Merge pull request #257 from jembi/TB-181-add-mapping-for-cr-candidates

Tb 181 add mapping for probabilistic patient matching

Author: bradsawadye

client-registry-jempi/README.md

@@ -46,6 +46,8 @@ via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (i
 
 POST http://localhost:3003/fhir/Patient
 
+The `candidateThreshold` can optionally be set in the request query. The default value is 0.9
+
 {
     "resourceType": "Patient",
     "gender": "male",
@@ -122,7 +124,7 @@ PATCH - http://localhost:50000/JeMPI/cr-update-fields
 via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
 
 ```sh
-PUT - http://localhost:3003/fhir/update/Patient/<PATIENT_GOLDEN_RECORD>
+PUT - http://localhost:3003/fhir/Patient/<PATIENT_GOLDEN_RECORD>
 
 {
     "resourceType": "Patient",
@@ -189,20 +191,83 @@ POST http://localhost:50000/JeMPI/cr-find
 via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
 
 ```sh
-POST http://localhost:3003/fhir/Patients
+GET http://localhost:3003/fhir/Patient
+
+Query parameters - family, given, telecom, identifier, gender, birthDate, address (city)
+```
+
+## Query patients probabilistic
+
+via the api (in JeMPI format)
+
+```sh
+POST - http://localhost:50000/JeMPI/cr-find
+
+{
+  "operand": {
+    "fn": "match",
+    "name": "givenName",
+    "value": "drake",
+    "distance": 2
+  },
+  "operands": [
+    {
+      "operator": "and",
+      "operand": {
+        "fn": "match",
+        "name": "familyName",
+        "value": "brake",
+        "distance": 2
+      }
+    }
+  ]
+}
+```
+
+via the [mapping mediator](https://github.com/jembi/openhim-mediator-mapping) (in fhir format)
+
+```sh
+
+POST http://localhost:3003/fhir/Patient/$match
 
 {
     "resourceType": "Parameters",
-    "parameters": [
+    "parameter": [
         {
-            "name": "and",                              // matches to the operator (options are "and" and "or")
-            "valueCode": "familyName",                  // matches to the field name (options are "givenName", "familyName", "dob", "nationalId", "gender", "city" and "phoneNumber")
-            "valueString": "creexxxeead"                // matches to value of the field
+            "name": "givenName",
+            "valueString": "drake",
+            "part": [
+                {
+                    "name": "operator",
+                    "valueString": "and"
+                },
+                {
+                    "name": "fn",
+                    "valueString": "match"
+                },
+                {
+                    "name": "distance",
+                    "valueInteger": 2
+                }
+            ]
         },
         {
-            "name": "and",
-            "valueCode": "city",
-            "valueString": "Indianapeeolis"
+            "name": "familyName",
+            "valueString": "brake",
+            "part": [
+                {
+                    "name": "operator",
+                    "valueString": "and"
+                },
+                {
+                    "name": "fn",
+                    "valueString": "match"
+                },
+                {
+                    "name": "distance",
+                    "valueInteger": 2
+                }
+            ]
         }
     ]
 }

client-registry-jempi/importer/mapping-mediator/docker-compose.config.yml

@@ -23,6 +23,10 @@ services:
         target: /searchAll.json
       - source: mediator-config-searchAllResponse.json
         target: /searchAllResponse.json
+      - source: mediator-config-searchAllProbabilistic.json
+        target: /searchAllProbabilistic.json
+      - source: mediator-config-searchAllProbabilisticResponse.json
+        target: /searchAllProbabilisticResponse.json
     networks:
       mapping-mediator:
     # This command will only attempt to import the config when the uptime responds with a 2xx
@@ -69,6 +73,16 @@ configs:
     name: mediator-config-searchAllResponse.json-${mediator_config_searchAllResponse_json_DIGEST:?err}
     labels:
       name: jempi
+  mediator-config-searchAllProbabilistic.json:
+    file: ./searchAllProbabilistic.json
+    name: mediator-config-searchAllProbabilistic.json-${mediator_config_searchAllProbabilistic_json_DIGEST:?err}
+    labels:
+      name: jempi
+  mediator-config-searchAllProbabilisticResponse.json:
+    file: ./searchAllProbabilisticResponse.json
+    name: mediator-config-searchAllProbabilisticResponse.json-${mediator_config_searchAllProbabilisticResponse_json_DIGEST:?err}
+    labels:
+      name: jempi
 
 networks:
   mapping-mediator:

