-11-12 12:02         ` Sebastian Christ
            0 siblings, 0 replies; 28+ messages in thread
          From: Sebastian Christ @ 2015-11-12 12:02 UTC (permalink / raw)
            To: emacs-orgmode
          
          >>>>> On Wed, 11 Nov 2015 15:58:24 -0500, Matt Price <moptop99@gmail.com> said:
          
            > I meant INTERLEAVE_PDF. I just opened an issue:
            > https://github.com/rudolfochrist/interleave/issues/13  so who knows,
            > maybe...
          
          Sound like a good idea. I'm currently a little short on time,but perhaps
          I can look into that this weekend.
          
          -Sebastian
          
          ^ permalink raw reply	[flat|nested] 28+ messages in thread

      • * Re: Org Mode and PDF Notes!
          2015-11-11 20:48     ` Kaushal Modi
          2015-11-11 20:58       ` Matt Price
        @ 2015-11-12 11:58       ` Sebastian Christ
          1 sibling, 0 replies; 28+ messages in thread
        From: Sebastian Christ @ 2015-11-12 11:58 UTC (permalink / raw)
          To: emacs-orgmode
        
        >>>>> On Wed, 11 Nov 2015 15:48:15 -0500, Kaushal Modi <kaushal.modi@gmail.com> said:
        
          > May be you can work with the interleave.el dev to add in your ideas
          > and code. I had worked with him to make interleave support pdf-tools
          > and it was a pleasure to work with him.
        
        You're so kind! It was also a pleasure for me.
        
        Best,
        Sebastian
        
        ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
    2015-11-11 14:59 ` Kaushal Modi
  @ 2015-11-11 15:06 ` Xebar Saram
    2015-11-11 15:10 ` Russell Adams
                     ` (4 subsequent siblings)
    6 siblings, 0 replies; 28+ messages in thread
  From: Xebar Saram @ 2015-11-11 15:06 UTC (permalink / raw)
    To: Matt Price; +Cc: Org Mode
  
  [-- Attachment #1: Type: text/plain, Size: 508 bytes --]
  
  thanks for the interesting post!
  
  you now have 0+1 readers (just subscribed via rss)  ;-)
  
  best
  
  Z
  
  On Wed, Nov 11, 2015 at 4:42 PM, Matt Price <moptop99@gmail.com> wrote:
  
  > I've just written up a post on my workflow for PDF's Since my blog has, I
  > think, a readership of 0 (surely there's a way to get emacsers to follow
  > me? ah well), I will post a link here in the hopes that someone will be
  > interested:
  >
  > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
  >
  > All best!
  > Matt
  >
  
  [-- Attachment #2: Type: text/html, Size: 1144 bytes --]
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
    2015-11-11 14:59 ` Kaushal Modi
    2015-11-11 15:06 ` Xebar Saram
  @ 2015-11-11 15:10 ` Russell Adams
    2015-11-11 16:40 ` Jeffrey DeLeo
                     ` (3 subsequent siblings)
    6 siblings, 0 replies; 28+ messages in thread
  From: Russell Adams @ 2015-11-11 15:10 UTC (permalink / raw)
    To: emacs-orgmode
  
  On Wed, Nov 11, 2015 at 09:42:13AM -0500, Matt Price wrote:
  > I've just written up a post on my workflow for PDF's Since my blog has, I
  > think, a readership of 0 (surely there's a way to get emacsers to follow
  > me? ah well), I will post a link here in the hopes that someone will be
  > interested:
  >
  > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
  >
  > All best!
  > Matt
  
  In the past I have just had the PDF open in emacs (docview?), made a
  bookmark, and inserted that into Org. It only links to the page
  though, not the text.
  
  Thanks.
  
  
  ------------------------------------------------------------------
  Russell Adams                            RLAdams@AdamsInfoServ.com
  
  PGP Key ID:     0x1160DCB3           http://www.adamsinfoserv.com/
  
  Fingerprint:    1723 D8CA 4280 1EC9 557F  66E8 1154 E018 1160 DCB3
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
                     ` (2 preceding siblings ...)
    2015-11-11 15:10 ` Russell Adams
  @ 2015-11-11 16:40 ` Jeffrey DeLeo
    2015-11-11 20:18   ` Matt Price
    2015-11-11 17:09 ` Memnon Anon
                     ` (2 subsequent siblings)
    6 siblings, 1 reply; 28+ messages in thread
  From: Jeffrey DeLeo @ 2015-11-11 16:40 UTC (permalink / raw)
    To: emacs-orgmode
  
  
  Matt Price <moptop99@gmail.com> writes:
  > I've just written up a post on my workflow for PDF's
  
  Thanks, this is helpful.
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• • * Re: Org Mode and PDF Notes!
      2015-11-11 16:40 ` Jeffrey DeLeo
    @ 2015-11-11 20:18   ` Matt Price
      0 siblings, 0 replies; 28+ messages in thread
    From: Matt Price @ 2015-11-11 20:18 UTC (permalink / raw)
      Cc: Org Mode
    
    [-- Attachment #1: Type: text/plain, Size: 455 bytes --]
    
    FWIW, I've just updated the post with
    - links that jump directly to the highlighted text
    - a new custom link type that opens highlights in a temporary buffer
    instead.
    
    http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
    
    On Wed, Nov 11, 2015 at 11:40 AM, Jeffrey DeLeo <JeffreyDeLeo@gmail.com>
    wrote:
    
    >
    > Matt Price <moptop99@gmail.com> writes:
    > > I've just written up a post on my workflow for PDF's
    >
    > Thanks, this is helpful.
    >
    >
    >
    
    [-- Attachment #2: Type: text/html, Size: 984 bytes --]
    
    ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
                     ` (3 preceding siblings ...)
    2015-11-11 16:40 ` Jeffrey DeLeo
  @ 2015-11-11 17:09 ` Memnon Anon
    2015-11-11 20:34   ` Matt Price
    2015-11-11 20:17 ` Ramon Diaz-Uriarte
    2015-11-12 11:30 ` Karl Voit
    6 siblings, 1 reply; 28+ messages in thread
  From: Memnon Anon @ 2015-11-11 17:09 UTC (permalink / raw)
    To: emacs-orgmode
  
  Matt Price <moptop99@gmail.com> writes:
  
  > [...] Since my blog
  > has, I think, a readership of 0 (surely there's a way to get emacsers
  > to follow me? ah well), I will post a link here [...]
  
  http://planet.emacsen.org/
  -- 
  /-------------------------------------------\
  | SDF and SDF-EU Public Access UNIX System  |
  | http://sdf.org   ||   http://sdf-eu.org   |
  =============================================
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• • * Re: Org Mode and PDF Notes!
      2015-11-11 17:09 ` Memnon Anon
    @ 2015-11-11 20:34   ` Matt Price
      2015-11-12 17:31     ` Memnon Anon
      0 siblings, 1 reply; 28+ messages in thread
    From: Matt Price @ 2015-11-11 20:34 UTC (permalink / raw)
      To: Org Mode
    
    [-- Attachment #1: Type: text/plain, Size: 435 bytes --]
    
    On Wed, Nov 11, 2015 at 12:09 PM, Memnon Anon <memnon+usenet@freeshell.org>
    wrote:
    
    > Matt Price <moptop99@gmail.com> writes:
    >
    > > [...] Since my blog
    > > has, I think, a readership of 0 (surely there's a way to get emacsers
    > > to follow me? ah well), I will post a link here [...]
    >
    > http://planet.emacsen.org/\ <http://planet.emacsen.org/>
    
    But I can't figure out how to add my blog to the list there! Can you tell
    me the secret?
    
    [-- Attachment #2: Type: text/html, Size: 933 bytes --]
    
    ^ permalink raw reply	[flat|nested] 28+ messages in thread

  • • * Re: Org Mode and PDF Notes!
        2015-11-11 20:34   ` Matt Price
      @ 2015-11-12 17:31     ` Memnon Anon
        0 siblings, 0 replies; 28+ messages in thread
      From: Memnon Anon @ 2015-11-12 17:31 UTC (permalink / raw)
        To: emacs-orgmode
      
      Matt Price <moptop99@gmail.com> writes:
      
      > On Wed, Nov 11, 2015 at 12:09 PM, Memnon Anon <
      > memnon+usenet@freeshell.org> wrote:
      >
      >     http://planet.emacsen.org/\
      >
      > But I can't figure out how to add my blog to the list there! Can you
      > tell me the secret?
      
      http://edward.oconnor.cx/2009/11/planet-emacsen-turns-3
      
      ,----
      | If you’d like me to add your Emacs feed to Planet Emacsen, send me an
      | email [mailto:hober0@gmail.com] and I’ll get right on it.
      `----
      
      While you are at it, please ask him to put that info somewhere more
      visible on the site itself...
      -- 
      /-------------------------------------------\
      | SDF and SDF-EU Public Access UNIX System  |
      | http://sdf.org   ||   http://sdf-eu.org   |
      =============================================
      
      ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
                     ` (4 preceding siblings ...)
    2015-11-11 17:09 ` Memnon Anon
  @ 2015-11-11 20:17 ` Ramon Diaz-Uriarte
    2015-11-11 20:33   ` Matt Price
    2015-11-12 11:30 ` Karl Voit
    6 siblings, 1 reply; 28+ messages in thread
  From: Ramon Diaz-Uriarte @ 2015-11-11 20:17 UTC (permalink / raw)
    To: Matt Price; +Cc: Org Mode
  
  Dear Matt,
  
  
  On Wed, 11-11-2015, at 15:42, Matt Price <moptop99@gmail.com> wrote:
  > I've just written up a post on my workflow for PDF's Since my blog has, I
  > think, a readership of 0 (surely there's a way to get emacsers to follow
  > me? ah well), I will post a link here in the hopes that someone will be
  
  Add another 1 :-)
  
  > interested:
  >
  > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
  >
  
  Really neat! A few comments/questions/ramblings:
  
  - The type of highlights you get from RepliGo contain the text itself. I
    mean, when in your pdf I use C-c C-a l, the buffer showing the contents
    of each highlight contain  the highlighted text.
  
    This is not what I get from, say, EzPDF (which is what I use on Android),
    or from highlighting from pdf-tools itself using C-c C-a h, or from
    highlighting from Okular. The contents just gives the rectangle). Hummmm...
  
  
    Because of this, when I use your code on my pdfs, I only get things
    such as
  
  Highlight
  ([[pdfview:/home/ramon/Zotero-data/storage/ESHHD4KW/Frank_2015_Commentary.pdf::5][Frank_2015_Commentary]],
  5)
  
  
    instead of the text. Bummer! I wonder if RepliGO gives you a lot more
    than the rest, or if I am doing something silly.
  
  
  - You have to call mwp/pdf-multi-extract on each file/set of files. I guess
    if I knew elisp, I'd find it trivial to iterate over a set of directories
    and subdirectories (and do this using a cron job at night), and also
    place everything in one single org file. Would this be something
    reasonable to do?
  
    (This might be related to your second Todo)
  
  
  - I know nothing about how it works, and it does not use pdf-tools, but in
    your first Todo you mention: "extend the pdfview link type (in
    org-pdfview) to permit me to specify the precise location of an
    annotation,".  PDF.js (https://mozilla.github.io/pdf.js/), which is
    used for instance by zotfile (http://zotfile.com/) does that and it works
    out of the box with Okular (but I've not been able to get it to work with
    pdftools).
  
