From abd709a4b9d82c901ffda2a291cacca876969154 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Wed, 11 Oct 2023 18:55:23 +0200 Subject: [PATCH 01/20] 1.0.0.0 release --- codex-process-data-transfer/pom.xml | 2 +- .../data_transfer/DataTransferProcessPluginDefinition.java | 2 +- codex-processes-ap1-test-data-generator/pom.xml | 2 +- pom.xml | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/codex-process-data-transfer/pom.xml b/codex-process-data-transfer/pom.xml index cb64f64..91e1ee9 100644 --- a/codex-process-data-transfer/pom.xml +++ b/codex-process-data-transfer/pom.xml @@ -8,7 +8,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0-SNAPSHOT + 1.0.0.0 diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java index f07e995..b21a881 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java @@ -18,7 +18,7 @@ public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition { public static final String VERSION = "1.0.0.0"; - public static final LocalDate DATE = LocalDate.of(2023, 9, 25); + public static final LocalDate DATE = LocalDate.of(2023, 10, 11); @Override public String getName() diff --git a/codex-processes-ap1-test-data-generator/pom.xml b/codex-processes-ap1-test-data-generator/pom.xml index 06758a3..d1c5fc7 100644 --- a/codex-processes-ap1-test-data-generator/pom.xml +++ b/codex-processes-ap1-test-data-generator/pom.xml @@ -6,7 +6,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0-SNAPSHOT + 1.0.0.0 diff --git a/pom.xml b/pom.xml index 108718b..59d3cb1 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0-SNAPSHOT + 1.0.0.0 pom From a8e1ea36cba9c87522054ce1be2e5593c8781cc8 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Sat, 16 Mar 2024 21:15:10 +0100 Subject: [PATCH 02/20] updated version to 1.0.0.1-SNAPSHOT --- codex-process-data-transfer/pom.xml | 2 +- codex-processes-ap1-test-data-generator/pom.xml | 2 +- pom.xml | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/codex-process-data-transfer/pom.xml b/codex-process-data-transfer/pom.xml index 91e1ee9..11fe347 100644 --- a/codex-process-data-transfer/pom.xml +++ b/codex-process-data-transfer/pom.xml @@ -8,7 +8,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0 + 1.0.0.1-SNAPSHOT diff --git a/codex-processes-ap1-test-data-generator/pom.xml b/codex-processes-ap1-test-data-generator/pom.xml index d1c5fc7..283f9a8 100644 --- a/codex-processes-ap1-test-data-generator/pom.xml +++ b/codex-processes-ap1-test-data-generator/pom.xml @@ -6,7 +6,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0 + 1.0.0.1-SNAPSHOT diff --git a/pom.xml b/pom.xml index 59d3cb1..d6b6337 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.0 + 1.0.0.1-SNAPSHOT pom @@ -20,7 +20,7 @@ ${project.basedir} 5.1.0 - 1.3.0 + 1.5.0 Business processes for the NUM RDP project (AP1) as plugins for the Data Sharing Framework. From 40f5b9be258d1a3ddc17b20f87a58a1c06c8abce Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Sat, 16 Mar 2024 21:18:38 +0100 Subject: [PATCH 03/20] replaced default SearchBundle to match up required searches for Risk Principe --- .../resources/fhir/Bundle/SearchBundle.xml | 24 +++---------------- 1 file changed, 3 insertions(+), 21 deletions(-) diff --git a/codex-process-data-transfer/src/main/resources/fhir/Bundle/SearchBundle.xml b/codex-process-data-transfer/src/main/resources/fhir/Bundle/SearchBundle.xml index 4372c16..ec284ed 100644 --- a/codex-process-data-transfer/src/main/resources/fhir/Bundle/SearchBundle.xml +++ b/codex-process-data-transfer/src/main/resources/fhir/Bundle/SearchBundle.xml @@ -3,7 +3,7 @@ - + @@ -15,31 +15,13 @@ - + - - - - - - - - - - - - - - - - - - - + From 19c89098d9d8745b62a8ea0af7c415e718a69bc7 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Sat, 16 Mar 2024 21:38:19 +0100 Subject: [PATCH 04/20] added basic support for Specimen resource --- .../data_transfer/service/send/ReadData.java | 35 +++++++------------ 1 file changed, 12 insertions(+), 23 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java index 68db13e..db224b5 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java @@ -25,51 +25,30 @@ import org.camunda.bpm.engine.delegate.BpmnError; import org.camunda.bpm.engine.delegate.DelegateExecution; -import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.*; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; import org.hl7.fhir.r4.model.Bundle.BundleType; import org.hl7.fhir.r4.model.Bundle.HTTPVerb; -import org.hl7.fhir.r4.model.CanonicalType; -import org.hl7.fhir.r4.model.Condition; import org.hl7.fhir.r4.model.Condition.ConditionEvidenceComponent; import org.hl7.fhir.r4.model.Condition.ConditionStageComponent; -import org.hl7.fhir.r4.model.Consent; import org.hl7.fhir.r4.model.Consent.ConsentVerificationComponent; import org.hl7.fhir.r4.model.Consent.provisionActorComponent; import org.hl7.fhir.r4.model.Consent.provisionComponent; import org.hl7.fhir.r4.model.Consent.provisionDataComponent; -import org.hl7.fhir.r4.model.DateTimeType; -import org.hl7.fhir.r4.model.DiagnosticReport; import org.hl7.fhir.r4.model.DiagnosticReport.DiagnosticReportMediaComponent; -import org.hl7.fhir.r4.model.DomainResource; -import org.hl7.fhir.r4.model.Encounter; import org.hl7.fhir.r4.model.Encounter.DiagnosisComponent; import org.hl7.fhir.r4.model.Encounter.EncounterHospitalizationComponent; import org.hl7.fhir.r4.model.Encounter.EncounterLocationComponent; import org.hl7.fhir.r4.model.Encounter.EncounterParticipantComponent; -import org.hl7.fhir.r4.model.IdType; -import org.hl7.fhir.r4.model.Identifier; -import org.hl7.fhir.r4.model.Immunization; import org.hl7.fhir.r4.model.Immunization.ImmunizationPerformerComponent; import org.hl7.fhir.r4.model.Immunization.ImmunizationProtocolAppliedComponent; import org.hl7.fhir.r4.model.Immunization.ImmunizationReactionComponent; -import org.hl7.fhir.r4.model.InstantType; -import org.hl7.fhir.r4.model.Medication; import org.hl7.fhir.r4.model.Medication.MedicationIngredientComponent; -import org.hl7.fhir.r4.model.MedicationAdministration; import org.hl7.fhir.r4.model.MedicationAdministration.MedicationAdministrationPerformerComponent; -import org.hl7.fhir.r4.model.MedicationStatement; -import org.hl7.fhir.r4.model.Meta; -import org.hl7.fhir.r4.model.Observation; -import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient.ContactComponent; import org.hl7.fhir.r4.model.Patient.PatientLinkComponent; -import org.hl7.fhir.r4.model.Procedure; import org.hl7.fhir.r4.model.Procedure.ProcedureFocalDeviceComponent; import org.hl7.fhir.r4.model.Procedure.ProcedurePerformerComponent; -import org.hl7.fhir.r4.model.Reference; -import org.hl7.fhir.r4.model.Resource; -import org.hl7.fhir.r4.model.Task; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -645,7 +624,6 @@ else if (resource instanceof Observation o) cleanUnsupportedReferences(o, "Observation.focus", Observation::hasFocus, Observation::setFocus); cleanUnsupportedReferences(o, "Observation.performer", Observation::hasPerformer, Observation::setPerformer); - cleanUnsupportedReference(o, "Observation.specimen", Observation::hasSpecimen, Observation::setSpecimen); cleanUnsupportedReference(o, "Observation.device", Observation::hasDevice, Observation::setDevice); cleanUnsupportedReferences(o, "Observation.derivedFrom", Observation::hasDerivedFrom, Observation::setDerivedFrom); @@ -674,6 +652,11 @@ else if (resource instanceof Procedure p) cleanUnsupportedReferences(p, "Procedure.usedReference", Procedure::hasUsedReference, Procedure::setUsedReference); } + else if (resource instanceof Specimen s) + { + // todo + + } else throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); } @@ -741,6 +724,12 @@ else if (resource instanceof Procedure p) p.setIdentifier(Collections.emptyList()); p.setSubject(patientRef); } + else if (resource instanceof Specimen s) + { + s.setIdentifier(Collections.emptyList()); + s.setAccessionIdentifier(null); + s.setSubject(patientRef); + } else throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); } From cea20b56a35613a3b1fc0b932f038b10a87c9294 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Sat, 16 Mar 2024 21:43:06 +0100 Subject: [PATCH 05/20] disabled tests, needs to be modified to use the tested SearchBundle and not the default one --- .../codex/processes/PolarDataTest.java | 2 ++ .../data_transfer/client/fhir/AbstractFhirClientTest.java | 2 ++ .../codex/processes/data_transfer/validation/MiiTest.java | 2 ++ .../data_transfer/validation/ValidateDataLearningTest.java | 2 ++ .../data_transfer/variables/PatientReferenceListTest.java | 2 ++ .../processes/data_transfer/variables/PatientReferenceTest.java | 2 ++ .../processes/fhir/profile/ActivityDefinitionProfileTest.java | 2 ++ .../codex/processes/fhir/profile/TaskProfileTest.java | 2 ++ 8 files changed, 16 insertions(+) diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/PolarDataTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/PolarDataTest.java index 2504c61..012ff9f 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/PolarDataTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/PolarDataTest.java @@ -54,6 +54,7 @@ import org.hl7.fhir.r4.model.Procedure; import org.hl7.fhir.r4.model.Reference; import org.hl7.fhir.r4.model.Resource; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -85,6 +86,7 @@ import de.rwh.utils.crypto.io.PemIo; import dev.dsf.fhir.validation.ValueSetExpanderImpl; +@Ignore public class PolarDataTest { private static final Logger logger = LoggerFactory.getLogger(PolarDataTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java index 7c4ea6b..f4d5c45 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java @@ -14,6 +14,7 @@ import java.util.Date; import org.hl7.fhir.r4.model.Bundle; +import org.junit.Ignore; import org.junit.Test; import org.mockito.Mockito; import org.slf4j.Logger; @@ -25,6 +26,7 @@ import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.domain.DateWithPrecision; import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; +@Ignore public class AbstractFhirClientTest { private static final Logger logger = LoggerFactory.getLogger(AbstractFhirClientTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java index f385c0d..ba3b27a 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java @@ -22,6 +22,7 @@ import java.util.stream.Stream; import org.bouncycastle.pkcs.PKCSException; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -37,6 +38,7 @@ import de.rwh.utils.crypto.io.PemIo; import dev.dsf.fhir.validation.ValueSetExpanderImpl; +@Ignore public class MiiTest { private static final Logger logger = LoggerFactory.getLogger(MiiTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java index b94938e..8c7cfa6 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java @@ -45,6 +45,7 @@ import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent; import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -66,6 +67,7 @@ import dev.dsf.fhir.validation.ValidationSupportWithCustomResources; import dev.dsf.fhir.validation.ValueSetExpanderImpl; +@Ignore public class ValidateDataLearningTest { private static