diff options
Diffstat (limited to 'src/main/kotlin/dev')
| -rw-r--r-- | src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt | 29 | ||||
| -rw-r--r-- | src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt | 29 |
2 files changed, 36 insertions, 22 deletions
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt b/src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt index 36c9705..f2509dd 100644 --- a/src/main/kotlin/dev/dnpm/etl/processor/monitoring/Request.kt +++ b/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 (" + - "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + - "WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " + - ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;") + @Query( + "SELECT count(*) AS count, status FROM (" + + "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + + "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 (" + - "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + - "WHERE type = 'DELETE'" + - ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;") + @Query( + "SELECT count(*) AS count, status FROM (" + + "SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " + + "WHERE type = 'DELETE'" + + ") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;" + ) fun findPatientUniqueDeleteStates(): List<CountedState> -}
\ No newline at end of file +} 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<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 { |