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
    Idea
    6
    Closed
    5
    89
    -c-a
    13
131
Interpretation automation
 
2020-06-30
2020-06-23
  • Incorporate coverage info from get-evidence dataset_reports in publication statistics
    9027
    Tapestry
    31
    Feature
    2
    New
    1
    131
    -c-a
    31
  • [Third party integration]
    Arvados job: download data from remote site into Keep
    8707
    Tapestry
    31
    Feature
    2
    In Progress
    2
    1.0
    1.0
    131
    -c-a
    31
  • [Third party integration]
    Trigger an arvados job to retrieve the data and import it into Keep
    8689
    Tapestry
    31
    Feature
    2
    In Progress
    2
    1.0
    1.0
    131
    -c-a
    31
  • [Publishing]
    Check for finished download/processing jobs
    8697
    Tapestry
    31
    Feature
    2
    In Progress
    2
    1.0
    1.0
    131
    -c-a
    31
  • When UserFile data is updated, if it has a suitable data type, submit report-generator jobs
    8698
    Tapestry
    31
    Feature
    2
    New
    1
    2.0
    2.0
    131
    -c-a
    31
  • Arvados job/pipeline generates ClinVar HTML report from VCF
    8701
    Tapestry
    31
    Feature
    2
    Closed
    5
    2.0
    2.0
    131
    -c-a
    31
  • Arvados job/pipeline generates GET-Evidence HTML report from VCF
    8700
    Tapestry
    31
    Feature
    2
    Closed
    5
    2.0
    2.0
    131
    -c-a
    31
  • [Publishing]
    Add report status/links to "show user_files" page
    8699
    Tapestry
    31
    Feature
    2
    Resolved
    3
    1.0
    1.0
    131
    -c-a
    31
  • [Third party integration]
    Accept authenticated API calls from data providers to add datasets to a public profile
    8688
    Tapestry
    31
    Feature
    2
    Resolved
    3
    2.0
    2.0
    131
    -c-a
    31
  • Check UserFiles too when checking for Datasets that are ready to publish
    8710
    Tapestry
    31
    Bug
    1
    Closed
    5
    0.5
    0.5
    131
    -c-a
    31
Product Backlog
  • LiveDownloading
    19925
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • opt-in participant survey reminders
    16554
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • Annotate l7g CWL pipeline
    14622
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • "There are 4 third party activities currently seeking participants." - but there are 5
    11152
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • Provide link to project/colleciton that datasets reside in that are public from users profile page
    10145
    Tapestry
    31
    Idea
    6
    New
    1
    -c-a
    31
  • Add "Genes for Good" support for genome report
    9241
    GET-Evidence
    13
    Feature
    2
    New
    1
    -c-a
    13
  • Specimens showing up in profile but not in "/specimens" page
    8322
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • Fix bulk mail "send" link
    8155
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • Set up sandbox development environment with a dummy keep server and some real data
    7134
    Tapestry
    31
    Idea
    6
    New
    1
    -c-a
    31
  • [Third party integration]
    Google survey participation link should work for newly created surveys, too
    6924
    Tapestry
    31
    Bug
    1
    In Progress
    2
    -c-a
    31
  • improve open humans flow
    6634
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • Edit history for some variants in GET-Evidence is broken
    6413
    GET-Evidence
    13
    Bug
    1
    New
    1
    -c-a
    13
  • [Improvements for admins]
    Admin cannot use UserFilesController#reprocess unless admin account is marked "enrolled"
    6412
    Tapestry
    31
    Bug
    1
    New
    1
    0.5
    0.5
    -c-a
    31
  • Add public facing database dump, cron job and Arvados upload
    6257
    Tapestry
    31
    Idea
    6
    In Progress
    2
    -c-a
    31
  • 'whget' still used in Tapestry. datasets.data_size is null.
    6226
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • 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
  • 'data_type' field in profile JSON report does not correctly have type
    5572
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • Add huID to 'aaData' entries in 'public_genetic_data.json' request
    5571
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • [Tapestry maintenance/fixes]
    hard-code link to personalgenomes.org/people
    2984
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • [Tapestry maintenance/fixes]
    attempting to authorize a disabled page should not redirect
    2980
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • When a waitlisted user revisits the eligibility questionnaire and removes their obstacle for eligibility, they are not automatically removed from the waitlist.
    2947
    Tapestry
    31
    Bug
    1
    New
    1
    1.0
    1.0
    -c-a
    31
  • broken links on /admin/removal_requests
    2545
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • add flag to choose locale
    2231
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • when Tapestry fails to send e-mail, user should not be presented with an "sorry, something went wrong" message
    1836
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • make it possible to disable/skip the eligiblity questionnaire
    1634
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • Make eligibility questionnaire customizable for a specific site's requirements
    1633
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • detect missing configuration variables on startup
    1632
    Tapestry
    31
    Feature
    2
    New
    1
    -c-a
    31
  • People who are not enrolled should not be able to use the 'withdraw' function
    1615
    Tapestry
    31
    Bug
    1
    New
    1
    +c-a
    31
  • auto-enrollment feature should be configurable
    1520
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • GeneTests
    1490
    GET-Evidence
    13
    Support
    3
    New
    1
    +c-a
    13
  • No feedback shown when failed Eligibility Questionnaire
    1483
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • nowhere to enter postal/zip code
    1478
    Tapestry
    31
    Bug
    1
    New
    1
    +c-a
    31
  • [Improvements for researchers]
    Researcher > Kits table content loads very slowly
    1471
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • Firefox compatibility problem in kit_design creation
    1461
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • When in /admin/users, menu choice for genetic data stats is messed up
    1457
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • [Improvements for admins]
    On user info page, clicking "Promote" should reload that page, not load the edit user page
    1454
    Tapestry
    31
    Bug
    1
    New
    1
    -c-a
    31
  • As an administrator, I can see the (not-actually-public) public profile page of a suspended participant / participant who withdrew and requested data removal
    1427
    Tapestry
    31
    Feature
    2
    New
    1
    1.0
    1.0
    -c-a
    31
  • Ruby 1.9 incompatibilities
    1412
    Tapestry
    31
    Bug
    1
    In Progress
    2
    -c-a
    31
  • 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
  • [Improvements for researchers]
    Selecting kit ranges at /kits should not be case-sensitive
    1116
    Tapestry
    31
    Bug
    1
    New
    1
    1.0
    1.0
    -c-a
    31
  • 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
  • handle xmlhttprequest timeouts gracefully
    451
    longupload
    16
    Bug
    1
    New
    1
    -c-a
    16
  • 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
  • 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
  • As a participant, I can remove traitwise survey results from my public profile
    1384
    Tapestry
    31
    Feature
    2
    New
    1
    2.0
    2.0
    -c-a
    31
  • [Enhance user interaction]
    As a participant, I can see a list of datasets contributed by 3rd party studies, which I can inspect (download) and release to my public profile
    1385
    Tapestry
    31
    Feature
    2
    New
    1
    5.0
    5.0
    -c-a
    31
  • Public profiles: add JSON for Absolute Pitch Survey
    5379
    Tapestry
    31
    Feature
    2
    New
    1
    0.5
    0.5
    -c-a
    31
  • Public profiles: add JSON for PHR data
    5377
    Tapestry
    31
    Feature
    2
    New
    1
    1.0
    1.0
    -c-a
    31
sprint
 
no end
no start
  • 0
    -c-a
  • January 13, 2023 07:00:04.3424609432220459 +0000