final Logger logger = LoggerFactory.getLogger(ValidateDataLearningTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceListTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceListTest.java index aad7e13..e31b3cb 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceListTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceListTest.java @@ -10,6 +10,7 @@ import java.util.UUID; import org.hl7.fhir.r4.model.Identifier; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -19,6 +20,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.json.JsonMapper; +@Ignore public class PatientReferenceListTest { private static final Logger logger = LoggerFactory.getLogger(PatientReferenceListTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceTest.java index 39b4314..abe0d61 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/variables/PatientReferenceTest.java @@ -9,6 +9,7 @@ import java.util.UUID; import org.hl7.fhir.r4.model.Identifier; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -18,6 +19,7 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.json.JsonMapper; +@Ignore public class PatientReferenceTest { private static final Logger logger = LoggerFactory.getLogger(PatientReferenceTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java index fd83870..0d13290 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java @@ -8,6 +8,7 @@ import org.hl7.fhir.r4.model.ActivityDefinition; import org.junit.ClassRule; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -21,6 +22,7 @@ import dev.dsf.fhir.validation.ResourceValidatorImpl; import dev.dsf.fhir.validation.ValidationSupportRule; +@Ignore public class ActivityDefinitionProfileTest { private static final Logger logger = LoggerFactory.getLogger(ActivityDefinitionProfileTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java index 93548e2..739e316 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java @@ -62,6 +62,7 @@ import org.hl7.fhir.r4.model.Task.TaskStatus; import org.hl7.fhir.r4.model.UnsignedIntType; import org.junit.ClassRule; +import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -78,6 +79,7 @@ import dev.dsf.fhir.validation.ResourceValidatorImpl; import dev.dsf.fhir.validation.ValidationSupportRule; +@Ignore public class TaskProfileTest { private static final Logger logger = LoggerFactory.getLogger(TaskProfileTest.class); From 56a883a8c73f6270794c21bcf387143dc251da40 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 18 Mar 2024 18:55:45 +0100 Subject: [PATCH 06/20] allow the usage of local pseudonyms --- .../DataTransferProcessPluginDefinition.java | 4 +- .../data_transfer/client/FttpClient.java | 2 + .../client/FttpClientFactory.java | 14 ++++- .../data_transfer/client/FttpClientImpl.java | 36 ++++++++++++ .../service/send/ResolvePsn.java | 58 +++++++++++++++---- 5 files changed, 99 insertions(+), 15 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java index b21a881..228342e 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java @@ -17,8 +17,8 @@ public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition { - public static final String VERSION = "1.0.0.0"; - public static final LocalDate DATE = LocalDate.of(2023, 10, 11); + public static final String VERSION = "1.0.0.1"; + public static final LocalDate DATE = LocalDate.of(2024, 3, 18); @Override public String getName() diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java index 236910f..1dba9d6 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClient.java @@ -18,5 +18,7 @@ public interface FttpClient */ Optional getDicPseudonym(String bloomFilter); + Optional getDicPseudonymForLocalPseudonym(String localPseudonym); + void testConnection(); } diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java index bbffd72..3a2eac6 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientFactory.java @@ -62,6 +62,18 @@ public Optional getDicPseudonym(String bloomFilter) return pseudonym; } + @Override + public Optional getDicPseudonymForLocalPseudonym(String localPseudonym) + { + Optional pseudonym = sha256(localPseudonym).map(p -> "dic_test/" + p); + + logger.warn( + "Returning simulated DIC pseudonym '{}' for local pseudonym '{}', fTTP connection not configured.", + pseudonym.orElseThrow(), localPseudonym); + + return pseudonym; + } + private Optional sha256(String original) { try @@ -142,7 +154,7 @@ public void testConnection() { logger.info( "Testing connection to fTTP with {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {}," - + " basicAuthUsername {}, basicAuthPassword {}, serverBase: {}, apiKey: {}, study: {}, target: {}, proxyUrl {}, proxyUsername, proxyPassword {}}", + + " basicAuthUsername: {}, basicAuthPassword: {}, serverBase: {}, apiKey: {}, study: {}, target: {}, proxyUrl: {}, proxyUsername: {}, proxyPassword: {}}", trustStorePath, certificatePath, privateKeyPath, privateKeyPassword != null ? "***" : "null", fttpBasicAuthUsername, fttpBasicAuthPassword != null ? "***" : "null", fttpServerBase, fttpApiKey != null ? "***" : "null", fttpStudy, fttpTarget, proxyUrl, proxyUsername, diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java index 5b95253..e5c9cb1 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/FttpClientImpl.java @@ -154,6 +154,18 @@ protected Parameters createParametersForPsnWorkflow(String dicSourceAndPseudonym return p; } + protected Parameters createParametersForPsnWorkflowLocalPseudonym(String localPseudonym) + { + Parameters p = new Parameters(); + p.addParameter("study", fttpStudy); + p.addParameter("original", localPseudonym); + p.addParameter("source", "local"); + p.addParameter("target", fttpTarget); + p.addParameter("apikey", fttpApiKey); + + return p; + } + @Override public Optional getDicPseudonym(String bloomFilter) { @@ -178,6 +190,30 @@ public Optional getDicPseudonym(String bloomFilter) } } + @Override + public Optional getDicPseudonymForLocalPseudonym(String localPseudonym) + { + Objects.requireNonNull(localPseudonym, "localPseudonym"); + + logger.info("Requesting DIC Pseudonym for local Pseudonym {} ...", localPseudonym); + + try + { + IGenericClient client = createGenericClient(); + + Parameters parameters = client.operation().onServer().named("requestPsnWorkflow") + .withParameters(createParametersForPsnWorkflowLocalPseudonym(localPseudonym)) + .accept(Constants.CT_FHIR_XML_NEW).encoded(EncodingEnum.XML).execute(); + + return getPseudonym(parameters).map(p -> fttpTarget + "/" + p); + } + catch (Exception e) + { + logger.error("Error while retrieving DIC pseudonym: {} - {}", e.getClass().getName(), e.getMessage()); + throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_FTTP_NOT_REACHABLE, e.getMessage()); + } + } + protected Parameters createParametersForBfWorkflow(String bloomFilter) { Parameters p = new Parameters(); diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java index aa0e14b..25b77bc 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java @@ -1,12 +1,6 @@ package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.send; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PATIENT_REFERENCE; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_PATIENT_NOT_FOUND; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_CODE; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_SYSTEM; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.*; import java.util.Objects; import java.util.Optional; @@ -94,8 +88,33 @@ private Optional getPseudonym(Patient patient) private String resolvePseudonymAndUpdatePatient(Patient patient) { - String bloomFilter = getBloomFilter(patient); - String pseudonym = resolveBloomFilter(bloomFilter); + String pseudonym; + // first try to find a bloom filter + Optional bloomFilter = getBloomFilter(patient); + if (bloomFilter.isPresent()) + { + pseudonym = resolveBloomFilter(bloomFilter.get()); + } + else + { + // otherwise try to find a local pseudonym + // --> no record linkage + logger.info( + "No bloom filter present for patient {}. Try to use the local pseudonym for data transfer without record linkage", + patient.getIdElement().getValue()); + Optional localPseudonym = getLocalPseudonym(patient); + if (localPseudonym.isPresent()) + { + pseudonym = resolveLocalPseudonym(localPseudonym.get()); + } + else + { + logger.info("No local pseudonym present for patient {}. Aborted", patient.getIdElement().getValue()); + throw new RuntimeException("Could not find pseudonym"); + } + + + } patient.getIdentifier().removeIf(i -> NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER.equals(i.getSystem())); patient.addIdentifier().setSystem(NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM).setValue(pseudonym).getType() @@ -107,12 +126,18 @@ private String resolvePseudonymAndUpdatePatient(Patient patient) return pseudonym; } - private String getBloomFilter(Patient patient) + private Optional getBloomFilter(Patient patient) { return patient.getIdentifier().stream().filter(Identifier::hasSystem) .filter(i -> NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER.equals(i.getSystem())).filter(Identifier::hasValue) - .findFirst().map(Identifier::getValue).orElseThrow(() -> new RuntimeException( - "No bloom filter present in patient " + patient.getIdElement().getValue())); + .findFirst().map(Identifier::getValue); + } + + private Optional getLocalPseudonym(Patient patient) + { + return patient.getIdentifier().stream().filter(Identifier::hasSystem) + .filter(i -> RFC_4122_SYSTEM.equals(i.getSystem())).filter(Identifier::hasValue).findFirst() + .map(Identifier::getValue); } private String resolveBloomFilter(String bloomFilter) @@ -123,6 +148,15 @@ private String resolveBloomFilter(String bloomFilter) "Unable to get DIC pseudonym for given BloomFilter")); } + private String resolveLocalPseudonym(String localPseudonym) + { + return fttpClientFactory.getFttpClient().getDicPseudonym(localPseudonym) + .orElseThrow(() -> new BpmnError( + CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER, + "Unable to get DIC pseudonym for given BloomFilter")); + } + + private void updatePatient(Patient patient) { dataStoreClientFactory.getDataStoreClient().getFhirClient().updatePatient(patient); From e21f00fa3a33dbb031f077d05d3d439f562ad12a Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:12:02 +0100 Subject: [PATCH 07/20] re-enabled tests --- .../client/fhir/AbstractFhirClientTest.java | 14 ++---- .../data_transfer/validation/MiiTest.java | 2 - .../validation/ValidateDataLearningTest.java | 21 +-------- .../ActivityDefinitionProfileTest.java | 2 - .../fhir/profile/TaskProfileTest.java | 2 - .../resources/fhir/Bundle/SearchBundle.xml | 46 +++++++++++++++++++ 6 files changed, 53 insertions(+), 34 deletions(-) create mode 100644 codex-process-data-transfer/src/test/resources/fhir/Bundle/SearchBundle.xml diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java index f4d5c45..95aae15 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java @@ -1,9 +1,7 @@ package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir; import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM; -import static org.junit.Assert.assertEquals; -import static org.junit.Assert.assertNotNull; -import static org.junit.Assert.assertTrue; +import static org.junit.Assert.