  
  - In case it matters, I have somewhat similar modus operandi.  I do a lot
    of PDF reading, including note-taking and highlighting, in android
    tablets ---I use EzPDF, which also embeds the notes in the PDF. I have a
    cron job that extracts all the highlights and annotations of all the PDFs
    and places them in a single org file. The kludge is explained here:
    https://github.com/rdiaz02/Adios_Mendeley#extracting-all-pdf-annotations-and-placing-them-in-an-org-mode-file
    The truth is I use two mechanisms for PDF annotation and highlighting
    extraction, since none is fully satisfactory to me, but the one that uses
    Ruby (i.e., that does not depend on poppler) is able to actually extract
    the text of the highlights.
  
  
  Best, and thanks again for sharing,
  
  
  R.
  
  
  
  
  
  > All best!
  > Matt
  
  
  -- 
  Ramon Diaz-Uriarte
  Department of Biochemistry, Lab B-25
  Facultad de Medicina
  Universidad Autónoma de Madrid 
  Arzobispo Morcillo, 4
  28029 Madrid
  Spain
  
  Phone: +34-91-497-2412
  
  Email: rdiaz02@gmail.com
         ramon.diaz@iib.uam.es
  
  http://ligarto.org/rdiaz
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

• • * Re: Org Mode and PDF Notes!
      2015-11-11 20:17 ` Ramon Diaz-Uriarte
    @ 2015-11-11 20:33   ` Matt Price
      2015-11-11 22:43     ` Matt Lundin
      2015-11-12 12:23     ` Ramon Diaz-Uriarte
      0 siblings, 2 replies; 28+ messages in thread
    From: Matt Price @ 2015-11-11 20:33 UTC (permalink / raw)
      To: Ramon Diaz-Uriarte; +Cc: Org Mode
    
    [-- Attachment #1: Type: text/plain, Size: 4622 bytes --]
    
    On Wed, Nov 11, 2015 at 3:17 PM, Ramon Diaz-Uriarte <rdiaz02@gmail.com>
    wrote:
    
    > Dear Matt,
    >
    >
    > On Wed, 11-11-2015, at 15:42, Matt Price <moptop99@gmail.com> wrote:
    > > I've just written up a post on my workflow for PDF's Since my blog has, I
    > > think, a readership of 0 (surely there's a way to get emacsers to follow
    > > me? ah well), I will post a link here in the hopes that someone will be
    >
    > Add another 1 :-)
    >
    > > interested:
    > >
    > > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
    > >
    >
    > Really neat! A few comments/questions/ramblings:
    >
    > - The type of highlights you get from RepliGo contain the text itself. I
    >   mean, when in your pdf I use C-c C-a l, the buffer showing the contents
    >   of each highlight contain  the highlighted text.
    >
    >   This is not what I get from, say, EzPDF (which is what I use on Android),
    >   or from highlighting from pdf-tools itself using C-c C-a h, or from
    >   highlighting from Okular. The contents just gives the rectangle).
    > Hummmm...
    >
    >
    >   Because of this, when I use your code on my pdfs, I only get things
    >   such as
    >
    > Highlight
    >
    > ([[pdfview:/home/ramon/Zotero-data/storage/ESHHD4KW/Frank_2015_Commentary.pdf::5][Frank_2015_Commentary]],
    > 5)
    >
    >
    >   instead of the text. Bummer! I wonder if RepliGO gives you a lot more
    >   than the rest, or if I am doing something silly.
    >
    > I think that there is no standard way of storing the highlight contents. I
    chose Repligo over EZPDF because it gives you access to the text of the
    highlights!
    
    Okular, I think, stores your annotations in its own database, rather than
    in the pdf. You can (I think!) attach the annotations to the pdf from
    inside Okular.  At leasts, that's what I remember from when I was looking
    around.
    
    Repligo stores the highlighted text in the "subject" field of the
    annotation. It's possible that the content of the annotation is stored in
    some other field, like "content".  Maybe you can try:
    
    M-: (pdf-annot-get-annots) and look at the output in the *Messages*
    buffer.  Can you see any evidence of the the text? Can you share what you
    learned?
    
    Politza and I are discussing this here:
    https://github.com/politza/pdf-tools/issues/137
    
    that might be a good place to ocntinue the conversation.
    
    
    >
    > - You have to call mwp/pdf-multi-extract on each file/set of files. I guess
    >   if I knew elisp, I'd find it trivial to iterate over a set of directories
    >   and subdirectories (and do this using a cron job at night), and also
    >   place everything in one single org file. Would this be something
    >   reasonable to do?
    >
    > for sure.  My elisp sucks too but I bet someone will answer you here on
    the list.
    
    
    >   (This might be related to your second Todo)
    >
    > well, wasn't what I was planning but would still be useful.
    
    >
    > - I know nothing about how it works, and it does not use pdf-tools, but in
    >   your first Todo you mention: "extend the pdfview link type (in
    >   org-pdfview) to permit me to specify the precise location of an
    >   annotation,".  PDF.js (https://mozilla.github.io/pdf.js/), which is
    >   used for instance by zotfile (http://zotfile.com/) does that and it
    > works
    >   out of the box with Okular (but I've not been able to get it to work with
    >   pdftools).
    >
    > Until I found pdf-tools, I had planned to write a node wrapper for pdf.js
    and grab the annotations that way.  But I don't really know how to do that,
    so this turned out to be easier :-)
    
    Anyway, I've judated the post, and it's now possible to create links to
    individualt annotations, though you will have to use my updated version of
    org-pdfview, until/unless Markus accepts my patch.
    
