Tapestry - Arvados

Story

New

Resolved

Sprint Impediments

2501

Much more flexible consent forms

Phil Hodgson

impediments

-c-a

2533

Basic clean-up of tests, as a foundation for working on specific ones

Phil Hodgson

impediments

-c-a

9673 9673 New consent doc for Harvard PGP New New 1 0.5 0.5 0.5 9673 31 63 3 0.5
9672 9672 Install extension to allow password reset on RT New New 1 9672 31 63 1
9411 9411 Change 30 day release window to 31 days New New 1 9411 31 63 3
9284 9284 Welcome e-mail feature New New 1 0.5 0.5 0.5 9284 31 63 2 0.5
7826 7826 Make sure that datasets which are served from Keep via get-evidence have collections New New 1 7826 31 63 1
7815 7815 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 in New New 1 7815 31 63 2
7673 7673 OH integration token appears to time out after a while, user is presented with 'refresh token' New New 1 7673 31 63 1
6467 6467 upgrade to reCAPTCHA v2 New New 1 0.5 0.5 0.5 6467 31 63 2 0.5
5683 5683 Trait surveys incomplete listed on a lot of entries in the WGS data page. Sounds like a bug. New New 1 5683 31 63 1
4979 4979 Improve sample tracking to allow for bulk marking of samples New New 1 2.0 2.0 2.0 4979 31 63 2 2.0
3025 3025 Add an admin interface feature to export all enrolled users + shipping address as a csv file. New New 1 3025 31 63 2
2850 2850 Phil Hodgson Phil Hodgson 80 Tapestry structural improv. 47 Tapestry structural improv. Comprehensive "Sectioning" of Tapestry New New 1 2850 31 80 63 6	2966 2966 Consider a section option for Absolute Pitch Survey Phil Hodgson 80 0 2850 1 31 -c-a 5 2595 2595 Specify desired authorizations scheme for Tapestry The related task of dividing Tapestry into "sections" necessarily involves another layer of a kind of security. If a section is disabled, it must be off limits. This related task will be considerably easier if authorizations are better defined and brought up to date. 0 2850 1 31 -c-a 5	3001 3001 Make the Enrollment process into a Section that can be disabled The idea is to disallow any enrollment process progress. It should freeze the state of everyone's enrollment when disabled. In theory this should not necessarily have to be enabled together with the "Signup" Section, i.e. it should be possible to enable or disable either one independently, if desired. Phil Hodgson 80 0 2850 3 31 -c-a 5
2552 2552 Phil Hodgson Phil Hodgson 80 Configurable mini-consent form and validations New New 1 2552 31 80 63 6
2544 2544 Phil Hodgson Phil Hodgson 80 The "site override" feature is tested New New 1 2544 31 80 63 6
2422 2422 exam automated tests New New 1 2422 31 63 2	2424 2424 write unit tests Phil Hodgson 80 0 2422 1 31 -c-a 5 2425 2425 write functional tests Phil Hodgson 80 0 2422 1 31 -c-a 5
2423 2423 enrollment step automated tests New New 1 2423 31 63 2	2427 2427 write functional tests Phil Hodgson 80 0 2423 1 31 -c-a 5 2426 2426 write unit tests Phil Hodgson 80 0 2423 1 31 -c-a 5
2428 2428 upgrade to ruby 1.9.3 New New 1 2428 31 63 2	3225 3225 Review 2930 Okay so I dug in and I've finally pursuaded all of the tests to pass. I did not go out of my way to create new tests, but I did fix every existing test and deprecation that was possible to fix, and in many controller classes the test coverage was significantly increased (from default generated and completely failing tests to at least a reasonably complete set of RESTful tests). It was a pretty big job, but it probably fixed at least a couple security holes and bugs in Tapestry. Mostly I just wanted to finally get the tests into a condition where we'd _notice_ if something went awry, going forward. It's hard to tell the difference between 376 tests failing and 379 tests failing, but the