*; import static org.mockito.Mockito.CALLS_REAL_METHODS; import static org.mockito.Mockito.when; @@ -14,7 +12,6 @@ import java.util.Date; import org.hl7.fhir.r4.model.Bundle; -import org.junit.Ignore; import org.junit.Test; import org.mockito.Mockito; import org.slf4j.Logger; @@ -26,7 +23,6 @@ import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.domain.DateWithPrecision; import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; -@Ignore public class AbstractFhirClientTest { private static final Logger logger = LoggerFactory.getLogger(AbstractFhirClientTest.class); @@ -38,7 +34,7 @@ public void testSetSearchBundleWithExportTo() throws Exception DataStoreClient dataClient = Mockito.mock(DataStoreClient.class); DataLogger dataLogger = Mockito.mock(DataLogger.class); when(dataClient.getSearchBundleOverride()) - .thenReturn(Paths.get("src/main/resources/fhir/Bundle/SearchBundle.xml")); + .thenReturn(Paths.get("src/test/resources/fhir/Bundle/SearchBundle.xml")); when(dataClient.getFhirContext()).thenReturn(fhirContext); AbstractFhirClient client = Mockito.mock(AbstractFhirClient.class, Mockito.withSettings().useConstructor(dataClient, dataLogger).defaultAnswer(CALLS_REAL_METHODS)); @@ -71,7 +67,7 @@ public void testSetSearchBundleWithExportFromAndExportTo() throws Exception DataStoreClient dataClient = Mockito.mock(DataStoreClient.class); DataLogger dataLogger = Mockito.mock(DataLogger.class); when(dataClient.getSearchBundleOverride()) - .thenReturn(Paths.get("src/main/resources/fhir/Bundle/SearchBundle.xml")); + .thenReturn(Paths.get("src/test/resources/fhir/Bundle/SearchBundle.xml")); when(dataClient.getFhirContext()).thenReturn(fhirContext); AbstractFhirClient client = Mockito.mock(AbstractFhirClient.class, Mockito.withSettings().useConstructor(dataClient, dataLogger).defaultAnswer(CALLS_REAL_METHODS)); @@ -106,7 +102,7 @@ public void testSetSearchBundleWithPatientIdAndExportFromAndExportTo() throws Ex DataStoreClient dataClient = Mockito.mock(DataStoreClient.class); DataLogger dataLogger = Mockito.mock(DataLogger.class); when(dataClient.getSearchBundleOverride()) - .thenReturn(Paths.get("src/main/resources/fhir/Bundle/SearchBundle.xml")); + .thenReturn(Paths.get("src/test/resources/fhir/Bundle/SearchBundle.xml")); when(dataClient.getFhirContext()).thenReturn(fhirContext); AbstractFhirClient client = Mockito.mock(AbstractFhirClient.class, Mockito.withSettings().useConstructor(dataClient, dataLogger).defaultAnswer(CALLS_REAL_METHODS)); @@ -142,7 +138,7 @@ public void testSetSearchBundleWithPseudonymIdAndExportFromAndExportTo() throws DataStoreClient dataClient = Mockito.mock(DataStoreClient.class); DataLogger dataLogger = Mockito.mock(DataLogger.class); when(dataClient.getSearchBundleOverride()) - .thenReturn(Paths.get("src/main/resources/fhir/Bundle/SearchBundle.xml")); + .thenReturn(Paths.get("src/test/resources/fhir/Bundle/SearchBundle.xml")); when(dataClient.getFhirContext()).thenReturn(fhirContext); AbstractFhirClient client = Mockito.mock(AbstractFhirClient.class, Mockito.withSettings().useConstructor(dataClient, dataLogger).defaultAnswer(CALLS_REAL_METHODS)); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java index ba3b27a..f385c0d 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/MiiTest.java @@ -22,7 +22,6 @@ import java.util.stream.Stream; import org.bouncycastle.pkcs.PKCSException; -import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -38,7 +37,6 @@ import de.rwh.utils.crypto.io.PemIo; import dev.dsf.fhir.validation.ValueSetExpanderImpl; -@Ignore public class MiiTest { private static final Logger logger = LoggerFactory.getLogger(MiiTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java index 8c7cfa6..a8a30de 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java @@ -14,15 +14,7 @@ import java.security.cert.Certificate; import java.security.cert.CertificateException; import java.security.cert.X509Certificate; -import java.util.Arrays; -import java.util.Comparator; -import java.util.EnumSet; -import java.util.HashSet; -import java.util.List; -import java.util.Map; -import java.util.Properties; -import java.util.Set; -import java.util.UUID; +import java.util.*; import java.util.function.Consumer; import java.util.function.Function; import java.util.stream.Collectors; @@ -31,21 +23,13 @@ import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService; import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport; import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain; -import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.*; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; -import org.hl7.fhir.r4.model.CanonicalType; -import org.hl7.fhir.r4.model.ElementDefinition; import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent; import org.hl7.fhir.r4.model.Enumerations.BindingStrength; -import org.hl7.fhir.r4.model.OperationOutcome; -import org.hl7.fhir.r4.model.Resource; -import org.hl7.fhir.r4.model.StringType; -import org.hl7.fhir.r4.model.StructureDefinition; -import org.hl7.fhir.r4.model.ValueSet; import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent; import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; -import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -67,7 +51,6 @@ import dev.dsf.fhir.validation.ValidationSupportWithCustomResources; import dev.dsf.fhir.validation.ValueSetExpanderImpl; -@Ignore public class ValidateDataLearningTest { private static final Logger logger = LoggerFactory.getLogger(ValidateDataLearningTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java index 0d13290..fd83870 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/ActivityDefinitionProfileTest.java @@ -8,7 +8,6 @@ import org.hl7.fhir.r4.model.ActivityDefinition; import org.junit.ClassRule; -import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -22,7 +21,6 @@ import dev.dsf.fhir.validation.ResourceValidatorImpl; import dev.dsf.fhir.validation.ValidationSupportRule; -@Ignore public class ActivityDefinitionProfileTest { private static final Logger logger = LoggerFactory.getLogger(ActivityDefinitionProfileTest.class); diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java index 739e316..93548e2 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/fhir/profile/TaskProfileTest.java @@ -62,7 +62,6 @@ import org.hl7.fhir.r4.model.Task.TaskStatus; import org.hl7.fhir.r4.model.UnsignedIntType; import org.junit.ClassRule; -import org.junit.Ignore; import org.junit.Test; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -79,7 +78,6 @@ import dev.dsf.fhir.validation.ResourceValidatorImpl; import dev.dsf.fhir.validation.ValidationSupportRule; -@Ignore public class TaskProfileTest { private static final Logger logger = LoggerFactory.getLogger(TaskProfileTest.class); diff --git a/codex-process-data-transfer/src/test/resources/fhir/Bundle/SearchBundle.xml b/codex-process-data-transfer/src/test/resources/fhir/Bundle/SearchBundle.xml new file mode 100644 index 0000000..05aebb5 --- /dev/null +++ b/codex-process-data-transfer/src/test/resources/fhir/Bundle/SearchBundle.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 833765ba179d9f2eab0c4b5d74792e89f5dba66f Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:12:58 +0100 Subject: [PATCH 08/20] add support for Specimen and contained resources --- .../data_transfer/service/send/ReadData.java | 52 +++++++++++++++++-- 1 file changed, 49 insertions(+), 3 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java index db224b5..f21be9b 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java @@ -25,6 +25,7 @@ import org.camunda.bpm.engine.delegate.BpmnError; import org.camunda.bpm.engine.delegate.DelegateExecution; +import org.hl7.fhir.instance.model.api.IBaseResource; import org.hl7.fhir.r4.model.*; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; import org.hl7.fhir.r4.model.Bundle.BundleType; @@ -155,6 +156,7 @@ protected Bundle toBundle(String pseudonym, Stream resourcesStre .collect(Collectors.toMap(r -> r.getIdElement().toUnqualifiedVersionless().getValue(), r -> "urn:uuid:" + UUID.randomUUID().toString())); + List resourcesWithTemporaryReferences = fixReferences(resources, resourcesById, uuidsById); List entries = resourcesWithTemporaryReferences.stream().map(r -> { @@ -219,12 +221,20 @@ else if (resource instanceof Observation o) Observation::setEncounter); fixReferences(o, uuidsById, "Observation.hasMember", Observation::hasHasMember, Observation::getHasMember, Observation::setHasMember); + fixReference(o, uuidsById, "Observation.specimen", Observation::hasSpecimen, Observation::getSpecimen, + Observation::setSpecimen); } else if (resource instanceof Procedure p) { fixReference(p, uuidsById, "Procedure.encounter", Procedure::hasEncounter, Procedure::getEncounter, Procedure::setEncounter); } + else if (resource instanceof Specimen s) + { + fixReferences(s, uuidsById, "Specimen.parent", Specimen::hasParent, Specimen::getParent, + Specimen::setParent); + } + return resource; } @@ -248,6 +258,18 @@ else if (oldReference.hasReference() && oldReference.getReference() == null && o { logger.debug("Not removing empty reference at {} with data-absent-reason extension", path); } + else if (!oldReference.getResource().isEmpty()) + { + String internalId = "#" + UUID.randomUUID(); + Reference fixedReference = new Reference(internalId); + IBaseResource oldContainedResource = clean((DomainResource) oldReference.getResource()); + oldContainedResource.setId(internalId); + fixedReference.setResource(oldContainedResource); + setReference.apply(resource, fixedReference); + logger.debug( + "Replacing reference to contained resource at {} from resource {} with bundle temporary id in transport bundle", + path, getAbsoluteId(resource).getValue()); + } else { logger.warn("Removing reference at {} from resource {} in transport bundle", path, @@ -286,6 +308,18 @@ else if (oldReference.hasReference() && oldReference.getReference() == null logger.debug("Not removing empty reference at {}[{}] with data-absent-reason extension", path, i); fixedReferences.add(oldReference); } + else if (!oldReference.getResource().isEmpty()) + { + String internalId = "#" + UUID.randomUUID(); + Reference fixedReference = new Reference(internalId); + IBaseResource oldContainedResource = clean((DomainResource) oldReference.getResource()); + oldContainedResource.setId(internalId); + fixedReference.setResource(oldContainedResource); + fixedReferences.add(fixedReference); + logger.debug( + "Replacing reference to contained resource at {}[{}] from resource {} with bundle temporary id in transport bundle", + path, i, getAbsoluteId(resource).getValue()); + } else { logger.warn("Removing reference at {}[{}] from resource {} in transport bundle", path, i, @@ -321,9 +355,10 @@ private R fixReferenceFromComponents(R resource, M i, getAbsoluteId(resource).getValue()); setReference.apply(component, new Reference(uuidsById.get(oldReference.getReference()))); } - else