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migrate to updated oauthNew1
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GET-Evidence pipeline code should be publicNew1
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23andMe report pipeline is brokenIn Progress2
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'Reprocess' does not workClosed5
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Port job submission to use ArvadosResolved3
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Automatically update GET-Evidence report pipeline with latest 'getev-latest.json.gz'Closed5
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Incorporate coverage info from get-evidence dataset_reports in publication statisticsNew1
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[Third party integration]Arvados job: download data from remote site into KeepIn Progress21.01.0
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[Third party integration]Trigger an arvados job to retrieve the data and import it into KeepIn Progress21.01.0
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[Publishing]Check for finished download/processing jobsIn Progress21.01.0
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When UserFile data is updated, if it has a suitable data type, submit report-generator jobsNew12.02.0
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Arvados job/pipeline generates ClinVar HTML report from VCFClosed52.02.0
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Arvados job/pipeline generates GET-Evidence HTML report from VCFClosed52.02.0
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[Publishing]Add report status/links to "show user_files" pageResolved31.01.0
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[Third party integration]Accept authenticated API calls from data providers to add datasets to a public profileResolved32.02.0
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Check UserFiles too when checking for Datasets that are ready to publishClosed50.50.5
Product Backlog
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googleNew1
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deleted project remains in My FavouritesNew1
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LiveDownloadingNew1
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opt-in participant survey remindersNew1
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Annotate l7g CWL pipelineNew1
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"There are 4 third party activities currently seeking participants." - but there are 5New1
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Provide link to project/colleciton that datasets reside in that are public from users profile pageNew1
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Add "Genes for Good" support for genome reportNew1
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Specimens showing up in profile but not in "/specimens" pageNew1
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Fix bulk mail "send" linkNew1
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Set up sandbox development environment with a dummy keep server and some real dataNew1
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[Third party integration]Google survey participation link should work for newly created surveys, tooIn Progress2
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improve open humans flowNew1
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Edit history for some variants in GET-Evidence is brokenNew1
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[Improvements for admins]Admin cannot use UserFilesController#reprocess unless admin account is marked "enrolled"New10.50.5
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Add public facing database dump, cron job and Arvados uploadIn Progress2
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'whget' still used in Tapestry. datasets.data_size is null.New1
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Use warehouse download link instead of directly calling arv-get for downloadsNew1
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Add 'nofollow' to download links for reportNew1
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'data_type' field in profile JSON report does not correctly have typeNew1
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Add huID to 'aaData' entries in 'public_genetic_data.json' requestNew1
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[Tapestry maintenance/fixes]hard-code link to personalgenomes.org/peopleNew1
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[Tapestry maintenance/fixes]attempting to authorize a disabled page should not redirectNew1
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When a waitlisted user revisits the eligibility questionnaire and removes their obstacle for eligibility, they are not automatically removed from the waitlist.New11.01.0
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broken links on /admin/removal_requestsNew1
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add flag to choose localeNew1
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when Tapestry fails to send e-mail, user should not be presented with an "sorry, something went wrong" messageNew1
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make it possible to disable/skip the eligiblity questionnaireNew1
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Make eligibility questionnaire customizable for a specific site's requirementsNew1
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detect missing configuration variables on startupNew1
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People who are not enrolled should not be able to use the 'withdraw' functionNew1
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auto-enrollment feature should be configurableNew1
-
GeneTestsNew1
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No feedback shown when failed Eligibility QuestionnaireNew1