difference between 0 and 3 is huge! I did notice thought that I probably spent too much time fixing controllers and their tests that may not even still be in use. There are so many dark corners to Tapestry! In any case, now we can choose to increase test coverage - the safer but more tedious option - or move on to upgrading to ruby 1.9.3 and 2 and also upgrading Rails upwards. I have not looked into tools for analyzing test coverage of code - perhaps this might be a good way to measure it. But certainly it would be good to know whether a lot of the more obscure controllers that don't seem to have active enrollment steps associated with them should still be maintained - or removed. (There are still some deprecation notices about some certain shoulda directives but it's just because we're caught between an old version of Ruby and newer gems, of course.) Ward Vandewege 1 0 2428 1 31 -c-a 5	2930 2930 Make all tests pass and without deprecation warnings in 1.8.7 Phil Hodgson 80 0 2428 3 31 -c-a 5
2429 2429 upgrade to rails 3.1 New New 1 2429 31 63 2
2431 2431 upgrade to ruby 2.1 New New 1 2431 31 63 2
2430 2430 upgrade to rails 3.2 New New 1 2430 31 63 2
8251 8251 fix FAQ link Resolved Resolved 3 8251 31 63 2
7674 7674 Ward Vandewege Ward Vandewege 1 disable releasing genomes as cagi option. Do not release the cagi genomes yet. Resolved Resolved 3 7674 31 1 63 1
6961 6961 Ward Vandewege Ward Vandewege 1 Simplify Tapestry/Open Humans account link flow Resolved Resolved 3 2.0 2.0 2.0 6961 31 1 63 2 2.0		7140 7140 review 6961-simplify-open-humans-account-link-flow Ward Vandewege 1 0 6961 3 31 -c-a 5
7424 7424 README that links to main repo Resolved Resolved 3 7424 31 63 2
7465 7465 canceling link on OH integration redirects to https://my-dev.pgp-hms.org/auth/open-humans/callback?error=access_denied which throws a 500 Resolved Resolved 3 7465 31 63 1
7462 7462 Always redirect Open Humans user back to OH Resolved Resolved 3 7462 31 63 2
7425 7425 Suffix .bz2 missing on downloaded genome file Resolved Resolved 3 7425 31 63 1
7395 7395 Tom Clegg Tom Clegg 3 Publishing 44 Publishing Fix wrong column headers and "real name" content in /exports/users.csv Resolved Resolved 3 0.5 0.5 0.5 7395 31 3 63 1 0.5		7396 7396 review 7395-users-csv-columns Ward Vandewege 1 0 7395 3 31 -c-a 5
4980 4980 Phil Hodgson Phil Hodgson 80 Users can connect their Tapestry account to Open Humans via OAuth2 Resolved Resolved 3 4980 31 80 63 6		4981 4981 Create UI for admin and users On the admin side, the same interface as will be used for #4766. On the user side, a way to handle the tokens (same as for #4766, likely), as well as a way via the "3rd party activities" section of Tapestry Phil Hodgson 80 0 4980 3 31 -c-a 5 4982 4982 Tests Phil Hodgson 80 0 4980 3 31 -c-a 5 5028 5028 Review 4980 Ward Vandewege 1 0 4980 3 31 -c-a 5 5282 5282 Make Open Humans appear just like other Third Party studies, and give it its own landing page Phil Hodgson 80 0 4980 3 31 -c-a 5
4766 4766 Phil Hodgson Phil Hodgson 80 Upgrade oauth1 code for google doc/spreadsheet sync to oauth2 Resolved Resolved 3 2.0 2.0 2.0 4766 31 80 63 2 2.0	5229 5229 Review 4766 Ward Vandewege 1 0 4766 1 31 -c-a 5	4983 4983 Repurpose current OAuth1 controllers and models for OAuth2 Phil Hodgson 80 0 4766 3 31 -c-a 5 4984 4984 Tests Phil Hodgson 80 0 4766 3 31 -c-a 5 4985 4985 Update wiki documentation Phil Hodgson 80 0 4766 3 31 -c-a 5
6914 6914 Ward Vandewege Ward Vandewege 1 When resigning consents (new version), the twin/recontact radioboxes should be prepopulated based on the previous consent Resolved Resolved 3 0.5 0.5 0.5 6914 31 1 63 1 0.5	6915 6915 review 6914-prepopulate-twin-recontact-fields-when-reconsenting Tom Clegg 3 0 6914 1 31 -c-a 5