if (oldReference.hasReference() && oldReference.getReference() == null + else if ((oldReference.hasReference() && oldReference.getReference() == null && oldReference.getReferenceElement_() .hasExtension("http://hl7.org/fhir/StructureDefinition/data-absent-reason")) + || oldReference.hasExtension("http://hl7.org/fhir/StructureDefinition/data-absent-reason")) { logger.debug("Not removing empty reference at " + path + " with data-absent-reason extension", i); } @@ -654,8 +689,17 @@ else if (resource instanceof Procedure p) } else if (resource instanceof Specimen s) { - // todo - + cleanUnsupportedReferences(s, "Specimen.request", Specimen::hasRequest, Specimen::setRequest); + cleanUnsupportedReferenceFromComponent(s, "Specimen.collection.collector", Specimen::hasCollection, + Specimen::getCollection, Specimen.SpecimenCollectionComponent::hasCollector, + Specimen.SpecimenCollectionComponent::setCollector); + cleanUnsupportedReferencesFromComponents(s, "Specimen.processing[{}].additive", Specimen::hasProcessing, + Specimen::getProcessing, Specimen.SpecimenProcessingComponent::hasAdditive, + Specimen.SpecimenProcessingComponent::setAdditive); + cleanUnsupportedReferenceFromComponents(s, "Specimen.container[{}].additiveReference", + Specimen::hasContainer, Specimen::getContainer, + Specimen.SpecimenContainerComponent::hasAdditiveReference, + Specimen.SpecimenContainerComponent::setAdditive); } else throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); @@ -734,6 +778,8 @@ else if (resource instanceof Specimen s) throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); } + ((DomainResource) resource).getContained().forEach(r -> setSubjectOrIdentifier(r, pseudonym)); + return resource; } From b89b225fe2dc4ad1cc7fcfff0aaf3ada478ae2cc Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:13:48 +0100 Subject: [PATCH 09/20] changed default packages to those required by risk principe --- .../data_transfer/spring/config/ValidationConfig.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java index 928fa7c..da2387b 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ValidationConfig.java @@ -75,7 +75,7 @@ public static enum TerminologyServerConnectionTestStatus private boolean validationEnabled; @ProcessDocumentation(description = "FHIR implementation guide package used to validated resources, specify as `name|version`", processNames = "wwwnetzwerk-universitaetsmedizinde_dataSend") - @Value("#{'${de.netzwerk.universitaetsmedizin.rdp.validation.package:de.basisprofil.r4|1.4.0,de.medizininformatikinitiative.kerndatensatz.diagnose|1.0.4,de.medizininformatikinitiative.kerndatensatz.fall|1.0.1,de.medizininformatikinitiative.kerndatensatz.laborbefund|1.0.6,de.medizininformatikinitiative.kerndatensatz.medikation|1.0.11,de.medizininformatikinitiative.kerndatensatz.person|1.0.16,de.medizininformatikinitiative.kerndatensatz.prozedur|1.0.7}'.trim().split('(,[ ]?)|(\\n)')}") + @Value("#{'${de.netzwerk.universitaetsmedizin.rdp.validation.package:de.basisprofil.r4|1.4.0,de.medizininformatikinitiative.kerndatensatz.meta|1.0.3,de.medizininformatikinitiative.kerndatensatz.person|2024.0.0-ballot,de.medizininformatikinitiative.kerndatensatz.fall|2024.0.0-ballot,de.medizininformatikinitiative.kerndatensatz.mikrobiologie|2024.0.0}'.trim().split('(,[ ]?)|(\\n)')}") private List validationPackages; @ProcessDocumentation(description = "FHIR implementation guide packages that do not need to be downloaded, list with `name|version` values", processNames = "wwwnetzwerk-universitaetsmedizinde_dataSend") @@ -200,6 +200,8 @@ public static enum TerminologyServerConnectionTestStatus @ProcessDocumentation(description = "List of ValueSet modifier classes, modifiers are executed before atempting to expand a ValueSet and after", processNames = "wwwnetzwerk-universitaetsmedizinde_dataSend") @Value("#{'${de.netzwerk.universitaetsmedizin.rdp.validation.valueset.expansion.modifierClasses:" + + "de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.KdsMikrobiologieBugFixer" + + "," + "de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.MissingEntriesIncluder" + "}'.trim().split('(,[ ]?)|(\\n)')}") private List valueSetModifierClasses; From 812c267d03ca908b5717ae44a337c2ee0b4a52f5 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:14:58 +0100 Subject: [PATCH 10/20] implement fix for invalid xhtml content until https://github.com/medizininformatik-initiative/kerndatensatzmodul-mikrobiologie/issues/18 is fixed --- .../data_transfer/validation/ValidationPackage.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java index 3f14aba..bd848bd 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java @@ -163,8 +163,10 @@ private Consumer doParseResources(FhirContext context, L try { - IBaseResource resource = context.newJsonParser() - .parseResource(new String(entry.getContent(), StandardCharsets.UTF_8)); + String resourceString = new String(entry.getContent(), StandardCharsets.UTF_8); + // fix profiles because their text contains invalid html + resourceString = resourceString.replaceAll("

[\\s\\w\\[\\]]*", ""); + IBaseResource resource = context.newJsonParser().parseResource(resourceString); if (resource instanceof CodeSystem) codeSystems.add((CodeSystem) resource); From e3d077419a362fced7108e0dadb73ce21c39142c Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:15:53 +0100 Subject: [PATCH 11/20] add workarounds until fixed kds mikrobiologie packages are released --- .../ValueSetExpansionClientWithModifiers.java | 4 ++- .../value_set/KdsMikrobiologieBugFixer.java | 36 +++++++++++++++++++ 2 files changed, 39 insertions(+), 1 deletion(-) create mode 100644 codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java index dde91d1..84db1c3 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValueSetExpansionClientWithModifiers.java @@ -11,6 +11,7 @@ import org.hl7.fhir.r4.model.ValueSet; import org.springframework.beans.factory.InitializingBean; +import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.KdsMikrobiologieBugFixer; import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.MissingEntriesIncluder; import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set.ValueSetModifier; import jakarta.ws.rs.WebApplicationException; @@ -18,13 +19,14 @@ public class ValueSetExpansionClientWithModifiers implements ValueSetExpansionClient, InitializingBean { public static final ValueSetModifier MISSING_ENTRIES_INCLUDER = new MissingEntriesIncluder(); + public static final KdsMikrobiologieBugFixer KDS_MIKROBIOLOGIE_BUG_FIXER = new KdsMikrobiologieBugFixer(); private final ValueSetExpansionClient delegate; private final List valueSetModifiers = new ArrayList<>(); public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate) { - this(delegate, Arrays.asList(MISSING_ENTRIES_INCLUDER)); + this(delegate, Arrays.asList(KDS_MIKROBIOLOGIE_BUG_FIXER, MISSING_ENTRIES_INCLUDER)); } public ValueSetExpansionClientWithModifiers(ValueSetExpansionClient delegate, diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java new file mode 100644 index 0000000..44bc8c7 --- /dev/null +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java @@ -0,0 +1,36 @@ +package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.validation.value_set; + +import java.util.Map; + +import org.hl7.fhir.r4.model.ValueSet; + +import ca.uhn.fhir.context.FhirContext; + +public class KdsMikrobiologieBugFixer implements ValueSetModifier +{ + + private final Map fixedValueSets = Map.of( + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc", + "mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json", + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-genotyp-loinc", + "mii-vs-mikrobio-empfindlichkeit.json", + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct", + "mii-vs-mikrobio-mre-klasse-snomedct.json"); + + @Override + public ValueSet modifyPreExpansion(ValueSet vs) + { + + if (vs.getUrl() != null && vs.getVersion() != null && vs.getVersion().equals("2024.0.0")) + { + String fileName = fixedValueSets.get(vs.getUrl()); + if (fileName != null) + { + return (ValueSet) FhirContext.forR4().newJsonParser() + .parseResource(getClass().getResourceAsStream("/bugfix/fhir/ValueSet/" + fileName)); + } + } + + return vs; + } +} From 6ca78a45546c7bafe977c9b1c1d1c51b799e1f51 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:16:41 +0100 Subject: [PATCH 12/20] added fixes for local pseudonyms and ensure compatibility with current blaze fhir server (remove version from id on update) --- .../data_transfer/client/fhir/AbstractFhirClient.java | 1 + .../processes/data_transfer/service/send/ResolvePsn.java | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java index 28717c5..cbc84f2 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java @@ -653,6 +653,7 @@ public void updatePatient(Patient patient) Objects.requireNonNull(patient, "patient"); String id = patient.getIdElement().toVersionless().getValue(); + patient.setId(id); logger.info("Updating patient {}", id); try diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java index 25b77bc..d277dbb 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java @@ -150,10 +150,10 @@ private String resolveBloomFilter(String bloomFilter) private String resolveLocalPseudonym(String localPseudonym) { - return fttpClientFactory.getFttpClient().getDicPseudonym(localPseudonym) + return fttpClientFactory.getFttpClient().getDicPseudonymForLocalPseudonym(localPseudonym) .orElseThrow(() -> new BpmnError( CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER, - "Unable to get DIC pseudonym for given BloomFilter")); + "Unable to get DIC pseudonym for given localPseudonym")); } From aafb7ec9b3599a399d410adc063f50c26118c3cf Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:17:16 +0100 Subject: [PATCH 13/20] added missing valuesets required for KdsMikrobiologieBugFixer --- ...krobio-empfindlichkeit-phenotyp-loinc.json | 55 +++++++++++++++++++ .../mii-vs-mikrobio-empfindlichkeit.json | 38 +++++++++++++ .../mii-vs-mikrobio-mre-klasse-snomedct.json | 48 ++++++++++++++++ 3 files changed, 141 insertions(+) create mode 100644 codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json create mode 100644 codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit.json create mode 100644 codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct.json diff --git a/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json new file mode 100644 index 0000000..f79e32c --- /dev/null +++ b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json @@ -0,0 +1,55 @@ +{ + "resourceType": "ValueSet", + "url": "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc", + "title": "MII VS Mikrobio Empfindlichkeit Phenotyp [LOINC]", + "name": "MII_VS_Mikrobio_Empfindlichkeit_Phenotyp_LOINC", + "status": "active", + "version": "2024.0.0", + "compose": { + "include": [ + { + "filter": [ + { + "property": "CLASS", + "op": "=", + "value": "ABXBACT" + }, + { + "property": "PROPERTY", + "value": "LP6870-2", + "op": "=" + }, + { + "property": "STATUS", + "value": "ACTIVE", + "op": "=" + }, + { + "property": "ORDER_OBS", + "value": "Observation", + "op": "=" + } + ], + "system": "http://loinc.org" + } + ], + "exclude": [ + { + "system": "http://loinc.org", + "filter": [ + { + "property": "METHOD_TYP", + "value": "LP28723-2", + "op": "=" + } + ] + } + ] + }, + "text": { + "status": "generated", + "div": "

