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feat: add stub of SANGER_READ_RUN workflow parameter variable (#459) #460

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Merged
merged 2 commits into from
Apr 4, 2025
Merged

feat: add stub of SANGER_READ_RUN workflow parameter variable (#459) #460

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fix: ensure that all possible workflow parameter variables are handle…
hunterckx Apr 4, 2025
78da645
feat: add stub of `SANGER_READ_RUN` workflow parameter variable (#459)
hunterckx Apr 4, 2025
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3 changes: 2 additions & 1 deletion .eslintrc.json
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,8 @@
"jsdoc/check-alignment": "error",
"jsdoc/check-param-names": "error",
"react-hooks/exhaustive-deps": "error",
"sonarjs/redundant-type-aliases": "warn"
"sonarjs/redundant-type-aliases": "warn",
"sonarjs/todo-tag": "warn"
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@hunterckx hunterckx Apr 4, 2025 •
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I put in a TODO comment on the placeholder switch case, so I had to add this so that ESLint would allow me to make a commit

(To be clear this is how we've handled this ESLint rule in other apps)

},
"overrides": [
{
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10 changes: 7 additions & 3 deletions app/utils/galaxy-api.ts
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Expand Up @@ -75,7 +75,9 @@ function paramVariableToRequestValue(
variable: WORKFLOW_PARAMETER_VARIABLE,
geneModelUrl: string | null,
referenceGenome: string
): WorkflowLandingsBodyRequestState[string] | undefined {
): WorkflowLandingsBodyRequestState[string] | null {
// Because this `switch` has no default case, and the function doesn't allow `undefined` as a return type,
// we ensure through TypeScript that all possible variables are handled.
switch (variable) {
case WORKFLOW_PARAMETER_VARIABLE.ASSEMBLY_ID:
return referenceGenome;
Expand All @@ -92,7 +94,9 @@ function paramVariableToRequestValue(
src: "url",
url: geneModelUrl,
}
: undefined;
: null;
case WORKFLOW_PARAMETER_VARIABLE.SANGER_READ_RUN:
return null; // TODO pass in necessary information and generate an actual value for this
}
}

Expand Down Expand Up @@ -120,7 +124,7 @@ function getWorkflowLandingsRequestState(
geneModelUrl,
referenceGenome
);
if (value !== undefined) result[key] = value;
if (value !== null) result[key] = value;
}
}
return result;
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1 change: 1 addition & 0 deletions catalog/build/py/generated_schema/schema.py
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Expand Up @@ -105,6 +105,7 @@ class WorkflowParameterVariable(str, Enum):
ASSEMBLY_ID = "ASSEMBLY_ID"
ASSEMBLY_FASTA_URL = "ASSEMBLY_FASTA_URL"
GENE_MODEL_URL = "GENE_MODEL_URL"
SANGER_READ_RUN = "SANGER_READ_RUN"


class WorkflowPloidy(str, Enum):
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1 change: 1 addition & 0 deletions catalog/schema/enums/workflow_parameter_variable.yaml
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Expand Up @@ -8,3 +8,4 @@ enums:
ASSEMBLY_ID:
ASSEMBLY_FASTA_URL:
GENE_MODEL_URL:
SANGER_READ_RUN:
1 change: 1 addition & 0 deletions catalog/schema/generated/schema.ts
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Expand Up @@ -29,6 +29,7 @@ export enum WorkflowParameterVariable {
ASSEMBLY_ID = "ASSEMBLY_ID",
ASSEMBLY_FASTA_URL = "ASSEMBLY_FASTA_URL",
GENE_MODEL_URL = "GENE_MODEL_URL",
SANGER_READ_RUN = "SANGER_READ_RUN",
};
/**
* Possible ploidies supported by workflows.
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3 changes: 2 additions & 1 deletion catalog/schema/generated/workflows.json
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Expand Up @@ -131,7 +131,8 @@
"enum": [
"ASSEMBLY_ID",
"ASSEMBLY_FASTA_URL",
"GENE_MODEL_URL"
"GENE_MODEL_URL",
"SANGER_READ_RUN"
],
"title": "WorkflowParameterVariable",
"type": "string"
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