Merge pull request #56 from mcode/dev

Dev

build.gradle

@@ -40,6 +40,7 @@ bootRun {
     }
 }
 
+ext['tomcat.version'] = '9.0.78'
 
 dependencies {
     implementation "io.github.http-builder-ng:http-builder-ng-core:1.0.3"
@@ -56,7 +57,10 @@ dependencies {
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-jpaserver-mdm:5.4.0'
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-testpage-overlay:5.4.0'
     implementation('org.springframework.boot:spring-boot-starter-data-jpa')
-    implementation 'org.springframework.boot:spring-boot-starter-web'
+    implementation ('org.springframework.boot:spring-boot-starter-web'){
+        exclude group: 'org.springframework.boot', module: 'spring-boot-starter-tomcat'
+	}
+    implementation 'org.springframework.boot:spring-boot-starter-jetty'
     implementation 'ch.qos.logback:logback-classic:1.2.3'
     implementation 'org.thymeleaf:thymeleaf:3.0.11.RELEASE'
     implementation 'org.springframework:spring-web'
@@ -93,7 +97,7 @@ dependencies {
     //implementation 'ca.uhn.hapi.fhir:hapi-fhir-testpage-overlay:4.2.0:war'
     implementation 'ca.uhn.hapi.fhir:hapi-fhir-testpage-overlay:4.2.0:classes'
 //    providedImplementation 'javax.servlet:javax.servlet-api:3.1.0'
-
+   // implementation group:'org.apache.tomcat', name:'tomcat-juli', version:property('tomcat.version')
     implementation 'javax.interceptor:javax.interceptor-api:1.2.2'
 }
 

dockerRunnerDev.sh

@@ -14,7 +14,7 @@ echo "Starting application in watch mode..."
 
 # Start load data process once server is running 
 echo "Starting continuous data loader..."
-( while ! grep -m1 "Tomcat started on port" < ./logs/runner.log; do
+( while ! grep -m1 "Started Application in " < ./logs/runner.log; do
     sleep 1
 done
 echo "loading data into test-ehr..."

dockerRunnerProd.sh

@@ -12,7 +12,7 @@ echo "*** Logs for 'gradle bootRun' ***" > ./logs/runner.log
 echo "Starting application in production mode..."
 
 # Start load data process once server is running 
-( while ! grep -m1 "Tomcat started on port" < ./logs/runner.log; do
+( while ! grep -m1 "Started Application in " < ./logs/runner.log; do
     sleep 1
 done
 echo "loading data into test-ehr..."

fhirResourcesToLoad/rems_snow_medication_ursodiol.json

@@ -0,0 +1,50 @@
+{
+  "resourceType": "Medication",
+  "id": "med-pat017-ursodiol",
+  "status": "active",
+  "code": {
+    "coding": [
+      {
+        "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+        "code": "1303740",
+        "display": "ursodiol 250 MG Oral Capsule"
+      }
+    ]
+  },
+  "form": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "858744",
+        "display": "Prolonged-release oral capsule"
+      }
+    ]
+  },
+  "ingredient": [
+    {
+      "itemCodeableConcept": {
+        "coding": [
+          {
+            "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+            "code": "11065",
+            "display": "Ursodiol"
+          }
+        ]
+      },
+      "strength": {
+        "numerator": {
+          "value": 70,
+          "system": "http://unitsofmeasure.org",
+          "code": "mg",
+          "unit": "mg"
+        },
+        "denominator": {
+          "value": 1,
+          "system": "http://terminology.hl7.org/CodeSystem/v3-orderableDrugForm",
+          "code": "ERTAB",
+          "unit": "Capsule"
+        }
+      }
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_medicationstatement_ursodiol.json

@@ -0,0 +1,93 @@
+{
+  "resourceType": "MedicationStatement",
+  "id": "medstate-pat017-ursodiol",
+  "status": "active",
+  "category": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/medication-statement-category",
+        "code": "outpatient",
+        "display": "Outpatient"
+      }
+    ]
+  },
+  "medicationReference": {
+    "reference": "Medication/med-pat017-ursodiol"
+  },
+  "subject": {
+    "reference": "Patient/pat017",
+    "display": "Jon Snow"
+  },
+  "effectiveDateTime": "2023-03-20",
+  "dateAsserted": "2021-03-22",
+  "informationSource": {
+    "reference": "Patient/pat017",
+    "display": "Jon Snow"
+  },
+  "reasonCode": [
+    {
+      "coding": [
+        {
+          "code": "39400004",
+          "system": "http://snomed.info/sct",
+          "display": "Injury of Liver"
+        }
+      ]
+    }
+  ],
+  "dosage": [
+    {
+      "sequence": 1,
+      "text": "70mg daily",
+      "timing": {
+        "repeat": {
+          "frequency": 1,
+          "period": 1,
+          "periodUnit": "d"
+        }
+      },
+      "route": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "code": "26643006",
+            "display": "Oral route"
+          }
+        ]
+      },
+      "doseAndRate": [
+        {
+          "type": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/dose-rate-type",
+                "code": "ordered",
+                "display": "Ordered"
+              }
+            ]
+          },
+          "doseQuantity": {
+            "value": 1,
+            "unit": "Capsule",
+            "system": "http://terminology.hl7.org/CodeSystem/v3-orderableDrugForm",
+            "code": "ERTAB"
+          },
+          "rateRatio": {
+            "numerator": {
+              "value": 1,
+              "unit": "pills"
+            },
+            "denominator": {
+              "value": 1,
+              "unit": "day",
+              "system": "http://unitsofmeasure.org",
+              "code": "d"
+
+            }
+
+          }
+        }
+      ]
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_procedure_ercp.json

