Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Matrix service integration with Data Browser #9

Closed
briandoconnor opened this issue Mar 12, 2018 · 5 comments
Closed

Matrix service integration with Data Browser #9

briandoconnor opened this issue Mar 12, 2018 · 5 comments
Assignees
@MillenniumFalconMechanic @NoopDog
Milestone
Sprint 12 - Octob...

Comments

@briandoconnor
Copy link

briandoconnor commented Mar 12, 2018 •
edited by hannes-ucsc
Loading

This needs to be scoped but users would expect integration

┆Issue Number: HCAB-6
@briandoconnor briandoconnor self-assigned this Mar 12, 2018
@theathorn
Copy link

theathorn commented Aug 13, 2018 •
edited
Loading

From 7/30 Data Browser meeting:

Proposed plan:

  • Create new button that would post the URL to the matrix server
    • The URL is all the matrix service needs to retrieve the manifest
    • Redirected to a page that gives stats, and a URL to check with, maybe ability to input an email address
    • No time estimation
    • Page can spin and wait, using the 301/302 retry after logic.
    • Matrix service could support the basic call in a few weeks (Sprint 8?)
  • Returns???
    • Won’t be available in “interactive time”
    • Signed URL will get returned
    • If the user submits a request that has already been requested (same url), and the work is the same as a previous request, then cached results will be returned.
    • Matrix service does not have plans to support email notification right now, but it could possibly be added (Marcus Kinsella)

Matrix Spec: https://docs.google.com/document/d/12gfF3UEgRZ0YJiBoScLMtcW6Cthv0_MZHQwj4WMYKPA/edit#heading=h.gk7s93eg9jfq

@theathorn theathorn assigned theathorn and unassigned briandoconnor Aug 21, 2018
@theathorn
Copy link

theathorn commented Aug 28, 2018 •
edited
Loading

Update from 8/27 meeting with @mckinsel, @brianraymor and @NoopDog:

  • Marcus has pull request for mock API out for review (Add initial mock API for orange box testing HumanCellAtlas/matrix-service#28)
  • "Version 0" (targeted for demo in Oct) will have Data Browser call Matrix APIs described below:
  • MatrixRequest "post" json will contain bundle fqids as input
  • MatrixRequest will not require any user-specified inputs; output file will be concatenated matrices only (very useful for SmartSeq2 one cell/bundle inputs)
  • MatrixFormat ("zarr", "parquet", "loom", "anndata", "singlecellexperiment") will use default value for Version 0
  • MatrixRequest API reply will return a "request ID" and "key" (eventually will be a link url to results)
  • Matrix "get" API used by UI to poll for completion status by providing "request ID" as input
  • need secondary analysis bundles generated by green box to test with (currently not present in prod)
  • TBD: call Matrix service APIs directly from browser or via azul webservice?

@theathorn theathorn assigned NoopDog and unassigned theathorn Aug 28, 2018
@theathorn
Copy link

@NoopDog Please review Marcus' PR for the Matrix API.

@theathorn theathorn assigned frano-m and unassigned NoopDog Sep 17, 2018
@theathorn theathorn added this to the Sprint 10 - September 28 milestone Sep 17, 2018
@frano-m
Copy link
Contributor

frano-m commented Sep 27, 2018

Skin complete - API TBC

@theathorn theathorn assigned NoopDog and unassigned frano-m Sep 27, 2018
@theathorn
Copy link

Use .zarray file type in links.json metadata in bundle to indicate presence of matrix-able data.
Select matrix files in Data Browser to enable "Matrix Service".
Request manifest returns url in response that can be passed to Matrix Service.

NoopDog pushed a commit that referenced this issue Mar 16, 2023
@BruceRodrigues
Project detail page/issue #9 (#15)
74ab83d 
* Initial structure. List and Detail pages + utils hooks. #3

* Container components + services + models. #3

* Adding List Page. #4

* Json component. #3

* Adding transformer and viewModels. #3

* Adding comments. #3

* Changing projectShortName to projectTitle. #3

* LinkTable component + list transformer. #4

* Fix. #4

* Adding vscode folder to gitignore #3

* generating static html

* adding prettier

* Config eslint

* Adding husky pre-commit. #8

* husky fixes. #8

* setting correct folder

* Build all detail pages. #9
NoopDog pushed a commit that referenced this issue Mar 16, 2023
@BruceRodrigues
Project index page/issue #10 (#16)
1d8edac 
* Initial structure. List and Detail pages + utils hooks. #3

* Container components + services + models. #3

* Adding List Page. #4

* Json component. #3

* Adding transformer and viewModels. #3

* Adding comments. #3

* Changing projectShortName to projectTitle. #3

* LinkTable component + list transformer. #4

* Fix. #4

* Adding vscode folder to gitignore #3

* generating static html

* adding prettier

* Config eslint

* Adding husky pre-commit. #8

* husky fixes. #8

* setting correct folder

* Build all detail pages. #9

* downgrading react and adding react-table. #10

* Adding react-table. #10

* React table type definition. #10

* Changing LinkTable to React-Table. #10
NoopDog pushed a commit that referenced this issue Mar 16, 2023
@BruceRodrigues
Basic layout/issue #12 (#24)
ae5e596 
* Initial structure. List and Detail pages + utils hooks. #3

* Container components + services + models. #3

* Adding List Page. #4

* Json component. #3

* Adding transformer and viewModels. #3

* Adding comments. #3

* Changing projectShortName to projectTitle. #3

* LinkTable component + list transformer. #4

* Fix. #4

* Adding vscode folder to gitignore #3

* generating static html

* adding prettier

* Config eslint

* Adding husky pre-commit. #8

* husky fixes. #8

* setting correct folder

* Build all detail pages. #9

* downgrading react and adding react-table. #10

* Adding react-table. #10

* React table type definition. #10

* Changing LinkTable to React-Table. #10

* Creating layout structure. #12

* Adding storybook. #12
Closed
2 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@MillenniumFalconMechanic MillenniumFalconMechanic

@NoopDog NoopDog

Labels
None yet
Projects
None yet
Milestone
Sprint 12 - October 26
Development

No branches or pull requests
5 participants
@briandoconnor @MillenniumFalconMechanic @NoopDog @frano-m @theathorn