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[CNDIT-1758] CDA mapper changes for ECR (#225)
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* CDA mapper changes

* Removing debug code

* Fixing sonar code smell and adding new tests for ecr poll
service

* Fixing sonar code smell

* Removed logback config file
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@rshanmugam-enquizit
rshanmugam-enquizit authored Sep 27, 2024
1 parent 623a532 commit 1d1d6ea
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Showing 16 changed files with 273 additions and 152 deletions.
37 changes: 20 additions & 17 deletions data-ingestion-service/src/main/java/gov/cdc/dataingestion/nbs/ecr/service/CdaMapper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,7 @@ private CdaContainerComp mapParentContainer(POCDMT000040ClinicalDocument1 clinic
clinicalDocument.getCode().setDisplayName("Public Health Case Report - PHRI");
clinicalDocument.setTitle(ST.Factory.newInstance());

clinicalDocument.getTitle().set(cdaMapHelper.mapToStringData("Public Health Case Report - Data from Legacy System to CDA"));
clinicalDocument.getTitle().set(cdaMapHelper.mapToPCData("Public Health Case Report - Data from Legacy System to CDA"));

clinicalDocument.setEffectiveTime(TS.Factory.newInstance());
clinicalDocument.getEffectiveTime().setValue(this.cdaMapHelper.getCurrentUtcDateTimeInCdaFormat());
Expand Down Expand Up @@ -237,28 +237,28 @@ private void mapCustodian(POCDMT000040ClinicalDocument1 clinicalDocument) throws

custodianValue = mapToTranslatedValue("CUS103");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewStreetAddressLine();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStreetAddressLineArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStreetAddressLineArray(k).set(cdaMapHelper.mapToPCData(custodianValue));
k = k+1;
custodianValue = mapToTranslatedValue("CUS104");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewStreetAddressLine();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStreetAddressLineArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStreetAddressLineArray(k).set(cdaMapHelper.mapToPCData(custodianValue));

k = 0;
custodianValue = mapToTranslatedValue("CUS105");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewCity();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getCityArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getCityArray(k).set(cdaMapHelper.mapToPCData(custodianValue));

custodianValue = mapToTranslatedValue("CUS106");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewState();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStateArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getStateArray(k).set(cdaMapHelper.mapToPCData(custodianValue));

custodianValue = mapToTranslatedValue("CUS107");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewPostalCode();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getPostalCodeArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getPostalCodeArray(k).set(cdaMapHelper.mapToPCData(custodianValue));

custodianValue = mapToTranslatedValue("CUS108");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().addNewCountry();
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getCountryArray(k).set(cdaMapHelper.mapToCData(custodianValue));
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getAddr().getCountryArray(k).set(cdaMapHelper.mapToPCData(custodianValue));

custodianValue = mapToTranslatedValue("CUS109");
clinicalDocument.getCustodian().getAssignedCustodian().getRepresentedCustodianOrganization().getTelecom().setValue(custodianValue);
Expand All @@ -277,7 +277,7 @@ private void mapAuthor(POCDMT000040ClinicalDocument1 clinicalDocument) throws Ec
clinicalDocument.getAuthorArray(0).getAssignedAuthor().addNewAssignedPerson().addNewName();
clinicalDocument.getAuthorArray(0).getAssignedAuthor().getAssignedPerson().getNameArray(0).addNewFamily();
value = mapToTranslatedValue("AUT102");
clinicalDocument.getAuthorArray(0).getAssignedAuthor().getAssignedPerson().getNameArray(0).getFamilyArray(0).set(cdaMapHelper.mapToCData(value));
clinicalDocument.getAuthorArray(0).getAssignedAuthor().getAssignedPerson().getNameArray(0).getFamilyArray(0).set(cdaMapHelper.mapToPCData(value));

OffsetDateTime now = OffsetDateTime.now();
String formattedDateTime = formatDateTime(now);
Expand All @@ -292,31 +292,34 @@ private static String formatDateTime(OffsetDateTime dateTime) {

private String convertXmlToString(ClinicalDocumentDocument1 clinicalDocument) {
XmlOptions options = new XmlOptions();
options.setSavePrettyPrint();
options.setSavePrettyPrintIndent(4); // Set indentation
// Use a default namespace instead of a prefixed one (like urn:)
options.setUseDefaultNamespace();
// Set to always use full tags instead of self-closing tags
options.setSaveNoXmlDecl();
options.setSaveOuter();