    >
    > - In case it matters, I have somewhat similar modus operandi.  I do a lot
    >   of PDF reading, including note-taking and highlighting, in android
    >   tablets ---I use EzPDF, which also embeds the notes in the PDF. I have a
    >   cron job that extracts all the highlights and annotations of all the PDFs
    >   and places them in a single org file. The kludge is explained here:
    >
    > https://github.com/rdiaz02/Adios_Mendeley#extracting-all-pdf-annotations-and-placing-them-in-an-org-mode-file
    >   The truth is I use two mechanisms for PDF annotation and highlighting
    >   extraction, since none is fully satisfactory to me, but the one that uses
    >   Ruby (i.e., that does not depend on poppler) is able to actually extract
    >   the text of the highlights.
    >
    > ah, man, that looks really cool and I'm sorry I didn't know about it
    earlier! I haven't read through your whole document but looks like there's
    a lot useful stuff there.
    
    
    
    >
    > Best, and thanks again for sharing,
    >
    > you're welcome & thank you!
    m
    
    [-- Attachment #2: Type: text/html, Size: 6761 bytes --]
    
    ^ permalink raw reply	[flat|nested] 28+ messages in thread

  • • * Re: Org Mode and PDF Notes!
        2015-11-11 20:33   ` Matt Price
      @ 2015-11-11 22:43     ` Matt Lundin
        2015-11-12 12:23     ` Ramon Diaz-Uriarte
        1 sibling, 0 replies; 28+ messages in thread
      From: Matt Lundin @ 2015-11-11 22:43 UTC (permalink / raw)
        To: Matt Price; +Cc: Ramon Diaz-Uriarte, Org Mode
      
      Matt Price <moptop99@gmail.com> writes:
      >
      > I think that there is no standard way of storing the highlight
      > contents. I chose Repligo over EZPDF because it gives you access to
      > the text of the highlights!
      
      > Okular, I think, stores your annotations in its own database, rather
      > than in the pdf. You can (I think!) attach the annotations to the pdf
      > from inside Okular. At leasts, that's what I remember from when I was
      > looking around.
      
      > Repligo stores the highlighted text in the "subject" field of the
      > annotation. It's possible that the content of the annotation is stored
      > in some other field, like "content". Maybe you can try:
      
      Repligo (as you say) grabs the text in the highlighted region and adds
      it to the "subject" connected to the highlight. I think it is rather
      unique in doing so. AFAIK, Okular, pdf-tools, or other android tools
      (mupdf, xodo reader) do not not do this. In other words, it is thanks of
      Repligo's previous extraction that the function on Matt's blog is able
      get the text of the highlighted region.
      
      Otherwise, you would need a means of going back into the region
      highlighted and extracting the embedded text. Pdf-tools doesn't
      currently extract the text, but it might not be that difficult to modify
      it to do so, since it already has the bounds of the highlighted region
      and can select and copy text embedded in the pdf.
      
      Best,
      Matt
      
      ^ permalink raw reply	[flat|nested] 28+ messages in thread

    • * Re: Org Mode and PDF Notes!
        2015-11-11 20:33   ` Matt Price
        2015-11-11 22:43     ` Matt Lundin
      @ 2015-11-12 12:23     ` Ramon Diaz-Uriarte
        2015-11-12 13:11       ` Matt Price
        2015-11-12 14:28       ` Matt Lundin
        1 sibling, 2 replies; 28+ messages in thread
      From: Ramon Diaz-Uriarte @ 2015-11-12 12:23 UTC (permalink / raw)
        To: Matt Price; +Cc: Ramon Diaz-Uriarte, Org Mode
      
      
      
      
      On Wed, 11-11-2015, at 21:33, Matt Price <moptop99@gmail.com> wrote:
      >>
      >>
      >>   instead of the text. Bummer! I wonder if RepliGO gives you a lot more
      >>   than the rest, or if I am doing something silly.
      >>
      >> I think that there is no standard way of storing the highlight contents. I
      > chose Repligo over EZPDF because it gives you access to the text of the
      > highlights!
      
      
      I'll try to see if I can get repligo (I had it a few years ago)
      
      >
      > Okular, I think, stores your annotations in its own database, rather than
      > in the pdf. You can (I think!) attach the annotations to the pdf from
      > inside Okular.  At leasts, that's what I remember from when I was looking
      > around.
      
      Actually, Okular stores the annotations in the PDF itself if you do "Save
      As". (It still keeps an internal db, but I never use it anymore). It is
      easy to check by doing that and then opening the file with another reader
      in another machine (e.g., in an android).
      
      
      
      >
      > Repligo stores the highlighted text in the "subject" field of the
      > annotation. It's possible that the content of the annotation is stored in
      > some other field, like "content".  Maybe you can try:
      >
      > M-: (pdf-annot-get-annots) and look at the output in the *Messages*
      > buffer.  Can you see any evidence of the the text? Can you share what you
      > learned?
      
      Nope, no evidence of the text. I get things such as
      
      (((buffer . #<buffer Frank_2015_Commentary.pdf>) (page . 13) (edges
      0.113553 0.31717 0.868657 0.361746) (type . highlight) (id . annot-13-0)
      (flags . 4) (color . "#ffff00") (contents . "") (modified 22081 45188)
      (label . "TF201") (subject . "Highlight") (opacity . 1.0) ...)
      
      
      so we get the location of the highlight (and its properties), but not the
      textual contents. And this is the case whether I make the annotation with
      EzPDF or Okular or, for that matter, with pdf-tools itself.
      
