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bwHealthCloud Backend REST API

1. Preliminaries:

1.1 MTBFile Model:

See the "shared spreadsheet" of MTB File parameters and their currently defined multiplicities and JSON representation.

1.2 Hypermedia

The bwHC backend includes experimental usage of Hypermedia to be truly RESTful, i.e. to allow easier discoverability and usage of API functions. The used representation for hypermedia content is essentially Hypertext Application Language (HAL) with custom extensions inspired from SIREN and CPHL to allow specifying actions on resources in addition to just links/relations.

The backend has a "hypermedia API entry point":

GET http://HOST:PORT/bwhc

from where hypermedia links to the various accessible sub-APIs can be followed:

{
  "_actions": {                            // Possible Actions:
    "logout": {                            // Logout
        "method": "POST",                  // HTTP Method
        "href": "/bwhc/user/api/logout"    // URI (relative)
    },
    ...
  },
  "_links": {
    "catalogs-api": {                     
        "href": "/bwhc/catalogs/api/"      // URI (relative) to Catalogs API
    },
    ...
    "etl-api": {
        "href": "/bwhc/etl/api/"           // URI (relative) to ETL API
    }
  }
}

For instance, following the link to the "etl-api"

GET http://HOST:PORT/bwhc/etl/api/

returns a description of Links/Actions available for this sub-API:

{
  "_actions": {
    "upload-mtbfile": {                                    // Action: Upload MTBFile
      "method": "POST"                                     // HTTP Method
      "href": "/bwhc/etl/api/MTBFile",                     // URI (relative)

      "formats": {                                         // Format specifications of request payloads for the Action
        "application/json": {
          "href": "/bwhc/etl/api/schema/upload-mtbfile"    // Link to JSON Schema specification for Content-Type 'application/json'
        }
      },
    },
    ...
    "delete-patient": {                                    // Action: Delete a Patient's data
      "method": "DELETE",
      "href": "/bwhc/etl/api/Patient/{id}"
    },
  },
  "_links": {
    ...
  }
}

2. Synthetic Data Examples API

Request a random-generated MTBFile JSON example

GET http://HOST:PORT/bwhc/fake/data/api/MTBFile

3 ETL API (Data upload and deletion)

IMPORTANT: This sub-API is not secured via a user login mechanism. Access to this URL path SHOULD be restricted in the reverse proxy.

3.1 Upload MTBFile

POST http://HOST:PORT/bwhc/etl/api/MTBFile

POST http://HOST:PORT/bwhc/etl/api/data/upload

Supported formats (HTTP Header "Content-type"):

  • application/json
  • application/fhir+json (experimental)

Response:

Case Status Code [and response payload]
Invalid JSON 400 Bad Request with list of syntax errors
Fatal data quality issues 422 Unprocessable Entity with DataQualityReport
Non-fatal Data quality issues 201 Created
No data quality issues 200 Ok

3.2 Delete a Patient's data

DELETE http://HOST:PORT/bwhc/etl/api/Patient/{PatientID}

DELETE http://HOST:PORT/bwhc/etl/api/MTBFile/{PatientID}

4. Data Quality Feedback API

4.1 Get Patients with Data Quality Issue reports

GET http://HOST:PORT/bwhc/mtb/api/data/Patient

4.2 Get a Patient's MTBFile

GET http://HOST:PORT/bwhc/mtb/api/data/MTBFile/{PatientID}

4.3 Get DataQualityReport for a given Patient's MTBFile

GET http://HOST:PORT/bwhc/mtb/api/data/DataQualityReport/{PatientID}

4.4 Delete a Patient's data

DELETE http://HOST:PORT/bwhc/mtb/api/data/Patient/{PatientID}

5. ZPM-QC-Reporting / Query API

5.1 Reporting

5.1.1 Get LocalQCReport (from local ZPM site)

GET http://HOST:PORT/bwhc/mtb/api/reporting/QCReport?scope=local

GET http://HOST:PORT/bwhc/mtb/api/reporting/LocalQCReport

5.1.2 Get GlobalQCReport (combined LocalQCReport of all ZPM sites)

GET http://HOST:PORT/bwhc/mtb/api/reporting/QCReport?scope=global

GET http://HOST:PORT/bwhc/mtb/api/reporting/GlobalQCReport

5.2 Evidence Querying API

5.2.1 Query Submission

POST http://HOST:PORT/bwhc/mtb/api/query

{
  "mode": {
      "code": "local",                  // Values: "local", "federated"
  },
  "parameters": {
      "diagnoses": [
          {
              "code": "C25.1",
          }
      ],
      "medicationsWithUsage": [
          {
              "medication": {
                  "code": "L01XX59",   // ATC code
              },
              "usage": {
                  "code": "used",      // Values: "used", "recommended"
              }
          }
      ],
      "mutatedGenes": [
          {
              "code": "HGNC:22",       // HGNC ID
          }
      ],
      "responses": [
          {
              "code": "SD",            // RECIST code 
          }
      ]
  }
}

