The cfde-deriva from nih-cfde

deployment and ops management of portal stack (AWS)

Start: 4/1/20
End: 7/1/20

dashboard - deploy to Production

Start: 6/1/20
End: 6/20/20

Deliverable is : nih-cfde/deliverables#112

2D and 3D visualizations, GSEA

Start: 7/1/20
End: 1/1/21

Milestone: 5

POC: Ma'ayan

(scripts linked to GH)

UI RFC+

Draft a one-page document to cover design and organizational issues for the UI focus area.

API Planning Doc

Draft a one-page document to cover design and organizational issues for the API focus area.

expose a REST API

Start: 1/1/20
End: 4/1/20

Milestone: 5

POC: ??

CFDE UI Landing Page

This is important as a base for the dashboard (#23) and portal (#16) functionality

Dashboard - Cia process

Start: 4/1/20
End: 11/1/20

MIlestone: 5

POC: @carlkesselman

work with Cia Romano: do user interviews and develop user preferences for the CFDE Dashboard.

Creates scripts to extract and annotate with metadata CF tools and workflows and creates a catalog of CF tools and workflows. Create a catalog of all CF DCC published bioinformatics tools and databases, and provide these for browsing and searching from the CFDE portal.

(4.2.6)

portal implementation

Start: 4/1/20
End: 7/1/20

Milestone: 5

POC: @mikedarcy

need to decompose

set of graphical plot renderings of statistical rollups and common queries.

Start: 1/1/20
End: 4/1/20

implement, deploy and operate a cloud-based identifier s/w i/f for CFDE

Start: 1/1/20
End: 1/1/21

Milestone: 5

POC: @mikedarcy

- #11
- #12
- #13

Remove schema assumptions in CfdeDataPackage

There are some assumptions about the schema of data being loaded into DERIVA, in the CfdeDataPackage, found specifically in the provision_denorm_tables method (e.g. column method must exist in table DataEvent in this code. These assumptions break the goal of this tool being generally C2M2-version agnostic, and are causing otherwise-valid data to fail to load into DERIVA.

The CfdeDataPackage should be modified to not require these columns in order to load data into DERIVA, so the tool doesn't need to be updated as the C2M2 changes.

portal - usability evaluation : user testing and feedback

Start: 7/1/20
End: 10/1/20

Milestone: 5

POC:

develop asset spec export tools

Start: 7/1/20
End: 1/1/21

depends on: nih-cfde/specifications-and-documentation#9 and nih-cfde/deliverables#66

implementation of asset spec at DCCs*

Start: 4/1/20
End: 1/1/21

depends on: nih-cfde/specifications-and-documentation#9 and nih-cfde/deliverables#66

finalize data model and presentation layer for catalog

support DCC ingest 3*

Start: 10/1/20
End: 1/1/21

depends on: #33

Authorization model

may affect data model (level 1? or higher?)

could survey models from DCCs

dbGaP

Phenotype driven use case to build on.

combinations may need to be made private (de-identified) to protect privacy.

support of ingest pipeline 2

Start: 4/1/20
End: 7/1/20

Concinuation of #29

support DCC ingest 2*

Start: 7/1/20
End: 10/1/20

depends on: #32

Improve Documentation for Public Beta Release

We are scheduled to release the portal to the public 9/30/20. These are the docs that should be available by then.

support DCC ingest 1*

Start: 4/1/20
End: 7/1/20

System infrastructure deployment

system diagram

waiting for STRIDES AWS accounts, but in the meantime

standup a VPC? need dedicated one for CFDE production deployment

UMB to set up local copy using our AWS account, Mike can provide access through firewall rules.

VPC environments? staging, devel, prod. Owned by STRIDES account

Need GLOBUS auth

portal - deploy to production

Start: 6/1/20
End: 9/20/20

Deliverable was: nih-cfde/deliverables#111 however the public release was delayed to 9/30/20

support of ingest pipeline 1

Start: 1/1/20
End: 4/1/20

identifier service - beta

new epic

Portal - Cia process

Start: 1/1/20
End: 4/1/20

work with Cia Romano: do user interviews and develop user preferences for the CFDE Portal.

Remove jargon from CFDE UI

@ACharbonneau , please add your list of jargon to be addressed to this issue when it's ready.

Identifier service - prototype

Start: 1/1/20
End: 4/1/20

Milestone: 5

POC: @mikedarcy

identifier service - production

Report for DCCs to evaluate their C2M2 data

I need to ask the DCCs to review their data in the C2M2 model, however it's not clear what we want/need them to review, or how they should go about doing that.

@abradyIGS has volunteered to create a first draft of a high level report we could give to DCCs to review

@owhite is going to compile a list of ideas for questions we might ask them to help us verify the data

develop CFDE UI documentation

Start: 6/1/20
End: 7/1/20

Milestone: 5

POC: @mikedarcy

https://github.com/nih-cfde/deliverables/issues/104

identifier strategy - develop and document

Start: 1/1/20
End: 4/1/20

Milestone: 6

POC: @rpwagner

relation to: https://github.com/nih-cfde/FAIR/issues/19 ??

dashboard - usability evaluation : user testing and feedback

Start: 6/1/20
End: 10/1/20

POC:

interface to create/run workflows

Start: 8-1-20
End: 1-1-21

Milestone: 5

POC: Ma'ayan

develop dashboard documentation

Start: 6/1/20
End: 7/1/20

Milestone: 5

POC: @victor73

produce deliverable : nih-cfde/deliverables#105

Collect all CF APIs documented with Swagger and SmartAPI

5.2.7 - Develops a prototype interface to create and run workflows#76
Internal Due Date: 12/18/20
NIH Due Date: 12/22/20

https://github.com/nih-cfde/deliverables/issues/76

Create a collection of workflows that integrate data and tools from at least 2 CF programs as example case studies

5.2.7 - Develops a prototype interface to create and run workflows#76
Internal Due Date: 12/18/20
NIH Due Date: 12/22/20

https://github.com/nih-cfde/deliverables/issues/76

tools for managing linkage and term sets (harmonize)

Start: 1/1/20
End: 7/1/20

scripts for ingest into C2M2

Start: 9/1/20
End: 12/1/20

depends on: #30

Infrastructure Planning Doc

Draft a one-page document to cover design and organizational issues for the Infrastructure focus area.

Planning Documentation Sprint

This is a sprint to create working docs that describe what we are focusing on, how we decide what we are focusing on, and how the work gets completed.

Nav bar improvements

For the demo web page, a few workarounds were added for the navbar since directly including it caused some styling collisions and other functionality to not work. The problem occurred because of a dependency on 2 different versions of bootstrap.css (3.3.7 and 4.7.0). Both were loaded into the environment side by side and that caused the clash in styles in navbar and some odd functionality with the modal's behavior since it's using a CSS solution to show/hide itself.

As a temporary solution, the navbar was placed inside of an <iframe> for the landing page and dashboard. This was done to scope the dependencies for the navbar so the version of bootstrap for the landing page and navbar could be different. This caused a few other issues, notably the navbar takes longer to load and the dropdowns in the navbar get clipped (so they are currently turned off).