Difference between revisions of "Issues-9/24/2013"

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=== WebApp - AC ===
 
=== WebApp - AC ===
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Note: gmap & pmap do not work

Latest revision as of 18:30, 24 September 2013

All meetings: WebDev Issues Meetings

Tuesday Sept 24th, 2pm, HL35

WS239 / Current Development

  • Pre-caching has begun

State of the Staging branch

Closed issues about to move to Master (Sept)

These closed issues will be moving to production soon. Take a quick look and make sure we're not pushing any big mistakes.

Note: Most GBrowse fixes were reverted and pushed back to WS240 together with GFF3 support

  • #737 - modENCODE track height - JB
  • #794 - PCR page update overlapping gene - JW
  • #983 - Other_name search - AC
  • #1006 - link outs blastp - AC
  • #1082 - transposon family summary pages - JW
  • #1114 - start_not_found/stop_not_found - JW
  • #1365 - Variation summary - JB
  • #1430 - Historical_gene - AC
  • #1511 - remove links to non-curated species strains - JW
  • #1629 - execute individual test - JB
  • #1644 - Error messages Sequence/Clone page - AC
  • #1677 - Webpage links case sensitive - AC
  • #1693 - phenotype legend filter - JW
  • #1694 - Natural isolates - AC
  • #1725 - Expr overview error on staging - AC
  • #1726 - Transgene page - AC
  • #1727 - Transgene reporter - AC
  • GFF databases, full name - JB, AC
  • Searching fix - add cutoff - AC

Open issues on staging

These need to be closed before we merge to master.

  • JD: #1603 - Pseudogene page
  • JD: #1709 - protein history

Other development

Issues (not on staging)

  • #741- lineage browser - JW
    • usable, wokring with Chris on final product
  • #1602 - sequence summary - JW
    • GFF research
  • #603 - Movies on expression pattern page - JW
    • try as sibling
  • #662 - Variation display - JW
    • researching
    • GFF databases
  • Various other issues - JB

Intermine Dev (JW)

  • Due Sept 27th
  • Generated sources/datafiles for FASTA and GFF3 for all species
  • loaded all FASTA
  • ran into error loading GFF3s
  • expanded data mappings for all classes loaded
    • gene/cds/tanscript/phen/exp clus/exp pattern/var/anatomy term/life stage
      • none of these loaded
  • Next: add RNA
  • adding orthologies
    • as it's own category
  • deadline might be pushed back to Sept 4

Visualisations (JB)

  • on hold

WS240 Development

GFF3

GBrowse - JB


  • Fixed landmarks
  • fixed hieght of non-coding/coding genes
  • fixed showing diff labels/desc for genomic featues
  • KH - working on redo-ing type and source assignments in GFF3
    • looking into alternative:
      • types - sequence ontology types
      • source always WormBase
      • might add GFF3 attribute to denote spec attr of feature
        • Testing things like this now
  • cannot search genomic features
    • worked after lunch!

WebApp - AC

Note: gmap & pmap do not work