MII VS Mikrobio Empfindlichkeit Phenotyp [LOINC]

https://www.medizininformatik-initiative.de/fhir/ext/modul-mikrobiologie/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc
" + }, + "id": "mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc", + "date": "2023-03-02T00:00:00.000Z" +} diff --git a/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit.json b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit.json new file mode 100644 index 0000000..531926d --- /dev/null +++ b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-empfindlichkeit.json @@ -0,0 +1,38 @@ +{ + "resourceType": "ValueSet", + "id": "mii-vs-mikrobio-empfindlichkeit-genotyp-loinc", + "text": { + "status": "generated", + "div": "

MII VS Mikrobio Empfänglichkeit Genotyp

https://www.medizininformatik-initiative.de/fhir/ext/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-genotyp-loinc
" + }, + "url": "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-genotyp-loinc", + "version": "2024.0.0", + "name": "MII_VS_Mikrobio_Empfänglichkeit_Genotyp_LOINC", + "title": "MII VS Mikrobio Empfänglichkeit Genotyp [LOINC]", + "status": "active", + "date": "2023-03-02T00:00:00.000Z", + "compose": { + "include": [ + { + "system": "http://loinc.org", + "filter": [ + { + "property": "CLASS", + "op": "=", + "value": "ABXBACT" + }, + { + "property": "PROPERTY", + "op": "=", + "value": "LP6870-2" + }, + { + "property": "METHOD_TYP", + "op": "=", + "value": "LP28723-2" + } + ] + } + ] + } +} \ No newline at end of file diff --git a/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct.json b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct.json new file mode 100644 index 0000000..ad52e8d --- /dev/null +++ b/codex-process-data-transfer/src/main/resources/bugfix/fhir/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct.json @@ -0,0 +1,48 @@ +{ + "resourceType": "ValueSet", + "url": "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct", + "title": "MII VS Mikrobio MRE Klasse [SNOMED CT]", + "name": "MII_VS_Mikrobio_MRE_Klasse_SNOMEDCT", + "status": "active", + "version": "2024.0.0", + "compose": { + "include": [ + { + "filter": [ + { + "property": "concept", + "op": "is-a", + "value": "409795000" + } + ], + "system": "http://snomed.info/sct" + }, + { + "filter": [ + { + "property": "concept", + "op": "is-a", + "value": "409794001" + } + ], + "system": "http://snomed.info/sct" + }, + { + "filter": [ + { + "property": "concept", + "op": "is-a", + "value": "409793007" + } + ], + "system": "http://snomed.info/sct" + } + ] + }, + "text": { + "status": "generated", + "div": "

MII VS Mikrobio MRE Klasse

https://www.medizininformatik-initiative.de/fhir/ext/modul-mikrobio/ValueSet/mii-vs-mikrobio-mre-klasse-snomedct
" + }, + "id": "mii-vs-mikrobio-mre-klasse-snomedct", + "date": "2023-03-02T00:00:00.000Z" +} \ No newline at end of file From 63b5deffad58f4aaff2f5088d21176c10dba7038 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:18:40 +0100 Subject: [PATCH 14/20] updated docker image versions --- .../docker-compose.yml | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/codex-processes-ap1-docker-test-setup/docker-compose.yml b/codex-processes-ap1-docker-test-setup/docker-compose.yml index 4457050..f40c528 100644 --- a/codex-processes-ap1-docker-test-setup/docker-compose.yml +++ b/codex-processes-ap1-docker-test-setup/docker-compose.yml @@ -74,7 +74,7 @@ services: dic-fhir: - image: ghcr.io/datasharingframework/fhir:1.3.0 + image: ghcr.io/datasharingframework/fhir:1.5.0 restart: "no" ports: - 127.0.0.1:5000:5000 @@ -136,7 +136,7 @@ services: - db - proxy dic-bpe: - image: ghcr.io/datasharingframework/bpe:1.3.0 + image: ghcr.io/datasharingframework/bpe:1.5.0 restart: "no" ports: - 127.0.0.1:5003:5003 @@ -220,7 +220,7 @@ services: aliases: - dic-fhir-store dic-fhir-store-blaze: - image: ghcr.io/num-codex/blaze + image: samply/blaze ports: - 127.0.0.1:8080:8080 environment: @@ -232,7 +232,7 @@ services: dts-fhir: - image: ghcr.io/datasharingframework/fhir:1.3.0 + image: ghcr.io/datasharingframework/fhir:1.5.0 restart: "no" ports: - 127.0.0.1:5001:5001 @@ -293,7 +293,7 @@ services: - db - proxy dts-bpe: - image: ghcr.io/datasharingframework/bpe:1.3.0 + image: ghcr.io/datasharingframework/bpe:1.5.0 restart: "no" ports: - 127.0.0.1:5004:5004 @@ -356,7 +356,7 @@ services: crr-fhir: - image: ghcr.io/datasharingframework/fhir:1.3.0 + image: ghcr.io/datasharingframework/fhir:1.5.0 restart: "no" ports: - 127.0.0.1:5002:5002 @@ -417,7 +417,7 @@ services: - db - proxy crr-bpe: - image: ghcr.io/datasharingframework/bpe:1.3.0 + image: ghcr.io/datasharingframework/bpe:1.5.0 restart: "no" ports: - 127.0.0.1:5005:5005 From eadce42b3ac82e2788ca5921ea3c38a1eba46000 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 09:19:58 +0100 Subject: [PATCH 15/20] add bundle with demo data for risk principe --- .../dic_fhir_store_demo_risk_principe.json | 2068 +++++++++++++++++ 1 file changed, 2068 insertions(+) create mode 100644 codex-process-data-transfer/src/test/resources/fhir/Bundle/dic_fhir_store_demo_risk_principe.json diff --git a/codex-process-data-transfer/src/test/resources/fhir/Bundle/dic_fhir_store_demo_risk_principe.json b/codex-process-data-transfer/src/test/resources/fhir/Bundle/dic_fhir_store_demo_risk_principe.json new file mode 100644 index 0000000..0193624 --- /dev/null +++ b/codex-process-data-transfer/src/test/resources/fhir/Bundle/dic_fhir_store_demo_risk_principe.json @@ -0,0 +1,2068 @@ +{ + "resourceType": "Bundle", + "type": "transaction", + "entry": [ + { + "fullUrl": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba", + "resource": { + "resourceType": "Patient", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/core/modul-person/StructureDefinition/PatientPseudonymisiert" + ] + }, + "identifier": [ + { + "type": { + "coding": [ + { + "code": "PSEUDED", + "system": "http://terminology.hl7.org/CodeSystem/v3-ObservationValue" + } + ] + }, + "system": "urn:ietf:rfc:4122", + "value": "07f602e0-579e-4fe3-95af-381728b00015" + } + ], + "gender": "other", + "_gender": { + "extension": [ + { + "url": "http://fhir.de/StructureDefinition/gender-amtlich-de", + "valueCoding": { + "code": "D", + "system": "http://fhir.de/CodeSystem/gender-amtlich-de", + "display": "divers" + } + } + ] + }, + "birthDate": "2022-12-01", + "managingOrganization": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "MHH" + } + } + }, + "request": { + "method": "POST", + "url": "Patient" + } + }, + { + "fullUrl": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2", + "resource": { + "resourceType": "Encounter", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/StructureDefinition/KontaktGesundheitseinrichtung" + ] + }, + "serviceType": { + "coding": [ + { + "system": "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/CodeSystem/Fachabteilungsschluessel", + "code": "3700", + "display": "Sonstige Fachabteilung", + "userSelected": false + } + ] + }, + "class": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "status": "finished", + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "identifier": [ + { + "type": { + "coding": [ + { + "code": "VN", + "system": "http://terminology.hl7.org/CodeSystem/v2-0203" + } + ] + }, + "system": "http://medizininformatik-initiative.de/fhir/NamingSystem/Aufnahmenummer/MusterKrankenhaus", + "value": "F_0000001" + } + ], + "diagnosis": [ + { + "use": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "condition": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "period": { + "start": "2020-01-08T07:00:00+01:00", + "end": "2020-01-11T05:00:00+01:00" + } + }, + "request": { + "method": "POST", + "url": "Encounter" + } + }, + { + "fullUrl": "urn:uuid:bb8e9846-9bc1-4a7a-8e1a-cf941c5fddb6", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mre-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mre-klasse" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1285113001", + "display": "Type of antimicrobial resistant organism (observable entity)" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "115329001", + "display": "Methicillin resistant Staphylococcus aureus" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mre-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:17e03942-3286-4b7c-86c2-9ff7f218a74e", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mre-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mre-klasse" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1285113001", + "display": "Type of antimicrobial resistant organism (observable entity)" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "113727004", + "display": "Vancomycin resistant Enterococcus" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mre-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:863d6462-1293-4999-b173-b37d0b817444", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "OBI" + } + ] + }, + "system": "https://example.org/fhir/sid/test-lab-results", + "value": "59826-8_1234567890", + "assigner": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "DIZ-ID" + } + } + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mrgn-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mrgn-klasse" + ] + }, + "identifier": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "OBI" + } + ] + }, + "system": "https://example.org/fhir/sid/test-lab-results", + "value": "59826-8_1234567890", + "assigner": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "DIZ-ID" + } + } + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "99780-9", + "display": "Multidrug resistant gram-negative organism classification [Type]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA33214-0", + "display": "2MRGN" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "OBI" + } + ] + }, + "system": "https://example.org/fhir/sid/test-lab-results", + "value": "59826-8_1234567890", + "assigner": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "DIZ-ID" + } + } + } + ], + "status": "final", + "performer": [ + { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifiers", + "value": "Charité" + } + } + ], + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mrgn-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:37a62b3c-2521-4c8c-b713-b3ae41f9224c", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mrgn-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mrgn-klasse" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "99780-9", + "display": "Multidrug resistant gram-negative organism classification [Type]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA33215-7", + "display": "3MRGN" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mrgn-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:e616f94e-534d-40a4-9d15-59a5dc271e48", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mrgn-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mrgn-klasse" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "99780-9", + "display": "Multidrug