schema.graphql

input AnatomyInput {
  id: [String!] = null
  name: [String!] = null
  description: [String!] = null
}

type AnatomyType {
  id: String!
  name: String!
  description: String
}

input AssayTypeInput {
  id: [String!] = null
  name: [String!] = null
  description: [String!] = null
}

type AssayTypeType {
  id: String!
  name: String!
  description: String
}

input BiosampleInput {
  idNamespace: [String!] = null
  localId: [String!] = null
  projectIdNamespace: [String!] = null
  projectLocalId: [String!] = null
  persistentId: [String!] = null
  creationTime: [String!] = null
  samplePrepMethod: [String!] = null
  anatomy: [AnatomyInput!] = null
  biofluid: [String!] = null
  subjects: [SubjectInput!] = null
  extra: [EnrichedBiosampleInput!] = null
}

type BiosampleType {
  idNamespace: String!
  localId: String!
  projectIdNamespace: String!
  projectLocalId: String!
  persistentId: String
  creationTime: String
  samplePrepMethod: String
  anatomy: AnatomyType
  biofluid: String
  subjects: [SubjectType!]!
  extra: EnrichedBiosampleType
}

input CollectionInput {
  biosamples: [BiosampleInput!] = null
  idNamespace: [String!] = null
  localId: [String!] = null
  persistentId: [String!] = null
  creationTime: [String!] = null
  abbreviation: [String!] = null
  name: [String!] = null
  description: [String!] = null
  lab: [String!] = null
  experimentType: [String!] = null
  experimentTarget: [String!] = null
  analyteClass: [String!] = null
  anatomy: [AnatomyInput!] = null
  subjects: [SubjectInput!] = null
  extra: [EnrichedCollectionInput!] = null
}

type CollectionType {
  biosamples: [BiosampleType!]!
  idNamespace: String!
  localId: String!
  persistentId: String
  creationTime: String
  abbreviation: String
  name: String!
  description: String
  lab: String
  experimentType: String
  experimentTarget: String
  analyteClass: String
  anatomy: [AnatomyType!]!
  subjects: [SubjectType!]!
  extra: EnrichedCollectionType
}

input DataTypeInput {
  id: [String!] = null
  name: [String!] = null
  description: [String!] = null
}

type DataTypeType {
  id: String!
  name: String!
  description: String
}

input DccInput {
  id: [String!] = null
  dccName: [String!] = null
  dccAbbreviation: [String!] = null
  dccDescription: [String!] = null
  contactEmail: [String!] = null
  contactName: [String!] = null
  dccUrl: [String!] = null
  projectIdNamespace: [String!] = null
  projectLocalId: [String!] = null
}

type DccType {
  id: String!
  dccName: String!
  dccAbbreviation: String!
  dccDescription: String
  contactEmail: String!
  contactName: String!
  dccUrl: String!
  projectIdNamespace: String!
  projectLocalId: String!
}

type DistinctFieldType {
  field: String!
  values: JSON!
}

input EnrichedBiosampleInput {
  encode: [EnrichedEncodeBiosampleInput!] = null
}

type EnrichedBiosampleType {
  encode: EnrichedEncodeBiosampleType
}

input EnrichedCollectionInput {
  fourdn: [EnrichedFourdnCollectionInput!] = null
  encode: [EnrichedEncodeCollectionInput!] = null
  hubmap: [EnrichedHubmapCollectionInput!] = null
}

type EnrichedCollectionType {
  fourdn: EnrichedFourdnCollectionType
  hubmap: EnrichedHubmapCollectionType
  encode: EnrichedEncodeCollectionType
}

input EnrichedEncodeBiosampleInput {
  biosampleType: [String!] = null
  biosampleTreatments: [String!] = null
  biosampleTreatmentsAmount: [String!] = null
  biosampleTreatmentsDuration: [String!] = null
  biosampleGeneticModifications: [String!] = null
  libraryMadeFrom: [String!] = null
  libraryDepletedIn: [String!] = null
  libraryExtractionMethod: [String!] = null
  libraryLysisMethod: [String!] = null
  libraryCrosslinkingMethod: [String!] = null
  libraryStrandSpecific: [String!] = null
  libraryFragmentationMethod: [String!] = null
  librarySizeRange: [String!] = null
}

type EnrichedEncodeBiosampleType {
  biosampleType: String
  biosampleTreatments: String
  biosampleTreatmentsAmount: String
  biosampleTreatmentsDuration: String
  biosampleGeneticModifications: String
  libraryMadeFrom: String
  libraryDepletedIn: String
  libraryExtractionMethod: String
  libraryLysisMethod: String
  libraryCrosslinkingMethod: String
  libraryStrandSpecific: String
  libraryFragmentationMethod: String
  librarySizeRange: String
}

input EnrichedEncodeCollectionInput {
  experimentTarget: [String!] = null
  project: [String!] = null
  platform: [String!] = null
  dbxrefs: [String!] = null
  rbnsProteinConcentration: [String!] = null
}

