The structure of the index file is simple. Each line can contain one filename. Blank lines are ignored. Lines starting with “#” are ignored as comments. To indicate that a file should be “demoted” to increase header levels, simply prefix it with the desired number of tabs (similar to the way the base header level metadata works).
A sample index file looks like:
# This is a comment (ignored)
introduction.txt
chapter1.txt
section1.txt
section2.txtThis indicates that section1.txt and section2.txt should be “children” of chapter1.txt.
Remember, metadata is ignored if it isn’t at the top of a file - when merging files, only the first file can contain metadata. Because of this, it may make sense to have the first file be a separate “metadata.txt” file that contains only metadata….
Let me know what you think.
F-
PS> This utility has been added to the github repository. You can get it now, or wait for the next “official” release - I’m not sure when that might be.
]]>For now, the repository will be accessible to the public, but I am still the only one with write access. This may or may not change in the future. But, as always, anyone is able to make their own changes to the source — either for their own use or to release for others.
I think I’ve updated the appropriate places on my website for the new download location.
As always, I welcome feedback!
]]>Corrected the case of SmartyPants.pl for compatibility with older machines/systems
Updated the templates to use $TM_FULLNAME rather than obsolete routines to try and determine the user’s name that no longer work.
A few other smaller issues…
Available at the project page
]]>First, try to install Parallels Tools in the usual way. If it works, then you have an updated version of Parallels Desktop, and don’t need this tip any more.
Otherwise, it will likely fail on installation of the video driver and Xorg configuration. But some of the features will be installed. From that point:
edit /etc/fstab and add to the end:
# Parallels Shared Folder mount
none /media/psf prl_fs sync,nosuid,nodev,noatime,share 0 0then, run the following:
sudo mkdir /media/psf
sudo mount /media/psfthen, recreate the link on the Desktop
cd ~/Desktop
ln -s /media/psf Parallels\ Shared\ FoldersAt this point, you may or may not need to reboot, but you can easily share your Mac folders with your virtual machine. The network should be working (though, I don’t think you need Parallels Tools for this technically). Once they update Parallels, you can install the new version and have the video/mouse integration restored.
]]>Most of these instructions were available elsewhere, and just had to be
cobbled together. The process took several hours days to
complete, including lots of trial and error. I’ll try and highlight some of
the “gotchas” that I discovered.
WARNING: You can really screw up your computer if you do this wrong. This is the approach I used, but I can’t guarantee I documented every little step. Read the pages I link to. Several times. Make sure you understand the approach, and follow along on these pages during the actual process so you don’t forget anything. I don’t guarantee that any of this will work for you, or that you won’t frag your drive.
WARNING: As with all activities like this, be sure you have a working backup before you start doing this. On more than one occasion, I had moments of panic when I worried that I may have wiped my OS X partition. In fact, I never lost any data (that I’m aware of yet, anyway). But you want to be darn sure you’re covered.
]]> Why Should One Do This?I recently bought an Eee PC and converted it to dual-boot Windows XP and Ubuntu. I enjoyed trying out Ubuntu again (it had been a while), but it was sort of cramped on the small screen. I decided I should try out booting a “real” installation of Ubuntu on a “real” laptop using Boot Camp and see what it was like.
I had never tried Boot Camp before, as I anticipated wanting to be able to launch Windows/Linux briefly, do a task, and then resume using Mac OS X, rather having to reboot every time I wanted to switch the OS.
But if I could run the same installation within Parallels and Boot Camp, that would be incredible!
After digging around on the internet, it appeared that what I wanted to do should be possible. And it is.
Linux, being an open-source project, is well suited to this. I am not an expert on Windows, but one potential gotcha is that your Windows installation may think it is running on two separate computers if you run it from Boot Camp and from Parallels. From what I read, Windows Genuine Advantage may cause problems with this - you can try Google to see if there will be a workaround for you.
Basically, I needed to:
It turned out to be somewhat complicated, but very possible.
The goal is to:
Delete files as necessary to create enough free space for your Linux and Windows partitions (I created approximately 45 Gb of free space to dedicate).
Use either Disk Utility or Boot Camp to create a partition for Windows at the end of your disk.
If you encounter errors in the resizing process, it may be caused by large files that cannot be moved off of the area of the disk being affected. In my case, when I removed some larger disk images (prior Parallels installations and large video files, for example) everything worked fine.
