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CNDIT-1786 Fix for schema, reduce cognitive complexity
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@sveselev
sveselev committed Sep 25, 2024
1 parent 3535e04 commit c69b676
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Showing 2 changed files with 92 additions and 109 deletions.
4 changes: 2 additions & 2 deletions liquibase-service/src/main/resources/db/rdb/tables/017-create_nrt_observation-003.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ IF EXISTS (SELECT 1 FROM sysobjects WHERE name = 'nrt_observation' and xtype = '
IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'cd_system_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
BEGIN
ALTER TABLE nrt_observation
ADD cd_system_desc_txt varchar(1000);
ADD cd_system_desc_txt varchar(100);
END;

IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'ctrl_cd_user_defined_1' AND object_id = Object_ID(N'nrt_observation'))
Expand All @@ -69,7 +69,7 @@ IF EXISTS (SELECT 1 FROM sysobjects WHERE name = 'nrt_observation' and xtype = '
IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd_system_cd' AND object_id = Object_ID(N'nrt_observation'))
BEGIN
ALTER TABLE nrt_observation
ADD alt_cd_system_cd varchar(1000);
ADD alt_cd_system_cd varchar(300);
END;

IF NOT EXISTS(SELECT 1 FROM sys.columns WHERE name = N'alt_cd_system_desc_txt' AND object_id = Object_ID(N'nrt_observation'))
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197 changes: 90 additions & 107 deletions ...ce/src/main/java/gov/cdc/etldatapipeline/observation/util/ProcessObservationDataUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,32 +42,27 @@ private void transformPersonParticipations(String personParticipations, String o
try {
JsonNode personParticipationsJsonArray = parseJsonArray(personParticipations, objectMapper);

if(personParticipationsJsonArray != null) {
for(JsonNode jsonNode : personParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));

if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd != null && subjectClassCd != null) {
if(typeCd.equals("ORD") && subjectClassCd.equals("PSN")) {
observationTransformed.setOrderingPersonId(jsonNode.get(ENTITY_ID).asLong());
}
if (typeCd.equals("PATSBJ") && subjectClassCd.equals("PSN")) {
observationTransformed.setPatientId(jsonNode.get(ENTITY_ID).asLong());
}
for (JsonNode jsonNode : personParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));

if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd != null && subjectClassCd != null) {
if(typeCd.equals("ORD") && subjectClassCd.equals("PSN")) {
observationTransformed.setOrderingPersonId(jsonNode.get(ENTITY_ID).asLong());
}
else {
logger.error("Type_cd or subject_class_cd is null for the personParticipations: {}", personParticipations);
if (typeCd.equals("PATSBJ") && subjectClassCd.equals("PSN")) {
observationTransformed.setPatientId(jsonNode.get(ENTITY_ID).asLong());
}
} else {
logger.error("Type_cd or subject_class_cd is null for the personParticipations: {}", personParticipations);
}
else {
logger.error("obsDomainCdSt1: {} is not valid for the personParticipations.", obsDomainCdSt1);
}
} else {
logger.error("obsDomainCdSt1: {} is not valid for the personParticipations.", obsDomainCdSt1);
}
}
else {
logger.info("PersonParticipations array is null.");
}
} catch (IllegalArgumentException ex) {
logger.info("PersonParticipations array is null.");
} catch (Exception e) {
logger.error("Error processing Person Participation JSON array from observation data: {}", e.getMessage());
}
Expand All @@ -77,36 +72,33 @@ private void transformOrganizationParticipations(String organizationParticipatio
try {
JsonNode organizationParticipationsJsonArray = parseJsonArray(organizationParticipations, objectMapper);

if(organizationParticipationsJsonArray != null) {
for(JsonNode jsonNode : organizationParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));
for(JsonNode jsonNode : organizationParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));