      So it seems RepliGO is actually giving you a lot more by default :-)
      
      
      >
      > Politza and I are discussing this here:
      > https://github.com/politza/pdf-tools/issues/137
      >
      > that might be a good place to ocntinue the conversation.
      >
      
      I'll do. In the meantime, I think this is a limitation coming from
      poppler. Other people have mentioned similar things (e.g.,
      http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using other
      tools that depend on poppler (such as Leela:
      https://github.com/TrilbyWhite/Leela) also will not give us the text
      itself. 
      
      
      
      >>
      >> Until I found pdf-tools, I had planned to write a node wrapper for pdf.js
      > and grab the annotations that way.  But I don't really know how to do that,
      > so this turned out to be easier :-)
      >
      > Anyway, I've judated the post, and it's now possible to create links to
      > individualt annotations, though you will have to use my updated version of
      > org-pdfview, until/unless Markus accepts my patch.
      
      
      I just updated packages, and things are working perfectly: I am jumping to
      the page and location.
      
      
      
      Thanks,
      
      
      R.
      
      
      
      
      -- 
      Ramon Diaz-Uriarte
      Department of Biochemistry, Lab B-25
      Facultad de Medicina
      Universidad Autónoma de Madrid 
      Arzobispo Morcillo, 4
      28029 Madrid
      Spain
      
      Phone: +34-91-497-2412
      
      Email: rdiaz02@gmail.com
             ramon.diaz@iib.uam.es
      
      http://ligarto.org/rdiaz
      
      ^ permalink raw reply	[flat|nested] 28+ messages in thread

    • • * Re: Org Mode and PDF Notes!
          2015-11-12 12:23     ` Ramon Diaz-Uriarte
        @ 2015-11-12 13:11       ` Matt Price
          2015-11-13  0:39         ` Ramon Diaz-Uriarte
          2015-11-12 14:28       ` Matt Lundin
          1 sibling, 1 reply; 28+ messages in thread
        From: Matt Price @ 2015-11-12 13:11 UTC (permalink / raw)
          To: Ramon Diaz-Uriarte; +Cc: Org Mode
        
        [-- Attachment #1: Type: text/plain, Size: 3669 bytes --]
        
        On Thu, Nov 12, 2015 at 7:23 AM, Ramon Diaz-Uriarte <rdiaz02@gmail.com>
        wrote:
        
        >
        >
        >
        > On Wed, 11-11-2015, at 21:33, Matt Price <moptop99@gmail.com> wrote:
        > >>
        > >>
        > >>   instead of the text. Bummer! I wonder if RepliGO gives you a lot more
        > >>   than the rest, or if I am doing something silly.
        > >>
        > >> I think that there is no standard way of storing the highlight
        > contents. I
        > > chose Repligo over EZPDF because it gives you access to the text of the
        > > highlights!
        >
        >
        > I'll try to see if I can get repligo (I had it a few years ago)
        >
        > >
        > > Okular, I think, stores your annotations in its own database, rather than
        > > in the pdf. You can (I think!) attach the annotations to the pdf from
        > > inside Okular.  At leasts, that's what I remember from when I was looking
        > > around.
        >
        > Actually, Okular stores the annotations in the PDF itself if you do "Save
        > As". (It still keeps an internal db, but I never use it anymore). It is
        > easy to check by doing that and then opening the file with another reader
        > in another machine (e.g., in an android).
        >
        >
        > my bad, thx.
        
        >
        > >
        > > Repligo stores the highlighted text in the "subject" field of the
        > > annotation. It's possible that the content of the annotation is stored in
        > > some other field, like "content".  Maybe you can try:
        > >
        > > M-: (pdf-annot-get-annots) and look at the output in the *Messages*
        > > buffer.  Can you see any evidence of the the text? Can you share what you
        > > learned?
        >
        > Nope, no evidence of the text. I get things such as
        >
        > (((buffer . #<buffer Frank_2015_Commentary.pdf>) (page . 13) (edges
        > 0.113553 0.31717 0.868657 0.361746) (type . highlight) (id . annot-13-0)
        > (flags . 4) (color . "#ffff00") (contents . "") (modified 22081 45188)
        > (label . "TF201") (subject . "Highlight") (opacity . 1.0) ...)
        >
        >
        > so we get the location of the highlight (and its properties), but not the
        > textual contents. And this is the case whether I make the annotation with
        > EzPDF or Okular or, for that matter, with pdf-tools itself.
        >
        > So it seems RepliGO is actually giving you a lot more by default :-)
        >
        >
        Try replacing
        
        (text (assoc-default 'subject annot))
        
        with
        
        (text (pdf-info-gettext page (assoc-default 'edges annot)))
        
        
        in the lambda function in pdf-annot-markups-as-org-text.  This will fail on
        cropped pdfs if you have added highlights using the most recent pdf-tools,
        which stores negative values in the 'edges field, but I've found it works
        otherwise.  I'd love to hear if it works for you too. (I know you're
        following the relevant bug report on the pdf-tools github repo).
        
        
        >
        > >
        > > Politza and I are discussing this here:
        > > https://github.com/politza/pdf-tools/issues/137
        > >
        > > that might be a good place to ocntinue the conversation.
        > >
        >
        > I'll do. In the meantime, I think this is a limitation coming from
        > poppler. Other people have mentioned similar things (e.g.,
        > http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using
        > other
        > tools that depend on poppler (such as Leela:
        > https://github.com/TrilbyWhite/Leela) also will not give us the text
        > itself.
        >
        >
        >
        > >>
        > >> Until I found pdf-tools, I had planned to write a node wrapper for
        > pdf.js
        > > and grab the annotations that way.  But I don't really know how to do
        > that,
        > > so this turned out to be easier :-)
        > >
        > > Anyway, I've judated the post, and it's now possible to create links to
        > > individualt annotations, though you will have to use my updated version
        > of
        > > org-pdfview, until/unless Markus accepts my patch.
        >
        >
        > I just updated packages, and things are working perfectly: I am jumping to
        > the page and location.
        >
        >
        >
        > Thanks,
        >
        >
        > R.
        >
        >
        >
        >
        >
        
