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hhundhhund
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Merge remote-tracking branch 'origin/develop' into issues/26_dnr_consent
2 parents 850a46d + 4b12c71 commit 513e01c

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‎codex-process-data-transfer/src/main/resources/fhir/StructureDefinition/highmed-task-base-0.4.0.xml‎

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<StructureDefinition xmlns="http://hl7.org/fhir">
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<meta>
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<tag>
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<system value="http://highmed.org/fhir/CodeSystem/authorization-role" />
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<code value="REMOTE" />
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</tag>
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</meta>
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<url value="http://highmed.org/fhir/StructureDefinition/task-base" />
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<version value="0.4.0" />
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<name value="TaskBase" />
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<status value="active" />
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<experimental value="false" />
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<date value="2021-01-26" />
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<fhirVersion value="4.0.1" />
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<kind value="resource" />
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<abstract value="true" />
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<type value="Task" />
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<baseDefinition value="http://hl7.org/fhir/StructureDefinition/Task" />
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<derivation value="constraint" />
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<differential>
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<element id="Task.instantiatesUri">
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<path value="Task.instantiatesUri" />
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<min value="1" />
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</element>
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<element id="Task.intent">
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<path value="Task.intent" />
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<fixedCode value="order" />
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</element>
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<element id="Task.authoredOn">
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<path value="Task.authoredOn" />
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<min value="1" />
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</element>
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<element id="Task.requester">
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<path value="Task.requester" />
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<min value="1" />
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<type>
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<code value="Reference" />
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<targetProfile value="http://highmed.org/fhir/StructureDefinition/organization" />
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</type>
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</element>
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<element id="Task.requester.reference">
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<path value="Task.requester.reference" />
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<max value="0" />
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</element>
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<element id="Task.requester.identifier">
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<path value="Task.requester.identifier" />
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<min value="1" />
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</element>
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<element id="Task.requester.identifier.system">
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<path value="Task.requester.identifier.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/NamingSystem/organization-identifier" />
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</element>
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<element id="Task.requester.identifier.value">
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<path value="Task.requester.identifier.value" />
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<min value="1" />
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</element>
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<element id="Task.restriction">
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<path value="Task.restriction" />
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<min value="1" />
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</element>
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<element id="Task.restriction.recipient">
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<path value="Task.restriction.recipient" />
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<min value="1" />
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<max value="1" />
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<type>
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<code value="Reference" />
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<targetProfile value="http://highmed.org/fhir/StructureDefinition/organization" />
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</type>
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</element>
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<element id="Task.restriction.recipient.reference">
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<path value="Task.restriction.recipient.reference" />
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<max value="0" />
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</element>
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<element id="Task.restriction.recipient.identifier">
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<path value="Task.restriction.recipient.identifier" />
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<min value="1" />
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</element>
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<element id="Task.restriction.recipient.identifier.system">
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<path value="Task.restriction.recipient.identifier.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/NamingSystem/organization-identifier" />
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</element>
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<element id="Task.restriction.recipient.identifier.value">
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<path value="Task.restriction.recipient.identifier.value" />
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<min value="1" />
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</element>
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<element id="Task.input">
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<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name">
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<valueString value="Parameter" />
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</extension>
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<path value="Task.input" />
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<slicing>
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<discriminator>
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<type value="value" />
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<path value="type.coding.system" />
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</discriminator>
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<discriminator>
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<type value="value" />
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<path value="type.coding.code" />
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</discriminator>
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<rules value="openAtEnd" />
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</slicing>
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<min value="1" />
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</element>
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<element id="Task.input:message-name">
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<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name">
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<valueString value="Parameter" />
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</extension>
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<path value="Task.input" />
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<sliceName value="message-name" />
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<min value="1" />
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<max value="1" />
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</element>
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<element id="Task.input:message-name.type">
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<path value="Task.input.type" />
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<binding>
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<extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
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<valueString value="TaskInputParameterType" />
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</extension>
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<strength value="required" />
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<valueSet value="http://highmed.org/fhir/ValueSet/bpmn-message" />
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</binding>
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</element>
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<element id="Task.input:message-name.type.coding">
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<path value="Task.input.type.coding" />
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<min value="1" />
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<max value="1" />
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</element>
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<element id="Task.input:message-name.type.coding.system">
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<path value="Task.input.type.coding.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/CodeSystem/bpmn-message" />
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</element>
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<element id="Task.input:message-name.type.coding.code">
