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fix: remove references to sampleId field removed from Azul backend #4928

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Merged
hannes-ucsc merged 3 commits into from
Aug 20, 2026
Merged

fix: remove references to sampleId field removed from Azul backend #4928

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eff6b5a
fix: remove references to sampleId field removed from Azul backend
hannes-ucsc Aug 17, 2026
4e3a131
fix: drop stale samples id from schema.org project fixture (#4928)
hannes-ucsc Aug 19, 2026
9f2f3df
fix: remove stale specimens id from aggregated response type (#4928)
hannes-ucsc Aug 19, 2026
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2 changes: 0 additions & 2 deletions __tests__/utils/schemaOrg/hcaProjectDataset.test.ts
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Expand Up @@ -250,7 +250,6 @@ describe("buildHcaProjectJsonLd", () => {
samples: [
{
disease: ["normal"],
id: ["s1"],
organ: ["brain"],
organPart: ["cortex"],
sampleEntityType: ["specimens"],
Expand All @@ -259,7 +258,6 @@ describe("buildHcaProjectJsonLd", () => {
specimens: [
{
disease: ["normal"],
id: ["s1"],
organ: ["brain"],
organPart: ["cortex"],
preservationMethod: [],
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2 changes: 0 additions & 2 deletions app/apis/azul/hca-dcp/common/aggregatedEntities.ts
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Expand Up @@ -120,7 +120,6 @@ export interface AggregatedSampleResponse {
cellLineType?: string[];
disease?: (string | null)[];
effectiveOrgan?: (string | null)[];
id: string[];
modelOrgan?: (string | null)[];
modelOrganPart?: (string | null)[];
organ?: string[];
Expand All @@ -144,7 +143,6 @@ export interface AggregatedSamplesResponse {
*/
export interface AggregatedSpecimenResponse {
disease: (string | null)[];
id: string[];
organ: string[];
organPart: (string | null)[];
preservationMethod: (string | null)[];
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1 change: 0 additions & 1 deletion app/apis/azul/hca-dcp/common/entities.ts
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Expand Up @@ -138,7 +138,6 @@ export interface SampleResponse {
cellLineType?: string;
disease?: (string | null)[];
effectiveOrgan: string | null;
id: string;
modelOrgan?: string | null;
modelOrganPart?: string | null;
organ?: string;
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2 changes: 0 additions & 2 deletions app/components/Index/common/constants.ts
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Expand Up @@ -32,7 +32,6 @@ const {
PHENOTYPIC_SEX,
PLATFORM,
REPORTED_ETHNICITY,
SAMPLE_ID,
SAMPLE_TYPE,
SELECTED_CELL_TYPE,
STUDY,
Expand Down Expand Up @@ -118,7 +117,6 @@ export const PLURALIZED_METADATA_LABEL = {
[PHENOTYPIC_SEX]: "phenotypic sexes",
[PLATFORM]: "platforms",
[REPORTED_ETHNICITY]: "reported ethnicities",
[SAMPLE_ID]: "sample ids",
[SAMPLE_TYPE]: "sample types",
[SELECTED_CELL_TYPE]: "cell types",
[STUDY]: "studies",
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1 change: 0 additions & 1 deletion app/components/Index/common/entities.ts
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Expand Up @@ -34,7 +34,6 @@ export enum METADATA_KEY {
PHENOTYPIC_SEX = "PHENOTYPIC_SEX",
PLATFORM = "PLATFORM",
REPORTED_ETHNICITY = "REPORTED_ETHNICITY",
SAMPLE_ID = "SAMPLE_ID",
SAMPLE_TYPE = "SAMPLE_TYPE",
SELECTED_CELL_TYPE = "SELECTED_CELL_TYPE",
SPECIES = "SPECIES",
Expand Down
27 changes: 0 additions & 27 deletions app/viewModelBuilders/azul/hca-dcp/common/viewModelBuilders.tsx
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Expand Up @@ -404,20 +404,6 @@
};
};

/**
* Build props for the aggregated sample ID NTagCell component from the given entity response.
* @param entityResponse - Response model return from the entity response API.
* @returns model to be used as props for the NTagCell component.
*/
export const buildAggregatedSampleId = (
entityResponse: ProjectsResponse | FilesResponse
): React.ComponentProps<typeof C.NTagCell> => {
return {
label: getPluralizedMetadataLabel(METADATA_KEY.SAMPLE_ID),
values: processAggregatedOrArrayValue(entityResponse.samples, "id"),
};
};

