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Merge pull request #260 from ao508/add-rec-coverage
Add recommended coverage to Sample view tables
2 parents 673d8c1 + e3919c2 commit 5d9eb85

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7 files changed

+61
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‎frontend/src/generated/graphql.ts‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1514,6 +1514,7 @@ export type DashboardSample = {
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custodianInformation?: Maybe<Scalars["String"]>;
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dbGapStudy?: Maybe<Scalars["String"]>;
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dmpPatientAlias?: Maybe<Scalars["String"]>;
1517+
dmpRecommendedCoverage?: Maybe<Scalars["String"]>;
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embargoDate?: Maybe<Scalars["String"]>;
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genePanel?: Maybe<Scalars["String"]>;
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historicalCmoSampleNames?: Maybe<Scalars["String"]>;
@@ -1573,6 +1574,7 @@ export type DashboardSampleInput = {
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custodianInformation?: InputMaybe<Scalars["String"]>;
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dbGapStudy?: InputMaybe<Scalars["String"]>;
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dmpPatientAlias?: InputMaybe<Scalars["String"]>;
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dmpRecommendedCoverage?: InputMaybe<Scalars["String"]>;
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embargoDate?: InputMaybe<Scalars["String"]>;
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genePanel?: InputMaybe<Scalars["String"]>;
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historicalCmoSampleNames?: InputMaybe<Scalars["String"]>;
@@ -11427,6 +11429,7 @@ export type DashboardSamplesQuery = {
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instrumentModel?: string | null;
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platform?: string | null;
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igoSampleStatus?: string | null;
11432+
dmpRecommendedCoverage?: string | null;
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validationReport?: string | null;
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validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11488,6 +11491,7 @@ export type DashboardSampleMetadataPartsFragment = {
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instrumentModel?: string | null;
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platform?: string | null;
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igoSampleStatus?: string | null;
11494+
dmpRecommendedCoverage?: string | null;
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validationReport?: string | null;
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validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11586,6 +11590,7 @@ export type UpdateDashboardSamplesMutation = {
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instrumentModel?: string | null;
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platform?: string | null;
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igoSampleStatus?: string | null;
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dmpRecommendedCoverage?: string | null;
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validationReport?: string | null;
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validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11716,6 +11721,7 @@ export const DashboardSampleMetadataPartsFragmentDoc = gql`
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instrumentModel
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platform
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igoSampleStatus
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dmpRecommendedCoverage
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validationReport
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validationStatus
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cancerType

‎frontend/src/pages/samples/config.tsx‎

Lines changed: 18 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -348,6 +348,12 @@ export const sampleColDefs: Array<ColDef<DashboardSample>> = [
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field: "igoSampleStatus",
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headerName: "IGO Sample Status",
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},
351+
{
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field: "dmpRecommendedCoverage",
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headerName: "Recommended Coverage",
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headerTooltip: "Recommended coverage for DMP samples",
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headerComponentParams: createCustomHeader(lockIcon + toolTipIcon),
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},
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];
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const dbGapPhenotypeColumns: Array<ColDef<DashboardSample>> = [
@@ -664,6 +670,12 @@ export const wesSampleColDefs: Array<ColDef<DashboardSample>> = [
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field: "igoSampleStatus",
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headerName: "IGO Sample Status",
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},
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{
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field: "dmpRecommendedCoverage",
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headerName: "Recommended Coverage",
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headerTooltip: "Recommended coverage for DMP samples",
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headerComponentParams: createCustomHeader(lockIcon + toolTipIcon),
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},
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];
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const accessSampleColDefs: Array<ColDef<DashboardSample>> = [
@@ -804,6 +816,12 @@ const accessSampleColDefs: Array<ColDef<DashboardSample>> = [
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field: "igoSampleStatus",
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headerName: "IGO Sample Status",
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},
819+
{
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field: "dmpRecommendedCoverage",
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headerName: "Recommended Coverage",
822+
headerTooltip: "Recommended coverage for DMP samples",
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headerComponentParams: createCustomHeader(lockIcon + toolTipIcon),
824+
},
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];
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809827
const editableSampleFields = new Set([