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<path value="Task.input.type.coding.code" />
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<min value="1" />
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<fixedCode value="message-name" />
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</element>
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<element id="Task.input:message-name.value[x]">
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<path value="Task.input.value[x]" />
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<type>
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<code value="string" />
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</type>
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</element>
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<element id="Task.input:business-key">
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<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name">
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<valueString value="Parameter" />
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</extension>
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<path value="Task.input" />
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<sliceName value="business-key" />
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<max value="1" />
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</element>
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<element id="Task.input:business-key.type">
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<path value="Task.input.type" />
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<binding>
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<extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
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<valueString value="TaskInputParameterType" />
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</extension>
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<strength value="required" />
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<valueSet value="http://highmed.org/fhir/ValueSet/bpmn-message" />
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</binding>
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</element>
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<element id="Task.input:business-key.type.coding">
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<path value="Task.input.type.coding" />
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<min value="1" />
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<max value="1" />
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</element>
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<element id="Task.input:business-key.type.coding.system">
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<path value="Task.input.type.coding.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/CodeSystem/bpmn-message" />
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</element>
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<element id="Task.input:business-key.type.coding.code">
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<path value="Task.input.type.coding.code" />
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<min value="1" />
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<fixedCode value="business-key" />
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</element>
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<element id="Task.input:business-key.value[x]">
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<path value="Task.input.value[x]" />
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<type>
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<code value="string" />
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</type>
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</element>
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<element id="Task.input:correlation-key">
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<extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-explicit-type-name">
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<valueString value="Parameter" />
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</extension>
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<path value="Task.input" />
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<sliceName value="correlation-key" />
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<max value="1" />
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</element>
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<element id="Task.input:correlation-key.type">
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<path value="Task.input.type" />
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<binding>
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<extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
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<valueString value="TaskInputParameterType" />
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</extension>
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<strength value="required" />
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<valueSet value="http://highmed.org/fhir/ValueSet/bpmn-message" />
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</binding>
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</element>
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<element id="Task.input:correlation-key.type.coding">
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<path value="Task.input.type.coding" />
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<min value="1" />
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<max value="1" />
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</element>
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<element id="Task.input:correlation-key.type.coding.system">
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<path value="Task.input.type.coding.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/CodeSystem/bpmn-message" />
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</element>
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<element id="Task.input:correlation-key.type.coding.code">
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<path value="Task.input.type.coding.code" />
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<min value="1" />
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<fixedCode value="correlation-key" />
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</element>
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<element id="Task.input:correlation-key.value[x]">
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<path value="Task.input.value[x]" />
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<type>
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<code value="string" />
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</type>
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</element>
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<element id="Task.output">
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<path value="Task.output" />
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<slicing>
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<discriminator>
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<type value="value" />
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<path value="type.coding.system" />
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</discriminator>
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<discriminator>
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<type value="value" />
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<path value="type.coding.code" />
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</discriminator>
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<rules value="openAtEnd" />
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</slicing>
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</element>
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<element id="Task.output:error">
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<path value="Task.output" />
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<sliceName value="error" />
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</element>
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<element id="Task.output:error.type">
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<path value="Task.output.type" />
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<binding>
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<extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
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<valueString value="TaskOutputParameterType" />
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</extension>
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<strength value="required" />
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<valueSet value="http://highmed.org/fhir/ValueSet/bpmn-message" />
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</binding>
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</element>
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<element id="Task.output:error.type.coding">
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<path value="Task.output.type.coding" />
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<min value="1" />
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<max value="1" />
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</element>
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<element id="Task.output:error.type.coding.system">
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<path value="Task.output.type.coding.system" />
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<min value="1" />
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<fixedUri value="http://highmed.org/fhir/CodeSystem/bpmn-message" />
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</element>
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<element id="Task.output:error.type.coding.code">
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<path value="Task.output.type.coding.code" />
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<min value="1" />
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<fixedCode value="error" />
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</element>
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<element id="Task.output:error.value[x]">
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<path value="Task.output.value[x]" />
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<type>
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<code value="string" />
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</type>
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</element>
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</differential>
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</StructureDefinition>

