89
Upgrade work
 
2015-03-09
2015-02-23
  • migrate to updated oauth
    5883
    GET-Evidence
    13
    Bug
    1
    New
    1
    89
    -c-a
    13
  • GET-Evidence pipeline code should be public
    5873
    GET-Evidence
    13
    Feature
    2
    New
    1
    89
    -c-a
    13
  • 23andMe report pipeline is broken
    5872
    GET-Evidence
    13
    Bug
    1
    In Progress
    2
    89
    -c-a
    13
  • 'Reprocess' does not work
    5345
    GET-Evidence
    13
    Bug
    1
    Closed
    5
    89
    -c-a
    13
  • Port job submission to use Arvados
    5287
    GET-Evidence
    13
    Bug
    1
    Resolved
    3
    89
    -c-a
    13
  • Automatically update GET-Evidence report pipeline with latest 'getev-latest.json.gz'
    5321
    GET-Evidence
    13
    Story
    6
    Closed
    5
    89
    -c-a
    13
Product Backlog
  • Add "Genes for Good" support for genome report
    9241
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Edit history for some variants in GET-Evidence is broken
    6413
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Use warehouse download link instead of directly calling arv-get for downloads
    6145
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Add 'nofollow' to download links for report
    6143
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • GeneTests
    1490
    GET-Evidence
    13
    Support
    3
    New
    1
    +c-a
    13
  • slowness when accessing /genomes as admin user
    1380
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • broken link
    1370
    GET-Evidence
    13
    Bug
    1
    New
    1
    +c-a
    13
  • slowness accessing http://evidence.personalgenomes.org/hu43860C
    1209
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Division by zero warning when computing progress percentage
    1104
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Add support for Family Tree DNA (FTDNA) data
    1085
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Add support for deCODE data
    1084
    GET-Evidence
    13
    Feature
    2
    New
    1
    +c-a
    13
  • Add non-reference variant counts to metadata
    1080
    GET-Evidence
    13
    Feature
    2
    New
    1
    +c-a
    13
  • Use compute cloud for back-end processing
    426
    GET-Evidence
    13
    Feature
    2
    In Progress
    2
    -c-a
    13
  • Work with Carlos et al. to integrate BioNotate annotations into GET-Evidence
    435
    GET-Evidence
    13
    Support
    3
    In Progress
    2
    -c-a
    13
  • xmlrpc server is careless with huge temp files
    466
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • latest-flat incorrectly displays non single-base substitution variants
    468
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • add “user manager” (control membership in groups: admin, curator, lab member)
    475
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • allow “lab members” group to upload/view publication PDFs
    476
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Keep "overall odds ratio" updated when editing individual sets of OR figures
    478
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • NSF-Lys702Asn shows wrong hapmap frequency
    479
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Test Internet Explorer, possibly use Chrome Frame to make editing features work in IE
    481
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • add “affects self (hom or dominant)” checkbox (vs “affects offspring”) on result page
    482
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Handle/prevent edit conflicts more effectively
    483
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Figure out better solution to HNF1A-Ser574Gly (genomes) vs. HNF1A-Gly574Ser (omim)
    484
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Don't let users add variant pages for genes that aren't in knownGene
    485
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • support publications without PMIDs (other namespaces? original contributions? OWW?)
    486
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Allow non-nsSNP variants
    488
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Classify web-hits as relevant/not-relevant
    490
    GET-Evidence
    13
    Feature
    2
    In Progress
    2
    -c-a
    13
  • Variant and Gene Removal
    493
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Warning about automatic logout
    494
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Allele frequency missing for rs41281314
    495
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Import and process raw reads for Jay Flatley genome
    496
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Import and process raw reads for YRI trio data
    497
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Show nucleotide positions for all dbSNP-keyed variants
    498
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Merge rsids and AA-variant pages
    499
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Trait-o-matic GET-E importer "AttributeError: 'tuple' object has no attribute 'remove'"
    500
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • GWAS - mark existing "not reviewed" variants as "pathogenic"
    501
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Update PGP2,3,5,7,8,10 on snp.med and evidence.PG
    502
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Import aachanges starting with termination (eg. METTL8-X379R)
    503
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Import aachanges containing periods (eg. HGC6.3-N156S)
    504
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Standardize gene names (correctly)
    506
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Report of insufficiently evaluated variants meeting autoscore thresholds
    507
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Clean up runt variants imported by PharmGKB
    509
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • ereg Deprecated in PHP 5.3.0
    514
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • 'Undefined' notices
    515
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Add conservation track from ucsc
    516
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Genome links should indicate which data set(s) actually support the variant call
    517
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Handle "data set is no longer public" during import_genomes
    518
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Use "BED" / "BED Detail" format instead of GFF
    519
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Interpret phased (haplotype) data
    529
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • PGP11 genome report has error messages
    533
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • call synonymous amino acids that match pathogenic reference alleles (e.g. F5 R534R)
    539
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Textile download link broken (404 Error) during install
    540
    GET-Evidence
    13
    Bug
    1
    In Progress
    2
    +c-a
    13
  • Visualization improvements
    556
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Improve reporting of variant/allele frequencies
    578
    GET-Evidence
    13
    Feature
    2
    Feedback
    4
    -c-a
    13
  • Find consensus nonref alleles & call when matching ref
    601
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Add Google Search API
    696
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Add spam-control measures
    714
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • https://evidence.personalgenomes.org/ should not show huPGP site
    775
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Error when saving edits or submitting
    835
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • Add EVS frequency data
    925
    GET-Evidence
    13
    Feature
    2
    In Progress
    2
    -c-a
    13
  • Update 1000 Genomes frequency data
    927
    GET-Evidence
    13
    Support
    3
    In Progress
    2
    -c-a
    13
sprint
 
no end
no start
  • 0
    -c-a
  • May 19, 2016 16:52:12.24938900566101074 +0000