Revision software revisited

So I decided to switch away from git and to start using bazaar. For some reason git wouldn't do commits for me (probably me being stupid). I find that working with bazaar is very intuitive. Perhaps this ease of use can be attributed to the fact that I'm not publishing my work via bazaar. This means that I don't have to worry about things like pushing the changes to a server etc. For those of you who use Windows, I suggest using Mercurial (Hg). Mercurial is apparently better for extremely large projects and installation on Windows isn't very difficult, also the syntax is the same as bazaar.


Bazaar Quickstart guide:

1. bzr whoami "name "
2. bzr init (run in project folder)
3. bzr add (add all project files in project folder to bzr)

 You've now started using bzr

• bzr commit -m "Short description of change" (this commits your changes to the next revision (ie from revision 1 to 2))
• bzr revert -r# (this changes the project back to revision #)
• bzr status (see what files have changed since your last commit)
• bzr diff (see what has changed IN the files since your last commit)
• bzr log (see history of changes)

edit: It suddenly occurs to me that this would be a good way to share the project. However, this would work well if I intended to share it so as to create a novel/story that was written by a social community. My intent is more that my writing can provide inspiration (a bit conceited of me, I know) to others, rather than creating a collaborative novel.

Brilliant ideas

So I was talking to a friend about pumps. In particular, we were talking about membrane-bound pumps (cellular biology). I thought about it for a moment and I could think of no examples of a non-membrane-bound pump. Of course, with my limited knowledge, that by no means indicates that there are none. At first I thought that the whole concept of a non-membrane-bound pump was kind of odd. If the pump didn't connect to the membrane, then what was the purpose? To keep the fluid that it was floating around in circulating? I tried thinking of non biological examples of pumps and then it hit me. Perhaps the most iconic pump of all is not membrane bound. A bike pump is a perfect example of this. It is a unattached pump that attaches to a membrane pore.

This is where my 'brilliant' idea came in. As a thought exercise, I thought of practical applications of a bike pump-like pump in terms of biology. I thought that it would be a great way to deliver drugs. You could use the pump as a way to target specific cells. In essence, a pill would contain two different compounds. One compound would be the pump. This pump would be a custom designed protein with two to three functional parts. The first would be a tissue-specific ligand that would bind to a pore or channel of sufficient size for the drug to pass through. The second part would forcefully open/activate the channel. Finally, the third would be a pump specifically designed for unidirectional transfer of the active drug. The second compound in the pill would, of course be the drug.

It seems like a no brainer when you think about it on the surface and it seemed, at least in my head, to work really well. Then when you delve deeper into it there are a variety of problems to overcome. First would be that making the custom pump would be ridiculously expensive and time consuming, probably better just to make a wide acting drug and let people deal with the side effects. The second problem would be finding a receptor or pore that is ONLY on the tissue you want. Another problem would be finding a way to make sure that you're pump doesn't attach permanently. This might actually solve itself, as some receptors are internalized after activation (which might be a problem in and of itself). Of course the biggest obstacle would be the fact that many drugs act on the receptors themselves, tricking the cell into doing a desired effect, which means that there is no need of a delivery system. Sigh so much for these brilliant ideas of mine.

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Another 'brilliant' idea I had recently was a slot machine dim sum restaurant. I figured that it would be a great way to introduce newbies into the world of dim sum. By leaving the choice to chance, they get an unbiased variety of dishes. Rather than being limited to the dishes that their friends or family want, they can try out more exotic dishes. Of course, this kind of defeats the purpose of dim sum whereby you choose the dishes as they come by but it doesn't have to be used by everybody. In addition to the slot machine dim sum, a rotation-sushi-like delivery system would be nice. It is unfortunate, though that such a delivery system kind of makes the dining experience kind of impersonal due to the fact that the participants are facing the conveyor belt rather than each other. Still, despite the problems, I think it would be a cool thing to do and not necessarily limited to dim sum. I could definitely see something like this used in conjunction with Microsoft Surface in restaurants.

Feeling dumb

So as some of you know, I wrote a little script to make my life easier during the process of writing this novel. The purpose of this script was to facilitate multiple versions of my novel. I have a nasty tendency to rewrite parts of my story and I wanted to be able to keep track. This was the script:

