Prioritized open issues

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# Project Tracker Status Priority Subject Assigned To % Done
  Urgent 1 Collapse all/Expand all
835 GET-Evidence Bug New Urgent Error when saving edits or submitting

  High 7 Collapse all/Expand all
468 GET-Evidence Bug New High latest-flat incorrectly displays non single-base substitution variants

15183 Arvados Bug New High [Workbench2] No errors reported when file is missing a block

16228 Arvados Bug New High NullPointerException while uploading file using Java SDK

16325 Arvados Bug New High Logs/outputs from Cancelled processes don't have properties.type="log"/"output"

17300 Arvados Bug New High array of array of File causes 'NoneType' object has no attribute 'resolved'

17396 Arvados Bug New High Favorites copy dialog further issues

17434 Arvados Bug New High project not shown in hierarchy on the left of wb2

  Normal 1698 Collapse all/Expand all
426 GET-Evidence Feature In Progress Normal Use compute cloud for back-end processing Tom Clegg

451 longupload Bug New Normal handle xmlhttprequest timeouts gracefully Tom Clegg

466 GET-Evidence Bug New Normal xmlrpc server is careless with huge temp files

478 GET-Evidence Bug New Normal Keep "overall odds ratio" updated when editing individual sets of OR figures Tom Clegg

479 GET-Evidence Bug New Normal NSF-Lys702Asn shows wrong hapmap frequency Tom Clegg

481 GET-Evidence Feature New Normal Test Internet Explorer, possibly use Chrome Frame to make editing features work in IE Tom Clegg

482 GET-Evidence Feature New Normal add “affects self (hom or dominant)” checkbox (vs “affects offspring”) on result page Tom Clegg

483 GET-Evidence Feature New Normal Handle/prevent edit conflicts more effectively Tom Clegg

484 GET-Evidence Feature New Normal Figure out better solution to HNF1A-Ser574Gly (genomes) vs. HNF1A-Gly574Ser (omim) Tom Clegg

485 GET-Evidence Feature New Normal Don't let users add variant pages for genes that aren't in knownGene Tom Clegg

486 GET-Evidence Feature New Normal support publications without PMIDs (other namespaces? original contributions? OWW?) Tom Clegg

488 GET-Evidence Feature New Normal Allow non-nsSNP variants Tom Clegg

490 GET-Evidence Feature In Progress Normal Classify web-hits as relevant/not-relevant Tom Clegg

493 GET-Evidence Feature New Normal Variant and Gene Removal Tom Clegg

494 GET-Evidence Bug New Normal Warning about automatic logout Tom Clegg

495 GET-Evidence Bug New Normal Allele frequency missing for rs41281314 Tom Clegg

498 GET-Evidence Feature New Normal Show nucleotide positions for all dbSNP-keyed variants Tom Clegg

499 GET-Evidence Feature New Normal Merge rsids and AA-variant pages Tom Clegg

500 GET-Evidence Bug New Normal Trait-o-matic GET-E importer "AttributeError: 'tuple' object has no attribute 'remove'" Tom Clegg

501 GET-Evidence Feature New Normal GWAS - mark existing "not reviewed" variants as "pathogenic" Tom Clegg

502 GET-Evidence Feature New Normal Update PGP2,3,5,7,8,10 on snp.med and evidence.PG Tom Clegg

503 GET-Evidence Bug New Normal Import aachanges starting with termination (eg. METTL8-X379R) Tom Clegg

506 GET-Evidence Bug New Normal Standardize gene names (correctly) Tom Clegg

507 GET-Evidence Feature New Normal Report of insufficiently evaluated variants meeting autoscore thresholds Tom Clegg

509 GET-Evidence Bug New Normal Clean up runt variants imported by PharmGKB Tom Clegg

514 GET-Evidence Bug New Normal ereg Deprecated in PHP 5.3.0 Tom Clegg

515 GET-Evidence Bug New Normal 'Undefined' notices Tom Clegg

516 GET-Evidence Feature New Normal Add conservation track from ucsc

517 GET-Evidence Feature New Normal Genome links should indicate which data set(s) actually support the variant call Tom Clegg

