Add sample allergyintolerance.json and test all samples

.github/workflows/test.yml

@@ -20,10 +20,8 @@ jobs:
     steps:
       - uses: actions/checkout@v4.1.7
 
-      - name: Build
-        run: |
-          # Start up the docker in docker
-          docker compose up -d
+      - name: Create containers with docker compose
+        run: docker compose up -d
 
       - name: Wait for application to be ready
         run: |
@@ -65,48 +63,66 @@ jobs:
             exit 1
           fi
 
-      - name: Test curl request to add new patient
+      - name: Test curl request to add new service
         run: |
-          # Perform PUT request to add a new patient
-          response=$(curl -s -o /dev/null -w "%{http_code}" -X PUT \
-            -T sample_data/example_patient.json \
-            -H "Content-Type: application/json" \
-            "http://${CONTAINER_IP}:${PORT}/${VERSION}/Patient/example")
-
-          # Check if the HTTP status code is 200
-          if [ "$response" -eq 200 ]; then
-            echo "Request successful with status code 200."
-          else
-            echo "Request failed with status code $response."
-            exit 1
-          fi
+          for filename_with_extension_and_path in sample_data/*.json; do
+            filename_with_extension="${filename_with_extension_and_path##*/}"
+            filename="${filename_with_extension%%.*}"
+
+            echo "Perform PUT request to add a new ${filename}"
+            response=$(curl -s -o /dev/null -w "%{http_code}" -X PUT \
+              -T ${filename_with_extension_and_path} \
+              -H "Content-Type: application/json" \
+              "http://${CONTAINER_IP}:${PORT}/${VERSION}/${filename}/example_${filename}")
+
+            # Check if the HTTP status code is 200
+            if [ "$response" -eq 200 ]; then
+              echo "Request ${filename} successful with status code 200."
+            else
+              echo "Request ${filename} failed with status code $response."
+              exit 1
+            fi
+          done
 
-      - name: Test curl request for existing patient
+      - name: Test curl request for existing service
         run: |
-          # Perform GET request get the newly added patient
-          response=$(curl -s -o /dev/null -w "%{http_code}" -X GET \
-            -H "Content-Type: application/json" \
-            "http://${CONTAINER_IP}:${PORT}/${VERSION}/Patient/example")
-
-          # Check if the HTTP status code is 200
-          if [ "$response" -eq 200 ]; then
-            echo "Request successful with status code 200."
-          else
-            echo "Request failed with status code $response."
-            exit 1
-          fi
+          for filename_with_extension_and_path in sample_data/*.json; do
+            filename_with_extension="${filename_with_extension_and_path##*/}"
+            filename="${filename_with_extension%%.*}"
+
+            echo "Perform GET request get the newly added ${filename}"
+            response=$(curl -s -o /dev/null -w "%{http_code}" -X GET \
+              -H "Content-Type: application/json" \
+              "http://${CONTAINER_IP}:${PORT}/${VERSION}/${filename}/example_${filename}")
+
+            # Check if the HTTP status code is 200
+            if [ "$response" -eq 200 ]; then
+              echo "Request ${filename} successful with status code 200."
+            else
+              echo "Request ${filename} failed with status code $response."
+              exit 1
+            fi
+          done
 
       - name: Test curl request for non-existing patient to fail
         run: |
-          # Perform GET request for a non-existing patient
-          response=$(curl -s -o /dev/null -w "%{http_code}" -X GET \
-            -H "Content-Type: application/json" \
-            "http://${CONTAINER_IP}:${PORT}/${VERSION}/Patient/no_show")
+          for filename_with_extension_and_path in sample_data/*.json; do
+            filename_with_extension="${filename_with_extension_and_path##*/}"
+            filename="${filename_with_extension%%.*}"
+
+            echo "Perform GET request for a non-existing ${filename}"
+            response=$(curl -s -o /dev/null -w "%{http_code}" -X GET \
+              -H "Content-Type: application/json" \
+              "http://${CONTAINER_IP}:${PORT}/${VERSION}/Patient/missing_${filename}")
+
+            # Check if the HTTP status code is 200
+            if [ "$response" -ne 200 ]; then
+              echo "Request ${filename} successful with status code $response (non 200)."
+            else
+              echo "Request ${filename} failed with undesired status code 200."
+              exit 1
+            fi
+          done
 
