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typeDefs.ts
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332 lines (295 loc) · 7.45 KB
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import { gql } from "apollo-server";
const GENERIC_TYPEDEFS = gql`
enum AgGridSortDirection {
asc
desc
}
input DashboardRecordContext {
fieldName: String
values: [String!]!
}
# Modeling after AG Grid's SortModel type
input DashboardRecordSort {
colId: String! # field name
sort: AgGridSortDirection!
}
input DashboardRecordColumnFilter {
# The field to filter on, e.g. "smileSampleId", "cmoPatientId", etc.
field: String!
# Can be a single value or an array of values to filter on. Comes from AG Grid's filter model object
filter: String!
}
`;
const SAMPLE_FIELDS = `
# (s:Sample)
smileSampleId: String!
revisable: Boolean
sampleCategory: String!
# (s:Sample)-[:HAS_METADATA]->(sm:SampleMetadata)
## Root-level fields
primaryId: String
cmoSampleName: String
importDate: String
cmoPatientId: String
investigatorSampleId: String
sampleType: String
species: String
genePanel: String
baitSet: String
preservation: String
tumorOrNormal: String
sampleClass: String
oncotreeCode: String
collectionYear: String
sampleOrigin: String
tissueLocation: String
sex: String
cfDNA2dBarcode: String
## Custom fields
recipe: String
altId: String
analyteType: String
historicalCmoSampleNames: String
instrumentModel: String
platform: String
igoSampleStatus: String
dmpRecommendedCoverage: String
## (sm:SampleMetadata)-[:HAS_STATUS]->(s:Status)
validationReport: String
validationStatus: Boolean
# Oncotree API
cancerType: String
cancerTypeDetailed: String
# (s:Sample)-[:HAS_TEMPO]->(t:Tempo)
## Root-level fields
billed: Boolean
costCenter: String
billedBy: String
custodianInformation: String
accessLevel: String
## Custom fields
initialPipelineRunDate: String
embargoDate: String
## (t:Tempo)-[:HAS_EVENT]->(bc:BamComplete)
bamCompleteDate: String
bamCompleteStatus: String
## (t:Tempo)-[:HAS_EVENT]->(mc:MafComplete)
mafCompleteDate: String
mafCompleteNormalPrimaryId: String
mafCompleteStatus: String
# (t:Tempo)-[:HAS_EVENT]->(qc:QcComplete)
qcCompleteDate: String
qcCompleteResult: String
qcCompleteReason: String
qcCompleteStatus: String
# (s:Sample)<-[:HAS_COHORT_SAMPLE]-(c:Cohort)
sampleCohortIds: String
# (s:Sample)-[:HAS_DBGAP]->(d:DbGap)
dbGapStudy: String
irbConsentProtocol: String
# (r:Request)-[:HAS_SAMPLE]->(s:Sample)
igoDeliveryDate: String
# (s:Sample)<-[:HAS_SAMPLE]-(p:Patient)<-[:IS_ALIAS]-(pa:PatientAlias)
## Custom fields
dmpPatientAlias: String
# Databricks
sequencingDate: String
molecularAccessionNumber: String
race: String
# results total
_total: Int
`;
const QUERY_RESULT_TYPEDEFS = gql`
type DashboardRequest {
igoRequestId: String!
igoProjectId: String
ilabRequestId: String
igoDeliveryDate: String
validationReport: String
validationStatus: Boolean
importDate: String
totalSampleCount: Int
projectManagerName: String
investigatorName: String
investigatorEmail: String
piEmail: String
dataAnalystName: String
dataAnalystEmail: String
genePanel: String
labHeadName: String
labHeadEmail: String
qcAccessEmails: String
dataAccessEmails: String
bicAnalysis: Boolean
isCmoRequest: Boolean
otherContactEmails: String
_total: Int
toleratedSampleErrors: [ToleratedSampleValidationError]
}
type ToleratedSampleValidationError {
primaryId: String!
validationStatus: Boolean
validationReport: String
}
type DashboardPatient {
smilePatientId: String!