518 GET-Evidence Bug New Normal Handle "data set is no longer public" during import_genomes Tom Clegg

519 GET-Evidence Feature New Normal Use "BED" / "BED Detail" format instead of GFF Tom Clegg

529 GET-Evidence Feature New Normal Interpret phased (haplotype) data Evan Maxwell

533 GET-Evidence Bug New Normal PGP11 genome report has error messages

539 GET-Evidence Feature New Normal call synonymous amino acids that match pathogenic reference alleles (e.g. F5 R534R)

540 GET-Evidence Bug In Progress Normal Textile download link broken (404 Error) during install

556 GET-Evidence Bug New Normal Visualization improvements

578 GET-Evidence Feature Feedback Normal Improve reporting of variant/allele frequencies

601 GET-Evidence Feature New Normal Find consensus nonref alleles & call when matching ref

696 GET-Evidence Feature New Normal Add Google Search API

714 GET-Evidence Feature New Normal Add spam-control measures

775 GET-Evidence Bug New Normal https://evidence.personalgenomes.org/ should not show huPGP site

925 GET-Evidence Feature In Progress Normal Add EVS frequency data Tom Clegg

927 GET-Evidence Support In Progress Normal Update 1000 Genomes frequency data

1080 GET-Evidence Feature New Normal Add non-reference variant counts to metadata Madeleine Ball

1084 GET-Evidence Feature New Normal Add support for deCODE data Madeleine Ball

1085 GET-Evidence Feature New Normal Add support for Family Tree DNA (FTDNA) data Madeleine Ball

1104 GET-Evidence Bug New Normal Division by zero warning when computing progress percentage Tom Clegg

1116 Tapestry Bug New Normal Selecting kit ranges at /kits should not be case-sensitive

1209 GET-Evidence Bug New Normal slowness accessing http://evidence.personalgenomes.org/hu43860C Ward Vandewege

1370 GET-Evidence Bug New Normal broken link

1380 GET-Evidence Bug New Normal slowness when accessing /genomes as admin user Ward Vandewege

1384 Tapestry Feature New Normal As a participant, I can remove traitwise survey results from my public profile

1385 Tapestry Feature New Normal 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

1427 Tapestry Feature New Normal As an administrator, I can see the (not-actually-public) public profile page of a suspended participant / participant who withdrew and requested data removal

1454 Tapestry Bug New Normal On user info page, clicking "Promote" should reload that page, not load the edit user page

1457 Tapestry Bug New Normal When in /admin/users, menu choice for genetic data stats is messed up

1461 Tapestry Bug New Normal Firefox compatibility problem in kit_design creation

1471 Tapestry Bug New Normal Researcher > Kits table content loads very slowly Tom Clegg

1478 Tapestry Bug New Normal nowhere to enter postal/zip code

1483 Tapestry Bug New Normal No feedback shown when failed Eligibility Questionnaire

1490 GET-Evidence Support New Normal GeneTests Tom Clegg

1520 Tapestry Bug New Normal auto-enrollment feature should be configurable Ward Vandewege

1615 Tapestry Bug New Normal People who are not enrolled should not be able to use the 'withdraw' function Ward Vandewege

1632 Tapestry Feature New Normal detect missing configuration variables on startup Ward Vandewege

1633 Tapestry Feature New Normal Make eligibility questionnaire customizable for a specific site's requirements

1836 Tapestry Bug New Normal when Tapestry fails to send e-mail, user should not be presented with an "sorry, something went wrong" message Ward Vandewege

2152 Arvados Task New Normal Set appropriate permissions on an instance of the GATK exome pipeline, and all of its jobs, inputs, and outputs.

2231 Tapestry Feature New Normal add flag to choose locale Ward Vandewege

2422 Tapestry Feature New Normal exam automated tests

2423 Tapestry Feature New Normal enrollment step automated tests

2424 Tapestry Task New Normal write unit tests Phil Hodgson

2425 Tapestry Task New Normal write functional tests Phil Hodgson

2426 Tapestry Task New Normal write unit tests Phil Hodgson

2427 Tapestry Task New Normal write functional tests Phil Hodgson

2428 Tapestry Feature New Normal upgrade to ruby 1.9.3

2429 Tapestry Feature New Normal upgrade to rails 3.1

2430 Tapestry Feature New Normal upgrade to rails 3.2

2431 Tapestry Feature New Normal upgrade to ruby 2.1

2544 Tapestry Story New Normal The "site override" feature is tested Phil Hodgson

2545 Tapestry Bug New Normal broken links on /admin/removal_requests

2552 Tapestry Story New Normal Configurable mini-consent form and validations Phil Hodgson

2595 Tapestry Task New Normal Specify desired authorizations scheme for Tapestry

2679 Arvados Story New Normal [API] If enabled by user via "preferences" checkbox in Workbench, notification service sends email to owner when a workflow finishes, fails, or is failing

2706 Arvados Feature New Normal [SDKs] Python SDK Keep client can enable "HEAD before PUT" mode when writing. Expose this as an arv-put option.

2822 Arvados Task New Normal [SDKs] Use Ruby SDK instead of google-api-client in arv-run-pipeline-instance

2850 Tapestry Story New Normal Comprehensive "Sectioning" of Tapestry Phil Hodgson

2889 Arvados Task New Normal Make other users' shared instances accessible via dashboard/home

2947 Tapestry Bug New Normal When a waitlisted user revisits the eligibility questionnaire and removes their obstacle for eligibility, they are not automatically removed from the waitlist.

2960 Arvados Feature New Normal Keep can stream GET and PUT requests

2966 Tapestry Task New Normal Consider a section option for Absolute Pitch Survey Phil Hodgson

2980 Tapestry Bug New Normal attempting to authorize a disabled page should not redirect Phil Hodgson

2984 Tapestry Feature New Normal hard-code link to personalgenomes.org/people Phil Hodgson

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