Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Platform/bill/16144 #16550

Merged
merged 17 commits into from
Nov 22, 2024
Merged

Platform/bill/16144 #16550

Show file tree
Hide file tree
Changes from 15 commits
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
e077e8a
[16144] Modifications for user story 16144 - Implement Translate Step…
wcutshall Nov 12, 2024
3322852
[16144] Change to attempt fix for existing unit and integration tests.
wcutshall Nov 13, 2024
9606328
[16144] Fixed unit tests in FHIRTranslatorTests.
wcutshall Nov 13, 2024
1102247
[16144] Fixed integration tests by modifying FHIRTranslator.
wcutshall Nov 13, 2024
d0517ec
[16144] Added code for tests.
wcutshall Nov 14, 2024
c860dd9
[16144] Added code to account for blob digest properly.
wcutshall Nov 18, 2024
978c899
Merge branch 'main' into platform/bill/16144
wcutshall Nov 18, 2024
6cdc85c
[16144] Checking in WIP.
wcutshall Nov 19, 2024
260604b
[16144] Checking in WIP.
wcutshall Nov 20, 2024
e1c5a70
[16144] Made change to FHIREngine to account for nullable reportEvent…
wcutshall Nov 20, 2024
c2de374
Merge branch 'main' into platform/bill/16144
wcutshall Nov 20, 2024
74b67f7
[16144] Updates based on PR review.
wcutshall Nov 20, 2024
9dc4049
[16144] Update based on PR review.
wcutshall Nov 20, 2024
8b29996
[16144] Changed url and digest to use correct reportdocument.
wcutshall Nov 20, 2024
7ce035d
[16144] Added additional checks to integration test.
wcutshall Nov 21, 2024
7f92ba3
Merge branch 'main' into platform/bill/16144
arnejduranovic Nov 21, 2024
97b21ad
[16144] Added additional check to integration tests.
wcutshall Nov 21, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 4 additions & 0 deletions prime-router/src/main/kotlin/azure/observability/event/ReportStreamEventData.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,9 @@ enum class ReportStreamEventProperties {
BUNDLE_DIGEST,
INGESTION_TYPE,
POISON_QUEUE_MESSAGE_ID,
ENRICHMENTS,
ORIGINAL_FORMAT,
TARGET_FORMAT,
;

@JsonKey
Expand All @@ -92,6 +95,7 @@ enum class ReportStreamEventName {
REPORT_NOT_PROCESSABLE,
ITEM_SENT,
PIPELINE_EXCEPTION,
ITEM_TRANSFORMED,
}

/**
Expand Down
2 changes: 1 addition & 1 deletion prime-router/src/main/kotlin/fhirengine/engine/FHIREngine.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -171,7 +171,7 @@ abstract class FHIREngine(
blobAccess ?: BlobAccess(),
azureEventService ?: AzureEventServiceImpl(),
reportService ?: ReportService(),
ReportStreamEventService(
reportEventService ?: ReportStreamEventService(
databaseAccess ?: databaseAccessSingleton,
azureEventService ?: AzureEventServiceImpl(),
reportService ?: ReportService()
Expand Down
47 changes: 41 additions & 6 deletions prime-router/src/main/kotlin/fhirengine/engine/FHIRTranslator.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@ import ca.uhn.hl7v2.model.Segment
import ca.uhn.hl7v2.util.Terser
import fhirengine.engine.CustomFhirPathFunctions
import fhirengine.engine.CustomTranslationFunctions
import gov.cdc.prime.reportstream.shared.BlobUtils
import gov.cdc.prime.reportstream.shared.QueueMessage
import gov.cdc.prime.router.ActionLogger
import gov.cdc.prime.router.CustomerStatus
Expand All @@ -21,16 +22,21 @@ import gov.cdc.prime.router.azure.DatabaseAccess
import gov.cdc.prime.router.azure.Event
import gov.cdc.prime.router.azure.db.Tables
import gov.cdc.prime.router.azure.db.enums.TaskAction
import gov.cdc.prime.router.azure.observability.bundleDigest.BundleDigestExtractor
import gov.cdc.prime.router.azure.observability.bundleDigest.FhirPathBundleDigestLabResultExtractorStrategy
import gov.cdc.prime.router.azure.observability.context.MDCUtils
import gov.cdc.prime.router.azure.observability.context.withLoggingContext
import gov.cdc.prime.router.azure.observability.event.AzureEventService
import gov.cdc.prime.router.azure.observability.event.AzureEventServiceImpl
import gov.cdc.prime.router.azure.observability.event.IReportStreamEventService
import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName
import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties
import gov.cdc.prime.router.common.Environment
import gov.cdc.prime.router.fhirengine.config.HL7TranslationConfig
import gov.cdc.prime.router.fhirengine.translation.hl7.FhirToHl7Context
import gov.cdc.prime.router.fhirengine.translation.hl7.FhirToHl7Converter
import gov.cdc.prime.router.fhirengine.translation.hl7.FhirTransformer
import gov.cdc.prime.router.fhirengine.translation.hl7.utils.CustomContext
import gov.cdc.prime.router.fhirengine.translation.hl7.utils.HL7Utils.defaultHl7EncodingFiveChars
import gov.cdc.prime.router.fhirengine.translation.hl7.utils.HL7Utils.defaultHl7EncodingFourChars
import gov.cdc.prime.router.fhirengine.utils.FhirTranscoder
Expand Down Expand Up @@ -113,12 +119,13 @@ class FHIRTranslator(
): FHIREngineRunResult {
logger.trace("Preparing to send original message")
val originalReport = reportService.getRootReport(message.reportId)
val bodyBytes = BlobAccess.downloadBlobAsByteArray(originalReport.bodyUrl)
val bodyAsString =
BlobAccess.downloadBlob(originalReport.bodyUrl, BlobUtils.digestToString(originalReport.blobDigest))

