Showing posts with label LaTeX. Show all posts
Showing posts with label LaTeX. Show all posts

2011/04/05

Automated creation of references with hyperlinks from Skim


In the post "Automated creation of a LaTeX compatible citation only from Skim! (with hyperlink included)" there is an AppleScript which creates a LaTeX reference in TextMate for the PDF file that you currently read in Skim. Now I will present an expanded and improved version of that AppleScript. Specifically the new AppleScript takes advantage of all my standardized notes in the first page of a PDF document.

These notes can be created automatically from the AppleScript in the post "How to create correctly the Skim notes which have the DEVONthink links, when you have already annotated the first page of the PDF document". Moreover you can find more information about these notes in my posts "How to put DevonThink links in Skim notes" and "Latin page numbers, Arabic page numbers and the fifth Skim note".

The references and hyperlinks that can be created from my new AppleScript are the following and correspond to the notes one through four:

1. A LaTeX reference to the exact PDF page which can be inserted in a MediaWiki page without any modifications or problems. Moreover, the necessary code for the creation of MediaWiki link is also included. An example is the following:
 (<rawtex>\cite{Deconstructing-the-Laws-of-Logic-Clark-2008a}</rawtex>: [x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=2 27])
A prerequisite for the use of this reference is to have installed and properly customized the Wiki2LaTeX MediaWiki extension. I will write more about this and its importance in a future post.

2. A LaTeX reference that can be inserted in a text file together with the proper LaTeX code for the creation of the corresponding hyperlink. An example is the following:
(\cite{Deconstructing-the-Laws-of-Logic-Clark-2008a}: \href{x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=2}{27})
3. A MediaWIki internal link to the wiki page of the source, followed by an external link to the PDF file itself. An example is the following:
([[Deconstructing the Laws of Logic - Clark]]: [x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=2 27]) 
4. A DEVONthink url

How to use this AppleScript

You should run the AppleScript when you read a PDF file in Skim and you want to make a reference to the current page. Additionally, a TextMate file should be opened. After the execution you can select from a menu which kind of reference you would like to be created. All the necessary numbers for the hyperlinks and the references are automatically created with the help of the fifth note. You can see this AppleScript in action in the following video:



The AppleScript code is the following:
--2011-04-05
--http://organognosi.blogspot.com

tell application "Skim"
    activate
    set numberOfNote5 to (get text for note 5 of page 1 of document 1) as string
   
    set RefType to my chooseRefType({"Latex for MediaWiki", "Latex", "MediaWiki", "DEVONthink link"})
    if RefType is 0 then return
   
    tell document 1
        set currentPageNumber to get index of current page
        set currentPageNumberText to currentPageNumber as text
        set pageDevonThinkNumber to currentPageNumber - 1
        set pageDevonThinkNumberText to pageDevonThinkNumber as text
        set DevonThinkLink to get text of note RefType of page 1
        set theRealPage to currentPageNumber + numberOfNote5 as string
       
        tell application "TextMate"
            activate
            if RefType is 1 then
                insert DevonThinkLink
                delay 1
                tell application "System Events"
                    key code 123
                    key code 123
                end tell
                delay 1
                insert pageDevonThinkNumberText & " " & theRealPage
                tell application "System Events"
                    key code 124
                    key code 124
                end tell
            else if RefType is 2 then
                insert DevonThinkLink
                delay 1
                tell application "System Events"
                    key code 123
                    key code 123
                    key code 123
                    key code 123
                end tell
                delay 1
                insert pageDevonThinkNumberText
                tell application "System Events"
                    key code 124
                    key code 124
                end tell
                delay 1
                insert theRealPage
                tell application "System Events"
                    key code 124
                    key code 124
                end tell
            else if RefType is 3 then
                insert DevonThinkLink
                delay 1
                tell application "System Events"
                    key code 123
                    key code 123
                end tell
                delay 1
                insert pageDevonThinkNumberText & " " & theRealPage
                tell application "System Events"
                    key code 124
                    key code 124
                end tell
            else if RefType is 4 then
                insert DevonThinkLink
                delay 1
                tell application "System Events"
                    key code 51
                end tell
                delay 1
                insert pageDevonThinkNumberText
               
            end if
        end tell
       
    end tell
   
   
   
end tell

on chooseRefType(typeList)
    tell application "Skim"
        set theResult to choose from list typeList with prompt "Reference type:"
        if theResult is false then return 0
        set refTypeNumber to theResult as string
        if refTypeNumber is "Latex for MediaWiki" then
            return 1
        else if refTypeNumber is "Latex" then
            return 2
        else if refTypeNumber is "MediaWiki" then
            return 3
        else if refTypeNumber is "DEVONthink link" then
            return 4
        end if
    end tell
    return RefType
end chooseRefType

2011/03/07

Automated creation of a LaTeX compatible citation only from Skim! (with hyperlink included)

In the post "DevonThink links in Skim notes and AppleScript" I presented how you can create to a PDF file a number of Skim notes with various versions of references to itself. An example of these notes is shown below:


Then you can insert manually the BibTeX cite command in the fist and the second note.


