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add long names to livd sync (#7210)
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@fzhao99
fzhao99 authored Jan 29, 2024
1 parent b641485 commit 736a99a
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Showing 3 changed files with 148 additions and 100 deletions.
4 changes: 4 additions & 0 deletions backend/src/main/java/gov/cdc/usds/simplereport/service/DeviceTypeSyncService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,8 @@ public void syncDevices(boolean dryRun) {
.equipmentUid(device.getEquipmentUid())
.equipmentUidType(device.getEquipmentUidType())
.testkitNameId(device.getTestKitNameId())
.testOrderedLoincLongName(device.getTestOrderedLoincLongName())
.testPerformedLoincLongName(device.getTestPerformedLoincLongName())
.build());
});

Expand Down Expand Up @@ -311,6 +313,8 @@ private DeviceType createDevice(
.testkitNameId(device.getTestKitNameId())
.equipmentUid(device.getEquipmentUid())
.equipmentUidType(device.getEquipmentUidType())
.testOrderedLoincLongName(device.getTestOrderedLoincLongName())
.testPerformedLoincLongName(device.getTestPerformedLoincLongName())
.build()))
.build();
log.info("Device created {}", createdDeviceType);
Expand Down
4 changes: 4 additions & 0 deletions backend/src/main/java/gov/cdc/usds/simplereport/service/model/reportstream/LIVDResponse.java
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,14 @@

import java.util.List;
import lombok.AllArgsConstructor;
import lombok.Builder;
import lombok.Getter;
import lombok.Setter;

@Getter
@Setter
@AllArgsConstructor
@Builder
public class LIVDResponse {
private String manufacturer;
private String model;
Expand All @@ -18,4 +20,6 @@ public class LIVDResponse {
private String testKitNameId;
private String equipmentUid;
private String equipmentUidType;
private String testOrderedLoincLongName;
private String testPerformedLoincLongName;
}
240 changes: 140 additions & 100 deletions ...end/src/test/java/gov/cdc/usds/simplereport/service/DeviceTypeServiceIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,9 @@ void setup() {
SupportedDiseaseTestPerformedInput.builder()
.supportedDisease(disease.getInternalId())
.testPerformedLoincCode("000000000")
.testPerformedLoincLongName("000000000 plus some extra stuff")
.testOrderedLoincCode("000000000")
.testOrderedLoincLongName("000000000 plus some extra stuff")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment Uid Type")
.testkitNameId("TestKit Uid")
Expand All @@ -100,6 +102,9 @@ void setup() {
SupportedDiseaseTestPerformedInput.builder()
.supportedDisease(disease.getInternalId())
.testPerformedLoincCode("258500001")
.testPerformedLoincLongName("258500001 plus some extra stuff")
.testOrderedLoincCode("253520011")
.testOrderedLoincLongName("253520011 plus some extra stuff")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment Uid Type")
.testkitNameId("TestKit Uid")
Expand All @@ -112,16 +117,19 @@ void setup() {
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_updatesDevices() {
LIVDResponse newDevice =
new LIVDResponse(
"Manufacturer A",
"Model A",
List.of(SPECIMEN_DESCRIPTION_ONE),
"influenza A RNA Result",
"7777777",
"8888888",
"Updated TestKit",
"Updated Equip",
"Updated Equip Type");
LIVDResponse.builder()
.manufacturer("Manufacturer A")
.model("Model A")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("influenza A RNA Result")
.testPerformedLoincCode("7777777")
.testPerformedLoincLongName("7777777 plus some extra stuff")
.testOrderedLoincCode("8888888")
.testOrderedLoincLongName("8888888 plus some extra stuff")
.testKitNameId("Updated TestKit")
.equipmentUid("Updated Equip")
.equipmentUidType("Updated Equip Type")
.build();

List<LIVDResponse> devices = List.of(newDevice);

Expand All @@ -141,23 +149,28 @@ void syncDevices_updatesDevices() {
assertThat(code.getTestkitNameId()).isEqualTo("Updated TestKit");
assertThat(code.getEquipmentUid()).isEqualTo("Updated Equip");
assertThat(code.getEquipmentUidType()).isEqualTo("Updated Equip Type");
assertThat(code.getTestOrderedLoincLongName()).isEqualTo("8888888 plus some extra stuff");
assertThat(code.getTestPerformedLoincLongName()).isEqualTo("7777777 plus some extra stuff");
}

