B-TECHBW · pmanko · Jul 8, 2022 · Jul 8, 2022 · Jul 25, 2022 · Aug 30, 2022
diff --git a/.env b/.env
@@ -1,3 +1,3 @@
-SHR_VERSION=v0.7.1
-FHIR_CONVERTER_VERSION=v3.2.1
-OMANG_SVC_VERSION=v1.6.3
+SHR_VERSION=v0.8.0
+FHIR_CONVERTER_VERSION=v3.3.0-beta
+OMANG_SVC_VERSION=v1.6.5
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -14,14 +14,14 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v1
+        uses: actions/checkout@v3
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v1
+        uses: docker/setup-buildx-action@v2
 
       -
         name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: ${{ secrets.GHCR_USER }}

diff --git a/.gitignore b/.gitignore
@@ -48,4 +48,6 @@ server/log
 
 *.tar
 
-data/*
+data/*
+
+*.bak
diff --git a/certs/selfsigned.crt b/certs/selfsigned.crt
@@ -0,0 +1,25 @@
+-----BEGIN CERTIFICATE-----
+MIIEMzCCAxugAwIBAgIUPZuJLyvfxhaedprEdyqgcvbVhIcwDQYJKoZIhvcNAQEL
+BQAwgagxCzAJBgNVBAYTAkJXMRMwEQYDVQQIDApTb21lLVN0YXRlMREwDwYDVQQH
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+SIb3DQEJARYUa2dha2dlLnRhbEBnbWFpbC5jb20wHhcNMjIwODIxMDM0MzUzWhcN
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+NtcZaOXfo9XGVIbKb6f05/w1PEan/qzJORAjnNUlUMa3eNJpTasGn/CcWkg86nnc
+aed05+c57GhxESS09eLxNaHvA9sAzb75uyZKjgslnla958JxPttU7fA3ynA4rhhr
+9ZtGEjg2VG9qw2JC9cwlCdYxpSyH4Ux1ntJNQviQfcuDaee/KDII4nN0pWqok46n
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+S0NPyB0NFIv4RlUEWF8hSZUE5J7EczA=
+-----END CERTIFICATE-----
diff --git a/certs/selfsigned.key b/certs/selfsigned.key
@@ -0,0 +1,28 @@
+-----BEGIN PRIVATE KEY-----
+MIIEvQIBADANBgkqhkiG9w0BAQEFAASCBKcwggSjAgEAAoIBAQClhu2wgLa2615/
+4LwI5n3sLa68NnIBoQzvHQvDVlQwc/GDh2Gfpf4uhmLaCj/wGzC4B6wQ0QWjDpRI
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+2aT6Ktg8kD1YagNzMbC4b0ninhyarbYEfOp48cxjJmIv6x142/IQTVjFXMrpNRYo
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+XOZPHZ7suxe6Ysa1ivyuj1M=
+-----END PRIVATE KEY-----
diff --git a/configs/opencr/PatientRelationship.json b/configs/opencr/PatientRelationship.json
@@ -0,0 +1,142 @@
+{
+    "resourceType": "Basic",
+    "id": "patientreport",
+    "meta": {
+      "versionId": "1",
+      "lastUpdated": "2019-07-30T07:34:24.098+00:00",
+      "profile": [
+        "http://ihris.org/fhir/StructureDefinition/iHRISRelationship"
+      ]
+    },
+    "extension": [
+      {
+        "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportDetails",
+        "extension": [
+          {
+            "url": "label",
+            "valueString": "Patient Report"
+          },
+          {
+            "url": "name",
+            "valueString": "patients"
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "gender"
+              },
+              {
+                "url": "name",
+                "valueString": "gender"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "birthDate"
+              },
+              {
+                "url": "name",
+                "valueString": "birthDate"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "given"
+              },
+              {
+                "url": "name",
+                "valueString": "name.where(use='official').last().given"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "family"
+              },
+              {
+                "url": "name",
+                "valueString": "name.where(use='official').last().family"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "fullname"
+              },
+              {
+                "url": "name",
+                "valueString": "name.where(use='official').last().text"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "phone"
+              },
+              {
+                "url": "name",
+                "valueString": "telecom.where(system='phone').value"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "artnumber"
+              },
+              {
+                "url": "name",
+                "valueString": "identifier.where(system='http://moh.bw.org/ext/identifier/pi').value"
+              }
+            ]
+          },
+          {
+            "url": "http://ihris.org/fhir/StructureDefinition/iHRISReportElement",
+            "extension": [
+              {
+                "url": "label",
+                "valueString": "nationalid"
+              },
+              {
+                "url": "name",
+                "valueString": "identifier.where(system='http://moh.bw.org/ext/identifier/omang').last().value"
+              }
+            ]
+          }
+        ]
+      }
+    ],
+    "code": {
+      "coding": [
+        {
+          "system": "http://ihris.org/fhir/ValueSet/ihris-resource",
+          "code": "iHRISRelationship"
+        }
+      ],
+      "text": "iHRISRelationship"
+    },
+    "subject": {
+      "reference": "StructureDefinition/Patient"
+    }
+  }
diff --git a/configs/opencr/config.json b/configs/opencr/config.json
@@ -44,32 +44,46 @@
   },
   "clients": [
     {
-      "id": "lis",
-      "displayName": "Lab Info System"
+      "id": "tester",
+      "displayName": "PIMS"
+    },
+    {
+      "id": "postman",
+      "displayName": "Postman"
+    },
+    {
+      "id": "shr-client",
+      "displayName": "Shared Health Record"
+    },
+    {
+      "id": "omang-api",
+      "displayName": "Omang Service"
     }
   ],
   "systems": {
     "CRBaseURI": "http://openclientregistry.org/fhir",
     "internalid": {
       "uri": [
-        "http://moh.bw.org/ext/identifier/omang"
+        "http://moh.bw.org/ext/identifier/mr",
+        "http://omang.bw.org/ext/identifier/internalid",
+        "http://openelis-global.org/pat_nationalId"
       ],
       "displayName": "Internal ID"
     },
     "nationalid": {
-      "uri": "http://health.go.ug/cr/natioanlid",
-      "displayName": "National ID"
+      "uri": "http://moh.bw.org/ext/identifier/omang",
+      "displayName": "National ID - OMANG"
     },
     "artnumber": {
-      "uri": "http://health.go.ug/cr/artnumber",
-      "displayName": "ART Number"
+      "uri": "http://moh.bw.org/ext/identifier/pi",
+      "displayName": "Patient Identifier"
     },
     "brokenMatch": {
       "uri": "http://clientregistry.org/brokenMatch"
     }
   },
   "sync": {
-    "lastFHIR2ESSync": "2022-08-31T19:24:26"
+    "lastFHIR2ESSync": "2023-04-04T22:03:09"
   },
   "__comments": {
     "matching.tool": "this tells if the app should use mediator algorithms or elasticsearch algorithms for matching, two options mediator and elasticsearch"

