refactor: several changes related to code style and readability (#152)

* refactor: extract provision code extraction
* refactor: catch exceptions by type without later type check
* refactor: further code cleanup
* chore: log error with error level, not debug level

build.gradle.kts

@@ -7,22 +7,22 @@ plugins {
     war
     id("org.springframework.boot") version "3.5.5"
     id("io.spring.dependency-management") version "1.1.7"
-    kotlin("jvm") version "1.9.25"
+    kotlin("jvm") version "2.2.10"
-    kotlin("plugin.spring") version "1.9.25"
+    kotlin("plugin.spring") version "2.2.10"
     jacoco
 }
 
 group = "dev.dnpm"
-version = "0.11.0"
+version = "0.12.0-SNAPSHOT"
 
 var versions = mapOf(
     "mtb-dto" to "0.1.0-SNAPSHOT",
-    "hapi-fhir" to "7.6.1",
+    "hapi-fhir" to "8.4.0",
-    "mockito-kotlin" to "5.4.0",
+    "mockito-kotlin" to "6.0.0",
-    "archunit" to "1.3.0",
+    "archunit" to "1.4.1",
     // Webjars
     "webjars-locator" to "0.52",
-    "echarts" to "5.4.3",
+    "echarts" to "6.0.0",
     "htmx.org" to "1.9.12"
 )
 

src/integrationTest/kotlin/dev/dnpm/etl/processor/web/HomeControllerTest.kt

@@ -282,6 +282,30 @@ class HomeControllerTest {
             assertThat(page.querySelectorAll("tbody tr")).isEmpty()
             assertThat(page.querySelectorAll("div.notification.info")).hasSize(1)
         }
+
+        @Test
+        @WithMockUser(username = "admin", roles = ["ADMIN"])
+        fun testShouldShowNoConsentStatusBadge() {
+            whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
+                PageImpl(
+                    listOf(
+                        Request(
+                            1L,
+                            randomRequestId(),
+                            PatientPseudonym("PSEUDO1"),
+                            PatientId("PATIENT1"),
+                            Fingerprint("ashdkasdh"),
+                            RequestType.MTB_FILE,
+                            RequestStatus.NO_CONSENT
+                        )
+                    )
+                )
+            )
+
+            val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
+            assertThat(page.querySelectorAll("tbody tr")).hasSize(1)
+            assertThat(page.querySelectorAll("tbody tr > td > small").first().textContent).isEqualTo("NO_CONSENT")
+        }
     }
 
 }

src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java

@@ -23,8 +23,6 @@ import ca.uhn.fhir.context.FhirContext;
 import ca.uhn.fhir.parser.IParser;
 import dev.dnpm.etl.processor.config.AppFhirConfig;
 import dev.dnpm.etl.processor.config.GPasConfigProperties;
-import java.net.URI;
-import java.net.URISyntaxException;
 import org.apache.commons.lang3.NotImplementedException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.hc.core5.net.URIBuilder;
@@ -39,9 +37,11 @@ import org.springframework.http.*;
 import org.springframework.retry.support.RetryTemplate;
 import org.springframework.web.client.HttpClientErrorException.BadRequest;
 import org.springframework.web.client.HttpClientErrorException.Unauthorized;
-import org.springframework.web.client.RestClientException;
 import org.springframework.web.client.RestTemplate;
 
+import java.net.URI;
+import java.net.URISyntaxException;
+
 public class GpasPseudonymGenerator implements Generator {
 
     private final FhirContext r4Context;
@@ -52,10 +52,10 @@ public class GpasPseudonymGenerator implements Generator {
     private final RestTemplate restTemplate;
     private final @NotNull String genomDeTanDomain;
     private final @NotNull String pidPsnDomain;
-    protected final static String createOrGetPsn = "$pseudonymizeAllowCreate";
+    protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate";
-    protected final static String createMultiDomainPsn = "$pseudonymize-secondary";
+    protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary";
-    private final static String SINGLE_PSN_PART_NAME = "pseudonym";
+    private static final String SINGLE_PSN_PART_NAME = "pseudonym";
-    private final static String MULTI_PSN_PART_NAME = "value";
+    private static final String MULTI_PSN_PART_NAME = "value";
 
     public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
         RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
@@ -85,7 +85,7 @@ public class GpasPseudonymGenerator implements Generator {
         switch (domainType) {
             case SINGLE_PSN_DOMAIN -> {
                 final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
+                final var responseEntity = getGpasPseudonym(requestBody, CREATE_OR_GET_PSN);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -93,7 +93,7 @@ public class GpasPseudonymGenerator implements Generator {
             }
             case MULTI_PSN_DOMAIN -> {
                 final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
-                final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
+                final var responseEntity = getGpasPseudonym(requestBody, CREATE_MULTI_DOMAIN_PSN);
                 final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
                     .parseResource(responseEntity.getBody());
 
