Using the flickr XML/API as a source of RSS feeds.

You may know that I seek from time to time royalty free pictures  on flickr.com for my other personal blog. The flickr API can be used to search for these images but it is currently not possible to generate a RSS feed to be alerted when a new image is posted on flickr.

The following XSLT stylesheet transforms the XML returned by www.flickr.com to a RSS feed (latest source: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/flickr/flickr2rss.xsl ):

<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:date="http://exslt.org/dates-and-times"
xmlns:dc="http://purl.org/dc/elements/1.1/" version="1.0">

<xsl:output method="xml" indent="yes" encoding="UTF-8"/>

<xsl:param name="title">No Title</xsl:param>


<xsl:template match="/">
<rss version="2.0">
<channel>

<title><xsl:value-of select="$title"/></title>
<link>http://www.flickr.com</link>
<description><xsl:value-of select="$title"/></description>
<pubDate><xsl:value-of select="date:date-time()"/></pubDate>
<lastBuildDate><xsl:value-of select="date:date-time()"/></lastBuildDate>
<generator>http://www.flickr.com/</generator>
<xsl:apply-templates select="rsp/photos/photo"/>
</channel>
</rss>
</xsl:template>

<xsl:template match="photo">
<item>
<title><xsl:value-of select="@title"/> : <xsl:value-of select="$title"/></title>
<link>http://www.flickr.com/photos/<xsl:value-of select="@owner"/>/<xsl:value-of select="@id"/>/</link>
<pubDate><xsl:value-of select="@datetaken"/></pubDate>

<author>
<xsl:choose>
<xsl:when test="@ownername"><xsl:value-of select="@ownername"/></xsl:when>
<xsl:otherwise><xsl:value-of select="@owner"/></xsl:otherwise>
</xsl:choose>
</author>
<guid isPermaLink="false">http://www.flickr.com/photos/<xsl:value-of select="@owner"/>/<xsl:value-of select="@id"/>/</guid>
<description>
<xsl:text><p><img </xsl:text>
<xsl:choose>
<xsl:when test="@height_s and @width_s">
<xsl:text> width='</xsl:text>
<xsl:value-of select="@width_s"/>
<xsl:text>' height='</xsl:text>
<xsl:value-of select="@height_s"/>
<xsl:text>' </xsl:text>
</xsl:when>
<xsl:when test="@height_m and @width_m">
<xsl:text> width='</xsl:text>
<xsl:value-of select="@width_m"/>
<xsl:text>' height='</xsl:text>
<xsl:value-of select="@height_m"/>
<xsl:text>' </xsl:text>
</xsl:when>
</xsl:choose>
<xsl:text> src='</xsl:text>
<xsl:choose>
<xsl:when test="@url_s"><xsl:value-of select="@url_s"/></xsl:when>
<xsl:otherwise>http://farm<xsl:value-of select="@farm"/>.staticflickr.com/<xsl:value-of select="@server"/>/<xsl:value-of select="@id"/>_<xsl:value-of select="@secret"/>_s.jpg</xsl:otherwise>
</xsl:choose>
<xsl:text>' /></p></xsl:text>
</description>
</item>
</xsl:template>

</xsl:stylesheet>

To invoke this stylesheet and generate the RSS feed, I wrote the following small quick'n dirty cgi-script "flickr.cgi". The script was made executable, installed into my public_html/cgi-bin directory. It also requires to get an API key from flickr.

#!/bin/sh
echo "Content-Type: application/rss+xml"
echo 

APIKEY=12345678910
TAGS=`echo ${QUERY_STRING}|tr "?&" "\n" | egrep '^tags=' | cut -d '=' -f 2 | sed 's/,/%2C/g'`
TEXT=`echo ${QUERY_STRING}|tr "?&" "\n" | egrep '^text=' | cut -d '=' -f 2 | tr " " "+"`

curl -s "http://api.flickr.com/services/rest/?method=flickr.photos.search&api_key=${APIKEY}&tags=${TAGS}&format=rest&extras=url_s,date_upload,date_taken,icon_server,owner_name&tag_mode=all&per_page=20&license=2,4,1,5,7&text=${TEXT}" |
xsltproc --novalid --stringparam title "${TAGS} ${TEXT}" flickr2rss.xsl -