type EnrichedEncodeCollectionType {
  project: String
  platform: String
  dbxrefs: String
  rbnsProteinConcentration: String
}

input EnrichedEncodeFileInput {
  assembly: [String!] = null
  fileFormatType: [String!] = null
  outputType: [String!] = null
  genomeAnnotation: [String!] = null
  controlledBy: [String!] = null
  s3Uri: [String!] = null
  azureUrl: [String!] = null
  fileAnalysisTitle: [String!] = null
  fileAnalysisStatus: [String!] = null
  readLength: [String!] = null
  mappedReadLength: [String!] = null
  runType: [String!] = null
  pairedEnd: [String!] = null
  pairedWith: [String!] = null
  indexOf: [String!] = null
  derivedFrom: [String!] = null
  auditWarning: [String!] = null
  auditNotCompliant: [String!] = null
  auditError: [String!] = null
}

type EnrichedEncodeFileType {
  assembly: String
  fileFormatType: String
  outputType: String
  genomeAnnotation: String
  controlledBy: String
  s3Uri: String
  azureUrl: String
  fileAnalysisTitle: String
  fileAnalysisStatus: String
  biologicalReplicates: String
  technicalReplicates: String
  readLength: String
  mappedReadLength: String
  runType: String
  pairedEnd: String
  pairedWith: String
  indexOf: String
  derivedFrom: String
  auditWarning: String
  auditNotCompliant: String
  auditError: String
}

input EnrichedFileInput {
  fourdn: [EnrichedFourdnFileInput!] = null
  encode: [EnrichedEncodeFileInput!] = null
  hubmap: [EnrichedHubmapFileInput!] = null
}

type EnrichedFileType {
  fourdn: EnrichedFourdnFileType
  encode: EnrichedEncodeFileType
  hubmap: EnrichedHubmapFileType
}

input EnrichedFourdnCollectionInput {
  displayTitle: [String!] = null
  targetedFactor: [String!] = null
  digestionEnzyme: [String!] = null
  crosslinkingMethod: [String!] = null
  crosslinkingTemperature: [String!] = null
  crosslinkingTime: [String!] = null
  ligationTemperature: [String!] = null
  ligationVolume: [String!] = null
  ligationTime: [String!] = null
  digestionTemperature: [String!] = null
  digestionTime: [String!] = null
  taggingMethod: [String!] = null
  fragmentationMethod: [String!] = null
  biotinRemoved: [String!] = null
  libraryPrepKit: [String!] = null
  averageFragmentSize: [String!] = null
  fragmentSizeRange: [String!] = null
  status: [String!] = null
  dateCreated: [String!] = null
}

type EnrichedFourdnCollectionType {
  displayTitle: String
  targetedFactor: [String!]
  digestionEnzyme: String
  crosslinkingMethod: String
  crosslinkingTemperature: String
  crosslinkingTime: String
  ligationTemperature: String
  ligationVolume: String
  ligationTime: String
  digestionTemperature: String
  digestionTime: String
  taggingMethod: String
  fragmentationMethod: String
  biotinRemoved: String
  libraryPrepKit: String
  averageFragmentSize: String
  fragmentSizeRange: String
  status: String
  dateCreated: String
}

input EnrichedFourdnFileInput {
  enrichedFileFormat: [String!] = null
  genomeAssembly: [String!] = null
  fileType: [String!] = null
  fileTypeDetailed: [String!] = null
  condition: [String!] = null
  biosourceName: [String!] = null
  dataset: [String!] = null
  replicateInfo: [String!] = null
  cellLineTier: [String!] = null
}

type EnrichedFourdnFileType {
  enrichedFileFormat: String
  genomeAssembly: String
  fileType: String
  fileTypeDetailed: String
  condition: String
  biosourceName: String
  dataset: String
  replicateInfo: String
  cellLineTier: String
  extraFiles: [ExtraFileType!]
}

input EnrichedHubmapCollectionInput {
  datasetType: [String!] = null
  pipeline: [String!] = null
  processing: [String!] = null
  groupName: [String!] = null
  analyteClass: [String!] = null
  visualization: [Boolean!] = null
}

type EnrichedHubmapCollectionType {
  pipeline: String
  processing: String
  groupName: String
  visualization: Boolean
  vitessceHints: [String!]
  metadata: JSON
}

input EnrichedHubmapFileInput {
  genomeAssembly: [String!] = null
  relPath: [String!] = null
  isDataProduct: [Boolean!] = null
}

type EnrichedHubmapFileType {
  genomeAssembly: String
  relPath: String
  isDataProduct: Boolean
}

type EnrichedHubmapSubjectType {
  ageValue: Float
  ageUnit: String
  sex: String
  race: String
  bodyMassIndexValue: Float
  bodyMassIndexUnit: String
  causeOfDeath: String
  deathEvent: String
  mechanismOfInjury: String
  medicalHistory: [String!]
  socialHistory: [String!]
  heightValue: Float
  heightUnit: String
  weightValue: Float
  weightUnit: String
}