-          # Check if the HTTP status code is 200
-          if [ "$response" -ne 200 ]; then
-            echo "Request successful with status code $response (non 200)."
-          else
-            echo "Request failed with undesired status code 200."
-            exit 1
-          fi
+      - name: Shutdown containers with docker compose
+        run: docker compose down

sample_data/allergyintolerance.json

@@ -0,0 +1,124 @@
+{
+  "resourceType": "AllergyIntolerance",
+  "id": "example_allergyintolerance",
+  "identifier": [
+    {
+      "system": "http://acme.com/ids/patients/risks",
+      "value": "49476534"
+    }
+  ],
+  "clinicalStatus": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-clinical",
+        "code": "active",
+        "display": "Active"
+      }
+    ]
+  },
+  "verificationStatus": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/allergyintolerance-verification",
+        "code": "confirmed",
+        "display": "Confirmed"
+      }
+    ]
+  },
+  "type": {
+    "coding": [
+      {
+        "system": "http://hl7.org/fhir/allergy-intolerance-type",
+        "code": "allergy",
+        "display": "Allergy"
+      }
+    ]
+  },
+  "category": ["food"],
+  "criticality": "high",
+  "code": {
+    "coding": [
+      {
+        "system": "http://snomed.info/sct",
+        "code": "227493005",
+        "display": "Cashew nuts"
+      }
+    ]
+  },
+  "patient": {
+    "reference": "Patient/example"
+  },
+  "onsetDateTime": "2004",
+  "recordedDate": "2014-10-09T14:58:00+11:00",
+  "recorder": {
+    "reference": "Practitioner/example"
+  },
+  "asserter": {
+    "reference": "Patient/example"
+  },
+  "note": [
+    {
+      "text": "The criticality is high becasue of the observed anaphylactic reaction when challenged with cashew extract."
+    }
+  ],
+  "reaction": [
+    {
+      "substance": {
+        "coding": [
+          {
+            "system": "http://www.nlm.nih.gov/research/umls/rxnorm",
+            "code": "1160593",
+            "display": "cashew nut allergenic extract Injectable Product"
+          }
+        ]
+      },
+      "manifestation": [
+        {
+          "concept": {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "39579001",
+                "display": "Anaphylactic reaction"
+              }
+            ]
+          }
+        }
+      ],
+      "description": "Challenge Protocol. Severe reaction to subcutaneous cashew extract. Epinephrine administered",
+      "onset": "2012-06-12",
+      "severity": "severe",
+      "exposureRoute": {
+        "coding": [
+          {
+            "system": "http://snomed.info/sct",
+            "code": "34206005",
+            "display": "Subcutaneous route"
+          }
+        ]
+      }
+    },
+    {
+      "manifestation": [
+        {
+          "concept": {
+            "coding": [
+              {
+                "system": "http://snomed.info/sct",
+                "code": "64305001",
+                "display": "Urticaria"
+              }
+            ]
+          }
+        }
+      ],
+      "onset": "2004",
+      "severity": "moderate",
+      "note": [
+        {
+          "text": "The patient reports that the onset of urticaria was within 15 minutes of eating cashews."
+        }
+      ]
+    }
+  ]
+}

sample_data/example_patient.json → sample_data/patient.json

@@ -1,6 +1,6 @@
 {
   "resourceType": "Patient",
-  "id": "example",
+  "id": "example_patient",
   "text": {
     "status": "generated",
     "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\">\n\t\t\t<table>\n\t\t\t\t<tbody>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Name</td>\n\t\t\t\t\t\t<td>Peter James \n              <b>Chalmers</b> (&quot;Jim&quot;)\n            </td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Address</td>\n\t\t\t\t\t\t<td>534 Erewhon, Pleasantville, Vic, 3999</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Contacts</td>\n\t\t\t\t\t\t<td>Home: unknown. Work: (03) 5555 6473</td>\n\t\t\t\t\t</tr>\n\t\t\t\t\t<tr>\n\t\t\t\t\t\t<td>Id</td>\n\t\t\t\t\t\t<td>MRN: 12345 (Acme Healthcare)</td>\n\t\t\t\t\t</tr>\n\t\t\t\t</tbody>\n\t\t\t</table>\n\t\t</div>"