// get a Report from the message
val (report, event, blobInfo) = Report.generateReportAndUploadBlob(
Event.EventAction.SEND,
bodyBytes,
bodyAsString.toByteArray(),
listOf(message.reportId),
receiver,
this.metadata,
Expand Down Expand Up @@ -148,10 +155,9 @@ class FHIRTranslator(
actionHistory: ActionHistory,
): FHIREngineRunResult {
logger.trace("Preparing to send translated message")
val bodyBytes =
getByteArrayFromBundle(
receiver, FhirTranscoder.decode(BlobAccess.downloadBlob(message.blobURL, message.digest))
)
val originalReport = reportService.getRootReport(message.reportId)
val bundle = FhirTranscoder.decode(BlobAccess.downloadBlob(message.blobURL, message.digest))
val bodyBytes = getByteArrayFromBundle(receiver, bundle)

val (report, event, blobInfo) = Report.generateReportAndUploadBlob(
Event.EventAction.BATCH,
Expand All @@ -163,6 +169,35 @@ class FHIRTranslator(
topic = message.topic
)

val bundleDigestExtractor = BundleDigestExtractor(
FhirPathBundleDigestLabResultExtractorStrategy(
CustomContext(
bundle,
bundle,
mutableMapOf(),
CustomFhirPathFunctions()
)
)
)
reportEventService.sendItemEvent(
eventName = ReportStreamEventName.ITEM_TRANSFORMED,
childReport = report,
pipelineStepName = TaskAction.translate
) {
parentReportId(message.reportId)
params(
mapOf(
ReportStreamEventProperties.RECEIVER_NAME to receiver.fullName,
ReportStreamEventProperties.BUNDLE_DIGEST
to bundleDigestExtractor.generateDigest(bundle),
ReportStreamEventProperties.ORIGINAL_FORMAT to originalReport.bodyFormat,
ReportStreamEventProperties.TARGET_FORMAT to receiver.translation.format.name,
ReportStreamEventProperties.ENRICHMENTS to listOf(receiver.translation.schemaName)
)
)
trackingId(bundle)
}

return FHIREngineRunResult(
event,
report,
Expand Down
6 changes: 5 additions & 1 deletion prime-router/src/test/kotlin/common/UniversalPipelineTestUtils.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@ package gov.cdc.prime.router.common
import assertk.assertThat
import assertk.assertions.hasSize
import assertk.assertions.isEqualTo
import gov.cdc.prime.reportstream.shared.BlobUtils.sha256Digest
import gov.cdc.prime.router.ClientSource
import gov.cdc.prime.router.CustomerStatus
import gov.cdc.prime.router.DeepOrganization
Expand Down Expand Up @@ -452,7 +453,8 @@ object UniversalPipelineTestUtils {
event,
Topic.FULL_ELR,
parentReport,
blobUrl
blobUrl,
reportContents,
)
}

Expand All @@ -464,6 +466,7 @@ object UniversalPipelineTestUtils {
topic: Topic,
parentReport: Report? = null,
bodyURL: String? = null,
reportContents: String,
): Report {
val report = Report(
fileFormat,
Expand Down Expand Up @@ -493,6 +496,7 @@ object UniversalPipelineTestUtils {
.setBodyUrl(report.bodyURL)
.setSendingOrg(universalPipelineOrganization.name)
.setSendingOrgClient("Test Sender")
.setBlobDigest(sha256Digest(reportContents.toByteArray(Charsets.UTF_8)))