‎codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/FhirBridgeTest.java‎

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package de.netzwerk_universitaetsmedizin.codex.processes;
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import org.hl7.fhir.r4.model.Bundle;
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import ca.uhn.fhir.context.FhirContext;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.FhirClientFactory;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.HapiFhirClientFactory;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.FhirBridgeClient;
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.fhir.FhirClientBuilder;
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public class FhirBridgeTest
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{
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private static final String BUNDLE_STRING = "{\"resourceType\":\"Bundle\",\"type\":\"transaction\",\"entry\":[{\"fullUrl\":\"urn:uuid:d2a06354-4514-482d-bdc9-26def09912b8\",\"resource\":{\"resourceType\":\"Patient\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/Patient\"]},\"text\":{\"status\":\"generated\",\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"><table class=\\\"hapiPropertyTable\\\"><tbody><tr><td>Identifier</td><td>0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5</td></tr><tr><td>Date of birth</td><td><span>30 September 1953</span></td></tr></tbody></table></div>\"},\"extension\":[{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/ethnic-group\",\"valueCoding\":{\"system\":\"http://snomed.info/sct\",\"code\":\"186019001\",\"display\":\"Other ethnic, mixed origin\"}},{\"url\":\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/age\",\"extension\":[{\"url\":\"dateTimeOfDocumentation\",\"valueDateTime\":\"2020-10-01\"},{\"url\":\"age\",\"valueAge\":{\"value\":67,\"unit\":\"years\",\"system\":\"http://unitsofmeasure.org\",\"code\":\"a\"}}]}],\"identifier\":[{\"system\":\"http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym\",\"value\":\"0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}],\"birthDate\":\"1953-09-30\"},\"request\":{\"method\":\"PUT\",\"url\":\"Patient?identifier=http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym|0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}},{\"fullUrl\":\"urn:uuid:fb4584cb-cc6e-4987-ad0e-fd62641b51c6\",\"resource\":{\"resourceType\":\"Condition\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/chronic-lung-diseases\"]},\"clinicalStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-clinical\",\"code\":\"active\",\"display\":\"Active\"}]},\"verificationStatus\":{\"coding\":[{\"system\":\"http://terminology.hl7.org/CodeSystem/condition-ver-status\",\"code\":\"confirmed\",\"display\":\"Confirmed\"},{\"system\":\"http://snomed.info/sct\",\"code\":\"410605003\",\"display\":\"Confirmed present (qualifier value)\"}]},\"category\":[{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"418112009\",\"display\":\"Pulmonary medicine\"}]}],\"code\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"413839001\",\"display\":\"Chronic lung disease\"}]},\"subject\":{\"identifier\":{\"system\":\"http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym\",\"value\":\"0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}},\"recordedDate\":\"2020-11-10T15:50:41.000+01:00\"},\"request\":{\"method\":\"PUT\",\"url\":\"Condition?_profile=https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/chronic-lung-diseases&recorded-date=2020-11-10T15:50:41.000+01:00&patient:identifier=http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym|0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}},{\"fullUrl\":\"urn:uuid:41a61a24-bd46-4090-92f3-edc556692d94\",\"resource\":{\"resourceType\":\"Observation\",\"meta\":{\"profile\":[\"https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr\"]},\"status\":\"final\",\"category\":[{\"coding\":[{\"system\":\"http://loinc.org\",\"code\":\"26436-6\"},{\"system\":\"http://terminology.hl7.org/CodeSystem/observation-category\",\"code\":\"laboratory\"}]}],\"code\":{\"coding\":[{\"system\":\"http://loinc.org\",\"code\":\"94500-6\",\"display\":\"SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection\"}],\"text\":\"SARS-CoV-2-RNA (PCR)\"},\"subject\":{\"identifier\":{\"system\":\"http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym\",\"value\":\"0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}},\"effectiveDateTime\":\"2020-11-10T15:50:41.000+01:00\",\"valueCodeableConcept\":{\"coding\":[{\"system\":\"http://snomed.info/sct\",\"code\":\"260373001\",\"display\":\"Detected (qualifier value)\"}],\"text\":\"SARS-CoV-2-RNA positiv\"}},\"request\":{\"method\":\"PUT\",\"url\":\"Observation?_profile=https://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/sars-cov-2-rt-pcr&date=2020-11-10T15:50:41.000+01:00&patient:identifier=http://www.netzwerk-universitaetsmedizin.de/sid/crr-pseudonym|0682c5f2076f099c34cfdd15a9e063849ed437a49677e6fcc5b4198c76575be5\"}}]}";
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public static void main(String[] args)
16+
{
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FhirContext fhirContext = FhirContext.forR4();
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HapiFhirClientFactory hapiFhirClientFactory = new HapiFhirClientFactory(fhirContext,
19+
"http://localhost:8888/fhir-bridge/fhir", null, null, null, 10_000, 10_000, 20_000, true);
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21+
FhirClientBuilder clientBuilder = (fc, clientFactory, searchBundleOverride) -> new FhirBridgeClient(fc,
22+
hapiFhirClientFactory, searchBundleOverride);
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FhirClientFactory clientFactory = new FhirClientFactory(hapiFhirClientFactory, fhirContext, null, null,
24+
clientBuilder);
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Bundle bundle = fhirContext.newJsonParser().parseResource(Bundle.class, BUNDLE_STRING);
27+
clientFactory.getFhirClient().storeBundle(bundle);
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}
29+
}