#!/bin/bash
IFS="
"
function findfile {
for word in $filetype; do
    case $word in
        .tex) find /home/ray/ -name *.tex | sort;;
        .odt) find /home/ray/ -name *.odt | sort;;
        .doc) find /home/ray/ -name *.doc | sort;;
        .html) find /home/ray/ -name *.html | sort;;
    esac
done
}

function editfile {
for word in $filetype; do
    case $word in
        .tex) gedit $response;;
        .odt) oowriter $response;;
        .doc) oowriter $response;;
        .html) oowriter $response;;
    esac
done
}

function makerevisions {
if [ -d $directory/Revisions/ ];
then
    echo "Revisions directory exists"
    mkdir $directory/Revisions/$(date +%F-%R)
    cp $response $directory/Revisions/$(date +%F-%R)/
else
    echo "Revisions directory does not exist"
    mkdir $directory/Revisions/
    mkdir $directory/Revisions/$(date +%F-%R)
    cp $response $directory/Revisions/$(date +%F-%R)/
fi
}

filetype=$(zenity \
--list \
--title="Select filetype" \
--column="Filetype" \
    .tex \
    .odt \
    .doc \
    .html)   
if [ "$filetype" == "" ]; then
    exit 1
fi

response=$(zenity \
--list \
--title="Select file" \
--column="File" \
    $(findfile))
filename=${response##/*/}
directory=${response%/*.***}
if [ "$response" == "" ]; then
    exit 1
fi

editfile $*
makerevisions

echo $filetype
echo $response
echo $filename
echo $directory

unset IFS

Anyways, to continue my story, I found out that I was being extraordinarily dumb. In many ways I was simply trying to reinvent the wheel. I forgot that there were many tools out there that did the exact same thing. Basically, what I was trying to do was a primitive version control script. I realized relatively recently (to may shame) that I could use things like git and svn to do the exact same thing, except better. So I took a look at a few different tools and I finally decided upon using git. I chose git because, well simply, it appeared to be the easiest to learn and I could use it offline. Now I have a script that I worked so hard on (a symptom of my amateurish scripting abilities) that's, for all intents and purposes, useless.

As a side note, it should be mentioned that git these 'software revision control' tools work particularly well because I am using LaTeX. I am unsure as to whether or not it would track changes just as well if it were regular doc, odt... etc. files.

Choosing a Perspective

When I started this endeavor I thought that it would be nice to write the bulk of the story in first person perspective. This would give the readers a unique look at the world while making sure that the narrator does not know everything. However, I found that my narrator knew too much about the story. There were thing that I, the writer, did not want to disclose but the character narrating had no reason to hide. This, of course, makes writing the part difficult and some of the scenes awkward. Therefore, I am contemplating whether or not to rewrite the sections in third person. While this perspective allows the narrator of the story to know everything, there are no constraints against what may or may not be disclosed.

Document conversion tool

So I was looking for a tool to convert between various document formats (ie .tex to .doc, .html, .pdf, .odt or any variation thereof) and I found that it was surprisingly difficult finding a tool to convert to .odt. Converting from pretty much anything to either html or pdf was a breeze, however to other formats was more difficult. To convert from .tex to .html, I chose to use latex2html rather than tex4ht because I found the output to be cleaner. Conversion from .tex to .pdf was quite a bit easier. There were a few options. I could either run latex, dvips, and ps2pdf; or latex and dvipdfm; or just pdflatex. These are the standard options. For some reason, when I used these methods the hyperlink table of contents that I created (via hyperref and \tableofcontents) wouldn't show up. I instead chose to use rubber instead. Rubber is a wrapper for LaTeX and some companion programs. With the '-d' option, I was able to make PDFs out of the .tex files that included they hyperlinked table of contents. I don't really understand why this worked and the other methods didn't but it did. Now was the hard part. Converting the .tex files into .odt or into .doc appeared to be near impossible to do cleanly. The best option I had heard was to convert first into HTML and then load it into Office and then save as the desired formats. I found this to work out extremely well. However, I had intended to automate the whole process of document conversion with a script, so this method was not very good for me especially since neither Microsoft Office nor Openoffice.org had very good command line interfaces. This was when I discovered a program called JODConverter. This is a Java program that utilizes Openoffice to convert from one format to another. While this does mean that I probably could have found a way to use Openoffice directly via command line, who was I to complain when there was a program out there to do it for me =D. In the end I wrote a small BASH script to help me with the conversions.

NOTES:
-written in BASH because I'm using Arch Linux
-uses zenity to provide a GUI but is not really necessary
-while this is tailored to my LaTeX usage it can probably be adapted for anything, although just using JODConverter is probably better if LaTeX is not an issue