I had errors when using Boot Camp to create the partition, so after deleting possible culprit files, I ran the 10.5 install disk and used Disk Utility to shrink my hard disk by 45 GB. Then, I grew the partition by 45 GB in order to return to the full size. This effectively moved all files out of the last 45 GB of disk space, “defragmenting” the empty space. Boot Camp ran fine after this.
Now, run the Boot Camp Assistant application. Create a partition big enough for your Windows Installation (we’ll do Linux later). Then, basically follow the instructions to install Windows. Reboot into Windows, make sure it’s all working, and that you’re happy with the setup.
NOTE: My Windows installation came from a DVD that was scripted to automatically install Windows and several other updates. It’s critical to follow the directions appropriately, and one of the steps is to reformat the Windows partition from within the Windows Installer. If you are not presented with this option, you can intentionally corrupt the Windows partition to force a reformat. I had to do this, using the command (be sure to read about this before using):
dd if=/dev/zero of=/dev/rdisk0s3 bs=1m count=100Be absolutely sure you chose the proper partition (e.g. rdisk0s3 in the example), or you could kill your Mac partition and wipe all data!! I then used NTFS as the format.
I wouldn’t spend too much time installing software or configuring things at this point. Just in case you have to try it over…
At this point, you can try running Parallels to configure it to work with your Boot Camp Windows installation. If you have Parallels 3, you can probably get it to work with a dual boot system, but I could not get it to work with a triple boot system (i.e. 2 non-Mac partitions). From the internet, it appeared that it should work, but I was unsuccessful.
Parallels 4.0, however, made this set up a snap.
When you run Parallels, it should have a setting for the Hard Disk that allows you to use your Boot Camp partition. Set it up for Windows, and run it to make sure everything seems to work properly. Again, don’t get too attached — if you’re adding Linux, you’re going to have to change the configuration later on.
At this point, you should have:
A working Mac OS X install on the first “real” partition of the boot drive
A working Windows Boot Camp installation on the last partition of the drive
A Parallels Virtual Machine that allows you to run your Boot Camp installation within the Mac OS.
This is a little bit trickier — but again, most of the effort was in figuring out what works…. I got most of this from http://fosswire.com/post/2009/3/how-to-ubuntu-810-on-white-macbook/. I recommend reading it thoroughly before beginning. Keep in mind that they overwrote the Windows Boot Camp partition to create a dual boot setup, whereas we are creating a new partition to build a triple boot machine. The overall process is the same.
Install rEFIt. This utility will help keep EFI and MBR in sync, allowing all this to work. It will save your life a couple of times during this process. Google to learn more about how it works - I can’t explain it well….
Use Apple Disk Utility to shrink your Mac Partition, freeing up enough space for Linux. You can create a new partition if you like, or you can leave the space empty. The empty space should be between the Mac disk (first visible partition) and the Windows (last visible partition).
Reboot from your Ubuntu Installation CD. I used Ubuntu 8.10. I had some trouble with Kubuntu 8.10 for some reason. I also had lots of trouble trying to build a custom install using Minimal Ubuntu. Ubuntu 9.04 should work, but Parallels Tools won’t build for it yet, so you might be better of waiting to upgrade for a bit.
Install Linux — you want to use the Manual option for the hard disk. You will want to reformat the Linux partition (should be called /dev/sda3) as ext3, and designate it as mount point /. If you already had a linux installation here, I do recommend reformatting the partition. I had strange errors when I didn’t…. NOTE: It is important that the GRUB bootloader be installed into the Linux partition (/dev/sda3). The default is into the MBR, which I understand would be really bad….
Once it’s installed, reboot and let the rEFIt menu come up. Go to the Partition Tool icon, and allow it to sync the MBR. Shut down the Mac for a few seconds and turn it back on.
Hold down the option key when you power up to load the Boot Camp selector. You should see two options (Mac/rEFIt and Windows). Choose Windows, and the result should be to come to a GRUB bootloader screen that allows you to select between Ubuntu and Windows. If so, boot into Linux and Windows and ensure that everything seems to be working.