5528 5528 The safety questionnaire isn't redirecting people to the page they were planning to go to Resolved Resolved 3 0.5 0.5 0.5 5528 31 63 1 0.5
4978 4978 Phil Hodgson Phil Hodgson 80 Distinguish pgp-originated and other files on public profiles Resolved Resolved 3 0.5 0.5 0.5 4978 31 80 63 2 0.5		5208 5208 Review 4978 Branch 4978-public-profile-data Ward Vandewege 1 0 4978 3 31 -c-a 5 5209 5209 Show new column with file origin By origin we mean showing whether something came from the Dataset model or the UserFile model Phil Hodgson 80 0 4978 3 31 -c-a 5 5210 5210 Render public profile as JSON Phil Hodgson 80 0 4978 3 31 -c-a 5
4662 4662 Phil Hodgson Phil Hodgson 80 Possible to disable Shipping Addresses as a section Resolved Resolved 3 4662 31 80 63 6		4663 4663 Review 4662 Ward Vandewege 1 0 4662 3 31 -c-a 5
4050 4050 Ward Vandewege Ward Vandewege 1 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. Resolved Resolved 3 1.0 1.0 1.0 4050 31 1 63 2 1.0		4052 4052 review 4050-real-names Tom Clegg 3 0 4050 3 31 -c-a 5 4053 4053 implement feature Ward Vandewege 1 0 4050 3 31 -c-a 5
2981 2981 Phil Hodgson Phil Hodgson 80 Tapestry maintenance/fixes 46 Tapestry maintenance/fixes family relations page redirects to public profile when toggling to "No" option Resolved Resolved 3 2981 31 80 63 1		2987 2987 Review 2981 Ward Vandewege 1 0 2981 3 31 -c-a 5
2979 2979 Phil Hodgson Phil Hodgson 80 Communication 38 Communication user email address on contact form should be used for reply-to:, from: should be configurable Resolved Resolved 3 2979 31 80 63 2	3011 3011 Review 2979 0 2979 1 31 -c-a 5
2962 2962 Phil Hodgson Phil Hodgson 80 Can deploy in a sub URI Resolved Resolved 3 2962 31 80 63 6		2963 2963 Adjust all hard-coded URLs relative to the root URL I.e. all URLs that start with "/" need to be examined. Phil Hodgson 80 0 2962 3 31 -c-a 5 2968 2968 Review 2962 PH: I also tested it using nginx and passenger, with and without a suburi - everything that I can test seems to work now exactly as expected Ward Vandewege 1 0 2962 3 31 -c-a 5
2549 2549 Phil Hodgson Phil Hodgson 80 Tapestry structural improv. 47 Tapestry structural improv. Configurable Signup Conditions Resolved Resolved 3 2549 31 80 63 6		2943 2943 Globally configurable postal ("zip") code validation There needs to be a central configuration reg-ex for postal codes, beyond the "site override" capabilities. Phil Hodgson 80 0 2549 3 31 -c-a 5 2550 2550 Configurable address fields and validations Phil Hodgson 80 0 2549 3 31 -c-a 5 2965 2965 An email can be configured to be sent to the user when the enrollment process has been completed. Phil Hodgson 80 0 2549 3 31 -c-a 5 2551 2551 Configurable minimum age of consent Phil Hodgson 80 0 2549 3 31 -c-a 5 2849 2849 Review 2550 The simple commit at ec1b87b2cd1fc525e67b37caa1ce7c9405a431d1 accompanied by the updated text at https://arvados.org/projects/tapestry/wiki/Customization and an explanatory email should meet the need of PGP UK to be able to not specify the "State" in the user Shipping Address Phil Hodgson 80 0 2549 3 31 -c-a 5 3003 3003 Review 2549 Ward Vandewege 1 0 2549 3 31 -c-a 5 2553 2553 Remove hard-coded internal references to "US" and "Boston" Phil Hodgson 80 0 2549 3 31 -c-a 5
2539 2539 Phil Hodgson Phil Hodgson 80 Cells can also be overridden Resolved Resolved 3 2539 31 80 63 6		2540 2540 Review 2539-can-override-cells Ward Vandewege 1 0 2539 3 31 -c-a 5 2535 2535 Add site-specific path for cells Phil Hodgson 80 0 2539 3 31 -c-a 5
