#294 - Update sq2cql to version v0.3.0

- follow redirects in curl in integration tests
- update blaze in tests to 0.27, flare to 2.2.0 and keycloak to 25.0
- update sq2cql dependency

.github/integration-test/docker-compose.yml

@@ -79,7 +79,7 @@ services:
       POSTGRES_DB: "codex_ui"
 
   blaze:
-    image: "samply/blaze:0.22"
+    image: "samply/blaze:0.27"
     environment:
       BASE_URL: "http://blaze:8080"
       JAVA_TOOL_OPTIONS: "-Xmx1g"
@@ -90,7 +90,7 @@ services:
       - "blaze-data:/app/data"
 
   flare:
-    image: ghcr.io/medizininformatik-initiative/flare:2.1.1
+    image: ghcr.io/medizininformatik-initiative/flare:2.2.0
     ports:
       - "8092:8080"
     environment:
@@ -110,8 +110,8 @@ services:
       - "feasibility-auth-db:/var/lib/postgresql/data"
 
   auth:
-    image: keycloak/keycloak:21.1
-    command: ["start", "--import-realm"]
+    image: quay.io/keycloak/keycloak:25.0
+    command: ["start-dev", "--import-realm"]
     restart: unless-stopped
     environment:
       KC_DB: "postgres"

.github/scripts/post-test-query.sh

@@ -14,37 +14,81 @@ response=$(curl -s -i \
   --header "Authorization: Bearer $access_token" \
   --header 'Content-Type: application/json' \
   --data '{
-            "version": "http://to_be_decided.com/draft-1/schema#",
-            "inclusionCriteria": [
+              "version": "http://to_be_decided.com/draft-1/schema#",
+              "display": "",
+              "inclusionCriteria":
               [
-                {
-                  "attributeFilters": [],
-                  "termCodes": [
-                    {
-                      "code": "263495000",
-                      "display": "Geschlecht",
-                      "system": "http://snomed.info/sct"
-                    }
-                  ],
-                  "context": {
-                    "code": "Patient",
-                    "display": "Patient",
-                    "system": "fdpg.mii.cds",
-                    "version": "1.0.0"
-                  },
-                  "valueFilter": {
-                    "selectedConcepts": [
+                  [
                       {
-                        "code": "male",
-                        "display": "Male",
-                        "system": "http://hl7.org/fhir/administrative-gender"
+                          "termCodes":
+                          [
+                              {
+                                  "code": "119373006",
+                                  "system": "http://snomed.info/sct",
+                                  "version": "http://snomed.info/sct/900000000000207008/version/20220930",
+                                  "display": "Amniotic fluid specimen"
+                              }
+                          ],
+                          "attributeFilters":
+                          [
+                              {
+                                  "criteria":
+                                  [
+                                      {
+                                          "termCodes":
+                                          [
+                                              {
+                                                  "code": "F40.01",
+                                                  "system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
+                                                  "version": "2023",
+                                                  "display": "Mit Panikstörung"
+                                              }
+                                          ],
+                                          "context":
+                                          {
+                                              "code": "Diagnose",
+                                              "system": "fdpg.mii.cds",
+                                              "version": "1.0.0",
+                                              "display": "Diagnose"
+                                          }
+                                      }
+                                  ],
+                                  "type": "reference",
+                                  "attributeCode":
+                                  {
+                                      "code": "festgestellteDiagnose",
+                                      "display": "Festgestellte Diagnose",
+                                      "system": "http://hl7.org/fhir/StructureDefinition"
+                                  }
+                              },
+                              {
+                                  "selectedConcepts":
+                                  [
+                                      {
+                                          "code": "C69",
+                                          "display": "Auge und Augenanhangsgebilde",
+                                          "system": "http://hl7.org/fhir/sid/icd-o-3"
+                                      }
+                                  ],
+                                  "type": "concept",
+                                  "attributeCode":
+                                  {
+                                      "code": "icd-o-3",
+                                      "display": "icd-o-3",
+                                      "system": "http://hl7.org/fhir/StructureDefinition"
+                                  }
+                              }
+                          ],
+                          "context":
+                          {
+                              "code": "Specimen",
+                              "system": "fdpg.mii.cds",
+                              "version": "1.0.0",
+                              "display": "Bioprobe"
+                          }
                       }
-                    ],
-                    "type": "concept"
-                  }
-                }
+                  ]
               ]
-            ]
           }
 ')
 

.github/scripts/wait-for-url.sh

@@ -9,7 +9,7 @@ eclipsed() {
 }
 
 # wait at maximum 240 seconds
-while [[ ($(eclipsed) -lt 240) && ("$(curl -s -o /dev/null -w '%{response_code}' "$URL")" != "200") ]]; do
+while [[ ($(eclipsed) -lt 240) && ("$(curl -L -s -o /dev/null -w '%{response_code}' "$URL")" != "200") ]]; do
   sleep 2
 done
 

pom.xml

@@ -26,7 +26,7 @@
     <java.version>17</java.version>
     <mockwebserver.version>4.10.0</mockwebserver.version>
     <okhttp3.version>4.10.0</okhttp3.version>
-    <ontology-tag>v2.1.27</ontology-tag>
+    <ontology-tag>v2.2.0-RC</ontology-tag>
   </properties>
 
   <dependencies>
@@ -224,7 +224,7 @@
     <dependency>
       <groupId>de.medizininformatik-initiative</groupId>
       <artifactId>sq2cql</artifactId>
-      <version>0.2.16</version>
+      <version>0.3.0-rc.1</version>
     </dependency>
 
     <dependency>

src/test/java/de/numcodex/feasibility_gui_backend/query/broker/direct/DirectBrokerClientCqlIT.java

@@ -42,7 +42,7 @@ class DirectBrokerClientCqlIT {
     private static final Long TEST_BACKEND_QUERY_ID = 1L;
 
     private final GenericContainer<?> blaze = new GenericContainer<>(
-        DockerImageName.parse("samply/blaze:0.25"))
+        DockerImageName.parse("samply/blaze:0.27"))
         .withImagePullPolicy(PullPolicy.alwaysPull())
         .withExposedPorts(8080)
         .waitingFor(Wait.forHttp("/health").forStatusCodeMatching(c -> c >= 200 && c <= 500))

src/test/java/de/numcodex/feasibility_gui_backend/query/broker/dsf/DSFFhirWebClientProviderTest.java

@@ -19,7 +19,7 @@
 public class DSFFhirWebClientProviderTest {
 
     @Container
-    private GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.25")
+    private GenericContainer<?> blaze = new GenericContainer<>("samply/blaze:0.27")
             .withExposedPorts(8080)
             .withNetwork(Network.newNetwork())
             .withReuse(true);