‎codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/FttpTest.java‎

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package de.netzwerk_universitaetsmedizin.codex.processes;
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import java.nio.file.Path;
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import java.nio.file.Paths;
5+
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import de.netzwerk_universitaetsmedizin.codex.processes.data_transfer.client.FttpClientFactory;
7+
8+
public class FttpTest
9+
{
10+
public static void main(String[] args)
11+
{
12+
Path trustStorePath = Paths
13+
.get("C:/Users/hhund/repositories/num-codex_gth-test/bpe/app/conf/fttp-num-ca_certificate.pem");
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Path certificatePath = Paths
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.get("C:/Users/hhund/repositories/num-codex_gth-test/bpe/app/conf/fttp-num-client_certificate.pem");
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Path privateKeyPath = Paths
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.get("C:/Users/hhund/repositories/num-codex_gth-test/bpe/app/conf/fttp-num-client_private-key.pem");
18+
19+
String fttpServerBase = "https://ip-test.ths.num.med.uni-greifswald.de/ttp-fhir/fhir";
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String fttpApiKey = "zpx9tlz07z0ebraw";
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String fttpStudy = "num";
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String fttpTarget = "codex";
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FttpClientFactory factory = new FttpClientFactory(trustStorePath, certificatePath, privateKeyPath, 10_000,
25+
10_000, 20_000, null, null, fttpServerBase, fttpApiKey, fttpStudy, fttpTarget, null, null, null, false);
26+
// factory.getFttpClient().testConnection();
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factory.getFttpClient().getCrrPseudonym("foo/bar");
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}
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}

‎codex-process-data-transfer/src/test/java/de/netzwerk_universitaetsmedizin/codex/processes/ToJson.java‎

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package de.netzwerk_universitaetsmedizin.codex.processes;
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import java.io.IOException;
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import java.io.InputStream;
5+
import java.nio.file.Files;
6+
import java.nio.file.Paths;
7+
8+
import org.hl7.fhir.r4.model.Task;
9+
10+
import ca.uhn.fhir.context.FhirContext;
11+
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public class ToJson
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{
14+
public static void main(String[] args) throws IOException
15+
{
16+
FhirContext fhirContext = FhirContext.forR4();
17+
try (InputStream in = Files
18+
.newInputStream(Paths.get("src/test/resources/fhir/Task/TaskStartDataSendWithIdentifierReference.xml")))
19+
{
20+
Task task = fhirContext.newXmlParser().parseResource(Task.class, in);
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String taskString = fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(task);
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System.out.println(taskString);
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}
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}
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}

‎codex-process-data-transfer/src/test/resources/fhir/Task/TaskStartDataSendWithAbsoluteReference.xml‎

Lines changed: 4 additions & 4 deletions
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22
<meta>
33
<profile value="http://www.netzwerk-universitaetsmedizin.de/fhir/StructureDefinition/task-start-data-send"/>
44
</meta>
5-
<instantiatesUri value="http://highmed.org/bpe/Process/dataSend/0.3.3"/>
5+
<instantiatesUri value="http://highmed.org/bpe/Process/dataSend/0.3.4"/>
66
<status value="requested"/>
77
<intent value="order"/>
8-
<authoredOn value="2021-04-07T12:30:00+01:00"/>
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<authoredOn value="2021-07-07T13:40:00+01:00"/>
99
<requester>
1010
<type value="Organization"/>
1111
<identifier>
@@ -54,7 +54,7 @@
5454
<code value="export-to"/>
5555
</coding>
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</type>
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<valueInstant value="2021-06-03T34:46:00+01:00"/>
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<valueInstant value="2021-07-07T13:40:00+01:00"/>
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</input>
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<!-- optional parameter specifying GECCO resources should be send starting
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at the defined date, resources older than the specified date will not be
@@ -66,6 +66,6 @@
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<code value="export-from"/>
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</coding>
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</type>
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<valueDateTime value="2021-04-07"/>
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<valueDateTime value="2021-01-01"/>
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</input> -->
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</Task>

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