‎graphql-server/src/generated/graphql.ts‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1513,6 +1513,7 @@ export type DashboardSample = {
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custodianInformation?: Maybe<Scalars["String"]>;
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dbGapStudy?: Maybe<Scalars["String"]>;
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dmpPatientAlias?: Maybe<Scalars["String"]>;
1516+
dmpRecommendedCoverage?: Maybe<Scalars["String"]>;
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embargoDate?: Maybe<Scalars["String"]>;
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genePanel?: Maybe<Scalars["String"]>;
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historicalCmoSampleNames?: Maybe<Scalars["String"]>;
@@ -1572,6 +1573,7 @@ export type DashboardSampleInput = {
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custodianInformation?: InputMaybe<Scalars["String"]>;
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dbGapStudy?: InputMaybe<Scalars["String"]>;
15741575
dmpPatientAlias?: InputMaybe<Scalars["String"]>;
1576+
dmpRecommendedCoverage?: InputMaybe<Scalars["String"]>;
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embargoDate?: InputMaybe<Scalars["String"]>;
15761578
genePanel?: InputMaybe<Scalars["String"]>;
15771579
historicalCmoSampleNames?: InputMaybe<Scalars["String"]>;
@@ -11426,6 +11428,7 @@ export type DashboardSamplesQuery = {
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instrumentModel?: string | null;
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platform?: string | null;
1142811430
igoSampleStatus?: string | null;
11431+
dmpRecommendedCoverage?: string | null;
1142911432
validationReport?: string | null;
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validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11487,6 +11490,7 @@ export type DashboardSampleMetadataPartsFragment = {
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instrumentModel?: string | null;
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platform?: string | null;
1148911492
igoSampleStatus?: string | null;
11493+
dmpRecommendedCoverage?: string | null;
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validationReport?: string | null;
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validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11585,6 +11589,7 @@ export type UpdateDashboardSamplesMutation = {
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instrumentModel?: string | null;
1158611590
platform?: string | null;
1158711591
igoSampleStatus?: string | null;
11592+
dmpRecommendedCoverage?: string | null;
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validationReport?: string | null;
1158911594
validationStatus?: boolean | null;
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cancerType?: string | null;
@@ -11715,6 +11720,7 @@ export const DashboardSampleMetadataPartsFragmentDoc = gql`
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instrumentModel
1171611721
platform
1171711722
igoSampleStatus
11723+
dmpRecommendedCoverage
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validationReport
1171911725
validationStatus
1172011726
cancerType

‎graphql-server/src/schemas/queries/samples.ts‎

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -59,6 +59,7 @@ const FIELDS_TO_SEARCH = [
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"cfDNA2dBarcode",
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"sampleCohortIds",
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"igoDeliveryDate",
62+
"dmpRecommendedCoverage",
6263
];
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6465
export function buildSamplesQueryBody({
@@ -300,7 +301,8 @@ export function buildSamplesQueryBody({
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latestMC[0] AS latestMC,
301302
latestQC[0] AS latestQC,
302303
coalesce(apoc.text.join([id IN sampleCohortIds WHERE id IS NOT NULL], ', '), '') AS sampleCohortIds,
303-
apoc.convert.fromJsonMap(latestSm.cmoSampleIdFields) AS cmoSampleIdFields
304+
apoc.convert.fromJsonMap(latestSm.cmoSampleIdFields) AS cmoSampleIdFields,
305+
apoc.convert.fromJsonMap(latestSm.additionalProperties).recommended_coverage AS dmpRecommendedCoverage
304306
305307
${bamCompleteDateColFilter && `WHERE ${bamCompleteDateColFilter}`}
306308
${mafCompleteDateColFilter && `WHERE ${mafCompleteDateColFilter}`}
@@ -321,6 +323,7 @@ export function buildSamplesQueryBody({
321323
latestQC,
322324
sampleCohortIds,
323325
cmoSampleIdFields,
326+
dmpRecommendedCoverage,
324327
d,
325328
r,
326329
@@ -366,6 +369,7 @@ export function buildSamplesQueryBody({
366369
validationReport: latestSt.validationReport,
367370
validationStatus: latestSt.validationStatus,
368371
igoSampleStatus: apoc.convert.fromJsonMap(latestSm.additionalProperties).igoSampleStatus,
372+
dmpRecommendedCoverage: dmpRecommendedCoverage,
369373
370374
smileTempoId: t.smileTempoId,
371375
billed: t.billed,

‎graphql-server/src/utils/typeDefs.ts‎

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Original file line numberDiff line numberDiff line change
@@ -59,6 +59,7 @@ const SAMPLE_FIELDS = `
5959
instrumentModel: String
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platform: String
6161
igoSampleStatus: String
62+
dmpRecommendedCoverage: String
6263
## (sm:SampleMetadata)-[:HAS_STATUS]->(s:Status)
6364
validationReport: String
6465
validationStatus: Boolean

‎graphql.schema.json‎

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Original file line numberDiff line numberDiff line change
@@ -13796,6 +13796,18 @@
1379613796
"isDeprecated": false,
1379713797
"deprecationReason": null
1379813798
},
13799+
{
13800+
"name": "dmpRecommendedCoverage",
13801+
"description": null,
13802+
"args": [],
13803+
"type": {
13804+
"kind": "SCALAR",
13805+
"name": "String",
13806+
"ofType": null
13807+
},
13808+
"isDeprecated": false,
13809+
"deprecationReason": null
13810+
},
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{
1380013812
"name": "embargoDate",
1380113813
"description": null,
@@ -14500,6 +14512,18 @@
1450014512
"isDeprecated": false,
1450114513
"deprecationReason": null
1450214514
},
14515+
{
14516+
"name": "dmpRecommendedCoverage",
14517+
"description": null,
14518+
"type": {
14519+
"kind": "SCALAR",
14520+
"name": "String",
14521+
"ofType": null
14522+
},
14523+
"defaultValue": null,
14524+
"isDeprecated": false,
14525+
"deprecationReason": null
14526+
},
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{
1450414528
"name": "embargoDate",
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"description": null,

‎graphql/operations.graphql‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -173,6 +173,7 @@ fragment DashboardSampleMetadataParts on DashboardSample {
173173
instrumentModel
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platform
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igoSampleStatus
176+
dmpRecommendedCoverage
176177
## (sm:SampleMetadata)-[:HAS_STATUS]->(s:Status)
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validationReport
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validationStatus

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