Manually update katsu's OpenAPI spec to v3.0 data model #239
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…the data model This has the following work done so far: 1. Move required field “primary_site” from Donor to Primary Diagnosis 2. Add optional “submitter_treatment_id” if the specimen was resected during surgery 3. Moved the conditional fields [“pathological_tumour_staging_system, “pathological_stage_group”, “pathological_t_category”, “pathological_n_category”, “pathological_m_category”] from Specimen to Primary Diagnosis
…ethod”, “number_lymph_nodes_positive”]
…ce_identifier”] Assuming there's no 64 character limit on the surgery_reference_identifier yet
[“recurrence_tumour_staging_system”, “recurrence_stage_group”, “recurrence_t_category”, “recurrence_n_category”, “recurrence_m_category”]
…ent_id from the SampleRegistrations I accidentally added it to
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## develop #239 +/- ##
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- Coverage 96.99% 96.64% -0.35%
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Files 35 36 +1
Lines 3561 3669 +108
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+ Hits 3454 3546 +92
- Misses 107 123 +16 ☔ View full report in Codecov by Sentry. |
- Switch pathological categories to be an enum - Switch actual/perscribed_cumulative_drug_dose to numbers
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Confused about why we are removing |
It'll be in the DonorWithClinicalData response under the NestedPrimaryDiagnosis schema, so to get the |
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Sorry, that last comment about the readme wasn't clear. I don't think we want to replace all of the instances of |
| To view the API documentation, simply open [schema.md](schema.md) or [Redoc](https://redocly.github.io/redoc/?url=https://raw.githubusercontent.com/CanDIG/katsu/feature/manual_schema/chord_metadata_service/mohpackets/docs/schema_manual.yml). | ||
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| > [!IMPORTANT] | ||
| > Katsu is currently being transitioned to MoH clinical data model v3.0.0. There is a manually created v3.0.0 of the OpenAPI schema at [schema_v3.yml](schema_v3.yml) that can be used as a reference in the interim period. This file will be replaced by the automatically generated schema documentaion files once katsu is fully transitioned to model v3.0.0. |
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@kcranston is this what you were thinking for the line in the README?
Description
This implements the CanDIGv3 data model changes as outlined in this document.
The updated schema can be found at this link (includes only the diffs to the schema).
Intended list of changes
Changes to the models includes:
Moving a few fields around:
primary_sitefrom donor to primary diagnosis, though the endpoints are still able to query based on itpathological_*[“days_per_cycle”, “number_of_cycles”],Removing a few fields:
submitter_specimen_idrecurrence_*[“line_of_treatment”, “treatment_setting”][“lymph_nodes_examined_status”, “lymph_nodes_examined_method”, “number_lymph_nodes_positive”]Adding a few fields:
submitter_treatment_id[“surgery_reference_database”, “surgery_reference_identifier”]And adding the new Systemic Therapy table, which supercedes (and removes) Chemo/Hormonal/Immunotherapy.
This PR does not address how the implementation of the new table, nor the new/changed endpoints, but only outlines what will need to be changed