Response: Created Query Object

{
    "id": "6033bc57-1ec5-4c32-a1e5-cf97355ee950",
    "querier": "082e1d9e-9d94-43a5-8a9f-1aed7118f6e8",
    "submittedAt": "2021-12-14T08:28:31.695372Z",
    "lastUpdate": "2021-12-14T08:28:31.695389Z",
    "mode": {
        "code": "local",
        "display": "Lokal",
        "system": "Query-Mode"
    },
    "parameters": {
        "diagnoses": [
            {
                "code": "C25.1",
                "display": "Bösartige Neubildung: Pankreaskörper",
                "system": "ICD-10-GM",
                "version": "2022"
            }
        ],
        "medicationsWithUsage": [
            {
                "medication": {
                    "code": "L01XX59",
                    "display": "Enasidenib",
                    "system": "ATC",
                    "version": "2021"
                },
                "usage": {
                    "code": "used",
                    "system": "Drug-Usage"
                }
            }
        ],
        "mutatedGenes": [
            {
                "code": "HGNC:22",
                "display": "adeno-associated virus integration site 1",
                "system": "HGNC"
            }
        ],
        "responses": [
            {
                "code": "SD",
                "display": "Stable Disease",
                "system": "RECIST"
            }
        ]
    },
    "filter": {
        "ageRange": {
            "l": 0,
            "r": 0
        },
        "genders": [],
        "vitalStatus": []
    },
    "zpms": []
    "_links": {
        "base": {
            "href": "/bwhc/mtb/api/query/"
        },
        "molecular-therapies": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/molecular-therapies"
        },
        "ngs-summaries": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/ngs-summaries"
        },
        "patients": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/patients"
        },
        "result-summary": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/result-summary"
        },
        "self": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950"
        },
        "therapy-recommendations": {
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/therapy-recommendations"
        }
    },
    "_actions": {
        "apply-filter": {
            "formats": {
                "application/json": {
                    "href": "/bwhc/mtb/api/query/schema/apply-filter"
                }
            },
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950/filter",
            "method": "POST"
        },
        "update": {
            "formats": {
                "application/json": {
                    "href": "/bwhc/mtb/api/query/schema/update"
                }
            },
            "href": "/bwhc/mtb/api/query/6033bc57-1ec5-4c32-a1e5-cf97355ee950",
            "method": "POST"
        }
    },
}

5.2.2 Get Query Object by ID

GET http://HOST:PORT/bwhc/mtb/api/query/{QueryID}

5.2.3 Update Query

POST http://HOST:PORT/bwhc/mtb/api/query/QUERY_ID

{
  "id": "6033bc57-1ec5-4c32-a1e5-cf97355ee950",
  "mode": {
      "code": .... 
  },
  "parameters": {
    ...
  }
}

5.2.4 Access to contents from Query ResultSet

See hypermedia links in example above

6 Catalogs and ValueSet API

6.1 Coding Systems (Catalogs)

GET http://HOST:PORT/bwhc/catalogs/api/Coding/SYSTEM[?pattern=CHARS][?version=VERSION]

GET http://HOST:PORT/bwhc/catalogs/api/Coding?system=SYSTEM[&pattern=CHARS][?version=VERSION]

SYSTEM must be any of:

System Name
ICD-10-GM
ICD-O-3-T
ICD-O-3-M
HGNC
ATC

Optional Parameter "pattern" filters for codings whose display label contains CHARS

Optional Parameter "version" indicated requested catalog version (only different ICD-10-GM versions a.t.m)

6.2 ValueSets

GET http://HOST:PORT/bwhc/catalogs/api/ValueSet

6.2.1 Fetch a given ValueSet NAME

GET http://HOST:PORT/bwhc/catalogs/api/ValueSet/NAME

GET http://HOST:PORT/bwhc/catalogs/api/ValueSet?name=NAME

ValueSet Names
Geschlecht
DiagnoseStadium
Verwandtschaftsgrad
TherapieLinie
LeitlinienTherapie-Abbruchsgrund
RECIST
ECOGPerformanceStatus
WHOGradingOfCNSTumors
LevelOfEvidence-Graduierung
LevelOfEvidence-Zusatzverweise
Proben-Art
Proben-Lokalisierung
Proben-Entnahmemethode
Kostenübernahme-Status
Kostenübernahme-Ablehnungsgrund
MolekularTherapie-Status
MolekularTherapie-Nichtumsetzungsgrund
MolekularTherapie-Abbruchsgrund