        [-- Attachment #2: Type: text/html, Size: 5449 bytes --]
        
        ^ permalink raw reply	[flat|nested] 28+ messages in thread

      • • * Re: Org Mode and PDF Notes!
            2015-11-12 13:11       ` Matt Price
          @ 2015-11-13  0:39         ` Ramon Diaz-Uriarte
            0 siblings, 0 replies; 28+ messages in thread
          From: Ramon Diaz-Uriarte @ 2015-11-13  0:39 UTC (permalink / raw)
            To: Matt Price; +Cc: Ramon Diaz-Uriarte, Org Mode
          
          
          
          
          On Thu, 12-11-2015, at 14:11, Matt Price <moptop99@gmail.com> wrote:
          >> >
          >> > M-: (pdf-annot-get-annots) and look at the output in the *Messages*
          >> > buffer.  Can you see any evidence of the the text? Can you share what you
          >> > learned?
          >>
          >> Nope, no evidence of the text. I get things such as
          >>
          >> (((buffer . #<buffer Frank_2015_Commentary.pdf>) (page . 13) (edges
          >> 0.113553 0.31717 0.868657 0.361746) (type . highlight) (id . annot-13-0)
          >> (flags . 4) (color . "#ffff00") (contents . "") (modified 22081 45188)
          >> (label . "TF201") (subject . "Highlight") (opacity . 1.0) ...)
          >>
          >>
          >> so we get the location of the highlight (and its properties), but not the
          >> textual contents. And this is the case whether I make the annotation with
          >> EzPDF or Okular or, for that matter, with pdf-tools itself.
          >>
          >> So it seems RepliGO is actually giving you a lot more by default :-)
          >>
          >>
          > Try replacing
          >
          > (text (assoc-default 'subject annot))
          >
          > with
          >
          > (text (pdf-info-gettext page (assoc-default 'edges annot)))
          >
          >
          > in the lambda function in pdf-annot-markups-as-org-text.  This will fail on
          > cropped pdfs if you have added highlights using the most recent pdf-tools,
          > which stores negative values in the 'edges field, but I've found it works
          > otherwise.  I'd love to hear if it works for you too. (I know you're
          > following the relevant bug report on the pdf-tools github repo).
          
          
          It works! I get the highlighted text (I have just tried with a pdf I
          highlighted with EzPDF, the one that, above, was giving just the location
          and properties). And it still does the correct thing in your pdf (the one
          from repligo).
          
          Awesome! Thanks.
          
          
          R.
          
          
          
          
          
          -- 
          Ramon Diaz-Uriarte
          Department of Biochemistry, Lab B-25
          Facultad de Medicina
          Universidad Autónoma de Madrid 
          Arzobispo Morcillo, 4
          28029 Madrid
          Spain
          
          Phone: +34-91-497-2412
          
          Email: rdiaz02@gmail.com
                 ramon.diaz@iib.uam.es
          
          http://ligarto.org/rdiaz
          
          ^ permalink raw reply	[flat|nested] 28+ messages in thread

      • * Re: Org Mode and PDF Notes!
          2015-11-12 12:23     ` Ramon Diaz-Uriarte
          2015-11-12 13:11       ` Matt Price
        @ 2015-11-12 14:28       ` Matt Lundin
          2015-11-12 22:52         ` Matt Price
          2015-11-12 23:55         ` Ramon Diaz-Uriarte
          1 sibling, 2 replies; 28+ messages in thread
        From: Matt Lundin @ 2015-11-12 14:28 UTC (permalink / raw)
          To: Ramon Diaz-Uriarte; +Cc: Org Mode
        
        Ramon Diaz-Uriarte <rdiaz02@gmail.com> writes:
        
        >
        > so we get the location of the highlight (and its properties), but not the
        > textual contents. And this is the case whether I make the annotation with
        > EzPDF or Okular or, for that matter, with pdf-tools itself.
        >
        > So it seems RepliGO is actually giving you a lot more by default :-)
        >
        >>
        >> Politza and I are discussing this here:
        >> https://github.com/politza/pdf-tools/issues/137
        >>
        >> that might be a good place to ocntinue the conversation.
        >>
        >
        > I'll do. In the meantime, I think this is a limitation coming from
        > poppler. Other people have mentioned similar things (e.g.,
        > http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using other
        > tools that depend on poppler (such as Leela:
        > https://github.com/TrilbyWhite/Leela) also will not give us the text
        > itself. 
        
        I don't think this is a limitation of poppler so much as the way that
        pdf annotations work. Typically, the subject/text field is not populated
        by the text of the highlighted region. Rather, a highlight annotation
        specifies bounds, color, style, etc. Basically what Repligo does (I
        wouldn't recommend using it, as it is closed source and severely out of
        date) is to grab the text *at the time of highlighting* and add it to
        the notes field. I don't know of any other annotation tool that does the
        same thing. Applications built on poppler could do it, though they
        currently do not.
        
