Post v1.0.0 bug fixes

[e-t-k]

This discussion is to track bugs, omissions, and errors in the interface design or reference implementation (Rust) that are still present in the 1.0.0 release and should be resolved.
This is not for new features (see #110 for that) and it is not for problems with any federation member's implementation of the interface.

Known Bugs

Diagnosis not available as search parameter for sample endpoint

Bug type Omission in interface design
Endpoint GET /sample?diagnosis=VALUE
Expected behavior Samples are filtered by the value of the "diagnosis" field
Current behavior per API spec Diagnosis is an UnsupportedField
Is fix a breaking change? No: a new parameter option will be added which clients may choose to ignore.
Will implementations need to update? Yes: if an implementation supports the sample endpoint and diagnosis is not yet a searchable parameter it will need to be added.
Date added June 24 2024
Current status fix not yet started as of June 24
Notes

Race Black or African American has the Asian description

Bug type Error in reference implementation
Endpoint The wiki: ccdi-federation-api / ccdi-federation-api-spec
Expected behavior wiki has the correct description for Black or African American
Current behavior wiki has the wrong description
Is fix a breaking change? No: fix applies to wiki only; no client needs to make a change.
Will implementations need to update? No; harmonized fields in metadata/fields/subject do not have a Description attribute.
Date added July 3 2024
Current status fix not yet started as of July 3
Notes
Comment block to be fixed is at:

ccdi-federation-api/packages/ccdi-cde/src/v1/subject/race.rs

Line 99 in d8163b9

/// `Asian`

Wikis (ccdi-federation-api / ccdi-federation-api-spec) have already been manually patched to correct this text.

[Ssandor13]

Tissue Type has a typo for Begin Date for Tumor
Bug type Error in reference implementation
Endpoint The wiki: [ccdi-federation-api / ccdi-federation-api-spec](https://github.com/stjudecloud/ccdi/wiki/Sample-Metadata-Fields#tissue_type)
Expected behavior 8/25/2016 should be formatted correctly
Current behavior Begin Date is not formatted correctly
Is fix a breaking change? No: fix applies to wiki only; no client needs to make a change.
Will implementations need to update? No
Date added July 8th, 2024
Current status fix not yet started as of July 8th, 2024

[e-t-k]

organization endpoint calls parameter 'name' but expects 'identifier'

Bug type misleading documentation in swagger.yml leading to inconsistent implementations
Endpoint GET /organization/
Problem swagger spec suggests that individual organization info should be retrieved using the name field (which can have special characters); however, reference implementation actually accepts identifier field. This inconsistency caused UCSC, StJude, PCDC to implement matching identifier and CHOP to implement matching name.
Resolution We will standardize on matching identifier and update the text in the swagger spec ; CHOP plans to update their implementation.
Is fix a breaking change? Yes - clients may have stored queries for CHOP matching old implementation
Will implementations need to update? CHOP only.
Date added July 17 2024
Current status fix not yet started as of July 17
Notes
Code to fix: https://github.com/CBIIT/ccdi-federation-api/blob/main/packages/ccdi-server/src/routes/organization.rs#L91

    path = "/organization/{name}",
    params(
        (
            "name" = String,
            description = "The name of the organization.",
        ),

[asafieva]

Bug type: index.html "title" and "description" HTML tags were not updated after changes in swagger.yml "info">>"title" and "info">>"description". This makes URL bookmarks appearance inconsistent with swagger website cbiit.github.io/ccdi-federation-api.
Endpoint: NA
Problem:
title YAML: "CCDI Data Federation: Participating Nodes API"
title index.html: "CCDI Data Federation API"
description in YAML: "The Childhood Cancer Data Initiative (CCDI) Data Federation API supports the querying of federated pediatric cancer within the broader community."
description in index.html: "An API for querying federated pediatric cancer data from the broader community.""
Resolution: Update index.html tags to match swagger.yml info title and description elements.
Is fix a breaking change? No
Will implementations need to update? No.
Date added: July 23 2024
Current status: fix not yet started as of July 23 2024

[asafieva]

Bug type: sample attributes "age_at_diagnosis" (3225640), "age_at_collection" (14473376), subject attribute "age_at_vital_status" (14480965) do not have CDEs references on wiki.
Endpoint: sample, subject
Problem: CDE missing references on API wiki pages.
Resolution: Add CDE missing references to harmonized values, on API wiki pages.
Is fix a breaking change? No
Will implementations need to update? Yes.
Date added: July 31 2024
Current status: fix not yet started as of July 31 2024

[asafieva]

Bug type: An attribute "depositions" is not defined as nullable. API group decided on a meeting 09/27/2024 that this is a bug, and "depositions" attributes shall be allowed to be nullable.
Endpoint: All using "models.metadata.common.Metadata" component.
Problem: An attribute "depositions" is not defined as nullable in the API spec.  But "null" values are sent in API responses besides KidsFirst server.
Resolution: "depositions" attributes shall be defined as nullable in the spec to allow returning the entities which are not related to dbGaP. The requirement to have not-null depositions would force API nodes to exclude a lot of entities to comply with this requirement.
Is fix a breaking change? No
Will implementations need to update? Yes, "swagger.yml" specification shall be updated.
Date added: Sep 27 2024
Current status: fix not yet started as of Sep 27 2024