{
  "index_patterns": ["overture-*"],
  "aliases": {
    "file_centric": {}
  },
  "mappings": {
    "properties": {
      "object_id": { "type": "keyword", "copy_to": ["file_autocomplete"] },
      "study_id": { "type": "keyword" },
      "data_type": { "type": "keyword" },
      "file_type": { "type": "keyword" },
      "file_access": { "type": "keyword" },
      "file_autocomplete": {
				"type": "keyword",
				"fields": {
					"analyzed": {
						"type": "text",
						"analyzer": "autocomplete_analyzed",
						"search_analyzer": "lowercase_keyword"
					},
					"lowercase": {
						"type": "text",
						"analyzer": "lowercase_keyword"
					},
					"prefix": {
						"type": "text",
						"analyzer": "autocomplete_prefix",
						"search_analyzer": "lowercase_keyword"
					}
				}
			},
      "analysis": {
        "properties": {
          "analysis_id": { "type": "keyword" },
          "analysis_type": { "type": "keyword" },
          "analysis_version": { "type": "integer" },
          "analysis_state": { "type": "keyword" },
          "updated_at": { "type": "date" },
          "first_published_at": { "type": "date" },
          "published_at": { "type": "date" },
          "experiment": {
            "properties": {
              "experimentalStrategy": { "type": "keyword" },
              "model": { "type": "keyword" },
              "platform": { "type": "keyword" },
              "sequencingCenter": { "type": "keyword" },
              "sequencingDate": { "type": "date" }
            }
          },
          "analysisStateHistory": {
            "type": "nested",
            "properties": {
              "initialState": { "type": "keyword" },
              "updatedState": { "type": "keyword" },
              "updatedAt": { "type": "date" }
            }
          },
          "collaborator": {
            "type": "nested",
            "properties": {
              "contactEmail": { "type": "keyword" },
              "name": { "type": "keyword" }
            }
          },
          "createdAt": { "type": "date" },
          "donor": {
            "properties": {
              "causeOfDeath": { "type": "keyword" },
              "primaryDiagnosis": {
                "type": "nested",
                "properties": {
                  "ageAtDiagnosis": { "type": "integer" },
                  "cancerTypeCode": { "type": "keyword" },
                  "clinicalStageGroup": { "type": "keyword" },
                  "clinicalTumourStagingSystem": { "type": "keyword" },
                  "followUp": {
                    "type": "nested",
                    "properties": {
                      "diseaseStatusAtFollowUp": { "type": "keyword" },
                      "intervalOfFollowUp": { "type": "integer" },
                      "relapseType": { "type": "keyword" },
                      "submitterFollowUpId": { "type": "keyword" },
                      "submitterTreatmentId": { "type": "keyword" }
                    }
                  },
                  "submitterPrimaryDiagnosisId": { "type": "keyword" },
                  "treatment": {
                    "type": "nested",
                    "properties": {
                      "chemotherapy": {
                        "type": "nested",
                        "properties": {
                          "drugName": { "type": "keyword" }
                        }
                      },
                      "responseToTreatment": { "type": "keyword" },
                      "submitterTreatmentId": { "type": "keyword" },
                      "treatmentDuration": { "type": "integer" },
                      "treatmentStartInterval": { "type": "integer" },
                      "treatmentType": { "type": "keyword" }
                    }
                  }
                }
              },
              "primarySite": { "type": "keyword" },
              "submitterDonorId": { "type": "keyword" },
              "survivalTime": { "type": "integer" },
              "vitalStatus": { "type": "keyword" }
            }
          },
          "publication": {
            "properties": {
              "doi": { "type": "keyword" },
              "publication": { "type": "keyword" }
            }
          },
          "specimen": {
            "properties": {
              "specimenAnatomicLocation": { "type": "keyword" },
              "submitterPrimaryDiagnosisId": { "type": "keyword" },
              "submitterSpecimenId": { "type": "keyword" },
              "tumourGrade": { "type": "keyword" },
              "tumourGradingSystem": { "type": "keyword" }
            }
          },
          "workflow": {
            "properties": {
              "genomeBuild": { "type": "keyword" },
              "inputs": {
                "type": "nested",
                "properties": {
                  "analysisType": { "type": "keyword" },
                  "normalAnalysisId": { "type": "keyword" },
                  "tumourAnalysisId": { "type": "keyword" }
                }
              },
              "runId": { "type": "keyword" },
              "sessionId": { "type": "keyword" },
              "workflowName": { "type": "keyword" },
              "workflowShortName": { "type": "keyword" },
              "workflowVersion": { "type": "keyword" }
            }
          }
        }
      },
      "file": {
        "properties": {
          "name": { "type": "keyword" },
          "md5sum": { "type": "keyword" },
          "size": { "type": "integer" },
          "data_type": { "type": "keyword" },
          "index_file": {
            "properties": {
              "object_id": { "type": "keyword" },
              "name": { "type": "keyword" },
              "file_type": { "type": "keyword" },
              "md5sum": { "type": "keyword" },
              "data_type": { "type": "keyword" },
              "size": { "type": "integer" },
              "dataCategory": { "type": "keyword" },
              "jbrowseCoordinates": { "type": "keyword" }
            }
          },
          "dataCategory": { "type": "keyword" },
          "jbrowseCoordinates": { "type": "keyword" }
        }
      },
      "repositories": {
        "type": "nested",
        "properties": {
          "code": { "type": "keyword" },
          "organization": { "type": "keyword" },
          "name": { "type": "keyword" },
          "type": { "type": "keyword" },
          "country": { "type": "keyword" },
          "url": { "type": "keyword" }
        }
      },
      "donors": {
        "type": "nested",
        "properties": {
          "donor_id": { "type": "keyword" },
          "submitter_donor_id": { "type": "keyword" },
          "gender": { "type": "keyword" },
          "specimens": {
            "type": "nested",
            "properties": {
              "specimen_id": { "type": "keyword" },
              "specimen_type": { "type": "keyword" },
              "submitter_specimen_id": { "type": "keyword" },
              "samples": {
                "type": "nested",
                "properties": {
                  "sample_id": { "type": "keyword" },
                  "submitter_sample_id": { "type": "keyword" },
                  "sample_type": { "type": "keyword" },
                  "matched_normal_submitter_sample_id": { "type": "keyword" }
                }
              },
              "tumour_normal_designation": { "type": "keyword" },
              "specimen_tissue_source": { "type": "keyword" }
            }
          }
        }
      },
      "dataCategory": { "type": "keyword" },
      "jbrowseCoordinates": { "type": "keyword" }
    }
  },
  "settings": {
    "analysis": {
      "analyzer": {
        "autocomplete_analyzed": {
          "filter": ["lowercase", "edge_ngram"],
          "tokenizer": "standard"
        },
        "autocomplete_prefix": {
          "filter": ["lowercase", "edge_ngram"],
          "tokenizer": "keyword"
        },
        "lowercase_keyword": {
          "filter": ["lowercase"],
          "tokenizer": "keyword"
        }
      },
      "filter": {
        "edge_ngram": {
          "max_gram": "20",
          "min_gram": "1",
          "side": "front",
          "type": "edge_ngram"
        }
      }
    },
    "index.max_result_window": 300000,
    "index.number_of_shards": 3
  }
}