if(typeCd != null && subjectClassCd != null) {
if(obsDomainCdSt1.equals(DOM_RESULT)) {
if(typeCd.equals("PRF") && subjectClassCd.equals("ORG")) {
observationTransformed.setPerformingOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
}
else if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd.equals("AUT") && subjectClassCd.equals("ORG")) {
observationTransformed.setAuthorOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
if(typeCd.equals("ORD") && subjectClassCd.equals("ORG")) {
observationTransformed.setOrderingOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
}
else {
logger.error("obsDomainCdSt1: {} is not valid for the organizationParticipations", obsDomainCdSt1);
if(typeCd != null && subjectClassCd != null) {
if(obsDomainCdSt1.equals(DOM_RESULT)) {
if(typeCd.equals("PRF") && subjectClassCd.equals("ORG")) {
observationTransformed.setPerformingOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
} else {
logger.error("Type_cd or subject_class_cd is null for the organizationParticipations: {}", organizationParticipations);
}
else if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd.equals("AUT") && subjectClassCd.equals("ORG")) {
observationTransformed.setAuthorOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
if(typeCd.equals("ORD") && subjectClassCd.equals("ORG")) {
observationTransformed.setOrderingOrganizationId(jsonNode.get(ENTITY_ID).asLong());
}
}
else {
logger.error("obsDomainCdSt1: {} is not valid for the organizationParticipations", obsDomainCdSt1);
}
} else {
logger.error("Type_cd or subject_class_cd is null for the organizationParticipations: {}", organizationParticipations);
}
}
else {
logger.info("OrganizationParticipations array is null.");
}
} catch (IllegalArgumentException ex) {
logger.info("OrganizationParticipations array is null.");
} catch (Exception e) {
logger.error("Error processing Organization Participation JSON array from observation data: {}", e.getMessage());
}
Expand All @@ -116,29 +108,25 @@ private void transformMaterialParticipations(String materialParticipations, Stri
try {
JsonNode materialParticipationsJsonArray = parseJsonArray(materialParticipations, objectMapper);

if(materialParticipationsJsonArray != null) {
for(JsonNode jsonNode : materialParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));
for(JsonNode jsonNode : materialParticipationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get(TYPE_CD));
String subjectClassCd = getNodeValue(jsonNode.get(SUBJECT_CLASS_CD));

if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd != null && subjectClassCd != null) {
if(typeCd.equals("SPC") && subjectClassCd.equals("MAT")) {
observationTransformed.setMaterialId(jsonNode.get(ENTITY_ID).asLong());
}
}
else {
logger.error("Type_cd or subject_class_cd is null for the materialParticipations: {}", materialParticipations);
if(obsDomainCdSt1.equals(DOM_ORDER)) {
if(typeCd != null && subjectClassCd != null) {
if(typeCd.equals("SPC") && subjectClassCd.equals("MAT")) {
observationTransformed.setMaterialId(jsonNode.get(ENTITY_ID).asLong());
}
}
else {
logger.error("obsDomainCdSt1: {} is not valid for the materialParticipations", obsDomainCdSt1);
} else {
logger.error("Type_cd or subject_class_cd is null for the materialParticipations: {}", materialParticipations);
}
}
else {
logger.error("obsDomainCdSt1: {} is not valid for the materialParticipations", obsDomainCdSt1);
}
}
else {
logger.info("MaterialParticipations array is null.");
}
} catch (IllegalArgumentException ex) {
logger.info("MaterialParticipations array is null.");
} catch (Exception e) {
logger.error("Error processing Material Participation JSON array from observation data: {}", e.getMessage());
}
Expand All @@ -148,34 +136,31 @@ private void transformFollowupObservations(String followupObservations, String o
try {
JsonNode followupObservationsJsonArray = parseJsonArray(followupObservations, objectMapper);

if(followupObservationsJsonArray != null) {
List<String> results = new ArrayList<>();
List<String> followUps = new ArrayList<>();
for (JsonNode jsonNode : followupObservationsJsonArray) {
String domainCdSt1 = getNodeValue(jsonNode.get("domain_cd_st_1"));
List<String> results = new ArrayList<>();
List<String> followUps = new ArrayList<>();
for (JsonNode jsonNode : followupObservationsJsonArray) {
String domainCdSt1 = getNodeValue(jsonNode.get("domain_cd_st_1"));