@ParameterizedTest
@MethodSource("deviceArgs")
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_createsDevices(String vendorAnalyteName, String expectedDiseaseName) {
LIVDResponse newDevice =
new LIVDResponse(
"New Device Manufacturer",
"New Device Model",
List.of(SPECIMEN_DESCRIPTION_ONE),
vendorAnalyteName,
"8888888",
"0123456",
"New TestKit",
"New Equip",
"New Equip Uid Type");
LIVDResponse.builder()
.manufacturer("New Device Manufacturer")
.model("New Device Model")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName(vendorAnalyteName)
.testPerformedLoincCode("8888888")
.testPerformedLoincLongName("8888888 plus some extra stuff")
.testOrderedLoincCode("0123456")
.testOrderedLoincLongName("0123456 plus some extra stuff")
.testKitNameId("New TestKit")
.equipmentUid("New Equip")
.equipmentUidType("New Equip Uid Type")
.build();
List<LIVDResponse> devices = List.of(newDevice);

when(dataHubClient.getLIVDTable()).thenReturn(devices);
Expand Down Expand Up @@ -189,27 +202,36 @@ void syncDevices_updatesSpecimenTypes() {
deviceSpecimenTypeRepository.findAllByDeviceTypeId(devA.getInternalId());
assertThat(deviceSpecimenTypes).hasSize(1);
LIVDResponse deviceOne =
new LIVDResponse(
devA.getManufacturer(),
devA.getModel(),
List.of(SPECIMEN_DESCRIPTION_ONE, SPECIMEN_DESCRIPTION_TWO),
"influenza A RNA Result",
"0123456",
"8888888",
"TestKit A",
"Equip A",
"Equip A Type");
LIVDResponse.builder()
.manufacturer(devA.getManufacturer())
.model(devA.getModel())
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE, SPECIMEN_DESCRIPTION_TWO))
.vendorAnalyteName("influenza A RNA Result")
.testPerformedLoincCode("0123456")
.testPerformedLoincLongName("0123456 plus some extra stuff")
.testOrderedLoincCode("8888888")
.testOrderedLoincLongName("8888888 plus some extra stuff")
.testKitNameId("TestKit A")
.equipmentUid("Equip A")
.equipmentUidType("Equip A Type")
.build();

LIVDResponse deviceTwo =
new LIVDResponse(
devB.getManufacturer(),
devB.getModel(),
List.of(SPECIMEN_DESCRIPTION_ONE, SPECIMEN_DESCRIPTION_THREE),
"influenza A RNA Result",
"0123456",
"8888888",
"TestKit A",
"Equip A",
"Equip A Type");
LIVDResponse.builder()
.manufacturer(devB.getManufacturer())
.model(devB.getModel())
.vendorSpecimenDescription(
List.of(SPECIMEN_DESCRIPTION_ONE, SPECIMEN_DESCRIPTION_THREE))
.vendorAnalyteName("influenza A RNA Result")
.testPerformedLoincCode("0123456")
.testPerformedLoincLongName("0123456 plus some extra stuff")
.testOrderedLoincCode("8888888")
.testOrderedLoincLongName("8888888 plus some extra stuff")
.testKitNameId("TestKit B")
.equipmentUid("Equip B")
.equipmentUidType("Equip B Type")
.build();

List<LIVDResponse> devices = List.of(deviceOne, deviceTwo);

when(dataHubClient.getLIVDTable()).thenReturn(devices);
Expand Down Expand Up @@ -249,16 +271,19 @@ void syncDevices_updatesSpecimenTypes() {
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_updatesAssociatedDeviceTypeDiseaseFields() {
LIVDResponse newDevice =
new LIVDResponse(
"Manufacturer A",
"Model A",
List.of(SPECIMEN_DESCRIPTION_ONE),
"influenza A RNA Result",
"7777777",
"8888888",
"Updated TestKit",
"Updated Equip",
"Updated Equip Type");
LIVDResponse.builder()
.manufacturer("Manufacturer A")
.model("Model A")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("influenza A RNA Result")
.testPerformedLoincCode("7777777")
.testPerformedLoincLongName("7777777 plus some extra stuff")
.testOrderedLoincCode("8888888")
.testOrderedLoincLongName("8888888 plus some extra stuff")
.testKitNameId("Updated TestKit")
.equipmentUid("Updated Equip")
.equipmentUidType("Updated Equip Type")
.build();

List<LIVDResponse> devices = List.of(newDevice);

Expand All @@ -284,16 +309,19 @@ void syncDevices_skipsNullUpdates() {
var updatedAt = existingDevice.getUpdatedAt();

LIVDResponse device =
new LIVDResponse(
existingDevice.getManufacturer(),
existingDevice.getModel(),
List.of(SPECIMEN_DESCRIPTION_ONE),
"covid",
"000000000",
"000000000",
"TestKit Uid",
"Equipment Uid",
"Equipment Uid Type");
LIVDResponse.builder()
.manufacturer(existingDevice.getManufacturer())
.model(existingDevice.getModel())
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("covid")
.testPerformedLoincCode("000000000")
.testPerformedLoincLongName("000000000 plus some extra stuff")
.testOrderedLoincCode("000000000")
.testOrderedLoincLongName("000000000 plus some extra stuff")
.testKitNameId("TestKit Uid")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment UID Type")
.build();