Now you are ready to capitalize on these four little notes!

The first way was presented in the post "Automated summary creation linked with the source pfd file" where the respective AppleScript use the fourth note:
 set pdfDevonThinkLink to (get text for note 4 of page 1 of document 1) as string
In the AppleScript of this post the second note will be used.

As you understand the numbering of these notes plays a fundamental role in the effective use of these AppleScripts. For this reason it is required that you create these notes when there are no annotations in the first page of the PDF file. Otherwise these four notes will take another index number and you will need to adjust accordingly the AppleScript (2011-04-05, an alternative solution is to use the AppleScript in my post "How to create correctly the Skim notes which have the DEVONthink links, when you have already annotated the first page of the PDF document").

One of the most important reasons for which I have chosen to write my essays using LaTeX is that it makes possible the creation of rich hypertexts. By rich I mean that the final PDF document can have all the sorts of different kinds of links as you can see in the lower part of my mind map "The many faces of links". In order to create these links you should use the Hyperref package.

If you are accustomed to the LaTeX markup code you will recognize that the second note includes a proper citation as it is required by the Hyperref package:

(\cite{Deconstructing-the-Laws-of-Logic-Clark-2008a}: \href{x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=}{})
The only things that are missing from the above citation are two numbers: the number for the DevonThink link and the the number of the referred page.

Now lets say that you would like to refer to the 27th page of the paper which is the third page of the PDF file. From now on you do not have to manually paste the necessary code and the appropriate numbers in your txt file but an AppleScript can do it for you!

There is only one but... you want the number that is shown in your text to be 27 but the number which is attached to the DevonThink link to be 2 (3-1: if you do not know why, read my post It's all about hyperlinks!). My AppleScript has the ability to recognize in which page you currently are but it cannot recognize the written number in the page! So you will have to enter it manually.

 The AppleScript code is the following:
--2011-03-07
--http://organognosi.blogspot.com

display dialog "Give the number which is written in you current page:" default answer "" buttons {"Cancel", "OK"} default button 2
set writtenNumber to text returned of the result as text

tell application "Skim"
    activate
   
    tell document 1
        set currentPageNumber to get index of current page
        set pageDevonThinkNumber to currentPageNumber - 1
        set pageDevonThinkNumberText to pageDevonThinkNumber as text
        set DevonThinkLink to get text of note 2 of page 1
       
        tell application "TextMate"
            activate
            insert DevonThinkLink
            tell application "System Events"
                key code 123
                key code 123
                key code 123
                key code 123
            end tell
            delay 0.5
            insert pageDevonThinkNumberText
            tell application "System Events"
                key code 124
                key code 124
            end tell
            delay 0.5
            insert writtenNumber
        end tell
    end tell
end tell

If you do not want to write even this number you can create a fifth note which will have only the written number of the first page and then the AppleScript can compute the rest.

--2011-03-07
--http://organognosi.blogspot.com

tell application "Skim"
    activate
   
    tell document 1
        set currentPageNumber to get index of current page
        set pageDevonThinkNumber to currentPageNumber - 1
        set pageDevonThinkNumberText to pageDevonThinkNumber as text
        set DevonThinkLink to get text of note 2 of page 1
        set writtenNumberOfFirstPage to (get text for note 5 of page 1) as string
        set currentPageWrittenNumber to currentPageNumber + writtenNumberOfFirstPage - 1 as string
       
       
        tell application "TextMate"
            activate
            insert DevonThinkLink
            tell application "System Events"
                key code 123
                key code 123
                key code 123
                key code 123
            end tell
            delay 0.5
            insert pageDevonThinkNumberText
            tell application "System Events"
                key code 124
                key code 124
            end tell
            delay 0.5
            insert currentPageWrittenNumber
        end tell
    end tell
end tell

Finally the easiest case is when the page numbers of the PDF file and the printed book coincide. In this case you can still use the above AppleScript if you write in the fifth note the number 1. If you do not want to use a fifth note the AppleScript is the following:

--2011-03-07
--http://organognosi.blogspot.com

tell application "Skim"
    activate
   
    tell document 1
        set currentPageNumber to get index of current page
        set pageDevonThinkNumber to currentPageNumber - 1
        set pageDevonThinkNumberText to pageDevonThinkNumber as string
        set currentPageNumberText to currentPageNumber as string
        set DevonThinkLink to get text of note 2 of page 1
       
       
        tell application "TextMate"
            activate
            insert DevonThinkLink
            tell application "System Events"
                key code 123
                key code 123
                key code 123
                key code 123
            end tell
            delay 0.5
            insert pageDevonThinkNumberText
            tell application "System Events"
                key code 124
                key code 124
            end tell
            delay 0.5
            insert currentPageNumberText
        end tell
    end tell
end tell
Before you execute any of the above AppleScripts you should have a TextMate document opened. Moreover the cursor should be at the point in which you want the citation to be inserted.