diff --git a/configs/opencr/decisionRules.json b/configs/opencr/decisionRules.json
@@ -0,0 +1,81 @@
+{
+    "__comments": {
+        "path": "Its a fhir path, for syntax refer to https://www.hl7.org/fhir/fhirpath.html",
+        "matchingType": "Must be specified, it can either",
+        "threshold": {
+            "levenshtein": "Lower the number, the closer the match, 0 being exact match, max threshold is 2",
+            "jaro-winkler": "number between 0 and 1, where 0 for no match and 1 for exact match"
+        },
+        "nullHandling": {
+            "description": "this option tells openCR what to do when a field is empty, when set at the top level of the rule then it will apply to all fields, if set at the respective field then it will apply for that particular field",
+            "values": "either conservative, moderate or greedy"
+        },
+        "nullHandlingBothFields": {
+            "description": "this option tells openCR what to do when both fields are empty and When this is set, then nullHandling applies to when only 1 of the fields is null, when set at the top level of the rule then it will apply to all fields, if set at the respective field then it will apply for that particular field",
+            "values": "either conservative, moderate or greedy"
+        },
+        "supported_algorithms": {
+            "elasticsearch": [
+                "https://github.com/intrahealth/similarity-scoring"
+            ]
+        }
+    },
+    "rules": [
+        {
+            "matchingType": "deterministic",
+            "fields": {
+                "nationalid": {
+                    "algorithm": "jaro-winkler-similarity",
+                    "threshold": 1,
+                    "fhirpath": "identifier.where(system='http://moh.bw.org/ext/identifier/omang').value",
+                    "null_handling": "conservative",
+                    "null_handling_both": "conservative",
+                    "espath": "nationalid"
+                }
+            },
+            "autoMatchThreshold": 2
+        },
+        {
+            "matchingType": "deterministic",
+            "fields": {
+                "given": {
+                    "algorithm": "jaro-winkler-similarity",
+                    "threshold": 0.8,
+                    "fhirpath": "name.where(use='official').given",
+                    "null_handling": "moderate",
+                    "null_handling_both": "moderate",
+                    "espath": "given"
+                },
+                "family": {
+                    "algorithm": "jaro-winkler-similarity",
+                    "threshold": 0.9,
+                    "fhirpath": "name.where(use='official').family",
+                    "null_handling": "moderate",
+                    "null_handling_both": "moderate",
+                    "espath": "family"
+                },
+                "birthdate": {
+                    "algorithm": "exact",
+                    "fhirpath": "birthDate",
+                    "null_handling": "moderate",
+                    "null_handling_both": "moderate",
+                    "espath": "birthDate"
+                },
+                "artnumber": {
+                    "algorithm": "exact",
+                    "fhirpath": "identifier.where(system='http://moh.bw.org/ext/identifier/pi').value",
+                    "null_handling": "moderate",
+                    "null_handling_both": "moderate",
+                    "espath": "artnumber"
+                }
+            },
+            "potentialMatchThreshold": 3,
+            "filters": {
+                "gender": {
+                    "fhirpath": "gender",
+                    "espath": "gender"
+                }
+            }
+        }
+    ]
+}
diff --git a/configs/openhim-console/default.json b/configs/openhim-console/default.json
@@ -2,9 +2,9 @@
     "version": "1.13.2",
     "minimumCoreVersion": "5.2.0",
     "protocol": "https",
-    "host": "core.moh.org.bw",
+    "host": "hie-pilot.gov.bw",
     "hostPath": "",
-    "port": "",
+    "port": "8090",
     "title": "Botswana HIE Admin Console",
     "footerTitle": "OpenHIM Administration Console",
     "footerPoweredBy": "<a href='http://openhim.org/' target='_blank'>Powered by OpenHIM</a>",
-Original file line number
+Diff line change
@@ Expand Up / @@ -48,4 +48,6 @@ server/log @@
     *.tar
-    data/*
+    data/*
+    *.bak