/**
* Build props for the aggregated model organ NTagCell component from the given entity response.
* @param entityResponse - Response model return from the entity response API.
Expand Down Expand Up @@ -1392,19 +1378,6 @@
};
};

/**
* Build props for sample identifier BasicCell component from the given sample response.
* @param samplesResponse - Response model return from samples API.
* @returns model to be used as props for the BasicCell component.
*/
export const buildSampleId = (
samplesResponse: SamplesResponse
): React.ComponentProps<typeof C.BasicCell> => {
return {
value: processEntityValue(samplesResponse.samples, "id"),
};
};

/**
* Build props for the model organ BasicCell component from the given samples response.
* @param samplesResponse - Response model return from the samples API.
Expand Down Expand Up @@ -1953,7 +1926,7 @@
cell: ({ column, row }) => (
<C.NTagCell
{...getNTagCellProps(
row.original as unknown as ProjectMatrixTableView, // TODO revisit type assertion here

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column.id,
METADATA_KEY.ANATOMICAL_ENTITY
)}
Expand All @@ -1975,7 +1948,7 @@
cell: ({ column, row }) => (
<C.NTagCell
{...getNTagCellProps(
row.original as unknown as ProjectMatrixTableView, // TODO revisit type assertion here

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column.id,
METADATA_KEY.CONTENT_DESCRIPTION
)}
Expand Down
2 changes: 0 additions & 2 deletions site-config/hca-dcp/category.ts
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Expand Up @@ -38,7 +38,6 @@ export const HCA_DCP_CATEGORY_KEY = {
PROJECT_TITLE: "projectTitle",
PUBLICATION_TITLE: "publicationTitle",
SAMPLE_ENTITY_TYPE: "sampleEntityType",
SAMPLE_ID: "sampleId",
SAMPLE_TYPE: "sampleType",
SELECTED_CELL_TYPE: "selectedCellType",
SPECIMEN_DISEASE: "specimenDisease",
Expand Down Expand Up @@ -84,7 +83,6 @@ export const HCA_DCP_CATEGORY_LABEL = {
PROJECT_TITLE: "Project Title",
PUBLICATION_TITLE: "Publication Title",
SAMPLE_ENTITY_TYPE: "Sample Type",
SAMPLE_ID: "Sample Id",
SAMPLE_TYPE: "Sample Type",
SELECTED_CELL_TYPE: "Selected Cell Type",
SPECIMEN_DISEASE: "Specimen Disease",
Expand Down
11 changes: 0 additions & 11 deletions site-config/hca-dcp/ma-dev/entities/files/columns.ts
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Expand Up @@ -214,16 +214,6 @@ const SAMPLE_ENTITY_TYPE: ColumnConfig<FilesResponse> = {
width: { max: "1fr", min: "120px" },
};

const SAMPLE_ID: ColumnConfig<FilesResponse> = {
componentConfig: {
component: C.NTagCell,
viewBuilder: V.buildAggregatedSampleId,
} as ComponentConfig<typeof C.NTagCell, FilesResponse>,
header: HCA_DCP_CATEGORY_LABEL.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
width: { max: "1fr", min: "120px" },
};

const SELECTED_CELL_TYPE: ColumnConfig<FilesResponse> = {
componentConfig: {
component: C.NTagCell,
Expand Down Expand Up @@ -274,7 +264,6 @@ export const COLUMNS: EntityConfig<FilesResponse>["list"]["columns"] = [
CONTENT_DESCRIPTION,
FILE_SOURCE,
PROJECT_TITLE,
SAMPLE_ID,
GENUS_SPECIES,
SAMPLE_ENTITY_TYPE,
SPECIMEN_ORGAN,
Expand Down
1 change: 0 additions & 1 deletion site-config/hca-dcp/ma-dev/entities/files/tableOptions.ts
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Expand Up @@ -11,7 +11,6 @@ export const TABLE_OPTIONS: EntityConfig<FilesResponse>["list"]["tableOptions"]
columnVisibility: {
[HCA_DCP_CATEGORY_KEY.FILE_FORMAT]: false,
[HCA_DCP_CATEGORY_KEY.FILE_SOURCE]: false,
[HCA_DCP_CATEGORY_KEY.SAMPLE_ID]: false,
[HCA_DCP_CATEGORY_KEY.GENUS_SPECIES]: false,
[HCA_DCP_CATEGORY_KEY.SAMPLE_ENTITY_TYPE]: false,
[HCA_DCP_CATEGORY_KEY.SPECIMEN_ORGAN]: false,
Expand Down
11 changes: 0 additions & 11 deletions site-config/hca-dcp/ma-dev/entities/samples/columns.ts
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Expand Up @@ -141,16 +141,6 @@ const SAMPLE_ENTITY_TYPE: ColumnConfig<SamplesResponse> = {
width: { max: "1fr", min: "124px" },
};