If you don’t get a successful boot via GRUB (I did not), then you need to reboot off of the Ubuntu installation CD, and choose the Ubuntu live option (first choice). Once Ubuntu is loaded, go to the Places->Computer menu, and then select the icons for your three partitions (they may be identified by their sizes, rather than real names) and mount them by right-clicking on one of them. Once all three are mounted, open a Terminal window and run the following (assuming that Linux is installed onto the third partition, counting the “invisible” EFI first partition). Again, read up about grub to feel comfortable that your commands are correct for your setup:
grub root (hd0,2) setup (hd0,2) quit
At this point, you should be able to reboot, hold down option, select Windows, and be presented with the GRUB menu. Boot into Linux, and ensure everything works.
Boot Windows again, and ensure everything works.
Now, you can boot back into the Mac OS, and create a new Parallels Virtual Machine to run Linux. In my testing, I had to select both Boot Camp partitions to be mounted in order for either Linux or Windows to boot. Attempt to run Linux within Parallels and make sure everything works properly.
Since you added a new partition, and moved the boot loader, your previous Windows Virtual Machine won’t work. You can create a new one, or simply configure the existing one to mount both the Linux and Windows partitions, and try again.
I have left rEFIt installed (in case I do any more tweaking). Any time you repartition your drive, you will need to use it to “resync” the MBR and EFI setups. However, if you’re happy with your partitions, I suppose you could remove it and use the option key whenever you wanted to boot to a non-Mac OS. I haven’t tried this yet.
Again, this was a tedious process (it took me a few days to get everything working properly). I tried to outline the process to save some time — now that I figured things out, I could probably do the whole thing within 4-5 hours, including time to install Windows/Linux and repartition drives. Now, I have a functional Windows installation and a Linux installation on my machine, either of which can run from boot, or within a Parallels Virtual Machine.
I realized that more and more of what I use a computer for can be accomplished in Firefox, Thunderbird, and a good text editor. I have Firefox and Thunderbird installed in every OS I use, and on a portable thumb drive for use at work. Now, I just need to find a text editor as good as TextMate for Linux and Windows….
]]>textutil, and it’s available to users on any operating system.
]]>
I recently bought an ASUS Eee PC1000HE. I wanted a new laptop, preferably something small and lightweight. I was also interested in getting a machine to run Ubuntu, and possibly even Windoze once in a while.
]]> After looking around (albeit briefly) at netbooks, this seemed like a reasonable machine for a reasonable price. I ordered it from Amazon, got it the next day, and got to work on setting it up the way I wanted it. I learned a few things, and figured I would share those here.The first thing I did was run Ubuntu off a USB stick and reformat the drive. It took some fiddling to find the options I wanted, and without spending all day doing bit-by-bit copies of empty space. But, eventually, I had a partition for Windows (that kept the preinstalled software), and an extended partition that contained the Ubuntu partitions set up by the installer. Unfortunately, I don’t remember exactly what options I chose, but everyone has their own needs anyway.
Then I was able to install Ubuntu, to create a dual boot machine.
Technically, I installed Easy Peasy. This is a customized version of Ubuntu specifically designed for netbooks. I read that it supported the Eee PC machines well.
Installation was easy and it worked without much difficulty.
One problem I did run into - the wireless connection was flaky with certain
routers. I discovered, through trial and error, that I could connect when the
machine first booted. But if it slept, upon awakening it could not obtain a
connection. The answer ended up being that I had to remove and then modprobe
the wireless driver in order to reconnect. I created a script to do this for
me, since I couldn’t get it to happen automatically:
(I need to look up this script)Other than installing my preferred software, I didn’t do a whole lot with this. I don’t plan on using the Windows too often. It seems to work well.
I installed Dropbox on both my Ubuntu and Windows partitions. This allows me to keep my active files synchronized between 2 machines (3 total operating systems) fairly easily.
Through the use of symlinks, it becomes possible to synchronize files outside of the main dropbox folder as well.
Since I was going to be using multiple operating systems, it made sense to emphasize cross-platform open source software.
I use Firefox as my primary web browser, so this was a no-brainer. I installed it in Windows and Ubuntu, and then used Foxmarks to synchronize my bookmarks and passwords across installations. On my main computer, I use [1Password](http://agilewebsolutions.com/products/1Password “Password Manager + Automatic Form Filler for Mac OS X”) to manage my passwords, so I had to manually reenter the passwords I wanted to keep synchronized within Firefox.
