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New consent doc for Harvard PGPNew10.50.5
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Install extension to allow password reset on RTNew1
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Change 30 day release window to 31 daysNew1
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Welcome e-mail featureNew10.50.5
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Make sure that datasets which are served from Keep via get-evidence have collectionsNew1
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If a dataset has been released to a user but they have not seen it yet, force-redirect to /specimen_analysis_data after they log inNew1
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OH integration token appears to time out after a while, user is presented with 'refresh token'New1
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upgrade to reCAPTCHA v2New10.50.5
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Trait surveys incomplete listed on a lot of entries in the WGS data page. Sounds like a bug.New1
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Improve sample tracking to allow for bulk marking of samplesNew12.02.0
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Add an admin interface feature to export all enrolled users + shipping address as a csv file.New1
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[Tapestry structural improv.]Comprehensive "Sectioning" of TapestryNew1
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Configurable mini-consent form and validationsNew1
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The "site override" feature is testedNew1
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exam automated testsNew1
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enrollment step automated testsNew1
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upgrade to ruby 1.9.3New1
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upgrade to rails 3.1New1
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upgrade to ruby 2.1New1
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upgrade to rails 3.2New1
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fix FAQ linkResolved3
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disable releasing genomes as cagi option. Do not release the cagi genomes yet.Resolved3
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Simplify Tapestry/Open Humans account link flowResolved32.02.0
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README that links to main repoResolved3
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canceling link on OH integration redirects to https://my-dev.pgp-hms.org/auth/open-humans/callback?error=access_denied which throws a 500Resolved3
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Always redirect Open Humans user back to OHResolved3
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Suffix .bz2 missing on downloaded genome fileResolved3
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[Publishing]Fix wrong column headers and "real name" content in /exports/users.csvResolved30.50.5
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Users can connect their Tapestry account to Open Humans via OAuth2Resolved3
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Upgrade oauth1 code for google doc/spreadsheet sync to oauth2Resolved32.02.0
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When resigning consents (new version), the twin/recontact radioboxes should be prepopulated based on the previous consentResolved30.50.5
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The safety questionnaire isn't redirecting people to the page they were planning to go toResolved30.50.5
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Distinguish pgp-originated and other files on public profilesResolved30.50.5
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Possible to disable Shipping Addresses as a sectionResolved3
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As a participant, I can choose to reveal my real name on my public profile. I can also remove my real name from my public profile.Resolved31.01.0
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[Tapestry maintenance/fixes]family relations page redirects to public profile when toggling to "No" optionResolved3
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[Communication]user email address on contact form should be used for reply-to:, from: should be configurableResolved3
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Can deploy in a sub URIResolved3
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[Tapestry structural improv.]Configurable Signup ConditionsResolved3
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Cells can also be overriddenResolved3
-
Basic clean-up of tests, as a foundation for working on specific onesResolved3
-
Make user-acceptance of TOS optionalResolved3
-
[Tapestry structural improv.]Make it possible to disable/enable "sections"Resolved3
-
[Tapestry structural improv.]Make all the site-specific labels configurableResolved3
-
Allow views and partials to be dynamically overriddenResolved3
-
Much more flexible consent formsResolved3
-
ci.curoverse.com automatically runs user model testsResolved3
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Public profiles: add JSON for Enrollment HistoryNew10.50.5
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Public profiles: add JSON for SamplesNew10.50.5
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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
-
googleNew1
-
deleted project remains in My FavouritesNew1
-
LiveDownloadingNew1
-
opt-in participant survey remindersNew1
-
Annotate l7g CWL pipelineNew1
-
"There are 4 third party activities currently seeking participants." - but there are 5New1
-
Provide link to project/colleciton that datasets reside in that are public from users profile pageNew1
-
Add "Genes for Good" support for genome reportNew1
-
Specimens showing up in profile but not in "/specimens" pageNew1
-
Fix bulk mail "send" linkNew1
-
Set up sandbox development environment with a dummy keep server and some real dataNew1
-
[Third party integration]Google survey participation link should work for newly created surveys, tooIn Progress2
-
improve open humans flowNew1
-
Edit history for some variants in GET-Evidence is brokenNew1
-
[Improvements for admins]Admin cannot use UserFilesController#reprocess unless admin account is marked "enrolled"New10.50.5
-
Add public facing database dump, cron job and Arvados uploadIn Progress2
-
'whget' still used in Tapestry. datasets.data_size is null.New1
-
Use warehouse download link instead of directly calling arv-get for downloadsNew1
-
Add 'nofollow' to download links for reportNew1
-
'data_type' field in profile JSON report does not correctly have typeNew1
-
Add huID to 'aaData' entries in 'public_genetic_data.json' requestNew1
-
[Tapestry maintenance/fixes]hard-code link to personalgenomes.org/peopleNew1
-
[Tapestry maintenance/fixes]attempting to authorize a disabled page should not redirectNew1
-
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
-
broken links on /admin/removal_requestsNew1
-
add flag to choose localeNew1
-
when Tapestry fails to send e-mail, user should not be presented with an "sorry, something went wrong" messageNew1
-
make it possible to disable/skip the eligiblity questionnaireNew1
-
Make eligibility questionnaire customizable for a specific site's requirementsNew1
-
detect missing configuration variables on startupNew1
-
People who are not enrolled should not be able to use the 'withdraw' functionNew1
-
auto-enrollment feature should be configurableNew1
-
GeneTestsNew1
-
No feedback shown when failed Eligibility QuestionnaireNew1
-
nowhere to enter postal/zip codeNew1
-
[Improvements for researchers]Researcher > Kits table content loads very slowlyNew1
-
Firefox compatibility problem in kit_design creationNew1
-
When in /admin/users, menu choice for genetic data stats is messed upNew1
-
[Improvements for admins]On user info page, clicking "Promote" should reload that page, not load the edit user pageNew1
-
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
-
Ruby 1.9 incompatibilitiesIn Progress2
-
slowness when accessing /genomes as admin userNew1
-
broken linkNew1
-
slowness accessing http://evidence.personalgenomes.org/hu43860CNew1
-
[Improvements for researchers]Selecting kit ranges at /kits should not be case-sensitiveNew11.01.0
-
Division by zero warning when computing progress percentageNew1
-
Add support for Family Tree DNA (FTDNA) dataNew1
-
Add support for deCODE dataNew1
-
Add non-reference variant counts to metadataNew1
-
Use compute cloud for back-end processingIn Progress2
-
handle xmlhttprequest timeouts gracefullyNew1
-
xmlrpc server is careless with huge temp filesNew1
-
latest-flat incorrectly displays non single-base substitution variantsNew1
-
allow “lab members” group to upload/view publication PDFsNew1
-
Keep "overall odds ratio" updated when editing individual sets of OR figuresNew1
-
NSF-Lys702Asn shows wrong hapmap frequencyNew1
-
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
-
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
-
Import aachanges containing periods (eg. HGC6.3-N156S)New1
-
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
-
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
-
call synonymous amino acids that match pathogenic reference alleles (e.g. F5 R534R)New1
-
Textile download link broken (404 Error) during installIn Progress2
-
Visualization improvementsNew1
-
Improve reporting of variant/allele frequenciesFeedback4
-
Find consensus nonref alleles & call when matching refNew1
-
Add Google Search APINew1
-
Add spam-control measuresNew1
-
https://evidence.personalgenomes.org/ should not show huPGP siteNew1
-
Error when saving edits or submittingNew1
-
Add EVS frequency dataIn Progress2
-
Update 1000 Genomes frequency dataIn Progress2
-
As a participant, I can remove traitwise survey results from my public profileNew12.02.0
-
[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