List<LIVDResponse> devices = List.of(device);

Expand All @@ -309,16 +337,19 @@ void syncDevices_skipsNullUpdates() {
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_skipsInvalidDiseases() {
LIVDResponse device =
new LIVDResponse(
"Some manufacturer",
"Some model",
List.of(SPECIMEN_DESCRIPTION_ONE),
"invalid disease!",
"000000000",
"000000000",
"TestKit Uid",
"Equipment Uid",
"Equipment Uid Type");
LIVDResponse.builder()
.manufacturer("Some manufacturer")
.model("Some model")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("invalid disease!")
.testPerformedLoincCode("000000000")
.testPerformedLoincLongName("000000000 plus some extra stuff")
.testOrderedLoincCode("000000000")
.testOrderedLoincLongName("000000000 plus some extra stuff")
.testKitNameId("TestKit Uid")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment UID Type")
.build();

List<LIVDResponse> devices = List.of(device);

Expand All @@ -334,16 +365,19 @@ void syncDevices_skipsInvalidDiseases() {
void syncDevices_avoidsDuplicateDeviceNames() {
// Define a device with a `model` matching a different value and a new `manufacturer`
LIVDResponse device =
new LIVDResponse(
"Shiny New Manufacturer",
"Device A",
List.of(SPECIMEN_DESCRIPTION_ONE),
"fluA",
"000000000",
"000000000",
"TestKit Uid",
"Equipment Uid",
"Equip Uid Type");
LIVDResponse.builder()
.manufacturer("Shiny New Manufacturer")
.model("Device A")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("fluA")
.testPerformedLoincCode("000000000")
.testPerformedLoincLongName("000000000 plus some extra stuff")
.testOrderedLoincCode("000000000")
.testOrderedLoincLongName("000000000 plus some extra stuff")
.testKitNameId("TestKit Uid")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment UID Type")
.build();

List<LIVDResponse> devices = List.of(device);

Expand All @@ -358,16 +392,19 @@ void syncDevices_avoidsDuplicateDeviceNames() {
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_skipsConfiguredDevices() {
LIVDResponse device =
new LIVDResponse(
"Applied BioCode, Inc.",
"BioCode CoV-2 Flu Plus Assay",
List.of(SPECIMEN_DESCRIPTION_ONE),
"fluA",
"000000000",
"000000000",
"TestKit Uid",
"Equipment Uid",
"Equipment Uid Type");
LIVDResponse.builder()
.manufacturer("Applied BioCode, Inc.")
.model("BioCode CoV-2 Flu Plus Assay")
.vendorSpecimenDescription(List.of(SPECIMEN_DESCRIPTION_ONE))
.vendorAnalyteName("fluA")
.testPerformedLoincCode("000000000")
.testPerformedLoincLongName("000000000 plus some extra stuff")
.testOrderedLoincCode("000000000")
.testOrderedLoincLongName("000000000 plus some extra stuff")
.testKitNameId("TestKit Uid")
.equipmentUid("Equipment Uid")
.equipmentUidType("Equipment UID Type")
.build();

List<LIVDResponse> devices = List.of(device);

Expand All @@ -382,16 +419,19 @@ void syncDevices_skipsConfiguredDevices() {
@SliceTestConfiguration.WithSimpleReportSiteAdminUser
void syncDevices_skipsForDryRuns() {
LIVDResponse newDevice =
new LIVDResponse(
"Dry Run Device Manufacturer",
"Dry Run Device Model",
List.of("not to be added (123456789^To Be Added^SCT)\r"),
"COVID-19",
"8888888",
"0123456",
"Dry Run TestKit",
"Dry Run Equip",
"Dry Run Equip Type");
LIVDResponse.builder()
.manufacturer("Dry Run Device Manufacturer")
.model("Dry Run Device Model")
.vendorSpecimenDescription(List.of("not to be added (123456789^To Be Added^SCT)\n"))
.vendorAnalyteName("OVID-19")
.testPerformedLoincCode("8888888")
.testPerformedLoincLongName("8888888 plus some extra stuff")
.testOrderedLoincCode("0123456")
.testOrderedLoincLongName("0123456 plus some extra stuff")
.testKitNameId("Dry Run TestKit")
.equipmentUid("Dry Run Equip")
.equipmentUidType("Dry Run Equip Type")
.build();

List<LIVDResponse> devices = List.of(newDevice);

Expand Down

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