I then installed Google Gears in order to keep copies of my Gmail, Google Calendar, and Google Docs information within each operating system for offline use while traveling.
I use Dropbox to synchronize my Thunderbird profile, so that I don’t have to update accounts on each copy separately, and so that the address books stay in synch whenever I make changes. I tend to still use Apple’s Mail primarily, but Thunderbird isn’t bad. And since I run Portable Thunderbird off a USB stick at work, it’s nice to have consistency.
I started off using Sunbird, but after installing Google Gears with Google Calendar, I gave up. Performance sucked, and it just wasn’t worth it.
All in all, it was nice to play with a new machine. I like the small size of the Eee PC, and it’s useful to have a linux installation that is not in a virtual machine. I’m trying to keep experimenting with open source software, and it’s interesting to have a machine that runs entirely free software and yet can still do almost everything I need.
]]>I am not actively maintaining my blosxom software any more, and was recently contacted by some developers who are. My plugins are now being hosted by the sourceforge development effort. Hopefully everything will get moved over and be more accessible and more up-to-date.
In any case, for now you can still access most of my blosxom software at my old site:
http://fletcher.freeshell.org/wiki/BlosxomPlugins
Here is a list of the plugins I have released to the public:
I needed to set the group id bit on the cgi scripts so they could write to the directories. This may or may not be a security issue.
I had to use /mt-static (no trailing slash) to identify where the mt-static directory would be.
I need to figure out exactly how to lock things down with htaccess for better security.
While I want part of my site to be a blog/journal/etc for posting periodic updates and thoughts, I want a large part of it to be more of a standard website.
To mimic this functionality with Movable Type, this is what I have discovered so far:
Decide on whether you like foo-bar or foo_bar and set the appropriate paths in the archive templates.
Change archiving to Entry
Disable the index page for archiving by adding something extra to the path so that it doesn’t overwrite manual pages
Archive pages to the appropriate folder/basename/index.html so that your pages create categories
Ensure that your categories and Pages match
Now you can have a custom page, and posts can be assigned that category in order to appear in the appropriate directory
Good explanation for how to clean up the URLs:
What I did is remove the html extension, and then ensure that each page is archive mapped to folder/page_basename/index so that the page doesn’t try to overwrite the category folder. If you create a home page named index, you can soft link index.html to index/index so that you don’t have to manually copy the home page after each update.
\indexI have written several modules for Oddmuse. Rather than duplicating effort at maintaining pages, those modules are now described solely at the Oddmuse site:
]]>AntiSpam Module - attempt to hide email addresses from spammers
ClusterMap Module - automatically generate a Site Map from your Clusters
CreationDate Module - permanently store the author and date that a page was created
FlickrGallery Module - automatically create an image gallery from a Flickr photo set
HtmlLinks Module - allow the use of raw HTML on specific pages
LogBannedContent Module - record information about people trying to spam your site
Login Module - require users to have an account and login before editing your site
Markdown Extension - originally written by Alex, now maintained by me. Allows you to use the MultiMarkdown syntax for your Oddmuse wiki.
PDF Module - use MultiMarkdown to generate a pdf version of pages in your site
PlainClusterRC Module
PlainSite Module - make your site appear less like a wiki and more like a “regular” site
Sitemap-index Module - add a plain text list of all pages in the wiki, suitable for indexing by Google
Static Hybrid Module - pregenerate pages as html files, greatly speeding up the time it takes to serve your site
TagMap Module - similar to the ClusterMap Module, this creates a map of the tags in use on your site, and automatically generates a hierarchy based on basic set theory
WrapperDiv Module - fixed a flaw in the layout of <divs> in Oddmuse (this has now been wrapped into the core Oddmuse functionality and this module is no longer required.)
For those who don’t know, in my “other life” I am an academic hospitalist. Having appropriate medical utilities on my iPhone is quite a boon - no more carrying my palm pilot AND cell phone around…
]]>(as of Aug 31, 2008)
This program has a large number of formulas and tools, and also has the handy “Favorites” ability. I certainly appreciate having a large selection of formulas on hand, but I also want a “short list” of the ones I actually use on a daily basis. In fact, some of the included formulas are ones I have not heard of - I have some reading to do….