        For extracting the text of highlighted regions *after the fact*, I've
        had good luck with this script that relies on the pdf-reader gem for
        ruby:
        
        https://gist.github.com/danlucraft/5277732
        
        Matt
        
        ^ permalink raw reply	[flat|nested] 28+ messages in thread

      • • * Re: Org Mode and PDF Notes!
            2015-11-12 14:28       ` Matt Lundin
          @ 2015-11-12 22:52         ` Matt Price
            2015-11-12 23:51           ` Ramon Diaz-Uriarte
            2015-11-12 23:55         ` Ramon Diaz-Uriarte
            1 sibling, 1 reply; 28+ messages in thread
          From: Matt Price @ 2015-11-12 22:52 UTC (permalink / raw)
            Cc: Org Mode
          
          [-- Attachment #1: Type: text/plain, Size: 1565 bytes --]
          
          On Thu, Nov 12, 2015 at 9:28 AM, Matt Lundin <mdl@imapmail.org> wrote:
          
          > Ramon Diaz-Uriarte <rdiaz02@gmail.com> writes:
          > >
          > > I'll do. In the meantime, I think this is a limitation coming from
          > > poppler. Other people have mentioned similar things (e.g.,
          > > http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using
          > other
          > > tools that depend on poppler (such as Leela:
          > > https://github.com/TrilbyWhite/Leela) also will not give us the text
          > > itself.
          >
          > I don't think this is a limitation of poppler so much as the way that
          > pdf annotations work. Typically, the subject/text field is not populated
          > by the text of the highlighted region. Rather, a highlight annotation
          > specifies bounds, color, style, etc. Basically what Repligo does (I
          > wouldn't recommend using it, as it is closed source and severely out of
          > date) is to grab the text *at the time of highlighting* and add it to
          > the notes field. I don't know of any other annotation tool that does the
          > same thing. Applications built on poppler could do it, though they
          > currently do not.
          >
          > For extracting the text of highlighted regions *after the fact*, I've
          > had good luck with this script that relies on the pdf-reader gem for
          > ruby:
          >
          > https://gist.github.com/danlucraft/5277732
          >
          > This looks interesting. It searches for file "./markup_receiver", but
          doesn't provide that file, which does not appear to be a gem.  Any hints?
          
          With politza's help am getting close to being able to extract annotation
          text from within pdf-tools, but am not quite there yet.
          
          
          > Matt
          >
          
          [-- Attachment #2: Type: text/html, Size: 2615 bytes --]
          
          ^ permalink raw reply	[flat|nested] 28+ messages in thread

        • • * Re: Org Mode and PDF Notes!
              2015-11-12 22:52         ` Matt Price
            @ 2015-11-12 23:51           ` Ramon Diaz-Uriarte
              0 siblings, 0 replies; 28+ messages in thread
            From: Ramon Diaz-Uriarte @ 2015-11-12 23:51 UTC (permalink / raw)
              To: Matt Price; +Cc: Org Mode
            
            
            
            
            On Thu, 12-11-2015, at 23:52, Matt Price <moptop99@gmail.com> wrote:
            > On Thu, Nov 12, 2015 at 9:28 AM, Matt Lundin <mdl@imapmail.org> wrote:
            >
            >> Ramon Diaz-Uriarte <rdiaz02@gmail.com> writes:
            >> >
            >> > I'll do. In the meantime, I think this is a limitation coming from
            >> > poppler. Other people have mentioned similar things (e.g.,
            >> > http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using
            >> other
            >> > tools that depend on poppler (such as Leela:
            >> > https://github.com/TrilbyWhite/Leela) also will not give us the text
            >> > itself.
            >>
            >> I don't think this is a limitation of poppler so much as the way that
            >> pdf annotations work. Typically, the subject/text field is not populated
            >> by the text of the highlighted region. Rather, a highlight annotation
            >> specifies bounds, color, style, etc. Basically what Repligo does (I
            >> wouldn't recommend using it, as it is closed source and severely out of
            >> date) is to grab the text *at the time of highlighting* and add it to
            >> the notes field. I don't know of any other annotation tool that does the
            >> same thing. Applications built on poppler could do it, though they
            >> currently do not.
            >>
            >> For extracting the text of highlighted regions *after the fact*, I've
            >> had good luck with this script that relies on the pdf-reader gem for
            >> ruby:
            >>
            >> https://gist.github.com/danlucraft/5277732
            >>
            >> This looks interesting. It searches for file "./markup_receiver", but
            > doesn't provide that file, which does not appear to be a gem.  Any hints?
            
            
            I think I got it from
            
            https://www.omniref.com/github/danlucraft/pyranine/HEAD/files/lib/pyranine/markup_receiver.rb
            
            >
            > With politza's help am getting close to being able to extract annotation
            > text from within pdf-tools, but am not quite there yet.
            
            
            Neat!
            
            
            R.
            
            
            >
            >
            >> Matt
            >>
            
            
            -- 
            Ramon Diaz-Uriarte
            Department of Biochemistry, Lab B-25
            Facultad de Medicina
            Universidad Autónoma de Madrid 
            Arzobispo Morcillo, 4
            28029 Madrid
            Spain
            
            Phone: +34-91-497-2412
            
            Email: rdiaz02@gmail.com
                   ramon.diaz@iib.uam.es
            
            http://ligarto.org/rdiaz
            
            ^ permalink raw reply	[flat|nested] 28+ messages in thread

        • * Re: Org Mode and PDF Notes!
            2015-11-12 14:28       ` Matt Lundin
            2015-11-12 22:52         ` Matt Price
          @ 2015-11-12 23:55         ` Ramon Diaz-Uriarte
            1 sibling, 0 replies; 28+ messages in thread
          From: Ramon Diaz-Uriarte @ 2015-11-12 23:55 UTC (permalink / raw)
            To: Matt Lundin; +Cc: Ramon Diaz-Uriarte, Org Mode
          
          
          