client-registry-jempi/importer/mapping-mediator/register-response.json

@@ -10,6 +10,7 @@
   },
   "inputTransforms": {
     "currentDate": "$now()",
+    "candidateThreshold": "$exists(query.candidateThreshold) ? query.candidateThreshold : constants.candidateThreshold",
     "sourcePatient": "$exists(requestBody.identifier) and $exists(requestBody.identifier[0]) and $exists(requestBody.identifier[0].value) ? {'patient': requestBody.identifier[0].value, 'facility': requestBody.identifier[0].system} : null",
     "nationalId": "$exists(requestBody.identifier) and $exists(requestBody.identifier[0]) and $count($filter(requestBody.identifier, function($v) {$contains($v.system, 'NationalID')})) > 0 ? $filter(requestBody.identifier, function($v) {$contains($v.system, 'NationalID')})[0].value : null",
     "name": "$exists(requestBody.name) and $exists(requestBody.name[0]) and $exists(requestBody.name[0].given[0]) ? requestBody.name[0].given[0] : null",
@@ -18,7 +19,7 @@
     "phoneNumber": "$exists(requestBody.telecom) and $exists(requestBody.telecom[0]) ? requestBody.telecom[0].value : null"
   },
   "inputMapping": {
-    "constants.candidateThreshold": "candidateThreshold",
+    "transforms.candidateThreshold": "candidateThreshold",
     "transforms.sourcePatient": "sourceId",
     "transforms.nationalId": "demographicData.nationalId",
     "transforms.familyName": "demographicData.familyName",
@@ -42,9 +43,6 @@
           "contentType": "application/fhir+json"
         },
         "url": "http://jempi-api:50000/JeMPI/cr-register"
-      },
-      "extract": {
-        "JeMPIResponse": "$.body"
       }
     }
   }

client-registry-jempi/importer/mapping-mediator/register.json

@@ -35,11 +35,16 @@
           "headers": {
             "contentType": "application/fhir+json"
           },
-          "url": "http://openhim-mapping-mediator:3003/register-response"
+          "url": "http://openhim-mapping-mediator:3003/register-response",
+          "params": {
+            "query": {
+              "candidateThreshold": {
+                "path": "query.candidateThreshold"
+              }
+            }
+          }
         },
-        "extract": {
-          "JeMPIResponse": "$.body"
-        }
+        "fhirResponse": true
       }
     ]
   }

client-registry-jempi/importer/mapping-mediator/search.json

@@ -2,7 +2,7 @@
   "name": "Search Patient by id",
   "endpoint": {
     "pattern": "/fhir/Patient/:patientId",
-    "method": "POST"
+    "method": "GET"
   },
   "transformation": {
     "input": "JSON",

client-registry-jempi/importer/mapping-mediator/searchAll.json

@@ -1,17 +1,12 @@
 {
-  "name": "Search Endpoint",
+  "name": "Search Endpoint deterministic",
   "endpoint": {
-    "pattern": "/fhir/Patients",
-    "method": "POST"
+    "pattern": "/fhir/Patient",
+    "method": "GET"
   },
   "transformation": {
-    "input": "JSON",
     "output": "JSON"
   },
-  "constants": {
-    "resourceType": "Bundle",
-    "type": "searchset"
-  },
   "inputTransforms": {
     "total": "$count(lookupRequests.jempiSearchAll.data.goldenRecords)",
     "entry": "$map(lookupRequests.jempiSearchAll.data.goldenRecords, function($v) {{'fullUrl': 'Patient/' & $v.goldenId, 'resource': {'resourceType': 'Patient','id': $v.goldenId,'name': {'given': [$v.demographicData.givenName],'family': $v.demographicData.familyName},'address': [{'city': $v.demographicData.city}],'birthDate': $v.demographicData.dob,'telecom': [{'value': $v.demographicData.phoneNumber,'system': 'phone'}],'identifier': [{'system': $v.sourceId.facility,'value': $v.sourceId.patient},{'system': 'NationalID','value': $v.demographicData.nationalId}],'gender': $v.demographicData.gender}}})"
@@ -22,20 +17,45 @@
     "transforms.total": "total",
     "transforms.entry": "entry"
   },
+  "constants": {
+    "resourceType": "Bundle",
+    "type": "searchset"
+  },
   "requests": {
     "lookup": [
       {
         "id": "jempiSearchAll",
-        "forwardExistingRequestBody": true,
         "config": {
-          "method": "post",
+          "method": "get",
           "headers": {
             "contentType": "application/json"
           },
+          "params": {
+            "query": {
+              "family": {
+                "path": "query.family"
+              },
+              "given": {
+                "path": "query.given"
+              },
+              "telecom": {
+                "path": "query.telecom"
+              },
+              "identifier": {
+                "path": "query.identifier"
+              },
+              "gender": {
+                "path": "query.gender"
+              },
+              "birthDate": {
+                "path": "query.birthDate"
+              },
+              "address": {
+                "path": "query.address"
+              }
+            }
+          },
           "url": "http://openhim-mapping-mediator:3003/search-response"
-        },
-        "extract": {
-          "JeMPIResponse": "$.body"
         }
       }
     ]