The list of included formulas is fairly comprehensive, and hopefully will continue to grow with each update. So far, this is looking to be my top utility (behind Epocrates Rx, of course). And because the overall app is working well, it should be fairly easy for the developer to continue to add in new features — this app could easily incorporate many of the functionality of some of the other medical “one shot” applications.
Well worth the $4.99. Especially since I was considering writing a program like this, and would much rather pay $5 than spend the hours it would have taken me to do this….
Update: Version 1.0.3 adds new features including a fairly complete pregnancy calculator. I am definitely happy every time I can get rid of an application that only does one thing in favor of an application that does the work of multiple other apps.
One complaint - how much longer until they release the iPhone equivalent of the Pro version - I paid for another year after being told that my subscription would transfer. That implies that there is a paid iPhone version, and not just a free version that doesn’t require a subscription….
http://home.comcast.net/~mdecaro/abg/
Just released today, this app fills a void in the “Palm-iPhone” gap. In addition to a basic acid-base interpretation, it includes a calculator to predict FiO2 requirements for a given PO2, and will also calculate some cardiac output related values.
My biggest complaint is that this app, like many of the other ABG interpreters available for the Palm, doesn’t perform a very thorough analysis of the ABG data. In my mind, this renders it useless for patient care, or for educational purposes. Hopefully, the author will update this function for the next release and make this a “best of breed” app.
This app is free, which is nice, but is pretty limited. BMI, Corrected Na, FeNa, MELD, and Parkland tools are all available in Mediquations. It does calculate a Bicarb deficit (honestly, I don’t think I have ever used this one), and corrects CSF WBC count (handy, and saves working it out by hand). Neither of these are deal-breakers for me, so I will stick with Mediquations for now.
On a more positive note - the Pregnancy Wheel in this program is quite nice, and much better than the also free OBWheel.
This application is also undergoing further development, so there will be additional features in the next version.
http://dr-chris.org/iPhone_Apps/iPhone_Apps.html
This app works, and shows gestation age and due date based on LMP. But, again, the pregnancy tools in Medical Calculator and Mediquations are more full-featured.
http://www.deathraypizza.com/deathraypizza/PubSearch_Home.html
I guess this is handy for searching PubMed from the iPhone, but since you can’t do much with the results it seems like a waste for right now. Perhaps the next version will be more useful?
Since writing this, a few new apps have come out. I have not tried them, so cannot say if they are better or worse than the ones I have used.
MediMath - http://www.medimath.com/MediMath/MediMath.html
Doctor’s Aid - no working web site available
Both of these of appear similar to the others by screen shots, and the lists of formulas are not yet as thorough as Mediquations. However, I am sure that subsequent releases will add more features. The difficulty is going to be when each app has one formula you need that the others don’t. I was hoping that a good open source calculator would come out that would allow users to contribute formulas. But I guess it’s better to have 4 options than 0 options….
]]>People and WhitePages Mobile have similar features, but People allows you to search for residential listings in your immediate area, without knowing names. Useful for finding new neighbors, etc.
SearchQuest GPS - this application has a lot of buried features: it can display the datafrom your GPS (lat, long, elevation, etc), it can email your location (a la Here I Am). It may or may not be able to replace several single trick GPS apps.
I like FastContacts better than My Street - it seems to do everything the latter can do, and much more.
The games I use the most are definitely the free ones - Morocco and Sol Free Solitaire lately. I shouldn’t have wasted money on the others, but wanted to see what the iPhone was capable of.
OmniFocus is fantastic - like many others, I missed having To Do’s on my iPhone, but in reality my computer based to do system was sorely lacking. I have made a concerted effort to try and be more organized — using OmniFocus and Omnifocus for iPhone has made a big difference. It’s far and away the most expensive iPhone app I have purchased, and it was completely worth it. I still believe that GTD is something of a cult, but there are a few tips and strategies in the system (and the book) that have influenced my approach to tasks and projects in a positive way.
Having my iPhone stolen (at gunpoint, no less) definitely reminded me of the need for security. I have passwords on the iPhone, as well as the SIM, and keep secure information inside of 1Password. Since I use 1Password on my computer, this is easily synchronized. Having secure notes inside of it also makes it easy to jott free form information there and I know it will be safe. Now, if only there were a “self-destruct” signal, similar to what I understand Blackberries to be capable of.
This will be where I track which applications I am using the most (subjectively), and leave comments about some of them.