resistant gram-negative organism classification [Type]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA33215-7", + "display": "3MRGN" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mrgn-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:a96ea433-8a27-4f67-9606-c19b0a4c12fa", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-kultur-nachweis" + ] + }, + "contained": [ + { + "resourceType": "Observation", + "id": "empf-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-empfindlichkeit" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "18868-0", + "display": "Aztreonam [Susceptibility]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueQuantity": { + "system": "http://unitsofmeasure.org", + "value": 32, + "code": "mg/L", + "unit": "mg/L" + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + }, + "interpretation": [ + { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "1306577009", + "display": "European Committee on Antimicrobial Susceptibility Testing category 2019 Susceptible, standard dosing regimen", + "version": "20240301" + } + ] + } + ] + }, + { + "resourceType": "Observation", + "id": "mrgn-1", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-mrgn-klasse" + ] + }, + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "99780-9", + "display": "Multidrug resistant gram-negative organism classification [Type]" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://loinc.org", + "code": "LA33215-7", + "display": "3MRGN" + } + ] + }, + "specimen": { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + }, + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason", + "valueCode": "unsupported" + } + ] + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "11475-1", + "display": "Microorganism identified in Specimen by Culture" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "260373001", + "display": "Detected (qualifier value)" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "hasMember": [ + { + "reference": "#empf-1" + }, + { + "reference": "#mrgn-1" + } + ], + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:09059c94-cf9e-4d9e-aefd-fff90ebe8873", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-molekulare-diagnostik" + ] + }, + "contained": [ + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "OBI" + } + ] + }, + "system": "https://example.org/fhir/sid/test-lab-results", + "value": "59826-8_1234567890", + "assigner": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "DIZ-ID" + } + } + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92253-4", + "display": "Microorganism identified in Isolate or Specimen by Molecular genetics method" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "10828004", + "display": "Positive" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "component": [ + { + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "398545005" + } + ] + }, + "valueQuantity": { + "value": 25.5, + "unit": "ng/mL", + "system": "http://unitsofmeasure.org", + "code": "ng/mL" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + }, + { + "fullUrl": "urn:uuid:7bc9bea7-852f-446e-83f9-9bab165b5c17", + "resource": { + "resourceType": "Observation", + "meta": { + "profile": [ + "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/StructureDefinition/mii-pr-mikrobio-molekulare-diagnostik" + ] + }, + "contained": [ + { + "resourceType": "Specimen", + "id": "probe-1", + "meta": { + "profile": [ + "http://hl7.org/fhir/StructureDefinition/Specimen" + ] + }, + "collection": { + "collectedDateTime": "2011-08-16T06:15:00Z" + } + } + ], + "identifier": [ + { + "type": { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "OBI" + } + ] + }, + "system": "https://example.org/fhir/sid/test-lab-results", + "value": "59826-8_1234567890", + "assigner": { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifier", + "value": "DIZ-ID" + } + } + } + ], + "status": "final", + "category": [ + { + "coding": [ + { + "system": "http://terminology.hl7.org/CodeSystem/observation-category", + "code": "laboratory", + "display": "Laboratory" + }, + { + "system": "http://loinc.org", + "code": "26436-6", + "display": "Laboratory studies (set)" + }, + { + "system": "http://loinc.org", + "code": "18725-2", + "display": "Microbiology studies" + } + ] + } + ], + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "92253-4", + "display": "Microorganism identified in Isolate or Specimen by Molecular genetics method" + } + ] + }, + "subject": { + "reference": "urn:uuid:1a4cef52-3418-4be7-b1e2-30dd9639f7ba" + }, + "effectiveDateTime": "2018-11-20T12:05:00+01:00", + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "10828004", + "display": "Positive" + } + ] + }, + "specimen": { + "reference": "#probe-1" + }, + "encounter": { + "reference": "urn:uuid:d7f5f52c-ce49-4e2e-8b2a-b5b4a602a6e2" + }, + "performer": [ + { + "identifier": { + "system": "https://www.medizininformatik-initiative.de/fhir/core/CodeSystem/core-location-identifiers", + "value": "Charité" + } + } + ], + "component": [ + { + "code": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "398545005" + } + ] + }, + "valueQuantity": { + "value": 25.5, + "unit": "ng/mL", + "system": "http://unitsofmeasure.org", + "code": "ng/mL" + } + }, + { + "code": { + "coding": [ + { + "system": "http://loinc.org", + "code": "89248-9" + } + ] + }, + "valueCodeableConcept": { + "coding": [ + { + "system": "http://snomed.info/sct", + "code": "840533007", + "display": "Severe acute respiratory syndrome coronavirus 2 (organism)" + } + ] + } + } + ] + }, + "request": { + "method": "POST", + "url": "Observation" + } + } + ] +} \ No newline at end of file From 725f0139b97be7237220023ab3ad81557ab648e8 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 12:18:07 +0100 Subject: [PATCH 16/20] implemented suggestions provided by @hhund --- codex-process-data-transfer/pom.xml | 2 +- .../data_transfer/ConstantsDataTransfer.java | 1 + .../DataTransferProcessPluginDefinition.java | 2 +- .../data_transfer/service/send/ReadData.java | 29 +++++++++++++++++-- .../service/send/ResolvePsn.java | 12 ++++++-- .../validation/ValidationPackage.java | 1 + .../value_set/KdsMikrobiologieBugFixer.java | 8 +++-- .../fhir/CodeSystem/data-transfer-error.xml | 5 ++++ .../client/fhir/AbstractFhirClientTest.java | 4 ++- .../validation/ValidateDataLearningTest.java | 19 ++++++++++-- .../pom.xml | 2 +- pom.xml | 2 +- 12 files changed, 74 insertions(+), 13 deletions(-) diff --git a/codex-process-data-transfer/pom.xml b/codex-process-data-transfer/pom.xml index 11fe347..48ab7fc 100644 --- a/codex-process-data-transfer/pom.xml +++ b/codex-process-data-transfer/pom.xml @@ -8,7 +8,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.1-SNAPSHOT + 1.1.0.0-SNAPSHOT diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java index 1ce6db9..c6bd630 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/ConstantsDataTransfer.java @@ -91,6 +91,7 @@ public interface ConstantsDataTransfer String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_BAD_PATIENT_REFERENCE = "bad-patient-reference"; String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_FTTP_NOT_REACHABLE = "fttp-not-reachable"; String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER = "no-dic-pseudonym-for-bloomfilter"; + String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_LOCAL_PSEUDONYM = "no-dic-pseudonym-for-local-pseudonym"; String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_VALIDATION_FAILED = "validation-failed"; String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_ECRYPTION_OF_DATA_FOR_CRR_FAILED = "ecryption-of-data-for-crr-failed"; String CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_DATA = "unable-to-store-ecrypted-data"; diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java index 228342e..d427dec 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/DataTransferProcessPluginDefinition.java @@ -17,7 +17,7 @@ public class DataTransferProcessPluginDefinition implements ProcessPluginDefinition { - public static final String VERSION = "1.0.0.1"; + public static final String VERSION = "1.1.0.0"; public static final LocalDate DATE = LocalDate.of(2024, 3, 18); @Override diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java index f21be9b..38cf7ff 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ReadData.java @@ -26,30 +26,52 @@ import org.camunda.bpm.engine.delegate.BpmnError; import org.camunda.bpm.engine.delegate.DelegateExecution; import org.hl7.fhir.instance.model.api.IBaseResource; -import org.hl7.fhir.r4.model.*; +import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; import org.hl7.fhir.r4.model.Bundle.BundleType; import org.hl7.fhir.r4.model.Bundle.HTTPVerb; +import org.hl7.fhir.r4.model.CanonicalType; +import org.hl7.fhir.r4.model.Condition; import org.hl7.fhir.r4.model.Condition.ConditionEvidenceComponent; import org.hl7.fhir.r4.model.Condition.ConditionStageComponent; +import org.hl7.fhir.r4.model.Consent; import org.hl7.fhir.r4.model.Consent.ConsentVerificationComponent; import org.hl7.fhir.r4.model.Consent.provisionActorComponent; import org.hl7.fhir.r4.model.Consent.provisionComponent; import org.hl7.fhir.r4.model.Consent.provisionDataComponent; +import org.hl7.fhir.r4.model.DateTimeType; +import org.hl7.fhir.r4.model.DiagnosticReport; import org.hl7.fhir.r4.model.DiagnosticReport.DiagnosticReportMediaComponent; +import org.hl7.fhir.r4.model.DomainResource; +import org.hl7.fhir.r4.model.Encounter; import org.hl7.fhir.r4.model.Encounter.DiagnosisComponent; import org.hl7.fhir.r4.model.Encounter.EncounterHospitalizationComponent; import org.hl7.fhir.r4.model.Encounter.EncounterLocationComponent; import org.hl7.fhir.r4.model.Encounter.EncounterParticipantComponent; +import org.hl7.fhir.r4.model.IdType; +import org.hl7.fhir.r4.model.Identifier; +import org.hl7.fhir.r4.model.Immunization; import org.hl7.fhir.r4.model.Immunization.ImmunizationPerformerComponent; import org.hl7.fhir.r4.model.Immunization.ImmunizationProtocolAppliedComponent; import org.hl7.fhir.r4.model.Immunization.ImmunizationReactionComponent; +import org.hl7.fhir.r4.model.InstantType; +import org.hl7.fhir.r4.model.Medication; import org.hl7.fhir.r4.model.Medication.MedicationIngredientComponent; +import org.hl7.fhir.r4.model.MedicationAdministration; import org.hl7.fhir.r4.model.MedicationAdministration.MedicationAdministrationPerformerComponent; +import org.hl7.fhir.r4.model.MedicationStatement; +import org.hl7.fhir.r4.model.Meta; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; import org.hl7.fhir.r4.model.Patient.ContactComponent; import org.hl7.fhir.r4.model.Patient.PatientLinkComponent; +import org.hl7.fhir.r4.model.Procedure; import org.hl7.fhir.r4.model.Procedure.ProcedureFocalDeviceComponent; import org.hl7.fhir.r4.model.Procedure.ProcedurePerformerComponent; +import org.hl7.fhir.r4.model.Reference; +import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.Specimen; +import org.hl7.fhir.r4.model.Task; import org.slf4j.Logger; import org.slf4j.LoggerFactory; @@ -778,7 +800,10 @@ else if (resource instanceof Specimen s) throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); } - ((DomainResource) resource).getContained().forEach(r -> setSubjectOrIdentifier(r, pseudonym)); + if (resource instanceof DomainResource d) + d.getContained().forEach(r -> setSubjectOrIdentifier(r, pseudonym)); + else + throw new RuntimeException("Resource of type " + resource.getResourceType().name() + " not supported"); return resource; } diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java index d277dbb..7459a5c 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/ResolvePsn.java @@ -1,6 +1,14 @@ package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.service.send; -import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.*; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_PATIENT_REFERENCE; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_LOCAL_PSEUDONYM; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_PATIENT_NOT_FOUND; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_CODE; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.IDENTIFIER_NUM_CODEX_DIC_PSEUDONYM_TYPE_SYSTEM; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_BLOOM_FILTER; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM; +import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.RFC_4122_SYSTEM; import java.util.Objects; import java.util.Optional; @@ -152,7 +160,7 @@ private String resolveLocalPseudonym(String localPseudonym) { return fttpClientFactory.getFttpClient().getDicPseudonymForLocalPseudonym(localPseudonym) .orElseThrow(() -> new BpmnError( - CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_BLOOMFILTER, + CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_NO_DIC_PSEUDONYM_FOR_LOCAL_PSEUDONYM, "Unable to get DIC pseudonym for given localPseudonym")); } diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java index bd848bd..79139ef 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackage.java @@ -165,6 +165,7 @@ private Consumer doParseResources(FhirContext context, L { String resourceString = new String(entry.getContent(), StandardCharsets.UTF_8); // fix profiles because their text contains invalid html + // Issue: https://github.com/medizininformatik-initiative/kerndatensatzmodul-mikrobiologie/issues/18 resourceString = resourceString.replaceAll("

[\\s\\w\\[\\]]*", ""); IBaseResource resource = context.newJsonParser().parseResource(resourceString); diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java index 44bc8c7..ff67fc1 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java @@ -6,9 +6,14 @@ import ca.uhn.fhir.context.FhirContext; +/** + * Replace a few ValueSets from MII KDS Mikrobiologie module. This ValueSetModifier currently resolves the following + * issues: * + * #15 * + * #16 + */ public class KdsMikrobiologieBugFixer implements ValueSetModifier { - private final Map fixedValueSets = Map.of( "https://www.medizininformatik-initiative.de/fhir/modul-mikrobio/ValueSet/mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc", "mii-vs-mikrobio-empfindlichkeit-phenotyp-loinc.json", @@ -20,7 +25,6 @@ public class KdsMikrobiologieBugFixer implements ValueSetModifier @Override public ValueSet modifyPreExpansion(ValueSet vs) { - if (vs.getUrl() != null && vs.getVersion() != null && vs.getVersion().equals("2024.0.0")) { String fileName = fixedValueSets.get(vs.getUrl()); diff --git a/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/data-transfer-error.xml b/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/data-transfer-error.xml index da25785..9e4356b 100644 --- a/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/data-transfer-error.xml +++ b/codex-process-data-transfer/src/main/resources/fhir/CodeSystem/data-transfer-error.xml @@ -81,6 +81,11 @@ + + + + + diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java index 95aae15..9f241dc 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClientTest.java @@ -1,7 +1,9 @@ package de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir; import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.NAMING_SYSTEM_NUM_CODEX_DIC_PSEUDONYM; -import static org.junit.Assert.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; import static org.mockito.Mockito.CALLS_REAL_METHODS; import static org.mockito.Mockito.when; diff --git a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java index a8a30de..b94938e 100644 --- a/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java +++ b/codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidateDataLearningTest.java @@ -14,7 +14,15 @@ import java.security.cert.Certificate; import java.security.cert.CertificateException; import java.security.cert.X509Certificate; -import java.util.*; +import java.util.Arrays; +import java.util.Comparator; +import java.util.EnumSet; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Properties; +import java.util.Set; +import java.util.UUID; import java.util.function.Consumer; import java.util.function.Function; import java.util.stream.Collectors; @@ -23,10 +31,17 @@ import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService; import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport; import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain; -import org.hl7.fhir.r4.model.*; +import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.CanonicalType; +import org.hl7.fhir.r4.model.ElementDefinition; import org.hl7.fhir.r4.model.ElementDefinition.TypeRefComponent; import org.hl7.fhir.r4.model.Enumerations.BindingStrength; +import org.hl7.fhir.r4.model.OperationOutcome; +import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.StringType; +import org.hl7.fhir.r4.model.StructureDefinition; +import org.hl7.fhir.r4.model.ValueSet; import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent; import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent; import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity; diff --git a/codex-processes-ap1-test-data-generator/pom.xml b/codex-processes-ap1-test-data-generator/pom.xml index 283f9a8..c521795 100644 --- a/codex-processes-ap1-test-data-generator/pom.xml +++ b/codex-processes-ap1-test-data-generator/pom.xml @@ -6,7 +6,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.1-SNAPSHOT + 1.1.0.0-SNAPSHOT diff --git a/pom.xml b/pom.xml index d6b6337..71e7e21 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ de.netzwerk-universitaetsmedizin.codex codex-processes-ap1 - 1.0.0.1-SNAPSHOT + 1.1.0.0-SNAPSHOT pom From 7e42a7581c98eff2540822768ad3c33a691120bc Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 12:21:00 +0100 Subject: [PATCH 17/20] javadoc formatting fix --- .../validation/value_set/KdsMikrobiologieBugFixer.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java index ff67fc1..c2962cb 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java @@ -8,8 +8,8 @@ /** * Replace a few ValueSets from MII KDS Mikrobiologie module. This ValueSetModifier currently resolves the following - * issues: * - * #15 * + * issues: + * #15 * #16 */ public class KdsMikrobiologieBugFixer implements ValueSetModifier From 3384d0cffafcfb0bb4432645526bd98809c61286 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 12:29:14 +0100 Subject: [PATCH 18/20] javadoc formatting fix to please format check --- .../validation/value_set/KdsMikrobiologieBugFixer.java | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java index c2962cb..f955e32 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/value_set/KdsMikrobiologieBugFixer.java @@ -8,8 +8,7 @@ /** * Replace a few ValueSets from MII KDS Mikrobiologie module. This ValueSetModifier currently resolves the following - * issues: - * #15 + * issues: #15 * #16 */ public class KdsMikrobiologieBugFixer implements ValueSetModifier From f3bacda15ee5275f1d83cda24d9e0dee8692420b Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 12:40:36 +0100 Subject: [PATCH 19/20] add comment explaining the versioned id issue with hapi client --- .../processes/data_transfer/client/fhir/AbstractFhirClient.java | 1 + 1 file changed, 1 insertion(+) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java index cbc84f2..57ee2ef 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/client/fhir/AbstractFhirClient.java @@ -653,6 +653,7 @@ public void updatePatient(Patient patient) Objects.requireNonNull(patient, "patient"); String id = patient.getIdElement().toVersionless().getValue(); + // set the patient id to versionless id to workaround a `If-Match`-header bug in hapi fhir client patient.setId(id); logger.info("Updating patient {}", id); From 4e5a6ff4fcb47384991cad40fc826030b09e9ae7 Mon Sep 17 00:00:00 2001 From: Simon Schweizer Date: Mon, 25 Mar 2024 13:20:34 +0100 Subject: [PATCH 20/20] improved logging by @hhund --- .../receive/StoreValidationErrorForDts.java | 9 +++++--- .../service/send/StoreDataForDts.java | 9 +++++--- .../service/translate/StoreDataForCrr.java | 9 +++++--- .../translate/StoreValidationErrorForDic.java | 23 +++++++++++++++---- .../spring/config/ReceiveConfig.java | 3 ++- .../spring/config/SendConfig.java | 2 +- .../spring/config/TranslateConfig.java | 4 ++-- ...nSnapshotGeneratorWithFileSystemCache.java | 2 +- .../ValidationPackageManagerImpl.java | 16 ++++++++++++- 9 files changed, 58 insertions(+), 19 deletions(-) diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java index 3dcafcd..ca61cc2 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/receive/StoreValidationErrorForDts.java @@ -15,7 +15,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import ca.uhn.fhir.context.FhirContext; +import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; import dev.dsf.bpe.v1.ProcessPluginApi; import dev.dsf.bpe.v1.activity.AbstractServiceDelegate; import dev.dsf.bpe.v1.constants.NamingSystems; @@ -26,12 +26,14 @@ public class StoreValidationErrorForDts extends AbstractServiceDelegate private static final Logger logger = LoggerFactory.getLogger(StoreValidationErrorForDts.class); private final String dtsIdentifierValue; + private final DataLogger dataLogger; - public StoreValidationErrorForDts(ProcessPluginApi api, String dtsIdentifierValue) + public StoreValidationErrorForDts(ProcessPluginApi api, String dtsIdentifierValue, DataLogger dataLogger) { super(api); this.dtsIdentifierValue = dtsIdentifierValue; + this.dataLogger = dataLogger; } @Override @@ -40,6 +42,7 @@ public void afterPropertiesSet() throws Exception super.afterPropertiesSet(); Objects.requireNonNull(dtsIdentifierValue, "dtsIdentifierValue"); + Objects.requireNonNull(dataLogger, "dataLogger"); } @Override @@ -72,7 +75,7 @@ private IdType createBinaryResource(Binary binary) } catch (Exception e) { - logger.debug("Binary to create {}", FhirContext.forR4().newJsonParser().encodeResourceToString(binary)); + dataLogger.logData("Binary to create", binary); logger.warn("Error while creating Binary resource: " + e.getMessage(), e); throw new BpmnError( diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/StoreDataForDts.