@@ -150,23 +150,22 @@ public class GpasPseudonymGenerator implements Generator {
                 log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
                 return responseEntity;
             }
-        } catch (RestClientException rce) {
+        } catch (BadRequest e) {
-            if (rce instanceof BadRequest) {
+            String msg = "gPas or request configuration is incorrect. Please check both."
-                String msg = "gPas or request configuration is incorrect. Please check both."
+                + e.getMessage();
-                    + rce.getMessage();
+            log.error(msg);
-                log.debug(
+            throw new PseudonymRequestFailed(msg, e);
-                    msg);
+        } catch (Unauthorized e) {
-                throw new PseudonymRequestFailed(msg, rce);
+            var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s"
-            }
+                .formatted(e.getMessage());
-            if (rce instanceof Unauthorized) {
+            log.error(msg);
-                var msg = "gPas access credentials are invalid  check your configuration. msg:  '%s".formatted(
+            throw new PseudonymRequestFailed(msg, e);
-                    rce.getMessage());
+        }
-                log.error(msg);
+        catch (Exception unexpected) {
-                throw new PseudonymRequestFailed(msg, rce);
-            }
-        } catch (Exception unexpected) {
             throw new PseudonymRequestFailed(
-                "API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
+                "API request due unexpected error unsuccessful gPas unsuccessful.",
+                unexpected
+            );
         }
         throw new PseudonymRequestFailed(
             "API request due unexpected error unsuccessful gPas unsuccessful.");

src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt

@@ -30,6 +30,7 @@ import org.springframework.data.relational.core.mapping.Table
 import org.springframework.data.repository.CrudRepository
 import org.springframework.data.repository.PagingAndSortingRepository
 import java.time.Instant
+import java.time.temporal.ChronoUnit
 import java.util.*
 
 @Table("request")
@@ -65,6 +66,12 @@ data class Request(
         processedAt: Instant
     ) :
             this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
+
+    fun isPendingUnknown(): Boolean {
+        return this.status == RequestStatus.UNKNOWN && this.processedAt.isBefore(
+            Instant.now().minus(10, ChronoUnit.MINUTES)
+        )
+    }
 }
 
 @JvmRecord
@@ -90,19 +97,23 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
     @Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
     fun countStates(): List<CountedState>
 
-    @Query("SELECT count(*) AS count, status FROM (" +
+    @Query(
-            "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
+        "SELECT count(*) AS count, status FROM (" +
-            "WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
+                "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
-            ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
+                "WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
+                ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
+    )
     fun findPatientUniqueStates(): List<CountedState>
 
     @Query("SELECT count(*) AS count, status FROM request WHERE type = 'DELETE' GROUP BY status ORDER BY status, count DESC;")
     fun countDeleteStates(): List<CountedState>
 
-    @Query("SELECT count(*) AS count, status FROM (" +
+    @Query(
-            "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
+        "SELECT count(*) AS count, status FROM (" +
-            "WHERE type = 'DELETE'" +
+                "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
-            ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
+                "WHERE type = 'DELETE'" +
+                ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
+    )
     fun findPatientUniqueDeleteStates(): List<CountedState>
 
 }

src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt

@@ -137,15 +137,7 @@ class ConsentProcessor(
             }
 
             val provisionComponent: ProvisionComponent = provisions.first()
-
+            val provisionCode = getProvisionCode(provisionComponent)
-            var provisionCode: String? = null
-            if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
-                val codableConcept: CodeableConcept = provisionComponent.code.first()
-                if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
-                    provisionCode = codableConcept.coding.first().code
-                }
-            }
-
             if (provisionCode != null) {
                 try {
                     val modelProjectConsentPurpose =
@@ -177,6 +169,17 @@ class ConsentProcessor(
         }
     }
 
+    private fun getProvisionCode(provisionComponent: ProvisionComponent): String? {
+        var provisionCode: String? = null
+        if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
+            val codableConcept: CodeableConcept = provisionComponent.code.first()
+            if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
+                provisionCode = codableConcept.coding.first().code
+            }
+        }
+        return provisionCode
+    }
+
     private fun setGenomDeSubmissionType(mtbFile: Mtb) {
         if (appConfigProperties.genomDeTestSubmission) {
             mtbFile.metadata.type = MvhSubmissionType.TEST
@@ -238,9 +241,9 @@ class ConsentProcessor(
             consent.provision.provision.filter { subProvision ->
                 isRequestDateInRange(requestDate, subProvision.period)
                 // search coding entries of current provision for code and system
-                subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
+                subProvision.code.map { c -> c.coding }.flatten().any { code ->
                     targetCode.equals(code.code) && targetSystem.equals(code.system)
-                } != null
+                }
             }.map { subProvision ->
                 subProvision
             }
@@ -257,11 +260,11 @@ class ConsentProcessor(
         researchAllowedPolicySystem: String?,
         policyRules: Collection<Coding>
     ): Boolean {
-        return policyRules.find { code ->
+        return policyRules.any { code ->
             researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
                 code.getCode()
             ))
-        } != null
+        }
     }
 
     fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {

src/main/resources/templates/index.html

@@ -52,8 +52,10 @@
                         <td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
                         <td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
-                        <td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
+                        <td th:if="${request.status.value == 'unknown' and not request.isPendingUnknown()}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
+                        <td th:if="${request.status.value == 'unknown' and request.isPendingUnknown()}" class="bg-yellow"><small>⏰ [[ ${request.status} ]] ⏰</small></td>
                         <td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
+                        <td th:if="${request.status.value == 'no-consent'}" class="bg-blue"><small>[[ ${request.status} ]]</small></td>
                         <td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>
                         <td th:if="not ${request.report}">[[ ${request.uuid} ]]</td>
                         <td th:if="${request.report}">