cmoPatientId: String
dmpPatientId: String
totalSampleCount: Int
cmoSampleIds: String
consentPartA: String
consentPartC: String
inDbGap: Boolean
mrn: String
anchorSequencingDate: String
anchorOncotreeCode: String
race: String
_total: Int
}
type DashboardCohort {
cohortId: String!
totalSampleCount: Int
billed: String
initialCohortDeliveryDate: String
importDate: String
endUsers: String
pmUsers: String
projectTitle: String
projectSubtitle: String
status: String
type: String
pipelineVersion: String
searchableSampleIds: String
_total: Int
_uniqueSampleCount: Int
}
type DashboardSample {
${SAMPLE_FIELDS}
}
type PatientIdsTriplet {
CMO_PATIENT_ID: String!
DMP_PATIENT_ID: String
MRN: String!
RACE: String
}
type AnchorSeqDateData {
MRN: String!
DMP_PATIENT_ID: String!
ANCHOR_SEQUENCING_DATE: String!
ANCHOR_ONCOTREE_CODE: String!
}
type SeqDateAccessionBySampleId {
DMP_SAMPLE_ID: String!
SEQUENCING_DATE: String!
MOLECULAR_ACCESSION_NUMBER: String
}
type TempoCohortSample {
primaryId: String!
cmoId: String
embargoDate: String
}
type TempoCohortRequest {
cohortId: String!
projectTitle: String!
projectSubtitle: String!
endUsers: String!
pmUsers: String!
type: String!
samples: [TempoCohortSample!]!
}
`;
const QUERY_TYPEDEFS = gql`
type Query {
dashboardRequests(
searchVals: [String!]
columnFilters: [DashboardRecordColumnFilter!]
sort: DashboardRecordSort!
limit: Int!
offset: Int!
): [DashboardRequest!]!
dashboardPatients(
searchVals: [String!]
columnFilters: [DashboardRecordColumnFilter!]
sort: DashboardRecordSort!
limit: Int!
offset: Int!
phiEnabled: Boolean
): [DashboardPatient!]!
dashboardCohorts(
searchVals: [String!]
columnFilters: [DashboardRecordColumnFilter!]
sort: DashboardRecordSort!
limit: Int!
offset: Int!
): [DashboardCohort!]!
dashboardSamples(
searchVals: [String!]
recordContexts: [DashboardRecordContext]
columnFilters: [DashboardRecordColumnFilter!]
sort: DashboardRecordSort!
limit: Int!
offset: Int!
phiEnabled: Boolean
includeDemographics: Boolean!
): [DashboardSample!]!
allAnchorSeqDateData(phiEnabled: Boolean): [AnchorSeqDateData!]!
allBlockedCohortIds: [String!]!
}
`;
// We have to define a separate "input" type for the mutation and can't reuse DashboardSample.
// For more context, see: https://stackoverflow.com/q/41743253
const MUTATION_TYPEDEFS = gql`
input DashboardSampleInput {
changedFieldNames: [String!]!
${SAMPLE_FIELDS}
}
input DashboardCohortInput {
changedFieldNames: [String!]!
cohortId: String!
totalSampleCount: Int
billed: String
initialCohortDeliveryDate: String
importDate: String
endUsers: String
pmUsers: String
projectTitle: String
projectSubtitle: String
status: String
type: String
pipelineVersion: String
searchableSampleIds: String
_total: Int
_uniqueSampleCount: Int
}
input TempoCohortSampleInput {
primaryId: String!
cmoId: String
embargoDate: String
}
input TempoCohortRequestInput {
cohortId: String!
projectTitle: String!
projectSubtitle: String!
endUsers: [String!]!
pmUsers: [String!]!
type: String!
samples: [TempoCohortSampleInput!]!
}
type Mutation {
updateDashboardSamples(
newDashboardSamples: [DashboardSampleInput]
): [DashboardSample]
updateTempoCohort(
dashboardCohort: DashboardCohortInput
): DashboardCohort
publishNewTempoCohortRequest(
tempoCohortRequest: TempoCohortRequestInput
): TempoCohortRequest
}
`;
export const typeDefs = [
GENERIC_TYPEDEFS,
QUERY_RESULT_TYPEDEFS,
QUERY_TYPEDEFS,
MUTATION_TYPEDEFS,
];