if (obsDomainCdSt1.equals(DOM_ORDER)) {
if (DOM_RESULT.equals(domainCdSt1)) {
Optional.ofNullable(jsonNode.get("result_observation_uid")).ifPresent(r -> results.add(r.asText()));
}
else {
Optional.ofNullable(jsonNode.get("result_observation_uid")).ifPresent(r -> followUps.add(r.asText()));
}
} else {
logger.error("obsDomainCdSt1: {} is not valid for the followupObservations", obsDomainCdSt1);
if (obsDomainCdSt1.equals(DOM_ORDER)) {
if (DOM_RESULT.equals(domainCdSt1)) {
Optional.ofNullable(jsonNode.get("result_observation_uid")).ifPresent(r -> results.add(r.asText()));
}
else {
Optional.ofNullable(jsonNode.get("result_observation_uid")).ifPresent(r -> followUps.add(r.asText()));
}
} else {
logger.error("obsDomainCdSt1: {} is not valid for the followupObservations", obsDomainCdSt1);
}
}

if(!results.isEmpty()) {
observationTransformed.setResultObservationUid(String.join(",", results));
}
if(!followUps.isEmpty()) {
observationTransformed.setFollowUpObservationUid(String.join(",", followUps));
}
if(!results.isEmpty()) {
observationTransformed.setResultObservationUid(String.join(",", results));
}
else {
logger.info("FollowupObservations array is null.");
if(!followUps.isEmpty()) {
observationTransformed.setFollowUpObservationUid(String.join(",", followUps));
}
} catch (IllegalArgumentException ex) {
logger.info("FollowupObservations array is null.");
} catch (Exception e) {
logger.error("Error processing Followup Observations JSON array from observation data: {}", e.getMessage());
}
Expand All @@ -185,41 +170,39 @@ private void transformParentObservations(String parentObservations, String obsDo
try {
JsonNode parentObservationsJsonArray = parseJsonArray(parentObservations, objectMapper);

if(parentObservationsJsonArray != null) {
for (JsonNode jsonNode : parentObservationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get("parent_type_cd"));
Optional.ofNullable(jsonNode.get("report_observation_uid")).ifPresent(id -> observationTransformed.setReportObservationUid(id.asLong()));
for (JsonNode jsonNode : parentObservationsJsonArray) {
String typeCd = getNodeValue(jsonNode.get("parent_type_cd"));
Optional.ofNullable(jsonNode.get("report_observation_uid")).ifPresent(id -> observationTransformed.setReportObservationUid(id.asLong()));

if (obsDomainCdSt1.equals(DOM_ORDER)) {
Optional<JsonNode> parentUid = Optional.ofNullable(jsonNode.get("parent_uid"));
if (obsDomainCdSt1.equals(DOM_ORDER)) {
Optional<JsonNode> parentUid = Optional.ofNullable(jsonNode.get("parent_uid"));

if(typeCd != null) {
if (typeCd.equals("SPRT")) {
parentUid.ifPresent(id -> observationTransformed.setReportSprtUid(id.asLong()));
} else if (typeCd.equals("REFR")) {
parentUid.ifPresent(id -> observationTransformed.setReportRefrUid(id.asLong()));
}
} else {
logger.error("Parent_type_cd is null for the parentObservations: {}", parentObservations);
if(typeCd != null) {
if (typeCd.equals("SPRT")) {
parentUid.ifPresent(id -> observationTransformed.setReportSprtUid(id.asLong()));
} else if (typeCd.equals("REFR")) {
parentUid.ifPresent(id -> observationTransformed.setReportRefrUid(id.asLong()));
}
} else {
logger.error("obsDomainCdSt1: {} is not valid for the parentObservations", obsDomainCdSt1);
logger.error("Parent_type_cd is null for the parentObservations: {}", parentObservations);
}
} else {
logger.error("obsDomainCdSt1: {} is not valid for the parentObservations", obsDomainCdSt1);
}
} else {
logger.info("ParentObservations array is null.");
}
} catch (IllegalArgumentException ex) {
logger.info("ParentObservations array is null.");
} catch (Exception e) {
logger.error("Error processing Parent Observations JSON array from observation data: {}", e.getMessage());
}
}

private JsonNode parseJsonArray(String jsonString, ObjectMapper objectMapper) throws JsonProcessingException {
private JsonNode parseJsonArray(String jsonString, ObjectMapper objectMapper) throws JsonProcessingException, IllegalArgumentException {
JsonNode jsonArray = jsonString != null ? objectMapper.readTree(jsonString) : null;
if (jsonArray != null) {
return jsonArray.isArray() ? jsonArray : null;
if (jsonArray != null && jsonArray.isArray()) {
return jsonArray;
} else {
return null;
throw new IllegalArgumentException();
}
}

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