          
          On Thu, 12-11-2015, at 15:28, Matt Lundin <mdl@imapmail.org> wrote:
          > Ramon Diaz-Uriarte <rdiaz02@gmail.com> writes:
          >
          >>
          >> so we get the location of the highlight (and its properties), but not the
          >> textual contents. And this is the case whether I make the annotation with
          >> EzPDF or Okular or, for that matter, with pdf-tools itself.
          >>
          >> So it seems RepliGO is actually giving you a lot more by default :-)
          >>
          >>>
          >>> Politza and I are discussing this here:
          >>> https://github.com/politza/pdf-tools/issues/137
          >>>
          >>> that might be a good place to ocntinue the conversation.
          >>>
          >>
          >> I'll do. In the meantime, I think this is a limitation coming from
          >> poppler. Other people have mentioned similar things (e.g.,
          >> http://coda.caseykuhlman.com/entries/2014/pdf-extract.html) and using other
          >> tools that depend on poppler (such as Leela:
          >> https://github.com/TrilbyWhite/Leela) also will not give us the text
          >> itself. 
          >
          > I don't think this is a limitation of poppler so much as the way that
          > pdf annotations work. Typically, the subject/text field is not populated
          > by the text of the highlighted region. Rather, a highlight annotation
          > specifies bounds, color, style, etc. Basically what Repligo does (I
          > wouldn't recommend using it, as it is closed source and severely out of
          > date) is to grab the text *at the time of highlighting* and add it to
          > the notes field. I don't know of any other annotation tool that does the
          > same thing. Applications built on poppler could do it, though they
          > currently do not.
          
          I stand corrected. You are right; sorry for the sloppiness in the wording
          and ideas.
          
          
          >
          > For extracting the text of highlighted regions *after the fact*, I've
          > had good luck with this script that relies on the pdf-reader gem for
          > ruby:
          >
          > https://gist.github.com/danlucraft/5277732
          
          That is also what I use for extracting the text from the highlighted
          regions.
          
          
          R.
          
          
          >
          > Matt
          
          
          -- 
          Ramon Diaz-Uriarte
          Department of Biochemistry, Lab B-25
          Facultad de Medicina
          Universidad Autónoma de Madrid 
          Arzobispo Morcillo, 4
          28029 Madrid
          Spain
          
          Phone: +34-91-497-2412
          
          Email: rdiaz02@gmail.com
                 ramon.diaz@iib.uam.es
          
          http://ligarto.org/rdiaz
          
          ^ permalink raw reply	[flat|nested] 28+ messages in thread

• * Re: Org Mode and PDF Notes!
    2015-11-11 14:42 Matt Price
                     ` (5 preceding siblings ...)
    2015-11-11 20:17 ` Ramon Diaz-Uriarte
  @ 2015-11-12 11:30 ` Karl Voit
    6 siblings, 0 replies; 28+ messages in thread
  From: Karl Voit @ 2015-11-12 11:30 UTC (permalink / raw)
    To: emacs-orgmode
  
  * Matt Price <moptop99@gmail.com> wrote:
  > --047d7b41411eff32e6052444d409
  > Content-Type: text/plain; charset=UTF-8
  >
  > I've just written up a post on my workflow for PDF's Since my blog has, I
  > think, a readership of 0 (surely there's a way to get emacsers to follow
  > me? ah well), I will post a link here in the hopes that someone will be
  > interested:
  >
  > http://matt.hackinghistory.ca/2015/11/11/note-taking-with-pdf-tools/
  
  Thanks for your blog post and the URL!
  
  I did something very similar a couple of years ago while writing my
  PhD thesis:
  https://github.com/novoid/extract_pdf_annotations_to_orgmode
  
  And I also have a blog which I use for Emacs/Org-mode stuff from
  time to time: http://karl-voit.at/
  
  This reminds me of implementing a tag-based RSS/Atom-feed for
  Emacs-related stuff to my blogging system ...
  
  -- 
  mail|git|SVN|photos|postings|SMS|phonecalls|RSS|CSV|XML to Org-mode:
         > get Memacs from https://github.com/novoid/Memacs <
  
  https://github.com/novoid/extract_pdf_annotations_to_orgmode + more on github
  
  ^ permalink raw reply	[flat|nested] 28+ messages in thread

end of thread, other threads:[~2015-11-16 10:07 UTC | newest]

Thread overview: 28+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2015-11-11 15:15 Org Mode and PDF Notes! Peter Davis
     [not found] <20@gmane.emacs.orgmode.nnrss>
2015-11-13  8:04 ` Matti Minkkinen
2015-11-16 10:07   ` Ramon Diaz-Uriarte
  -- strict thread matches above, loose matches on Subject: below --
2015-11-11 14:42 Matt Price
2015-11-11 14:59 ` Kaushal Modi
2015-11-11 20:38   ` Matt Price
2015-11-11 20:48     ` Kaushal Modi
2015-11-11 20:58       ` Matt Price
2015-11-12 12:02         ` Sebastian Christ
2015-11-12 11:58       ` Sebastian Christ
2015-11-11 15:06 ` Xebar Saram
2015-11-11 15:10 ` Russell Adams
2015-11-11 16:40 ` Jeffrey DeLeo
2015-11-11 20:18   ` Matt Price
2015-11-11 17:09 ` Memnon Anon
2015-11-11 20:34   ` Matt Price
2015-11-12 17:31     ` Memnon Anon
2015-11-11 20:17 ` Ramon Diaz-Uriarte
2015-11-11 20:33   ` Matt Price
2015-11-11 22:43     ` Matt Lundin
2015-11-12 12:23     ` Ramon Diaz-Uriarte
2015-11-12 13:11       ` Matt Price
2015-11-13  0:39         ` Ramon Diaz-Uriarte
2015-11-12 14:28       ` Matt Lundin
2015-11-12 22:52         ` Matt Price
2015-11-12 23:51           ` Ramon Diaz-Uriarte
2015-11-12 23:55         ` Ramon Diaz-Uriarte
2015-11-12 11:30 ` Karl Voit

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