@@ -0,0 +1,35 @@
+{
+  "resourceType": "Procedure",
+  "id": "pr-4",
+  "status": "completed",
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "386718000",
+        "display": "Endoscopic retrograde cholangiopancreatography (Procedure)"
+      }
+    ],
+    "text": "Endoscopic retrograde cholangiopancreatography"
+  },
+  "subject": {
+    "reference": "Patient/pat017"
+  },
+  "performedDateTime": "2023-04-05",
+  "recorder": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "asserter": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "performer": [
+    {
+      "actor": {
+        "reference": "Practitioner/example",
+        "display": "Dr Cecil Surgeon"
+      }
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_procedure_hida.json

@@ -0,0 +1,35 @@
+{
+  "resourceType": "Procedure",
+  "id": "pr-5",
+  "status": "completed",
+  "code": {
+    "coding": [
+      {
+        "system": "http://www.ama-assn.org/go/cpt",
+        "code": "78226",
+        "display": "Hepatobiliary iminodiacetic acid scan"
+      }
+    ],
+    "text": "HIDA Scan"
+  },
+  "subject": {
+    "reference": "Patient/pat017"
+  },
+  "performedDateTime": "2023-04-05",
+  "recorder": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "asserter": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "performer": [
+    {
+      "actor": {
+        "reference": "Practitioner/example",
+        "display": "Dr Cecil Surgeon"
+      }
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_procedure_liver_biospy.json

@@ -0,0 +1,35 @@
+{
+  "resourceType": "Procedure",
+  "id": "pr-3",
+  "status": "completed",
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "86259008",
+        "display": "Liver Biopsy (Procedure)"
+      }
+    ],
+    "text": "Liver Biopsy"
+  },
+  "subject": {
+    "reference": "Patient/pat017"
+  },
+  "performedDateTime": "2023-04-05",
+  "recorder": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "asserter": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "performer": [
+    {
+      "actor": {
+        "reference": "Practitioner/example",
+        "display": "Dr Cecil Surgeon"
+      }
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_procedure_liver_imaging.json

@@ -0,0 +1,35 @@
+{
+  "resourceType": "Procedure",
+  "id": "pr-2",
+  "status": "completed",
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "441802002",
+        "display": "Imaging of liver (Procedure)"
+      }
+    ],
+    "text": "Imaging of liver"
+  },
+  "subject": {
+    "reference": "Patient/pat017"
+  },
+  "performedDateTime": "2023-04-05",
+  "recorder": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "asserter": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "performer": [
+    {
+      "actor": {
+        "reference": "Practitioner/example",
+        "display": "Dr Cecil Surgeon"
+      }
+    }
+  ]
+}

fhirResourcesToLoad/rems_snow_procedure_liver_ultrasound.json

@@ -0,0 +1,50 @@
+{
+  "resourceType": "Procedure",
+  "id": "pr-1",
+  "status": "completed",
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "105377009",
+        "display": "Ultrasonography of liver (Procedure)"
+      }
+    ],
+    "text": "Ultrasonography of liver"
+  },
+  "subject": {
+    "reference": "Patient/pat017"
+  },
+  "performedDateTime": "2023-04-05",
+  "recorder": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "asserter": {
+    "reference": "Practitioner/example",
+    "display": "Dr Cecil Surgeon"
+  },
+  "performer": [
+    {
+      "actor": {
+        "reference": "Practitioner/example",
+        "display": "Dr Cecil Surgeon"
+      }
+    }
+  ],
+  "reasonCode": [
+    {
+      "text": "Generalized abdominal pain 24 hours. Localized in RIF with rebound and guarding"
+    }
+  ],
+  "followUp": [
+    {
+      "text": "ROS 5 days  - 2023-04-10"
+    }
+  ],
+  "note": [
+    {
+      "text": "Routine liver ultrasound - everything normal"
+    }
+  ]
+}