I can know add some new RSS feeds into thunderbird and receive the new items: for example http://localhost/~me/cgi-bin/flickr.cgi?tags=science

<rss version="2.0" xmlns:date="http://exslt.org/dates-and-times" xmlns:dc="http://purl.org/dc/elements/1.1/" version="2.0" >
<channel>
<title>science </title>
<link>http://www.flickr.com</link>
<description>science </description>
<pubDate>2012-07-09T23:09:58+02:00</pubDate>
<lastBuildDate>2012-07-09T23:09:58+02:00</lastBuildDate>
<generator>http://www.flickr.com/</generator>
<item>
<title>2012 NOAA HABs Forecast : science </title>
<link>http://www.flickr.com/photos/41398337@N07/7537830696/</link>
<pubDate>2012-07-05 10:16:56</pubDate>
<author>Ohio Sea Grant and Stone Laboratory</author>
<guid isPermaLink="false">http://www.flickr.com/photos/41398337@N07/7537830696/</guid>
<description><p><img width='240' height='160' src='http://farm8.staticflickr.com/7252/7537830696_2a66783e70_m.jpg' /></p></description>
</item>
<item>
<title>2012 NOAA HABs Forecast : science </title>
<link>http://www.flickr.com/photos/41398337@N07/7537829638/</link>
<pubDate>2012-07-05 10:18:37</pubDate>
<author>Ohio Sea Grant and Stone Laboratory</author>
<guid isPermaLink="false">http://www.flickr.com/photos/41398337@N07/7537829638/</guid>
<description><p><img width='240' height='160' src='http://farm8.staticflickr.com/7252/7537829638_4c6dd535b4_m.jpg' /></p></description>
</item>
<item>
(...)
</item>
</channel>
</rss>

That's it,

Pierre

A CGI-version of samtools tview.

I've created a lightweight CGI-based web-application for samtools tview. This C++ program named ngsproject.cgi uses the samtools api, it allows any user to visualize all the alignments in a given NGS project. The projects and their BAMS are defined on the server side using a simple XML document. e.g:

<?xml version="1.0"?>
<projects>
 <reference id="hg19">
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.fa</path>
 </reference>
 <bam id="b1">
  <sample>Sample 1</sample>
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.bam</path>
 </bam>
 <bam id="b2">
  <sample>Sample 2</sample>
  <path>/home/lindenb/samtools-0.1.18/examples/ex1.bam</path>
 </bam>
 <project id="1">
  <name>Test 1</name>
  <description>Test</description>
  <bam ref="b1"/>
  <bam ref="b2"/>
  <reference ref="hg19" />
 </project>
 <project id="2">
  <name>Test 2</name>
  <description>Test</description>
  <bam ref="b2"/>
  <reference ref="hg19" />
 </project>
</projects>

Once the CGI has been installed, the user can visualize the reads of each samples.

This tool is available in the variation toolkit at http://code.google.com/p/variationtoolkit/.

That's it.

Pierre

xul4wikipedia

I've added a few more individuals in my History Of Science and I've also tried to generate an iCal version of this dataset to display the birth/death dates of all those persons (http://lindenb.integragen.org/xulhistory/history.ical) however there is a bug in this file as the events are not correctly displayed in google-calendar. Does anyone knows why ?

There is now a new beautiful version of freebase but it is a little bit slower and as I want to edit a large number of individual, the procedure takes now too much time for me. I received a kind mail of Robert Cook from metaweb about this problem telling me that they're working on this issue. I also noticed that, just like wikipedia, they are now much more concerned about the origin of the pictures. That's fair but I wish I could add a picture to all those individuals :-) . I could draw them but there would be still a problem of rights :-)

Meanwhile, I've added some infoboxes in wikipedia. I also created a simple web form at http://lindenb.integragen.org/xul4wikipedia/xul4wikipedia.cgi to create on the fly a firefox extension. This add-on will append some custom items in the contextual popup menu when editing an article in wikipedia. Each of those items is used to insert a custom text in the textarea of the edited article, for example you won't have to find, copy and paste your favorite Template:Infobox Person, this template will now be always available in your menu. The source code is available here and is broadly inspired from one of my previous post.

Pierre