type EnrichedSubjectType {
  hubmap: EnrichedHubmapSubjectType
}

type ExtraFileType {
  href: String
  md5sum: String
  fileSize: Int
  fileFormat: String
}

input FileFormatInput {
  id: [String!] = null
  name: [String!] = null
  description: [String!] = null
}

type FileFormatType {
  id: String!
  name: String!
  description: String
}

input FileMetadataInput {
  dcc: [DccInput!] = null
  collections: [CollectionInput!] = null
  project: [ProjectInput!] = null
  idNamespace: [String!] = null
  localId: [String!] = null
  projectIdNamespace: [String!] = null
  projectLocalId: [String!] = null
  persistentId: [String!] = null
  creationTime: [String!] = null
  sizeInBytes: [Int!] = null
  sha256: [String!] = null
  md5: [String!] = null
  filename: [String!] = null
  fileFormat: [FileFormatInput!] = null
  compressionFormat: [String!] = null
  dataType: [DataTypeInput!] = null
  assayType: [AssayTypeInput!] = null
  analysisType: [String!] = null
  mimeType: [String!] = null
  bundleCollectionIdNamespace: [String!] = null
  bundleCollectionLocalId: [String!] = null
  dbgapStudyId: [String!] = null
  accessUrl: [String!] = null
  dataAccessLevel: [String!] = null
  genomeAssembly: [String!] = null
  genomeAnnotation: [String!] = null
  outputType: [String!] = null
  outputTypeDetail: [String!] = null
  biologicalReplicates: [String!] = null
  technicalReplicates: [String!] = null
  assayInfo: [String!] = null
  condition: [String!] = null
  extra: [EnrichedFileInput!] = null
}

type FileMetadataType {
  dcc: DccType!
  collections: [CollectionType!]!
  project: ProjectType
  idNamespace: String!
  localId: String!
  projectIdNamespace: String!
  projectLocalId: String!
  persistentId: String
  creationTime: String
  sizeInBytes: Int
  sha256: String
  md5: String
  filename: String!
  fileFormat: FileFormatType
  compressionFormat: String
  dataType: DataTypeType
  assayType: AssayTypeType
  analysisType: String
  mimeType: String
  bundleCollectionIdNamespace: String
  bundleCollectionLocalId: String
  dbgapStudyId: String
  accessUrl: String
  status: String
  dataAccessLevel: String
  genomeAssembly: String
  genomeAnnotation: String
  outputType: String
  outputTypeDetail: String
  biologicalReplicates: String
  technicalReplicates: String
  assayInfo: String
  condition: String
  extra: EnrichedFileType
}

"""
The `JSON` scalar type represents JSON values as specified by [ECMA-404](https://ecma-international.org/wp-content/uploads/ECMA-404_2nd_edition_december_2017.pdf).
"""
scalar JSON @specifiedBy(url: "https://ecma-international.org/wp-content/uploads/ECMA-404_2nd_edition_december_2017.pdf")

input NcbiTaxonomyInput {
  id: [String!] = null
  name: [String!] = null
  clade: [String!] = null
}

type NcbiTaxonomyType {
  id: String!
  name: String!
  clade: String
  description: String
}

scalar ObjectIdScalar

input ProjectInput {
  idNamespace: [String!] = null
  localId: [String!] = null
  name: [String!] = null
  abbreviation: [String!] = null
  description: [String!] = null
}

type ProjectType {
  idNamespace: String!
  localId: String!
  name: String!
  abbreviation: String
  description: String
  persistentId: String
}

type Query {
  files(input: [FileMetadataInput!] = null, page: Int! = 0, pageSize: Int! = 25): [FileMetadataType!]!
  file(id: ObjectIdScalar!): FileMetadataType
  distinctValues(fields: [String!]!, input: [FileMetadataInput!] = null): [DistinctFieldType!]!
}

input SubjectInput {
  idNamespace: [String!] = null
  localId: [String!] = null
  projectIdNamespace: [String!] = null
  projectLocalId: [String!] = null
  persistentId: [String!] = null
  creationTime: [String!] = null
  granularity: [String!] = null
  sex: [String!] = null
  ethnicity: [String!] = null
  ageAtEnrollment: [Float!] = null
  ageAtSampling: [Float!] = null
  race: [String!] = null
  taxonomy: [NcbiTaxonomyInput!] = null
}

type SubjectType {
  idNamespace: String!
  localId: String!
  projectIdNamespace: String!
  projectLocalId: String!
  persistentId: String
  creationTime: String
  granularity: String
  sex: String
  ethnicity: String
  ageAtEnrollment: Float
  ageAtSampling: Float
  race: [String!]!
  taxonomy: NcbiTaxonomyType
  extra: EnrichedSubjectType
}