WebDev 2016.02.23-Agenda and Minutes

From WormBaseWiki
Revision as of 15:41, 23 February 2016 by Awright (talk | contribs) (→‎Database migration)
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigationJump to search


Administrative notes

Web development

-WS252 widget related issues mostly resolved, except (please don't cache them):

  • genetic widget on variation page and
  • Sequence widgets on CDS, transcript, protein (working on a bug fix)

- Issues with multiple strains (bioproject) from the same species are resolved.

  • they have own species index page, ftp links, gbrowse links
  • integrated search for their gene and protein under their strain (not mixed up with the default strain)

- Had conversation with GO people about gene model graph, will work on this visualization after WS252 development

- Will discuss with Daniala and TransgeneOme about pulling data from their API

Data visualization

  • committed gbrowse config files for WS252

- jbrowse:

  • jq tool:
    • really easy to insert a field into all JSON objects (all non-modencode tracks are now downloadable over whole chromosomes)
    • doubles as a JSON validator, helped fixing some formatting issues
  • found and fixed 2 missing tracks for WS252
  • Installed test instance of JBrowse 1.12.0 (currently using 1.11.6)
  • Working with WebApollo people on handling subtracks, there is an example in the 1.12.0 test instance here. Note that several issues remain, the most notable of which is that it won't draw data until you zoom or pan around.

Database migration

  1. Working with Juancarlos to get him access to Datomic REST API
  2. Split repo into one repo per project:
    • ACeDB to Datomic
      • Took reorganized the folder structure when I took away the non ACeDB to Datomic from this repo .
      • Need to make sure that documentation reflects changes and is up to date.
      • Will create a WS252 DynamoDB database In order to make sure the reorganized code still works and to make sure the documentation is accurate.
  3. Will finish setting up DynamoDB ready to run ACeDB to Datomic, needs to:
    • I need to make a table called WormBase. The current Table in DynamoDB is called WS251 because I thought the table name was the database name but, it turns out, a DynamoDB table contains databases. (Can't change a table name once create so have to make fresh table)
  4. Creating WS252 DynamoDB database
    • working on setting getting the the model file and ACeDB dump for WS252
    • Once I get these I will be running the ACeDB to Datomic tool to directly create a DynamoDB Datomic Database for WS252
    • configure transactor for DynamoDB. This needs to be done to reflect the new table name and shouldn't have to be done again.
  5. Working on documentation
    • I have started documentation on the WormBase wiki. This will need to be expanded significantly as the project progress'.
  6. Meeting with Matthew (EBI)
    • Trying to make a meeting this week with Matthew to have both Sybil and I introduce ourselves.

Intermine / InterMOD progress

Outstanding issues

Nothing needs discussion.