Co-op Documentation

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Current Tasks

Tasks In Progress

  • Refining Interactions widget:
    • Details:
      • If the number of interactions is too high, only show the minimal table (hide Cytoscape?) and add "Show More"/"Show Neighbouring Interactions"? option
      • Otherwise, show all interactions(nearby interactions included) and Cytoscape plugin
      • Need to scale distance based from current gene based on connectedness(number of interactions)
        • Shouldn't cluster by gene class (problems arise from classes like "let" where genes are necessarily related so grouping is misleading)
    • Progress:
      • Looking into BLASTP field in Homology Widget on Protein page that uses similar mechanism
      • Split interactions into 2 methods, one for those involving current gene and one for nearby interactions
      • If local interactions exceeds 400 100(after merging duplicates), doesn't load nearby (e.g. unc-26(82) vs. daf-16 without nearby(433) vs. daf-16 with nearby(1386))
      • Combined duplicate edges (duplicate implies matching source node, target node, direction, type, & phenotype)
      • Changed table: "Details" column with single link to interaction object -> "Citations" column with list of links to duplicate interactions
      • Modified tooltip
        • Removed interaction number and link to page (misleading for multiple)
        • Added phenotype and number of citations to tooltip
      • Added "edge width based on number of citations" feature
        • Set 15 as max number of citations; anything higher will be scaled down
      • Incorporate toggle
  • Gene page alterations
    • Details:
      • Making corrections to Gene page interface based on curator consultation
      • Interactions:
        • Add legend to describe edge colours in cytoscape image
        • Hide no_interactions when "All" option is selected and possibly remove/hide no_interactions from drop-down
      • Phenotype:
        • Add evidence information
          • Gene Ontology widget uses similar mechanism
          • Check for build_evidence method in Object.pm
        • Standardize look and feel of tables (convert to data tables)
      • Reagents:
        • Drop the word "found" whenever we use search results
        • Switch search results to actual list of results(expand if too many)
          • See/learn how this was done for the Expression widget
    • Progress:
      • Pending consultation from curators. Teleconference: 11:30 am EST Wednesday, January 18th, 2012
      • Phenotype:
        • Changed Phenotypes and Phenotypes_not_observed tables to use build_data_table
        • Modified corresponding API methods to return compatible data for build_data_table
        • Currently modifying RNAi table
  • Interface Corrections
    • Details:
      • Look into rearranging the elements in widgets so that they do not appear strange/distorted when switched from one- to two-column views or using smaller displays
      • Will require modifying the templates
  • Homology Widget
    • Needs to be modified; Contains too much information that shouldn't necessarily be grouped this way
    • May need to move orthologs to separate widget
  • Cytoscape plugin
    • Incorporate button/option to open pop-up for larger view (e.g. in case user has small screen or is using 2-column layout)
    • Also, add plugin to interaction page (may need to wait until interactions are merged)

Other Tasks

Additional tasks that require further investigation

Getting Started

See WormBase Staff Resources.

Members/Contacts

Meetings

  • WormBase OICR Developers Teleconference
    • Mondays, 3:00PM
    • Phone-in 1-800-747-5150 id: 6738514
  • WormBase OICR Developers Teleconference with Lincoln
  • WormBase International Groups Teleconference
    • Every other Thursday, 11:30AM
    • Lincoln's Office
  • Group Meeting
    • Fridays, 3:00PM
    • HL31 Conference Room/TBA

Tools

The following are some of the tools with which many major aspects of WormBase are developed. You should familiarize yourself with them through documentation and examples.

Perl

There is significant documentation on getting started with Perl. One starting point is PerlMonks.

Catalyst

Catalyst is the web development framework used to develop WormBase. To get started, read and try examples from

Git

Git is a version control system used for collaboration and backup in the development process. One starting point is the progit tutorial

Given that we have modified two files a.txt and b.txt but do not wish to keep the changes made to b.txt

git status
git checkout b.txt
git add a.txt
git commit -m “Added change1 and change2 to a.txt”
git push

If we have did not have the most recent version, then we will run into an issue when trying to push. In this case we can:

git fetch
git merge
git push

Note: pull is similar to using fetch + merge

Browser (Debugging)

Many browsers provide useful tools to developers that can be used for debugging
Chrome

  • Tools->Developer Tools/JavaScript Console

Firefox

  • Firefox->Web Developer->Web Console/Error Console

Other

Some other tools that you should be aware of but may not be required to know/interact with include:

  • JavaScript
  • ACeDB
  • MySQL
  • Xapian
  • GFF
  • Cytoscape Web
    • Cytoscape Tutorial
    • Plugin generally used for pathway analysis
    • This plugin is used in the Interactions widget on the Gene page ([WormBase dir]/root/templates/classes/gene/interactions.tt2)
    • Installation directory (for updating): [WormBase dir]/root/js/jquery/plugins/

General Concepts

Widget Data Loading

Widget Loading

REST Controller:

  1. Catches internal url (/rest/widget/...)
  2. Determines the class and widget from the url
  3. From class and widget, determines which fields are required from the configuration file (wormbase.conf)
  4. API methods request data from appropriate databases, process/format/package the data, and then return it(/lib/WormBase/API/Object/[Class].pm)
  5. Sends data to the template to be used in rendering the widget (/root/templates/classes/[Class]/[Widget].tt2)

Other Info

Useful Macros when editing templates can be found in:

  • /root/templates/config/main
  • /root/templates/shared/page_elements.tt2

Useful files for debugging include:

  • /logs/wb-dev-catalyst.log

Other:

  • If the port you have been using appears to be busy but the server is not running,
ps -aux|grep -XXXX
kill -9 ID

where XXXX is the port number(e.g. 8023) and ID is the process id that is using the port(e.g. 10361) NOTE: Do not kill other users' processes if you are using a shared dev machine (e.g. wb-dev)

  • To dump data in API methods include Data::Dumper
use Data::Dumper
...
warn(Dumper(\@data));
  • Sometimes firewall blocks certain ports, so you may be unable to connect to your dev server on the wb-dev machine through the browser
ssh -L 8080:localhost:8023 wb-dev.oicr.on.ca

Then go to localhost:8080 in browser