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Archive for the ‘news’ Category

blog was down, blog is up again

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OK, the title for this post sucks.

You know what else sucks?

When your blog goes down all of a sudden due to a line in an .htaccess file that had worked fine for months.

I had to change this:

Options All +Indexes

to this:

Options +Indexes

Thanks to the technician at Godaddy.com for figuring out it was my .htaccess file.

I still had to debug it by myself after that, but I never would have guessed a functional .htaccess file would all of a sudden make my site throw a 500 Internal Server Error.

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Written by nitin

August 31st, 2011 at 7:29 pm

Posted in news

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MXMLiszt version 0.9.2 released

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If anyone's interested, MXMLiszt version 0.9.2 is now available for download.

MXMLiszt is a web-based delivery and search/retrieval environment for MusicXML files and their manifestations.

The documentation and source-code download links are available here.

Here's the changelog:

0.9.2
- included Bach and Schubert MusicXML files from MusicSQL project (http://musicsql.googlecode.com/).
    - For the Bach, cleaned up diacritics (in titles only) and changed "Soprano", etc. to "Soprano", etc.
        - diacritics are still messed up in lyrics. I'm too lazy to fix them. :]
    - For the Schubert, changed "Part_1" through "Part_4" to "Violin 1", "Violin 2", "Viola", and "Cello".
    - original files available here:

http://musicsql.googlecode.com/files/Bach_SATB-1.0.zip

http://musicsql.googlecode.com/files/Schubert_quartets-1.0.zip

- adjusted <hr> rules in style.css to accomodate Internet Explorer 9
    - Removed "optimized for Firefox" in welcome.php since MXMLiszt now works well in IE, Firefox, Chrome, Safari, and Opera (see below).
- fixed generateIndex.php so the <img> tag now closes in this line:
        echo nl2br('<img src="png/' . $filenamePlain . '.pre.png" />'); //line #12
    - This was the only reason the Index view wasn't working in Opera.
        - Opera was the only browser that caught this error. :]
- made "Results" header for search results an <h2>, just as with the MIR results header.
- added two modules: startWatch.php and stopWatch.php to reduce coding redundancy in regard to reporting the time it takes for actions to finish.
- changed mxml2mods.xsl to output the MODS namespace.
    - adjusted mods.xsl, loadMODSasDC.php, and XQuery syntax as needed.
    - Sample XQueries using a namespace prefix:

        This is a Faust query example:
                    declare namespace mods = "http://www.loc.gov/mods/v3";
                    for $x in doc("../concat/concatMODS.xml")/hyperMODS/hypoMODS/mods:mods
                    let $x1 := $x//mods:subTitle
                    return $x1

        This is a Dante example:
                    declare namespace mods = "http://www.loc.gov/mods/v3";
                    for $x in doc("../concat/concatMODS.xml")/hyperMODS/hypoMODS
                    let $x1 := $x/mods:mods
                    where $x1//mods:subTitle contains text "You"
                    return data($x/@file)

- simplified some of the built in MODS related XQueries (same functionality, just less wordy).
- changed order of MODS search drop down terms on Search page.
- changed <i> and <b> to <em> and <strong>, respectively.
- replaced "pop1", etc. with better-named CSS variables like stickyNote and IndexPopup, etc. in style.css.
- added a streamed comment in each module with a one or two sentence description of what it does.
- added .htaccess file.
    - to hide root folder.
    - to make the "/~foo.xml" forward (with masking) to:"transmuteMXML.php$fname=musicXML/foo.xml".
        - adjusted mxml2mods.xsl accordingly.
    - to hide directory icons.
    - to use fancy indexing.
- changed displayMODS.php to display MODS files via an <iframe> only as a fallback if PHP XSL processing not available on server.
_______________________________________________________________________
0.9.1
- created mods.css file to display MODS on a transparent background.
- changed displayMODS.php to display MODS files via an <iframe>.
    - The previous version was using the mods.xsl stylesheet to parse the MODS element values in real-time.
_______________________________________________________________________
0.9.0
- this was the first version - that worked!
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Written by nitin

July 23rd, 2011 at 10:29 am

Posted in music notation,news,scripts

Tagged with ,

Go Daddy and database connection problems

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It's funny that GoDaddy.com uses a race car driver as their spokesperson, given that their service doesn't always "go".

Anyway, I created a new MySQL db in my Go Daddy account and I had all kinds of connectivity errors. Sometimes my PHP script would retrieve the data I wanted from the db and other times a connection just couldn't be established.

This seemed weird since my WordPress blog is using a MySQL db hosted by Go Daddy and I don't have any problems with connectivity and my blog.

