Got some bug reports this week and am procrastinating other stuff by looking at them. The content of this post will change as I use it to reply to this update Dec 30 8:26PM 2018 [pmid-refs key=redenti_18 wrap=ol showlink=false] 2017 [pmid-refs key=redenti_17 wrap=ol showlink=false] 2016 [pmid-refs key=redenti_16 wrap=ol showlink=false] other [pmid-refs key=27590350 wrap=ul] [pmid-refs key=27879490 wrap=ul]
Category Archives: web development
phpmyadmin hybrid install (apt + manual) on Ubuntu
While migrating our websites to the new Ubuntu box, I set up phpmyadmin using apt-get. But that package is 4.5x while the latest version is 4.8x. Not surprisingly, the Nessus security scan needed to get http and https ports opened through the TAMU firewall detected security exploits that I hope have been fixed in the […]
JSmol2wp plugin released at wordpress.org
A while ago I wrote a WordPress shortcode plugin to embed Bob Hanson’s JSmol molecular structure viewer into WordPress posts and pages. Last weekend I finally got it into the wordpress.org plugin repository. The basic usage for proteins is via a shortcode like this: [[jsmol pdb=’1LMB’]] The plugin fetches the appropriate record from the PDB […]
WP PubMed Reflist
I committed a couple of updates to my WordPress plugin for getting reference lists from PubMed. The new version allows customization of the display. I preloaded some templates that approximate a few popular formats NIH format [pmid-refs key=’jimhu’ style=NIH limit=5] ASM format [pmid-refs key=’jimhu’ style=ASM limit=5] PNAS format [pmid-refs key=’jimhu’ style=PNAS limit=5] Notes The formatting […]
Your spambot needs debugging
Found an amusing spam in my comment moderation queue. Excerpt: { {I have|I’ve} been {surfing|browsing} online more than {three|3|2|4} hours today, yet I never found any interesting article like yours. {It’s|It is} pretty worth enough for me. {In my opinion|Personally|In my view}, if all {webmasters|site owners|website owners|web owners} and bloggers made good content as you did, […]
WordPress shortcode plugins with multiple instances
I’ve been working on the JSmol2wp plugin used in these previous posts. There have been a couple of challenges associated with putting multiple copies of the JSmol viewer applet in the same post, and in having multiple posts with viewers. The WordPress shortcode API doesn’t provide an obvious way for a shortcode to know its […]
More JSmol2wp testing
As of version 0.7, I wonder whether having two posts with viewers causes applet name clashes. The prediction is that this would work while viewing one post, but not on the home page. This prediction turned out to be true. This first item loaded the first one from the next post, while the first item […]
Updating to Mavericks Server
We have a mini that we got to support a program to train undergrads in bioinformatics. Over the past week or so I’ve been working on updating it to run Mavericks and Mavericks Server. I first decided to go with OSX servers back when I had a G5 blade running Panther Server for the user-friendly GUI […]
Weird, given Marissa Mayer’s rep from Google
I first heard of Marissa Mayer from a podcast of this talk from the Stanford Entrepreneurial Thought Leaders series. As I recall, one of the intereresting things was the way Google tested UI options and gathered data about what did or did not work for users. Given that, I am kind of surprised how hideous […]
Fix for Macports 2.2.0 upgrade problems (if /opt/local is a symlink)
I was having trouble updating MacPorts on one of our OSX servers. Error: org.macports.extract for port gnupg returned: command execution failed Please see the log file for port gnupg for details: /opt/local/var/macports/logs/_Volumes_r4_opt_local_var_macports_sources_rsync.macports.org_release_ports_mail_gnupg/gnupg/main.log Error: Unable to upgrade port: 1 To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets It turns out that version 2.2.0 doesn’t like symlinks to /opt/local that didn’t bother earlier […]