client-registry-jempi/importer/mapping-mediator/searchAllProbabilistic.json

@@ -0,0 +1,41 @@
+{
+  "name": "Search Endpoint probabilistic",
+  "endpoint": {
+    "pattern": "/fhir/Patient/$match",
+    "method": "POST"
+  },
+  "transformation": {
+    "input": "JSON",
+    "output": "JSON"
+  },
+  "constants": {
+    "resourceType": "Bundle",
+    "type": "searchset"
+  },
+  "inputTransforms": {
+    "total": "$count(lookupRequests.jempiSearchAllProbabilistic.data.goldenRecords)",
+    "entry": "$map(lookupRequests.jempiSearchAllProbabilistic.data.goldenRecords, function($v) {{'fullUrl': 'Patient/' & $v.goldenId, 'resource': {'resourceType': 'Patient','id': $v.goldenId,'name': {'given': [$v.demographicData.givenName],'family': $v.demographicData.familyName},'address': [{'city': $v.demographicData.city}],'birthDate': $v.demographicData.dob,'telecom': [{'value': $v.demographicData.phoneNumber,'system': 'phone'}],'identifier': [{'system': $v.sourceId.facility,'value': $v.sourceId.patient},{'system': 'NationalID','value': $v.demographicData.nationalId}],'gender': $v.demographicData.gender}}})"
+  },
+  "inputMapping": {
+    "constants.resourceType": "resourceType",
+    "constants.type": "type",
+    "transforms.total": "total",
+    "transforms.entry": "entry"
+  },
+  "requests": {
+    "lookup": [
+      {
+        "id": "jempiSearchAllProbabilistic",
+        "forwardExistingRequestBody": true,
+        "config": {
+          "method": "post",
+          "headers": {
+            "contentType": "application/json"
+          },
+          "url": "http://openhim-mapping-mediator:3003/search-response-probabilistic"
+        },
+        "fhirResponse": true
+      }
+    ]
+  }
+}

client-registry-jempi/importer/mapping-mediator/searchAllProbabilisticResponse.json

@@ -0,0 +1,74 @@
+{
+  "name": "Search Response Endpoint deterministic",
+  "endpoint": {
+    "pattern": "/search-response-probabilistic",
+    "method": "POST"
+  },
+  "transformation": {
+    "input": "JSON",
+    "output": "JSON"
+  },
+  "inputValidation": {
+    "type": "object",
+    "properties": {
+      "requestBody": {
+        "type": "object",
+        "properties": {
+          "parameter": {
+            "type": "array",
+            "items": {
+              "type": "object",
+              "properties": {
+                "name": {
+                  "type": "string"
+                },
+                "valueString": {
+                  "type": "string"
+                },
+                "part": {
+                  "type": "array",
+                  "items": {
+                    "type": "object",
+                    "properties": {
+                      "name": {
+                        "type": "string"
+                      },
+                      "valueString": {
+                        "type": "string"
+                      },
+                      "valueInteger": {
+                        "type": "number"
+                      }
+                    },
+                    "required": ["name"]
+                  }
+                }
+              },
+              "required": ["name", "valueString", "part"]
+            },
+            "minItems": 1
+          }
+        },
+        "required": ["parameter"]
+      }
+    }
+  },
+  "inputTransforms": {
+    "operands": "$append([], $map(requestBody.parameter, function($v) {{'operator': $single($v.part, function($v) {$v.name = 'operator'}).valueString, 'operand': {'fn': $single($v.part, function($v) {$v.name = 'fn'}).valueString, 'distance': $single($v.part, function($v) {$v.name = 'distance'}).valueInteger, 'name': $v.name, 'value': $v.valueString}}}))"
+  },
+  "inputMapping": {
+    "transforms.operands": "operands",
+    "transforms.operands[0].operand": "operand"
+  },
+  "requests": {
+    "response": [
+      {
+        "id": "jempiSearchAllProbabilisticResponse",
+        "config": {
+          "method": "post",
+          "url": "http://jempi-api:50000/JeMPI/cr-find"
+        }
+      }
+    ]
+  }
+}