Set default to no params

Lucas0T · Lucas0T · commit 04d4b6267a8e · 2025-07-08T08:08:06.000Z
diff --git a/README.md b/README.md
diff --git a/src/main/java/de/medizininformatikinitiative/torch/config/AppConfig.java b/src/main/java/de/medizininformatikinitiative/torch/config/AppConfig.java
@@ -391,12 +391,13 @@ public Clock systemDefaultZone() {
 
 
     @Bean
-    ExchangeFilterFunction oauthExchangeFilterFunction(
-            @Value("${torch.fhir.oauth.issuer.uri:}") String issuerUri,
-            @Value("${torch.fhir.oauth.client.id:}") String clientId,
-            @Value("${torch.fhir.oauth.client.secret:}") String clientSecret) {
+    ExchangeFilterFunction oauthExchangeFilterFunction(TorchProperties torchProperties) {
+        String issuerUri = torchProperties.fhir().oauth().issuer().uri();
+        String clientId = torchProperties.fhir().oauth().client().id();
+        String clientSecret = torchProperties.fhir().oauth().client().secret();
+
         if (!issuerUri.isEmpty() && !clientId.isEmpty() && !clientSecret.isEmpty()) {
-            logger.debug("Enabling OAuth2 authentication (issuer uri: '{}', client id: '{}').",
+            logger.info("Enabling OAuth2 authentication (issuer uri: '{}', client id: '{}').",
                     issuerUri, clientId);
             var clientRegistration = ClientRegistrations.fromIssuerLocation(issuerUri)
                     .registrationId(REGISTRATION_ID)
@@ -414,7 +415,7 @@ ExchangeFilterFunction oauthExchangeFilterFunction(
 
             return oAuthExchangeFilterFunction;
         } else {
-            logger.debug("Skipping OAuth2 authentication.");
+            logger.info("Skipping OAuth2 authentication.");
             return (request, next) -> next.exchange(request);
         }
     }
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -5,32 +5,32 @@ server:
 torch:
   base:
     url:
-      http://localhost:8080
+
   profile:
     dir: structureDefinitions
   mapping:
     consent: mappings/consent-mappings_fhir.json
     type_to_consent: mappings/type_to_consent.json
   search_parameters_file: search-parameters.json
   fhir:
-    user: ""
-    password: ""
+    user:
+    password:
     oauth:
       issuer:
-        uri: ""
+        uri:
       client:
-        id: ""
-        secret: ""
+        id:
+        secret:
 
-    url: http://localhost:8081/fhir
+    url:
     page:
       count: 500
     max:
       connections: 5
     disable:
       async: false
   flare:
-    url: http://localhost:8084
+    url:
   results:
     dir: output/
     persistence: PT2160H # Time Block in ISO 8601 format
@@ -54,5 +54,3 @@ logging:
 spring:
   profiles:
     active: active
-  codec:
-    max-in-memory-size: 100MB
diff --git a/src/test/java/de/medizininformatikinitiative/torch/util/ReferenceHandlerIT.java b/src/test/java/de/medizininformatikinitiative/torch/util/ReferenceHandlerIT.java
@@ -3,16 +3,13 @@
 
 import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
-import de.medizininformatikinitiative.torch.consent.ConsentValidator;
-import de.medizininformatikinitiative.torch.management.CompartmentManager;
 import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedAttribute;
 import de.medizininformatikinitiative.torch.model.crtdl.annotated.AnnotatedAttributeGroup;
 import de.medizininformatikinitiative.torch.model.management.PatientResourceBundle;
 import de.medizininformatikinitiative.torch.model.management.ReferenceWrapper;
 import de.medizininformatikinitiative.torch.model.management.ResourceBundle;
 import de.medizininformatikinitiative.torch.model.management.ResourceGroup;
 import de.medizininformatikinitiative.torch.model.management.ResourceGroupWrapper;
-import de.medizininformatikinitiative.torch.service.DataStore;
 import org.hl7.fhir.r4.model.Medication;
 import org.hl7.fhir.r4.model.Organization;
 import org.hl7.fhir.r4.model.Patient;
@@ -22,7 +19,6 @@
 import org.junit.jupiter.api.TestInstance;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.context.SpringBootTest;
-import org.springframework.boot.test.mock.mockito.MockBean;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.ActiveProfiles;
 import reactor.core.publisher.Flux;
@@ -101,26 +97,15 @@ class ReferenceHandlerIT {
     public static final String PAT_REFERENCE = "Patient/VHF00006";
     public static final String REFERENCE_MEDICATION = "Medication/testMedication";
 
-    @MockBean
-    private DataStore dataStore;
-
     @Autowired
     private ProfileMustHaveChecker profileMustHaveChecker;
 
-    @Autowired
-    private CompartmentManager compartmentManager;
-
-    @MockBean
-    private ConsentValidator consentValidator;
-
 
     private ReferenceHandler referenceHandler;
 
     private IParser parser;
 
     AnnotatedAttributeGroup patientGroup;
-    private Organization organization;
-    private AnnotatedAttribute medicationID;
     private AnnotatedAttribute referenceAttribute;
     Map<String, AnnotatedAttributeGroup> attributeGroupMap = new HashMap<>();
 