]]> (This table is created using my usual glicko technique.)| iPhone Application | Rating | RD |
|---|---|---|
| NetNewsWire | 1903 | 221 |
| OmniFocus | 1839 | 219 |
| Google Mobile App | 1836 | 226 |
| Stanza | 1810 | 226 |
| 1796 | 212 | |
| Epocrates Rx | 1791 | 223 |
| Morocco | 1778 | 230 |
| Sol Free Solitaire | 1770 | 225 |
| FastContacts | 1722 | 192 |
| WeatherBug | 1710 | 188 |
| Koi Pond | 1646 | 215 |
| People | 1630 | 219 |
| Jott for iPhone | 1624 | 214 |
| IM+ All-in-One Mobile | 1575 | 223 |
| TouchFS | 1557 | 213 |
| Dashbuster | 1554 | 218 |
| Mediquations | 1541 | 204 |
| Wikipanion | 1484 | 214 |
| iPhrase - Touch Poetry | 1467 | 217 |
| Caissa Chess | 1452 | 192 |
| Yelp | 1451 | 225 |
| Now Playing | 1428 | 198 |
| WhitePages Mobile | 1416 | 204 |
| Weight Tracker | 1405 | 185 |
| 1Password | 1395 | 221 |
| AP Mobile News Network | 1395 | 222 |
| Remote | 1373 | 220 |
| Exposure | 1355 | 200 |
| Taxi! | 1345 | 214 |
| Medical Calculator | 1310 | 214 |
| SearchQuest GPS | 1305 | 179 |
| PubSearch | 1296 | 230 |
| Midomi | 1255 | 219 |
| Super Monkey Ball | 1209 | 226 |
| Talking Spanish Phrasebook | 1189 | 209 |
| Here I Am | 1189 | 225 |
| Trism | 1180 | 206 |
| OBWheel | 1098 | 204 |
| Evernote | 1097 | 206 |
I have thus far not been able to redirect my old URL’s to these new ones for automatic updating…
]]>However, that seems unlikely to happen any time soon, unfortunately.
]]> Specifically, I was having trouble meeting the following criteria:content-type needs to be application/xhtml+xml for Firefox and other
real browserscontent-type needs to be text/html for IEBecause I want MathML to work on my site (more as a matter of pride than for
any real purpose), I have to serve the content as application/xhtml+xml.
With this content type, a real browser (e.g. Firefox) knows what to expect and
handles it appropriately. This allows the display of mathematical formulas,
such as:
However, as soon as I enabled the proper serving of XHTML 1.1, it effectively
turned off access to my site from Internet Explorer. Instead of accessing a
page, the user was offered the chance to download the page as an unusable
file. Therefore, IE needs the content served as text/html.
I could have two versions of the content, one ending in .html and one in
.xhtml so that different browsers are served the appropriate version, but
that would be a pain to keep up with. So this “solution” was not acceptable to
me.
I think, finally, that today I have solved this problem.
After much digging on the internet, I finally found a solution that I was able
to implement on my site via .htaccess.
I had already set the default data type:
DefaultType application/xhtml+xmlThen I had to change the content-type to text/html for requests from IE:
# Make Internet Explorer Happy
# If getting homepage
RewriteCond %{HTTP_USER_AGENT} .*MSIE.*
RewriteCond %{REQUEST_URI} ^/?$
RewriteRule ^$ index.html [T=text/html]
# If asking for a directory, serve back the index (it has no extension here)
RewriteCond %{HTTP_USER_AGENT} .*MSIE.*
RewriteCond %{REQUEST_URI} ..*\/$
RewriteRule (.*)/$ $1/index [T=text/html]
# Otherwise, try to just send the file as html
RewriteCond %{HTTP_USER_AGENT} .*MSIE.*
RewriteRule .* - [T=text/html]I have multiple steps in order to match certain request. Step 1 matches
the home page, which is stored in /index.html. Step 2 matches directories,
which store their main page in the directory in a file named index with no
extension. Step 3 matches everything else (which might cause problems with
images and other files down the road, but I’ll deal with that later….)
This seems to work so far - I still have access to MathML from Firefox, and I seem to be able to access the site from IE on Windows. But it’s still a crock to have to do this.
(Of course, getting the layout and other features right is another story. But for now, I’ll settle for seeing that the site exists!)
]]>