2533 2533 Phil Hodgson Phil Hodgson 80 Basic clean-up of tests, as a foundation for working on specific ones Resolved Resolved 3 2533 31 80 63 6		2546 2546 Review remaining code from refactor-tests branch Following up on #2419/#2420, we'll want to merge that code into master, so that the basic changes that allowed `rake test` to run can be part of Phil's efforts to further the coding of other tests. 0 2533 3 31 -c-a 5
2526 2526 Phil Hodgson Phil Hodgson 80 Make user-acceptance of TOS optional Resolved Resolved 3 2526 31 80 63 6		2537 2537 Add config.yml entry for "ensure_tos" and hook it up to the authorization filter Phil Hodgson 80 0 2526 3 31 -c-a 5 2538 2538 Review 2526-optional-tos Phil Hodgson 80 0 2526 3 31 -c-a 5
2503 2503 Phil Hodgson Phil Hodgson 80 Tapestry structural improv. 47 Tapestry structural improv. Make it possible to disable/enable "sections" Resolved Resolved 3 2503 31 80 63 6		2851 2851 Review 2503 As agreed in email between Ward and Phil, because of an inadvertent merge we're going finish this story one up more or less at the stage it is at. At least, based on the story title, we can say that it is now "possible" to define sections of Tapestry, and that we're evolving a methodology for doing this. This story will be continued in #2850. Phil Hodgson 80 0 2503 3 31 -c-a 5 2542 2542 Reference configuration when rendering partials and cells Phil Hodgson 80 0 2503 3 31 -c-a 5 2541 2541 Identify "modules" and assign config.yml keys Phil Hodgson 80 0 2503 3 31 -c-a 5 2543 2543 Reference configuration when authorizing controllers Phil Hodgson 80 0 2503 3 31 -c-a 5
2502 2502 Phil Hodgson Phil Hodgson 80 Tapestry structural improv. 47 Tapestry structural improv. Make all the site-specific labels configurable Resolved Resolved 3 2502 31 80 63 6		2534 2534 Turn non-view, site-specific string literals into translations Hard-coded strings outside of app/views should definitely use translations. Meanwhile it is becoming apparent that it is not worth doing this to the views, since almost all of the text is arguably site-specific, and this has been taken care of with #2518 Phil Hodgson 80 0 2502 3 31 -c-a 5 2536 2536 Review 2502-site-labels Phil Hodgson 80 0 2502 3 31 -c-a 5
2518 2518 Phil Hodgson Phil Hodgson 80 Allow views and partials to be dynamically overridden Resolved Resolved 3 2518 31 80 63 2		2527 2527 review view/partial override code Ward Vandewege 1 0 2518 3 31 -c-a 5 2529 2529 Allow views and partials to be overridden by putting files in a specific location on the server Phil Hodgson 80 0 2518 3 31 -c-a 5
2501 2501 Phil Hodgson Phil Hodgson 80 Much more flexible consent forms Resolved Resolved 3 2501 31 80 63 2		2504 2504 Make the consent form allow for (an) additional question(s) This is a necessary, immediate-term improvement. There is an additional question that PGPC needs for their consent form. Ideally this will manifest in the database as something dynamic, unlike the responses to other consent form questions which are stored in dedicated fields in a dedicated table. The long-term plan is to make _all_ of the steps and elements of the enrollment process behave in a more dynamic fashion. Bearing this in mind, it would make sense for this immediate-term solution to be a first step in that direction. Phil Hodgson 80 0 2501 3 31 -c-a 5 2528 2528 review more flexible consent form code Phil Hodgson 80 0 2501 3 31 -c-a 5 2532 2532 Site-specific validation for additional consent questions Phil Hodgson 80 0 2501 3 31 -c-a 5 2530 2530 Text and textarea helpers for more flexible consent forms Phil Hodgson 80 0 2501 3 31 -c-a 5
2419 2419 Ward Vandewege Ward Vandewege 1 ci.curoverse.com automatically runs user model tests Resolved Resolved 3 2419 31 1 63 2		2420 2420 get user model tests in shape; rake test Phil Hodgson 80 0 2419 3 31 -c-a 5 2421 2421 set up tapestry on ci.curoverse.com Ward Vandewege 1 0 2419 3 31 -c-a 5