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/StoreDataForDts.java index 265e0bc..db3a61e 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/StoreDataForDts.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/send/StoreDataForDts.java @@ -15,7 +15,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import ca.uhn.fhir.context.FhirContext; +import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; import dev.dsf.bpe.v1.ProcessPluginApi; import dev.dsf.bpe.v1.activity.AbstractServiceDelegate; import dev.dsf.bpe.v1.constants.NamingSystems; @@ -27,12 +27,14 @@ public class StoreDataForDts extends AbstractServiceDelegate private static final Logger logger = LoggerFactory.getLogger(StoreDataForDts.class); private final String dtsIdentifierValue; + private final DataLogger dataLogger; - public StoreDataForDts(ProcessPluginApi api, String dtsIdentifierValue) + public StoreDataForDts(ProcessPluginApi api, String dtsIdentifierValue, DataLogger dataLogger) { super(api); this.dtsIdentifierValue = dtsIdentifierValue; + this.dataLogger = dataLogger; } @Override @@ -41,6 +43,7 @@ public void afterPropertiesSet() throws Exception super.afterPropertiesSet(); Objects.requireNonNull(dtsIdentifierValue, "dtsIdentifierValue"); + Objects.requireNonNull(dataLogger, "dataLogger"); } @Override @@ -72,7 +75,7 @@ private IdType createBinaryResource(Binary binary) } catch (Exception e) { - logger.debug("Binary to create {}", FhirContext.forR4().newJsonParser().encodeResourceToString(binary)); + dataLogger.logData("Binary to create", binary); logger.warn("Error while creating Binary resource: " + e.getMessage(), e); throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_DATA, diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreDataForCrr.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreDataForCrr.java index 0bb0a77..1172352 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreDataForCrr.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreDataForCrr.java @@ -15,7 +15,7 @@ import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import ca.uhn.fhir.context.FhirContext; +import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; import dev.dsf.bpe.v1.ProcessPluginApi; import dev.dsf.bpe.v1.activity.AbstractServiceDelegate; import dev.dsf.bpe.v1.constants.NamingSystems; @@ -27,12 +27,14 @@ public class StoreDataForCrr extends AbstractServiceDelegate private static final Logger logger = LoggerFactory.getLogger(StoreDataForCrr.class); private final String crrIdentifierValue; + private final DataLogger dataLogger; - public StoreDataForCrr(ProcessPluginApi api, String crrIdentifierValue) + public StoreDataForCrr(ProcessPluginApi api, String crrIdentifierValue, DataLogger dataLogger) { super(api); this.crrIdentifierValue = crrIdentifierValue; + this.dataLogger = dataLogger; } @Override @@ -41,6 +43,7 @@ public void afterPropertiesSet() throws Exception super.afterPropertiesSet(); Objects.requireNonNull(crrIdentifierValue, "crrIdentifierValue"); + Objects.requireNonNull(dataLogger, "dataLogger"); } @Override @@ -72,7 +75,7 @@ private IdType createBinaryResource(Binary binary) } catch (Exception e) { - logger.debug("Binary to create {}", FhirContext.forR4().newJsonParser().encodeResourceToString(binary)); + dataLogger.logData("Binary to create", binary); logger.warn("Error while creating Binary resource: " + e.getMessage(), e); throw new BpmnError(CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_DATA, diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreValidationErrorForDic.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreValidationErrorForDic.java index b153cbe..bd1d5d3 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreValidationErrorForDic.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/service/translate/StoreValidationErrorForDic.java @@ -4,6 +4,8 @@ import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.BPMN_EXECUTION_VARIABLE_BUNDLE; import static de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.ConstantsDataTransfer.CODESYSTEM_NUM_CODEX_DATA_TRANSFER_ERROR_VALUE_UNABLE_TO_STORE_ECRYPTED_VALIDATION_ERROR; +import java.util.Objects; + import org.camunda.bpm.engine.delegate.BpmnError; import org.camunda.bpm.engine.delegate.DelegateExecution; import org.hl7.fhir.r4.model.Binary; @@ -12,21 +14,34 @@ import org.hl7.fhir.r4.model.ResourceType; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.InitializingBean; -import ca.uhn.fhir.context.FhirContext; +import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.logging.DataLogger; import dev.dsf.bpe.v1.ProcessPluginApi; import dev.dsf.bpe.v1.activity.AbstractServiceDelegate; import dev.dsf.bpe.v1.constants.NamingSystems; import dev.dsf.bpe.v1.variables.Variables; import jakarta.ws.rs.core.MediaType; -public class StoreValidationErrorForDic extends AbstractServiceDelegate +public class StoreValidationErrorForDic extends AbstractServiceDelegate implements InitializingBean { private static final Logger logger = LoggerFactory.getLogger(StoreValidationErrorForDic.class); - public StoreValidationErrorForDic(ProcessPluginApi api) + private DataLogger dataLogger; + + public StoreValidationErrorForDic(ProcessPluginApi api, DataLogger dataLogger) { super(api); + + this.dataLogger = dataLogger; + } + + @Override + public void afterPropertiesSet() throws Exception + { + super.afterPropertiesSet(); + + Objects.requireNonNull(dataLogger, "dataLogger"); } @Override @@ -60,7 +75,7 @@ private IdType createBinaryResource(Binary binary) } catch (Exception e) { - logger.debug("Binary to create {}", FhirContext.forR4().newJsonParser().encodeResourceToString(binary)); + dataLogger.logData("Binary to create", binary); logger.warn("Error while creating Binary resource: " + e.getMessage(), e); throw new BpmnError( diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ReceiveConfig.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ReceiveConfig.java index 1073cfc..7f1311e 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ReceiveConfig.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/ReceiveConfig.java @@ -84,7 +84,8 @@ public EncryptValidationError encryptValidationError() @Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE) public StoreValidationErrorForDts storeValidationErrorForDts() { - return new StoreValidationErrorForDts(api, transferDataConfig.dtsIdentifierValue()); + return new StoreValidationErrorForDts(api, transferDataConfig.dtsIdentifierValue(), + transferDataConfig.dataLogger()); } @Bean diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/SendConfig.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/SendConfig.java index b5ef9fc..58daee3 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/SendConfig.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/SendConfig.java @@ -125,7 +125,7 @@ public AfterDryRunEndListener afterDryRunEndListener() @Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE) public StoreDataForDts storeDataForDts() { - return new StoreDataForDts(api, transferDataConfig.dtsIdentifierValue()); + return new StoreDataForDts(api, transferDataConfig.dtsIdentifierValue(), transferDataConfig.dataLogger()); } @Bean diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/TranslateConfig.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/TranslateConfig.java index 8528204..4b6eeac 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/TranslateConfig.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/spring/config/TranslateConfig.java @@ -52,7 +52,7 @@ public ReplacePseudonym replacePseudonym() @Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE) public StoreDataForCrr storeDataForCodex() { - return new StoreDataForCrr(api, transferDataConfig.crrIdentifierValue()); + return new StoreDataForCrr(api, transferDataConfig.crrIdentifierValue(), transferDataConfig.dataLogger()); } @Bean @@ -108,7 +108,7 @@ public DownloadValidationErrorFromCrr downloadValidationErrorFromCrr() @Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE) public StoreValidationErrorForDic storeValidationErrorForDic() { - return new StoreValidationErrorForDic(api); + return new StoreValidationErrorForDic(api, transferDataConfig.dataLogger()); } @Bean diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java index 32541da..2c031b3 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/PluginSnapshotGeneratorWithFileSystemCache.java @@ -105,7 +105,7 @@ private SnapshotWithValidationMessages generateSnapshotAndWriteToCache(Structure if (PublicationStatus.DRAFT.equals(snapshot.getSnapshot().getStatus())) { - logger.info("Not writing StructureDefinition {}|{} with snapshot and status {} to cache", + logger.warn("Not writing StructureDefinition {}|{} with snapshot and status {} to cache", snapshot.getSnapshot().getUrl(), snapshot.getSnapshot().getVersion(), snapshot.getSnapshot().getStatus()); return snapshot; diff --git a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManagerImpl.java b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManagerImpl.java index 661286b..666e79b 100644 --- a/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManagerImpl.java +++ b/codex-process-data-transfer/src/main/java/de/netzwerk_universitaetsmedizin/codex/processes/data_transfer/validation/ValidationPackageManagerImpl.java @@ -17,6 +17,7 @@ import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport; import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain; import org.hl7.fhir.r4.model.Enumerations.BindingStrength; +import org.hl7.fhir.r4.model.Enumerations.PublicationStatus; import org.hl7.fhir.r4.model.StructureDefinition; import org.hl7.fhir.r4.model.ValueSet; import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent; @@ -367,9 +368,22 @@ private void createSnapshot(ValidationPackageWithDepedencies packageWithDependen definitions.stream() .filter(sd -> !sd.equals(diff) && !sd.getUrl().equals(diff.getBaseDefinition()) && !(sd.getUrl() + "|" + sd.getVersion()).equals(diff.getBaseDefinition())) - .map(sd -> sd.getUrl() + "|" + sd.getVersion()).sorted() + .map(sd -> sd.getUrl() + "|" + sd.getVersion()).distinct().sorted() .collect(Collectors.joining(", ", "[", "]"))); + String dependenciesWithDifferentStatus = definitions.stream() + .filter(sd -> !sd.equals(diff) && !sd.getUrl().equals(diff.getBaseDefinition()) + && !(sd.getUrl() + "|" + sd.getVersion()).equals(diff.getBaseDefinition())) + .filter(sd -> !sd.getStatus().equals(diff.getStatus())) + .map(sd -> sd.getUrl() + "|" + sd.getVersion() + ": " + sd.getStatus().toCode()).distinct().sorted() + .collect(Collectors.joining(", ")); + + if (PublicationStatus.ACTIVE.equals(diff.getStatus()) && !dependenciesWithDifferentStatus.isEmpty()) + { + logger.warn("StructureDefinition {}|{}, has dependencies with no active status [{}]", diff.getUrl(), + diff.getVersion(), dependenciesWithDifferentStatus); + } + definitions.stream().filter(sd -> sd.hasDifferential() && !sd.hasSnapshot() && !snapshots.containsKey(sd.getUrl() + "|" + sd.getVersion())).forEach(sd -> {