#!/bin/bash
cd /home/ray/Documents/Novel/Tex/
response=$(zenity --list --title="Choose File" --column=File \
$(ls --hide=*.pdf --hide=*.odt --hide=*.html --hide=Revisions --hide=Output /home/ray/Documents/Novel/Tex/) )
input=$(zenity --list --title="Choose File Type" --checklist --column=Files --column=Description \
TRUE PDF \
TRUE HTML \
TRUE ODT \
TRUE DOC)
cd /home/ray/Documents/Novel/Tex/
IFS='|' ; for word in $input ; do
case $word in
PDF) rubber -f -s -d /home/ray/Documents/Novel/Tex/$response;;
HTML) latex2html -split 0 -no_navigation -dir /home/ray/Documents/Novel/Tex/ $response
sed s_${response%.*x}.html#_#_ <${response%.*x}.html>${response%.*x}.html.new
rm index.html
rm ${response%.*x}.html
mv ${response%.*x}.html.new ${response%.*x}.html;;
ODT)latex2html -split 0 -no_navigation -dir /home/ray/Documents/Novel/Tex/ $response
sed s_${response%.*x}.html#_#_ <${response%.*x}.html>${response%.*x}.html.new
rm index.html
rm ${response%.*x}.html
mv ${response%.*x}.html.new ${response%.*x}.html
soffice -headless -accept="socket,host=127.0.0.1,port=8100;urp;" -nofirststartwizard &
jodconverter /home/ray/Documents/Novel/Tex/${response%.*x}.html /home/ray/Documents/Novel/Tex/${response%.*x}.odt
pkill soffice;;
DOC)latex2html -split 0 -no_navigation -dir /home/ray/Documents/Novel/Tex/ $response
sed s_${response%.*x}.html#_#_ <${response%.*x}.html>${response%.*x}.html.new
rm index.html
rm ${response%.*x}.html
mv ${response%.*x}.html.new ${response%.*x}.html
soffice -headless -accept="socket,host=127.0.0.1,port=8100;urp;" -nofirststartwizard &
jodconverter /home/ray/Documents/Novel/Tex/${response%.*x}.html /home/ray/Documents/Novel/Tex/${response%.*x}.doc
pkill soffice;;
esac
unset IFS
cd /home/ray/Documents/Novel/Tex/
rm $(ls --hide=*.tex --hide=*.sh --hide=*.html --hide=*.odt --hide=*.pdf --hide=*.doc --hide=Output --hide=Revisions)
mkdir Output/$(date +%F-%R)
cp $(ls --hide=*.tex --hide=Revisions --hide=Output) /home/ray/Documents/Novel/Tex/Output/$(date +%F-%R)/
#
#echo "-------------------- EXTRA STEPS --------------------"
#echo "1. Open HTML with OpenOffice.org Writer"
#echo "2. Add first-line indent"
#echo "3. Save file as Master.odt"
#echo "4. Export Master.odt to GoogleDocs"
#echo "-----------------------------------------------------"
#cd ~
done

File Hosting

So here's the deal. Blogger is a great place to write stuff down but it's a pretty terrible place to share files that aren't images/videos. If you want any files in which you can edit you can, as always, go to the GoogleDoc linked on the right-hand panel OR you can follow the other link to my website. This website will be a central place in which you can find all files related to the novel as well as other miscellaneous information.

Update

Hello my non-existent readers. I would just like to give everyone an update. I've changed the layout of the blog a bit. I've added a page where you can access the completed story (well completed so far). I will keep the link to the GoogleDocs version of the story in case you wish to download/edit/distribute the story.

Next section of the novel is forthcoming.

Warning: Techy stuff ahead

If you've read my previous post: A Note on Writing Software, you'll know that I am currently using LaTeX to write my story. There are many tools that I use. The three main programs that I use are pdflatex (makes PDFs), oolatex (makes ODT [OpenDocumentText file]), and latex2html (makes a HTML file). The ease in which I can convert into all of these filetypes is one reason why I use LaTeX. Recently though, I discovered something. For those of you who know, oolatex is a part of Tex4ht, which is itself capable of making an HTML file via the htlatex command. Now I have found that when copy/pasting the html produced by the htlatex command into Blogspot, the paragraphs get all messed up. This is why I turned to latex2html. The only caveat with latex2html is that the Table of Contents hyperlinks do not work (keyed to file). This problem was quickly solved by a few sed commands replacing part of the HTML code that tied the links to the file. Anyways I wrote a little bash script so that I can easily convert my .tex file into .odt, .pdf, and .html all in one go. Here is said script


#!/bin/bash
cd /home/ray/Documents/Novel/Tex/
sed "s_\\\usepackage_%\\\usepackage_" Master.tex.new
sed "s_\\\hypersetup_%\\\hypersetup_" Master.tex
mk4ht oolatex Master.tex
sed "s_%\\\usepackage_\\\usepackage_" Master.tex.new
sed "s_%\\\hypersetup_\\\hypersetup_" Master.tex
pdflatex Master.tex
#htlatex Master.tex
latex2html -split 0 -no_navigation -dir /home/ray/Documents/Novel/Tex/ Master.tex
sed 's_Master.html#_#_' Master.html.new
rm index.html
rm Master.html
mv Master.html.new Master.html
rm $(ls --hide=*.tex --hide=*.sh --hide=*.html --hide=*.odt --hide=*.pdf)
cd ~

Now there's probably an easier way to do all of this, and I welcome suggestions, but this is the one I've settled upon for now.