ReportStreamTestDatabaseContainer.testDatabaseAccess.insertReportFile(
reportFile, txn, action
Expand Down
61 changes: 61 additions & 0 deletions prime-router/src/test/kotlin/fhirengine/azure/FHIRTranslatorIntegrationTests.kt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
package gov.cdc.prime.router.fhirengine.azure

import assertk.assertThat
import assertk.assertions.hasSize
import assertk.assertions.isEqualTo
import assertk.assertions.isInstanceOf
import assertk.assertions.isNotEqualTo
import assertk.assertions.isNotNull
import assertk.assertions.isNull
Expand All @@ -22,7 +24,10 @@ import gov.cdc.prime.router.azure.db.enums.TaskAction
import gov.cdc.prime.router.azure.db.tables.Task
import gov.cdc.prime.router.azure.observability.event.AzureEventService
import gov.cdc.prime.router.azure.observability.event.InMemoryAzureEventService
import gov.cdc.prime.router.azure.observability.event.ReportStreamEventName
import gov.cdc.prime.router.azure.observability.event.ReportStreamEventProperties
import gov.cdc.prime.router.azure.observability.event.ReportStreamEventService
import gov.cdc.prime.router.azure.observability.event.ReportStreamItemEvent
import gov.cdc.prime.router.cli.tests.CompareData
import gov.cdc.prime.router.common.TestcontainersUtils
import gov.cdc.prime.router.common.UniversalPipelineTestUtils
Expand Down Expand Up @@ -191,6 +196,20 @@ class FHIRTranslatorIntegrationTests : Logging {
QueueAccess.sendMessage(any(), any())
}

// check events
assertThat(azureEventService.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!).hasSize(1)
assertThat(
azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first()
).isInstanceOf<ReportStreamItemEvent>()
val event = azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first() as ReportStreamItemEvent
assertThat(event.params[ReportStreamEventProperties.ORIGINAL_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.TARGET_FORMAT]).isEqualTo("HL7")
assertThat(event.params[ReportStreamEventProperties.RECEIVER_NAME]).isEqualTo("phd.x")
val enrichments = event.params[ReportStreamEventProperties.ENRICHMENTS] as List<*>
arnejduranovic marked this conversation as resolved.
Show resolved Hide resolved
assertThat(enrichments).hasSize(1)

// check action table
UniversalPipelineTestUtils.checkActionTable(listOf(TaskAction.receive, TaskAction.translate))

Expand Down Expand Up @@ -289,6 +308,20 @@ class FHIRTranslatorIntegrationTests : Logging {
QueueAccess.sendMessage(any(), any())
}

// check events
assertThat(azureEventService.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!).hasSize(1)
assertThat(
azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first()
).isInstanceOf<ReportStreamItemEvent>()
val event = azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first() as ReportStreamItemEvent
assertThat(event.params[ReportStreamEventProperties.ORIGINAL_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.TARGET_FORMAT]).isEqualTo("HL7")
assertThat(event.params[ReportStreamEventProperties.RECEIVER_NAME]).isEqualTo("phd.x")
val enrichments = event.params[ReportStreamEventProperties.ENRICHMENTS] as List<*>
assertThat(enrichments).hasSize(1)

// check action table
UniversalPipelineTestUtils.checkActionTable(listOf(TaskAction.receive, TaskAction.translate))

Expand Down Expand Up @@ -364,6 +397,20 @@ class FHIRTranslatorIntegrationTests : Logging {
QueueAccess.sendMessage(any(), any())
}

// check events
assertThat(azureEventService.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!).hasSize(1)
assertThat(
azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first()
).isInstanceOf<ReportStreamItemEvent>()
val event = azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first() as ReportStreamItemEvent
assertThat(event.params[ReportStreamEventProperties.ORIGINAL_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.TARGET_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.RECEIVER_NAME]).isEqualTo("phd.x")
val enrichments = event.params[ReportStreamEventProperties.ENRICHMENTS] as List<*>
assertThat(enrichments).hasSize(1)

// check action table
UniversalPipelineTestUtils.checkActionTable(listOf(TaskAction.receive, TaskAction.translate))

Expand Down Expand Up @@ -449,6 +496,20 @@ class FHIRTranslatorIntegrationTests : Logging {
QueueAccess.sendMessage(any(), any())
}

// check events
assertThat(azureEventService.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!).hasSize(1)
assertThat(
azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first()
).isInstanceOf<ReportStreamItemEvent>()
val event = azureEventService
.reportStreamEvents[ReportStreamEventName.ITEM_TRANSFORMED]!!.first() as ReportStreamItemEvent
assertThat(event.params[ReportStreamEventProperties.ORIGINAL_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.TARGET_FORMAT]).isEqualTo("FHIR")
assertThat(event.params[ReportStreamEventProperties.RECEIVER_NAME]).isEqualTo("phd.x")
val enrichments = event.params[ReportStreamEventProperties.ENRICHMENTS] as List<*>
assertThat(enrichments).hasSize(1)

// check action table
UniversalPipelineTestUtils.checkActionTable(listOf(TaskAction.receive, TaskAction.translate))

Expand Down
Loading