@@ -134,7 +119,7 @@ void setUp() {
         AnnotatedAttribute conditionSubject = new AnnotatedAttribute("Condition.subject", "Condition.subject", "Condition.subject", true, List.of("Patient1"));
         AnnotatedAttributeGroup conditionGroup = new AnnotatedAttributeGroup("Condition1", "https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose", List.of(conditionSubject), List.of(), null);
 
-        medicationID = new AnnotatedAttribute("Medication.id", "Medication.id", "Medication.id", true, List.of());
+        AnnotatedAttribute medicationID = new AnnotatedAttribute("Medication.id", "Medication.id", "Medication.id", true, List.of());
         AnnotatedAttribute medicationAdherence = new AnnotatedAttribute("Medication.adherence", "Medication.adherence", "Medication.adherence", true, List.of());
         AnnotatedAttributeGroup medicationGroup = new AnnotatedAttributeGroup("Medication1", "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication", List.of(medicationID), List.of(), null);
         AnnotatedAttributeGroup medicationGroup2 = new AnnotatedAttributeGroup("Medication2", "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication", List.of(medicationID, medicationAdherence), List.of(), null);
@@ -144,7 +129,7 @@ void setUp() {
         attributeGroupMap.put("Medication1", medicationGroup);
         attributeGroupMap.put("Medication2", medicationGroup2);
 
-        organization = new Organization();
+        Organization organization = new Organization();
         organization.setId("evilInc");
 
 
diff --git a/src/test/resources/application.yml b/src/test/resources/application.yml
@@ -5,15 +5,14 @@ server:
 torch:
   base:
     url:
-      http://localhost:8080
   profile:
     dir: structureDefinitions
   mapping:
     consent: mappings/consent-mappings_fhir.json
     type_to_consent: mappings/type_to_consent.json
   search_parameters_file: search-parameters.json
   fhir:
-    url: http://localhost:8082/fhir
+    url:
     page:
       count: 500
     max:
@@ -24,12 +23,12 @@ torch:
       path: src/test/resources/BlazeBundle.json
     oauth:
       issuer:
-        uri: "https://auth.localhost:444/realms/blaze"
+        uri:
       client:
-        id: "test"
-        secret: "tast"
+        id:
+        secret:
   flare:
-    url: http://localhost:8084
+    url:
   results:
     dir: output/
     persistence: PT2160H # Time Block in ISO 8601 format
@@ -51,6 +50,3 @@ logging:
     ca.uhn.fhir: WARN
     org.hl7.fhir: WARN
 
-spring:
-  codec:
-    max-in-memory-size: 100MB

Name	Default	Description
SERVER_PORT	8080	The Port of the server to use
TORCH_PROFILE_DIR	structureDefinitions	The directory for profile definitions.
TORCH_MAPPING_CONSENT	mappings/consent-mappings_fhir.json	The file for consent mappings in FHIR format.
TORCH_MAPPING_TYPE_TO_CONSENT	mappings/type_to_consent.json	The file mapping Resource Types to time fields against which the consent is checked
TORCH_FHIR_USER	""	The FHIR server user.
TORCH_FHIR_PASSWORD	""	The FHIR server password.
TORCH_FHIR_OAUTH_ISSUER_URI	""	The URI for the OAuth issuer.
TORCH_FHIR_OAUTH_CLIENT_ID	""	The client ID for OAuth.
TORCH_FHIR_OAUTH_CLIENT_SECRET	""	The client secret for OAuth.
TORCH_FHIR_URL	http://localhost:8081/fhir	The base URL of the FHIR server to use.
TORCH_FHIR_MAX_CONNECTIONS	5	The maximum number of concurrent connections to use - has to be (TORCH_MAXCONCURRENCY + 1)
TORCH_FHIR_PAGE_COUNT	500	The number of pages in a FHIR search response.
TORCH_FHIR_DISABLE_ASYNC	false	Set to `true` in order to disable use of Asynchronous Interaction Request Pattern.
TORCH_FLARE_URL	http://localhost:8084	The base URL of the FLARE server to use.
TORCH_RESULTS_DIR	output/	The directory for storing results.
TORCH_RESULTS_PERSISTENCE	PT2160H	Time Block for result persistence in ISO 8601 format in hours/minutes/seconds. Default 90 days
TORCH_BATCHSIZE	500	The batch size used for processing data.
TORCH_MAXCONCURRENCY	4	The maximum concurrency level for processing.
TORCH_MAPPINGS_FILE	ontology/mapping_cql.json	The file for ontology mappings using CQL.
TORCH_BUFFERSIZE	100	Size in MB of the webclientbuffer that interacts with the FHIR server
TORCH_CONCEPT_TREE_FILE	ontology/mapping_tree.json	The file for the concept tree mapping.
TORCH_DSE_MAPPING_TREE_FILE	ontology/dse_mapping_tree.json	The file for DSE concept tree mapping.
TORCH_USE_CQL	true	Flag indicating if CQL should be used.
TORCH_BASE_URL	http://localhost:8080	The server name before the proxy from which torch is accessed
TORCH_OUTPUT_FILE_SERVER_URL	http://localhost:8080/output	The URL to access Result location TORCH_RESULTS_DIR served by a proxy/fileserver
LOG_LEVEL	info	Log level for torch core functionality.
LOG_LEVEL _CA_UHN_FHIR	error	Log level for HAPI FHIR library.
SPRING_PROFILES_ACTIVE	active	The active Spring profile.
SPRING_CODEC_MAX_IN_MEMORY_SIZE	100MB	The maximum in-memory size for Spring codecs.