clevercanary / hca-atlas-tracker

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Add validation for the HCA Data Repository for network and atlas #419

Closed NoopDog closed 1 month ago

NoopDog commented 2 months ago

Need

The HCA Data Explorer shows the atlases and BioNetworks that are associated with a given study. The HCA data wranglers require a report to indicate the atlases and BioNetworks that are missing from projects in the HCA Data repository.

Approach

  1. Add a new HCA Data Repository validation called "Link project to HCA BioNeworks and Atlases."
  2. Validate each source study's project.
  3. Make the validation depends on if the project exists in the HCA Data Repository (skip the validation until the project exists)
  4. Validate the project on save of a source study or when the projects refresh normally happens.
  5. Crate a saved filter, "HCA Data Repository - Missing Network or Atlas that filters on todo instances of this event.

Validating a project's networks in the HCA Data Repository

Every project corresponding to a tracker's source study should have one or more atlases listed in the Azul response in the project's bionetworkName field for example:

 "bionetworkName": [
    "Genetic Diversity",
    "Immune"
 ],

Validating a projects atlas's are listed in the HCA Data Repository

Every project associated with a source study should have one or more atlases listed in the projects Azul response like:

"tissueAtlas": [
                        {
                            "atlas": Lung,
                            "version": "v1.0"
                        },
                        {
                            "atlas": "Blood",
                            "version": "v1.0"
                        }
                    ],

Description

For the expected and actual in the description, make a sentence like.

Missing Networks: Lung Missing Atlases Lung v1.0, Lung v2.0, Brain v1.0

NoopDog commented 1 month ago

Complete