2011-04-05
There is an improved version of the above AppleScript in my post "Automated creation of references with hyperlinks from Skim"


2011/02/20

How to put DevonThink links in Skim notes


For every book or paper that I read I create a new page in my wiki. The name of this page is created under the following template: Title - Author, for example "Deconstructing the Laws of Logic - Clark". In this page I keep all my notes and my thoughts concerning this paper. The pdf file is inside a DevonThink database. When I am reading a pdf I want to be able to use the DevonThink link without leaving Skim. To this end I wrote an AppleScript, which creates in the first page of a pdf four Skim notes, containing four different ways of constructing references using DevonThink links.
The fourth note is the simplest and contains the DevonThink url (x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=0). Its extended text contains the title of the wiki page. 

The third note contains a MediaWIki internal link to the wiki page of this pdf followed by an external link to the pdf file itself.

The second note contains the necessary Latex code for creating a proper bibliography reference and a link to the exact pdf page using the hyperref package. The only things that are missing from the above code are the cite key (between the opening parenthesis and the colon) and the page numbers. As an example the complete second note is the following: 

(\cite{Deconstructing-the-Laws-of-Logic-Clark-2008a}: \href{x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=}{})

As you can notice the cite key "Deconstructing-the-Laws-of-Logic-Clark-2008a" is quite long. I have chosen this because I want to recognize the reference just by looking in its cite key and not by trying to remember for example which paper Clark wrote on 2008...

The code for a bibliography reference to the third page of this paper which is in the 27th page of the Philosophy Journal is the following:

(\cite{Deconstructing-the-Laws-of-Logic-Clark-2008a}: \href{x-devonthink-item://CDEC17B7-1EEE-42E1-B8C9-86A24C172BF3?page=2}{27})

The first note contains the necessary MediaWiki code for creating a link to the excact pdf page which is compatible with LaTeX whenever you want to export the wiki text to Latex (more about this in a quite distant in time post...)

Now every time I want to create a link to a pdf file everything is at hand in one of these notes! 

The AppleScript code which makes all the above possible is the following: 
tell application id "com.devon-technologies.thinkpro2"
    set these_items to the selection
    if these_items is {} then error "Please select some contents."
   
    repeat with this_item in these_items
       
        set RecordLink to the reference URL of this_item
        set DevonThinkLink to RecordLink & "?page=0"
        set PdfPath to get the path of this_item
        set PdfName to the name of this_item
       
       
        tell application "Skim"
            open PdfPath
            tell page 1 of document 1
                make note with properties {type:anchored note, bounds:{523, 820, 540, 820}, text:"(<rawtex></rawtex>: [" & RecordLink & "?page=])", extended text:DevonThinkLink}
                delay 0.1
                make note with properties {type:anchored note, bounds:{523, 800, 540, 800}, text:"(: \\href{" & RecordLink & "?page=}{})"}
                delay 0.1
                make note with properties {type:anchored note, bounds:{523, 780, 540, 780}, text:"([[" & PdfName & "]]: [" & RecordLink & "?page=])"}
                delay 0.1
                make note with properties {type:anchored note, bounds:{523, 760, 540, 760}, text:DevonThinkLink, extended text:PdfName}
            end tell
            save document 1
            delay 1
            close document 1
           
        end tell
    end repeat
end tell
2011-04-02 
In my post "How to create correctly the Skim notes which have the DEVONthink links, when you have already annotated the first page of the PDF document" there is an improved version of the above AppleScript. The newer one solves a problem which appears when you want a third AppleScript to use the aforementioned Skim notes like the AppleScript in my post "Automated creation of a LaTeX compatible citation only from Skim! (with hyperlink included)". Moreover it creates a fifth note for which there is detailed information in my post "Latin page numbers, Arabic page numbers and the fifth Skim note".

2011/02/15

A road map for my blog - The many faces of links

In the following mind map you can see the various kinds of links that I am able to use and the respective programs that are required in order to create each of them. Moreover I have added some hyperlinks in the nodes for which I have posted relevant information.



From A Digital Workflow for Academic Research

You can download this mind map in its native Mind Manager file format from here  and as a PDF from here (right click + Save as).

Finally, you can view this mind map as a roadmap for my blogspots... post by post I will try to present how you can create and use these different ways of cross-linking your thoughts, notes, writings and also your sources into an integrated whole!  

2011/02/12

Some tools of the trade

I use the following hardware:
  • a MacBook Pro 17in
  • a MacMini (as a server for my wikis and my ebooks library)
  • an iPad
  • a Time Capsule
  • an iPhone 3G
  • several external hard drives (for backup)
  • a 27in LG monitor

In my academic workflow I use the following programs:
  • Skim: for reading papers and books (in pdf format)
  • Calibre: for organizing all my ebooks (read and unread)
  • DevonThink: for organizing everything that I have read
  • BibDesk: for reference management and automated bibliography creation
  • MediaWIki: for notes management
  • TextMate and LaTex: for writing my papers
  • AppleScript: for automating my workflow