Customer service was, of course, a waste of time. I got the generic, stock answers about verifying my PHP connection string … but if it connects sometimes but not all the times isn't is clear the issue isn't with my connection string? Worthless.

So what I did was cheat …

Since Go Daddy does make it easy to install WordPress or various other PHP/MySQL applications, I just installed one (OpenDB) that I didn't intend to use. In other words, I made Go Daddy create the db.

I then just deleted all the files on my server related to OpenDB.

Then, I used phpMyAdmin to drop all the tables in the db created for OpenDB as described here.

After that, I imported my tables and it seems that this workaround will allow me to access a MySQL db hosted by Go Daddy without PHP connection problems.

I wasted so much time on the weekend over this issue that I hope this post helps others deal with the issue if they have the same problem.

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Written by nitin

June 26th, 2011 at 10:56 am

Posted in news,technophilia

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Musescore: way better Lilypond export than before

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When MuseScore first came out, I think a lot of people knew it was going to be great.

And it is. It's also getting better all the time.

One thing that wasn't great initially was the Lilypond export. But MuseScore version 1.0's Lilypond export seems really good from initial experiments I've done.

And let's face it – that's the holy grail of music notation: a GUI score editor with good Lilypond export … AND MusicXML support … and command line options.

So in other words, a one-stop shop for music notation that supports the best tool (Lilypond) for output in terms of aesthetics and the more widely supported XML format in MusicXML … as well as those command line options for using on a server.

Well, well done people.

Keep it up.

:)

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Written by nitin

June 26th, 2011 at 9:52 am

Posted in music notation,news

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PubMed2XL 1.0 available

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I've uploaded a new version of PubMed2XL, a Windows application that converts article lists from PubMed.gov into Microsoft Excel files.

Unlike downloading the CSV directly from PubMed.gov, PubMed2XL gives users (OK … advanced users) the ability to customize the output but even the default format includes Abstract, links to each article, and even links to related articles, and reviews.

Here's an example of a spreadsheet made with PubMed2XL and here's the source file used to make it. The source file was downloaded from PubMed.gov using a search for "Mexican flu".

If you'd like to use the software you can download it for free.

If you notice any bugs or have any questions or remarks, please feel free to leave a comment on the site. Thanks!

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Written by nitin

June 18th, 2011 at 2:28 pm

Posted in news,scripts

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tweaking Simple Download Manager, a WordPress plugin

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I wanted a way to track downloads available through my blog without having to do a lot of work and without having to check server access logs.

So I installed Simple Download Manager (v. 0.21). It's great.

I did do one thing a little differently than the instructions in regard to editing my .htaccess file.

Here are the instructions:

The last step involves editing the '.htaccess' file. The default '.htaccess' skips default WordPress processing for existing files, which means that direct-linked files would get downloaded directly, without Simple Download Monitor ever learning about it. You need to modify the '.htaccess' file so that downloads are passed through Simple Download Monitor. This is easy enough to do: Open your '.htaccess' file and locate line RewriteCond %{REQUEST_FILENAME} !-f Add this line directly above it: RewriteRule ^(files/.*) /index.php?sdmon=$1 [L] (replace 'files/' with your download directory).

Other than changing the "files" folder to "uploads", I altered the line to read like this:

RewriteRule ^(uploads/.*\..*) /index.php?sdmon=$1 [L]

The reason for this is that using the default line would have prevented users from directly browsing directories through their browser. And that would have been a problem since with some projects I provide a link to a directory so people can download past versions of software.

For example:

Click here to download the latest Windows self-installer.

Click here to download the latest ZIP file.

Older versions can be accessed here.

Simple Download Manager will still track downloads for the types of files I've asked it to track whether the user downloads the file via clicking a link in a blog post or by downloading the file from the directory. That's exactly what I wanted.

I'm pretty lousy with regular expressions, so for my own notes here goes …

There are three parts, as I see it, to this regex:

.*\..*

Those parts are:

  1. .*
  2. \.
  3. .*

The first matches anything, the second makes sure the match ends with a dot, and the third means the match can have anything after the dot.

This matches filenames a la "filename.ext" but excludes directories.

By the way, this means I cannot name directories with a dot in the directory name, otherwise the RewriteRule will kick in on the directory – which won't work and the user won't be able to traverse that directory.

I guess I should learn the regex to allow me to create directories with dots in the directory name …

:/

Update, June 12, 2011: Actually, I've since reconsidered. I only want to track ZIP and EXE downloads. Doing otherwise would force users to have to download other file types like text and XML files. That's not a user-friendly approach. So, the addition to the .htaccess file now reads:

RewriteRule ^(uploads/.*\.zip) /index.php?sdmon=$1 [L]
RewriteRule ^(uploads/.*\.exe) /index.php?sdmon=$1 [L]

The two lines ensure that only ZIP and EXE files are processed by Simple Download Manager … and I can now make directory names with dots in them.