const SAMPLE_ID: ColumnConfig<SamplesResponse> = {
componentConfig: {
component: C.BasicCell,
viewBuilder: V.buildSampleId,
} as ComponentConfig<typeof C.BasicCell, SamplesResponse>,
header: HCA_DCP_CATEGORY_LABEL.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
width: { max: "1fr", min: "120px" },
};

const SELECTED_CELL_TYPE: ColumnConfig<SamplesResponse> = {
componentConfig: {
component: C.NTagCell,
Expand Down Expand Up @@ -192,7 +182,6 @@ const WORKFLOW: ColumnConfig<SamplesResponse> = {
};

export const COLUMNS: EntityConfig<SamplesResponse>["list"]["columns"] = [
SAMPLE_ID,
PROJECT_TITLE,
GENUS_SPECIES,
SAMPLE_ENTITY_TYPE,
Expand Down
2 changes: 1 addition & 1 deletion site-config/hca-dcp/ma-dev/entities/samples/tableOptions.ts
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Expand Up @@ -23,7 +23,7 @@ export const TABLE_OPTIONS: EntityConfig<SamplesResponse>["list"]["tableOptions"
sorting: [
{
desc: SORT_DIRECTION.ASCENDING,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.PROJECT_TITLE,
},
],
},
Expand Down
10 changes: 0 additions & 10 deletions site-config/lungmap/dev/index/filesEntityConfig.ts
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Expand Up @@ -100,15 +100,6 @@ export const filesEntityConfig: EntityConfig = {
id: HCA_DCP_CATEGORY_KEY.PROJECT_TITLE,
width: { max: "2fr", min: "240px" },
},
{
componentConfig: {
component: C.NTagCell,
viewBuilder: V.buildAggregatedSampleId,
} as ComponentConfig<typeof C.NTagCell, FilesResponse>,
header: HCA_DCP_CATEGORY_LABEL.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
width: { max: "1fr", min: "120px" },
},
{
componentConfig: {
component: C.NTagCell,
Expand Down Expand Up @@ -250,7 +241,6 @@ export const filesEntityConfig: EntityConfig = {
columnVisibility: {
[HCA_DCP_CATEGORY_KEY.FILE_FORMAT]: false,
[HCA_DCP_CATEGORY_KEY.FILE_SOURCE]: false,
[HCA_DCP_CATEGORY_KEY.SAMPLE_ID]: false,
[HCA_DCP_CATEGORY_KEY.GENUS_SPECIES]: false,
[HCA_DCP_CATEGORY_KEY.SAMPLE_ENTITY_TYPE]: false,
[HCA_DCP_CATEGORY_KEY.SPECIMEN_ORGAN]: false,
Expand Down
11 changes: 1 addition & 10 deletions site-config/lungmap/dev/index/samplesEntityConfig.ts
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Expand Up @@ -25,15 +25,6 @@ export const samplesEntityConfig: EntityConfig = {
label: "Samples",
list: {
columns: [
{
componentConfig: {
component: C.BasicCell,
viewBuilder: V.buildSampleId,
} as ComponentConfig<typeof C.BasicCell, SamplesResponse>,
header: HCA_DCP_CATEGORY_LABEL.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
width: { max: "1fr", min: "120px" },
},
{
componentConfig: {
component: C.Link,
Expand Down Expand Up @@ -207,7 +198,7 @@ export const samplesEntityConfig: EntityConfig = {
sorting: [
{
desc: SORT_DIRECTION.ASCENDING,
id: HCA_DCP_CATEGORY_KEY.SAMPLE_ID,
id: HCA_DCP_CATEGORY_KEY.PROJECT_TITLE,
},
],
},
Expand Down
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