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nowhere to enter postal/zip codeNew1
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[Improvements for researchers]Researcher > Kits table content loads very slowlyNew1
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Firefox compatibility problem in kit_design creationNew1
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When in /admin/users, menu choice for genetic data stats is messed upNew1
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[Improvements for admins]On user info page, clicking "Promote" should reload that page, not load the edit user pageNew1
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As an administrator, I can see the (not-actually-public) public profile page of a suspended participant / participant who withdrew and requested data removalNew11.01.0
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Ruby 1.9 incompatibilitiesIn Progress2
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slowness when accessing /genomes as admin userNew1
-
broken linkNew1
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slowness accessing http://evidence.personalgenomes.org/hu43860CNew1
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[Improvements for researchers]Selecting kit ranges at /kits should not be case-sensitiveNew11.01.0
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Division by zero warning when computing progress percentageNew1
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Add support for Family Tree DNA (FTDNA) dataNew1
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Add support for deCODE dataNew1
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Add non-reference variant counts to metadataNew1
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Use compute cloud for back-end processingIn Progress2
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handle xmlhttprequest timeouts gracefullyNew1
-
xmlrpc server is careless with huge temp filesNew1
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latest-flat incorrectly displays non single-base substitution variantsNew1
-
allow “lab members” group to upload/view publication PDFsNew1
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Keep "overall odds ratio" updated when editing individual sets of OR figuresNew1
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NSF-Lys702Asn shows wrong hapmap frequencyNew1
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Test Internet Explorer, possibly use Chrome Frame to make editing features work in IENew1
-
add “affects self (hom or dominant)” checkbox (vs “affects offspring”) on result pageNew1
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Handle/prevent edit conflicts more effectivelyNew1
-
Figure out better solution to HNF1A-Ser574Gly (genomes) vs. HNF1A-Gly574Ser (omim)New1
-
Don't let users add variant pages for genes that aren't in knownGeneNew1
-
support publications without PMIDs (other namespaces? original contributions? OWW?)New1
-
Allow non-nsSNP variantsNew1
-
Classify web-hits as relevant/not-relevantIn Progress2
-
Variant and Gene RemovalNew1
-
Warning about automatic logoutNew1
-
Allele frequency missing for rs41281314New1
-
Import and process raw reads for Jay Flatley genomeNew1
-
Import and process raw reads for YRI trio dataNew1
-
Show nucleotide positions for all dbSNP-keyed variantsNew1
-
Merge rsids and AA-variant pagesNew1
-
Trait-o-matic GET-E importer "AttributeError: 'tuple' object has no attribute 'remove'"New1
-
GWAS - mark existing "not reviewed" variants as "pathogenic"New1
-
Update PGP2,3,5,7,8,10 on snp.med and evidence.PGNew1
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Import aachanges starting with termination (eg. METTL8-X379R)New1
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Import aachanges containing periods (eg. HGC6.3-N156S)New1
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Standardize gene names (correctly)New1
-
Report of insufficiently evaluated variants meeting autoscore thresholdsNew1
-
Clean up runt variants imported by PharmGKBNew1
-
ereg Deprecated in PHP 5.3.0New1
-
'Undefined' noticesNew1
-
Add conservation track from ucscNew1
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Genome links should indicate which data set(s) actually support the variant callNew1
-
Handle "data set is no longer public" during import_genomesNew1
-
Use "BED" / "BED Detail" format instead of GFFNew1
-
Interpret phased (haplotype) dataNew1
-
PGP11 genome report has error messagesNew1
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call synonymous amino acids that match pathogenic reference alleles (e.g. F5 R534R)New1
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Textile download link broken (404 Error) during installIn Progress2
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Visualization improvementsNew1
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Improve reporting of variant/allele frequenciesFeedback4
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Find consensus nonref alleles & call when matching refNew1
-
Add Google Search APINew1
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Add spam-control measuresNew1
-
https://evidence.personalgenomes.org/ should not show huPGP siteNew1
-
Error when saving edits or submittingNew1
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Add EVS frequency dataIn Progress2
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Update 1000 Genomes frequency dataIn Progress2
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As a participant, I can remove traitwise survey results from my public profileNew12.02.0
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[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 profileNew15.05.0
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Public profiles: add JSON for Absolute Pitch SurveyNew10.50.5
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Public profiles: add JSON for PHR dataNew11.01.0