Bioinformatics Links




Updating the JVM used for CFGraph in ColdFusion 5

ColdFusion 5 uses a built-in version of JRun and Generator to render the images created by CFGraph. That built-in JRun server (version 3.02a) is configured in the file to use the jre that ships with ColdFusion 5.

That version of the CF5 built-in jre on Solaris is 1.3.0_02. That version of jre may be unstable in certain enviroments or circumstances, and can lead to the jvm crashing. When that happens you may get a "Cannot connect to JRun proxy" error in the place of the expected graph.


Linux Magazine: Subscription Woes

For the third year I've been receiving a subscription to Linux Magazine, however for about 6 months I'd not actually received it, but the subscripton was still valid and I did not change any of my customer data such as the address. It took me a while to realize that something was wrong, and I just bought it off the rack during that time.

I finally got around to writing to their customer support email address, and the response I got was completely underwhelming. Most email responses were to the effect of "sorry, can't find you in our database", with no further questions or follow up. I'd reply back with details about my mailing address, billing information, and information directly off the mailing label, and I sent this to a wider distribution as I began searching for all related Linux Mag emails that I could find. Replies to this varied widely. One told me that I had a subscription and it was valid until Feb 04 but with no follow up on my request for missing back issues. Another reply to the same email said that they still couldn't find my customer id in their database, again, with no follow-up.


RedHat Ships Outdated Apache

Saw some discussion today of the RedHat 8 and 9 distributions. Each of these distributions ships Apache 2.0.40, however has released a number of revisions with important security fixes and the like.

Does RedHat continue to support the distribution if you upgrade the httpd package to something more recent, say 2.0.46?

Compiling the Apache Connector Module for CFMX

Found an excellent step by step procedure for Compiling and Installing the Apache module for CFMX from source code on CFDEV today. This explains more carefully how to perform the procedure first described in the ColdFusion MX wsconfig FAQ.

See my more recent blog entry for a script you can use to more easily build the connector.

CFUN03 Celebrity Squares Trivia

CF Celebrity Squares At the recent CFUN03 conference, I was asked again this year to create the trivia questions to be used in the game show parody, this year entitled Celebrity Squares. The following is a list of questions prepared for the game.

1) The CFML tags CFDUMP, CFLOG, and CFFLUSH first became available in what version of ColdFusion?
Answer: ColdFusion 5 (a little bathroom humor to warm up !)
2) CFMAIL can be used to send large volumes of unsolicited mail, often known as spam. How did junk email come to be known as "spam"?


DSNs in CFMX Getting Out of Sync

Ray Camden just posed an interesting problem to the CFGuru mailing list regarding DSNs failing after a restart of CF. It just happens that I ran into this problem a while back and eventually uncovered the problem with jrun-resources.xml.

The longer explanation based on my test is the following:

This sounds like the jrun-resources.xml and neo-query.xml are out of sync. Check jrun-resources.xml to confirm that there is only 1 datasource node for that particular datasource. I have seen some cases where a manual or externally automated modification to jrun-resources.xml (say an ISP custom script for adding dsn's or someone at home tinkering with the service factory, or ??) can end up creating duplicate nodes for a particular datasource, each with slightly different settings. ColdFusion MX only expects one node for the datasource. On start up it reads jrun-resources.xml, finds the (top-most) node (#1) for a datasource, and updates neo-query with that data. When you edit the datasource from the admin, those modifications will cause the top-most node (#1) to be removed and a new node (#3) to be written, while leaving the previous bottom-most node (#2) which makes it node #1 for that datasource. In other words it reads from the top and writes to the bottom. If the !

new node data is good, then you'll run for as long as CF is up, but when you restart, the top node (#1(#2)) will be read and used, not #3. If there was only one node for a datasource, then it would do the right thing... remove it and rewrite it, but instead there are multiple nodes being shuffled.

This behavior will not occur in the next update as all relevant datasource info will be kept in neo-query.xml without trying to synch it with jrun-resources.xml.

First Blog!!

Let's kick things off with a first blog! Spent a few hours today creating a personalized "talkingtree" green style by getting my feet wet with CFXML_Blog. What appeals most to me about this blogging project is that its built in ColdFusion so extending and modifying it is easy, and secondly that it uses XML to hold all the blog data so no database is necessary.

Tomorrow evening I'll be driving from Boston to Gaithersburg, Maryland to attend the annual CFUN03, a ColdFusion conference. I've attended this conference for the last two years and it just keeps getting better every time. This year there are several "tracks" to choose from, not to mention a keynote address from the ColdFusion Community Leader, Christian Cantrell. Last year I created the questions for the CF Celebrity Jeopardy game. This year, Michael Smith asked me to write the Celebrity Squares questions, which I'll post here after the game.