Update, November 26, 2011: I need to mention that this addition to the .htaccess file should not go in the WordPress block otherwise it will get periodically overwritten, preventing the download manager from working. It maybe better to just see an example …

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
# END WordPress

#Notes: don't put anything in the WordPress block per: http://www.webpronews.com/keep-wordpress-from-overwriting-custom-htaccess-rules-2007-06

#Simple Download Manager
RewriteRule ^(uploads/.*\.zip) /index.php?sdmon=$1 [L]
RewriteRule ^(uploads/.*\.exe) /index.php?sdmon=$1 [L]
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Written by nitin

June 12th, 2011 at 10:25 am

Posted in news,technophilia

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PubMed2XL 0.9.1 available

5 comments

I've uploaded a new version of PubMed2XL, a Windows application that converts article lists from pubmed.gov into Microsoft Excel files.

If you'd like to use the software you can download it for free.

For those who are interested, here's the changelog:

0.9.1
- worked with Björn Carlsson on a few things:
    - added length checker for <getElement> so that abstracts greater than 32k characters would get truncated to the first 30k characters.
        - see: http://blog.humaneguitarist.org/2011/03/16/dealing-with-a-pubmed2xl-bug/
    - added <getAttributeByElementPosition> element.
        - Updated schema.
- removed code that displayed the "aboutMessage" variable on the command line if command line options are used.
    - This is because the diacritic in Mr. Carlsson's name caused encoding errors with the default Windows command prompt.
- added <hyperlinkSuffix> element so that alternate views of PubMed data could be passed via the URL.
    - updated schema.
    - For example, see this: http://www.ncbi.nlm.nih.gov/pubmed/21069543 then this: http://www.ncbi.nlm.nih.gov/pubmed/21069543?report=medline
        - The hyperlink suffix of ?report=medline changes the display!
        - For more information, see:
            - PubMed Help — PubMed Help — NCBI Bookshelf. Retrieved November 13, 2010, from http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=helppubmed&part=pubmedhelp&rendertype=table&id=pubmedhelp.T40
            - pm_workbook.pdf. Retrieved November 13, 2010, from http://www.nlm.nih.gov/pubs/manuals/pm_workbook.pdf (see page 135).
- updated py2exe "setup.py" to automatically name the command line/console version correctly (i.e. with the "-CL" suffix).
- removed "src" folder and placed Python files in same folder as .exe's.
_______________________________________________________________________
0.9.0
- this was the first version - that worked!
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Written by nitin

April 3rd, 2011 at 5:40 pm

Posted in news,scripts

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PubMed CSV option added

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It looks like things are afoot at PubMed.gov. They've apparently added a CSV option for downloading citations. This is great and will facilitate people getting citations into spreadsheets. Having this new option sure beats that FLink thing.

I'm not sure it's totally up and running though as the RSS feed for their News and Noteworthy shows a link to a post called "CSV File Selection" from March 24th but there's no post there, it just redirects to the home page.

Interestingly, this all seems to have happened a few days after someone from the NIH – according to Google Analytics – spent a good bit of time on this blog looking for information on how to get PubMed citations into a spreadsheet. Boy, would I like to believe that had something to do with it!

Of course, the data in the CSV file is still limited and non-customizable. You still can't get abstracts, it seems. That makes no sense of course since it is available in the XML format. If they've already got the data in a granular fashion, why not offer users better options?

For now, if you want abstracts and customized output you can try PubMed2XL. By the way, I'll be uploading an updated version in a few days. I just moved to a new town and I'm not quite settled enough to update some documentation and do some light programming work.

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Written by nitin

March 31st, 2011 at 10:04 am

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opensourcelibrarian.org: back online

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My other site, opensourcelibrarian.org, is back online.

I'm actually glad I had to have my VPS provider, KickAssVPS, rebuild my VPS and that I, in turn, had to reinstall the site, including the MXMLiszt project. The reason being that the first time around I didn't document a few trouble spots in regard to getting MXMLiszt up and running on Windows Server 2003, the OS my VPS uses. So, this time around I hope I wrote down all the things I didn't document the first time!

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Written by nitin

March 5th, 2011 at 12:26 pm

opensourcelibrarian.org: closed 3/3/2011 to 3/5/2011

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My other site – opensourcelibrarian.org – will be down for a few days.

It runs on a VPS and the VPS has to get rebuilt due to a security breach.

The MXMLiszt project runs on the VPS, so that will be down for a few days as well.

Update, March 5, 2011: opensourcelibrarian.org is back online.

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Written by nitin

March 4th, 2011 at 6:25 pm

Posted in news

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