OpenWetWare:Software/Milestones/March 2008

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Development Items

Lab Notebook

  • Create a model group lab notebook for IGEM users
    • Work with Ricardo to do the design
  • Evaluate using a simplified entry form for daily log entries
    • Does not require adding the template calls to the beginning and end of daily lab notebook sections.
    • Also provides a drop-down list of all current projects
  • Add auto-create of a Project page
    • No need to enter or edit mediawiki text on project creation


  • Track down problem related to email messages sent to new users or rejected users.

User Poll

  • Add a small user poll to the OWW front page just below the current search box
    • When a person responds, the current poll stats will be shown as a histogram.
    • Poll will not be limited to OWW members.
    • Will revise as needed if abuse is detected.
    • Will use existing Ajax-based PHP/JavaScript/MySQL script
    • Reports for all polls will be maintained in an OWW MediaWiki special page
      • All new poll questions will be added via the special page
      • Results will be stored in the OWW database


  • Complete poll to determinne whether we should eliminate the Ajax Google-suggest-inspired search
    • The idea of prompted search is sound but the implementation has been criticized by several users
  • Jason R. Kelly 17:18, 22 March 2008 (CDT):Should we consider moving to google search? We could have "Go" and "Search", but search would point to a google search. I did some informal testing and google seems much better, what's the tech dev position on this?

Invite User

  • Complete work on the "invite" extension
  • Use the HTML form Ilya and Reed worked on
  • The inviting member will be alerted when a user that member invites joins OWW

Contact Us

  • Fix the 'navigation' sidebar icon.
    • Part of the problem may be related to caching pages.
    • Also may be related to how labels are stored in the MySQL database and the MediaWiki: namespace

File Upload

  • Deploy a test version of the abbreviated file upload process
    • Provide a way to use it within the editor
    • Try out the Java-based drag-and-drop upload.
      • Radlinks has a closed source but still pretty useful component that fits the bill.
      • The initial 'trial' version is limited to small files.
      • Price for the full version is $69.00

Fix Google Search

  • Was incapacitated when the "search from current page" feature was added.
    • The code is in the Special:Search page. This is a matter of moving part of the OWW modified version of the page into the OWW subclassed OWWSpecialSearch php page.

User Interface

  • Install the FCKEditor
    • Requires MW1.11
      • Notify Steering Committee
    • Solicit input.

Community Features

  • Add configurable header text to the Feedback tag.
    • The text will appear in the MediaWiki: namespace

Filename conflict resolution

    • Investigate providing a way for users to see filenames minus any disambiguation tagging.
    • Other users will see the full name.
    • Evaluate in light of the MW1.11 Image programming model change.

Deprecate support for Flash Video

  • Decided to just use youtube or google video, rather than host anything ourselves.

System Management

Upgrade OWW Linux Server at Rackspace

  • Complete upgrade agreement/service order
    • Work with MIT legal to do this
      • Send a message to her immediately
      • Get back agreement
      • Return to Rackspace
  • Move OWW Server to RHEL5
    • Currently on RHEL4
    • 2 weeks to complete the work
    • Move /data directory
    • Reconfigure MySQL
      • Standard on RHEL5
      • Currently on MySQL 4.1
    • Reconfigure PHP5
      • Will use the native RHEL5 PHP5 package
    • Install sudo and other packages needed
    • Load all Databases
    • Test Mediawiki
      • Test all extensions

Complete upgrade to Mediawiki 1.11.2 (or most recent release)

  • Load all Databases
  • Test Mediawiki
    • Test all extensions

Modify backup procedures

  • Add all MySQL backups to the /data rsync process back to MIT
  • Move local MIT copy of /data to MIT Bionet server (nightly backup)
  • Move rsync job from (RHEL4) to (RHEL5)
  • Investigate MySQL replication between MIT and Rackspace

Speak to Sasha at Harvard Church Lab re: MySQL database replication

  • Explore how this may be accomplished
  • Church Lab has excellent web server Internet access and backup facilities

SSL Certificate for OWW

  • Price out certificate
    • Verisign: 1 Year: $399 for 1 year
    • Rackspace/Thawte: $249 for 2 years
      • wjf 13:10, 16 March 2008 (CDT) Based upon the Rackspace Price, I ordered a 2 year SSL certificate.
    • Details of the certificate will be present in the certificate itself:
    • Rackspace will invoice/install this week.
    • No issue moving the certificate to another server that I'm aware or
      • Certificate does not contain the IP address, just the DNS name
    • This will allow user logins to OWW to be protected.
    • We don't anticipate deploying SSL for all OWW transactions.
    • The basis for this is non-repudiation and authentication but not general encryption.

Research items


  • Evaluate Wikipedia's Lucene Search for OWW
    • Provides for Relevance-ranked searching
  • Evaluate Google Custom Search
    • We can create multiple custom searches, each for a major site area such as
      • Materials
      • Protocols
      • Courses

Subscribe to Page Range

  • Evaluate a way to subscribe to changes for a range of pages rather than from a specific page.
    • Uses the "Recent Changes" page and a filter

OWW Chat

  • Work with Austin to integrate the new Jabber chat features with OWW
    • Figure out what to do about the current Wiki:Chat PHP/HTML/Javascript search
  • Is there an way to implement/reserve a way to schedule voice chats?
    • Skype works but is proprietary
      • Most OWW members have access to it.
      • Other VOIP methods?