From 3d9d84438d2c17f09c3ccf02c8a6337320367659 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Thu, 4 Sep 2025 12:47:56 +0200 Subject: [PATCH] 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 --- .../pseudonym/GpasPseudonymGenerator.java | 49 +++++++++---------- .../processor/services/ConsentProcessor.kt | 29 ++++++----- 2 files changed, 40 insertions(+), 38 deletions(-) diff --git a/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java b/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java index 6a2b947..ea0d20f 100644 --- a/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java +++ b/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 = "$pseudonymizeAllowCreate"; - protected final static String createMultiDomainPsn = "$pseudonymize-secondary"; - private final static String SINGLE_PSN_PART_NAME = "pseudonym"; - private final static String MULTI_PSN_PART_NAME = "value"; + protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate"; + protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary"; + private static final String SINGLE_PSN_PART_NAME = "pseudonym"; + 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) { - if (rce instanceof BadRequest) { - String msg = "gPas or request configuration is incorrect. Please check both." - + rce.getMessage(); - log.debug( - msg); - throw new PseudonymRequestFailed(msg, rce); - } - if (rce instanceof Unauthorized) { - var msg = "gPas access credentials are invalid check your configuration. msg: '%s".formatted( - rce.getMessage()); - log.error(msg); - throw new PseudonymRequestFailed(msg, rce); - } - } catch (Exception unexpected) { + } catch (BadRequest e) { + String msg = "gPas or request configuration is incorrect. Please check both." + + e.getMessage(); + log.error(msg); + throw new PseudonymRequestFailed(msg, e); + } catch (Unauthorized e) { + var msg = "gPas access credentials are invalid check your configuration. msg: '%s" + .formatted(e.getMessage()); + log.error(msg); + throw new PseudonymRequestFailed(msg, e); + } + 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."); diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt index 2ed21eb..381f38a 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt +++ b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt @@ -137,15 +137,7 @@ class ConsentProcessor( } val provisionComponent: ProvisionComponent = provisions.first() - - 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 - } - } - + val provisionCode = getProvisionCode(provisionComponent) 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 ): 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 {