Completed IT Tasks

As the ComputingTodo list gets too long we will move some of the completed tasks here.

  • DONEDevelop plan to bring up new server
  • DONEBring up new server
  • DONESet up procedure so that server gets correct time. Must also correctly set the computer's hardware clock. Server fell back an hour after a recent reboot. (added 24 June 2004 by Jeff)
  • DONEDevelop or acquire a server monitoring tool that can send email to on call pager if trouble is detected (added 10 Jun 2004)
  • DONEDevelop after-hours server support plan (e.g., provide cell phone numbers to selected users or rotating responsibility to check 3 times each evening). (10 Jun 2004: partially done - we now have a pager that can receive email and a very simple job that is checking on the server every 30 minutes)
  • DONEMake appropriate changes to Preventive Medicine web pages so that everything can be found as it should. We should leave faculty pages with links to Biostatistics so that they can be found. (for Dale, added 5 May 2004)
  • DONEDocument backup configuration and procedures (with links to product and company) (Jeff and Dale) BiostatServerOps
  • DONEMake LDAP recovery more robust when server crashes. (15 Apr 2004) Jeff
  • Set appropriate protection on Twiki pages that need to be protected.
  • DONEHow can we get a particular twiki template to come up for new users? (Dale) - Cole has set things up so that new users get the template page as their default user page. They can use and modify that template or roll their own.
  • DONEMake user template easy to get (Dale)
  • DONEAdd df-alert to cron; one for non-essential partitions, and one for critical partitions. (16 Apr 2004) Jeff
  • DONEAdd phpmyadmin to website
  • DONEis there a twiki plug-in front end to MySQL? (Jeff)
    • try the DatabasePlugin
    • this plugin requires phpMyAdmin in order for users to edit tables, as well as DBI and DBD-mysql from CPAN
  • Look into other twiki plugins (07 Apr 2004)
    • DONEMathModePlugin - This plugin allows you to include mathematics in a TWiki page, with a format very similar to LaTeX. It requires latex2html and the Digest::MD5 module from CPAN. (Cole)
    • DONEImplement a BibTeX citation plugin for twiki. A page containing \cite{x,y} ... \cite{z} would link to Frank's primary bibliographic database (cvs bib project file feh.bib) or to http://biostat.mc.vanderbilt.edu/twiki/pub/Main/RmS/fehbib.html and would replace \cite{ } with auto-sequenced references that appear as superscripts in the text but link to bibliographic citations that would automatically be created at the bottom of the screen after a horizontal line. Tags inside \cite{} are BibTeX article keys. Check first if anyone has done anything like this. -- This has been partially implemented with EmbedBibPlugin, which requires BibTool and Bib2html. See instructions about how to use this plugin. (Jeff and Cole)
  • Note this should be updated to refer to http://citeulike.org
      • DONEInstall BibTool and Bib2html (6 May 2004 Jeff)
    • DONEPowerEditPlugin - This plugin enables a Java 1.1 applet text editor. Java must be installed on the client for this to work. It has been decided that this plugin is not very beneficial. It can be used by removing it from the Disabled Plugins list on the twiki prefererences page. In addition, under the line Edit in /usr/local/www/twiki/templates/view.tmpl, a link to the plugin is needed. (Cole)
    • DONEInstall SectionalEditPlugin (14 June 2004 Cole)

  • DONEUpdate cvs to latest secure release on server (Jeff)
  • DONENeed cron job to shutdown database, make backup to some place that gets saved by the remote backup process, restart database. Then remove /var/whatever from the list of trees getting backed up. (6 May 2004 Jeff)
  • DONELook into workstation backup issues (All) - as of 5 May 2004 client is installed on server and backups will begin tonight.
  • DONESend out informational e-mail introducing the mailing lists (28 Apr 2004 Dale)
  • DONEAdd anonymous CVS browsing to the website. (15 Apr 2004) Jeff
  • DONEFinish documentation for CVS and LDAP. (Jeff and Cole)
  • DONEChange backup procedure to make sure disk space on / is not completely consumed. (Dale & Jeff)
  • DONEChange page redirection method being used to redirect biostat.mc.vanderbilt.edu to the twiki front page. Currently, index.html just does a simple minded redirect after 3 seconds. Some folks don't like being redirected, the delay is annoying, and some browsers complain. (done by Jeff 4/30/2004)
  • DONEAdd documentation for Xprint, the server that facilitates printing in Mozilla products. (16 Apr 2004) Jeff
  • DONEMake a mailing list called "biostat-it". Members will be Jeff, Cole, and Dale. (done by dale 4/14/2004)
  • DONEAutomate (cron?) backup of web site files (07 Apr 2004) (Jeff)
    • Documentation for this will be found on the Restricted Web.
  • DONETry out Frank's win4lin hint. Add a how-to. (Cole)
    • Process involves copying appwrapper.exe into ~/win/windows and, within this folder, replacing the line shell=Explorer.exe with shell=/path/to/executable in the system.ini file
    • This is only useful for someone who exclusively uses one Windows' application, otherwise the system.ini file needs to be modified when the user wants to run other applications. It seems unlikely that this would provide much benefit, as the time it takes to modify the system.ini file is greater than the time it takes a user to open and close an application. This also takes up one of the win4lin licenses.
  • DONEDefine specifications for a new server 13-apr-2004 (Here is a ServerQuote. What do you think?)
  • DONEMake these redirections in the Twiki:
  • DONE Set reply in lists to go to the list (Cole)
  • DONE Look into rekall (Cole)
  • DONEDouble check that the biostat-all e-mail list is really going to everyone; one report from a member of phdfac indicated non-receipt of a message sent to biostat-all.
  • DONEMake a better title for this (07 Apr 2004)
    • What about 2DLFWTN2BDR2DCR? or maybe just Current IT Tasks? (Cole)
  • DONEOrder spare consumables for Xerox printer (Dale) (8Apr2004)
  • DONEPurchase 3 more Win4Lin seats
  • DONEset up xerox phaser 6250 dp (PhaserNotes)
  • DONEmake a template for user page (Dale) (see UserpageTemplate)
  • DONEget email notification of changes working (need to do cron setup on server)
  • DONEget email notification of registration working
  • DONEFileMaker - add a filemaker user on the server for saving databases (Dale)
  • DONEdevelop a department standard sources.list
  • DONEAdd a cron job on biostat and biostat2 to email the output from /usr/tibs/tera -Q to biostat-it once a day. Should run at 7:00 a.m. or so to check status of backup jobs.
  • DONESee about web calendar issue: Say an assistant places an appointment on user A's calendar. User A can delete this appointment but cannot edit it. This needs fixing.
  • DONEDevelop a departmental FAQ: what applications we support, where to get help, how to request that a file be restored, etc.
  • DONESet up an "admin share".
  • DONEMove color1 printer to 4th floor.
  • DONEUse rsync to copy workstation home areas to server to facilitate workstation backup. DONEWill need to get more space for the server (Jeff and Dale)
  • DONEChange web calendar default reminder time to 4 hrs, 15 minutes. This makes it more convenient to set a short reminder period while leaving the default at about 4 hrs. (Edited /usr/local/www/html/calendar/includes/site_extras.php.)
  • DONEMake "cheat sheet" of common and helpful commands (e.g. command to stop and restart apache, make a tar repository of all files in a directory tree, stop and restart firewall, etc.)
  • DONELook into xforms? (Dale) (see ToDoXforms for some notes. More will come as it is actually tried out.)
  • DONELook into the feasibility of adding a plug-in for the graphviz dot executable for generating directed graphs (dendograms). The users guide for dot states that it can produce png files directly. The png image would be inserted at the point of the dot commands. In a few tests png and jpeg files looked fuzzy (partially because they didn't have some fonts available) so it may be best to output a pdf file that can easily be referenced, using dot -Tps foo.dot -o foo.ps && convert foo.ps foo.pdf. Example invocation:
<dot>
digraph G {
    subgraph cluster_c0 {a0 -> a1 -> a2 -> a3;}
    subgraph cluster_c1 {b0 -> b1 -> b2 -> b3;}
    x -> a0;
    x -> b0;
    a1 -> a3;
    a3 -> a0;
}
</dot>
  • Try to generalize this. For example:
<exec cmd="R --vanilla" out="my.pdf,my2.pdf" label="Make 2 plots">
pdf('my.pdf')
plot(runif(100))
dev.off()
pdf('my2.pdf')
hist(rnorm(10000), nclass=50)
dev.off()
</exec>
This passes the 6 lines to cmd as stdin; creates 3 buttons - one hyperlinking to /foo/my.pdf, one to /foo/my2.pdf, one to re-run the script, using Make 2 plots as the name of the button. The script is only run when the Make 2 plots button is pressed, so at first the 2 hyperlinks will point to nowhere. In addition to .pdf, the script could create .txt, .html, and many other file types. cd to /foo before invoking cmd. /foo is something like /var/www/html/twiki/execout. For out files that are known inline-displayed formats (e.g. png) display as inline images automatically, without a hyperlink button.

In a future version allow passing of user-entered values:
<exec .... data="Number of observations:N; Mean:mean">
x <- rnorm(`N`, mean=`mean`)
...
A pop-up window would look like
Number of observations:____________
Mean:____________
and `N` and `mean` in the script would be replaced with the user-entered values before running cmd. The data would need to be stored somewhere so that you could tell what the output meant without re-running the script.
Topic revision: r4 - 14 May 2019, DalePlummer
 

This site is powered by FoswikiCopyright © 2013-2017 by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding Vanderbilt Biostatistics Wiki? Send feedback