String xmlOutput = clinicalDocument.xmlText(options);

xmlOutput = xmlOutput.replaceAll("<STRING[^>]*>([^<]+)</STRING>", "$1");// NOSONAR // remove string tag
xmlOutput = xmlOutput.replaceAll("<CDATA[^>]*>(.*?)</CDATA>", "$1");// NOSONAR // replace CDATA with real CDATA
xmlOutput = xmlOutput.replaceAll("\\[CDATA\\](.*?)\\[CDATA\\]", "<![CDATA[$1]]>");// NOSONAR // replace CDATA with real CDATA
xmlOutput = xmlOutput.replaceAll("<CDATA[^>]*>(.*?)</CDATA>", "<![CDATA[$1]]>");// NOSONAR // replace CDATA with real CDATA
xmlOutput = xmlOutput.replaceAll("<(\\w+)></\\1>", "");// NOSONAR // remove empty <tag></tag>
xmlOutput = xmlOutput.replaceAll("<(\\w+)/>", "");// NOSONAR // remove empty <tag/>
xmlOutput = xmlOutput.replaceAll("<STUD xmlns=\"\">STUD</STUD>", "");// NOSONAR // remove STUD tag
xmlOutput = xmlOutput.replaceAll("<stud xmlns=\"\">stud</stud>", "");// NOSONAR // remove STUD tag
xmlOutput = xmlOutput.replaceAll("(?m)^\\s*$[\n\r]{1,}", "");// NOSONAR // remove new line

xmlOutput = xmlOutput.replaceAll("sdtcxmlnamespaceholder=\""+ XML_NAME_SPACE_HOLDER +"\"", "xmlns:sdtcxmlnamespaceholder=\""+XML_NAME_SPACE_HOLDER+"\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("sdt=\"urn:hl7-org:sdtc\"", "xmlns:sdt=\"urn:hl7-org:sdtc\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xsi=\"http://www.w3.org/2001/XMLSchema-instance\"", "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xmlns:xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"", "xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xmlns:xmlns", "xmlns");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xmlns:urn=\"urn:hl7-org:v3\"", "");// NOSONAR

xmlOutput = xmlOutput.replaceAll("schemaLocation=\""+ XML_NAME_SPACE_HOLDER +" CDA_SDTC.xsd\"", "xsi:schemaLocation=\""+XML_NAME_SPACE_HOLDER +" CDA_SDTC.xsd\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("<section xmlns=\"\">", "<section>");// NOSONAR

xmlOutput = xmlOutput.replaceAll("<xmlns=\"\">", "");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xmlns=\"\"", "");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xsi:type=\"urn:CE\"", "xsi:type=\"CE\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xsi:type=\"urn:ST\"", "xsi:type=\"ST\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xsi:type=\"urn:II\"", "xsi:type=\"II\"");// NOSONAR
xmlOutput = xmlOutput.replaceAll("xsi:type=\"urn:TS\"", "xsi:type=\"TS\"");// NOSONAR

xmlOutput = xmlOutput.replaceAll("\\^NOT_MAPPED", "");// NOSONAR
xmlOutput = xmlOutput.replaceAll("NOT_MAPPED","");// NOSONAR
Expand Down
15 changes: 6 additions & 9 deletions ...vice/src/main/java/gov/cdc/dataingestion/nbs/ecr/service/helper/CdaCaseMappingHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,9 +13,7 @@
import gov.cdc.dataingestion.nbs.repository.model.dto.EcrMsgCaseParticipantDto;
import gov.cdc.dataingestion.nbs.repository.model.dto.lookup.PhdcQuestionLookUpDto;
import gov.cdc.nedss.phdc.cda.*;
import org.apache.xmlbeans.XmlCursor;

import javax.xml.namespace.QName;
import java.util.List;
import java.util.Map;

Expand Down Expand Up @@ -55,7 +53,7 @@ public CdaCaseMapper mapToCaseTop(EcrSelectedRecord input, POCDMT000040ClinicalD
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getCode().setCodeSystem(CODE_SYSTEM);
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getCode().setCodeSystemName(CODE_SYSTEM_NAME);
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getCode().setDisplayName("Clinical Information");
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getTitle().set(cdaMapHelper.mapToStringData("CLINICAL INFORMATION"));
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getTitle().set(cdaMapHelper.mapToPCData("CLINICAL INFORMATION"));

componentCounter = c;

Expand Down Expand Up @@ -528,12 +526,11 @@ private void setMessageAnswerDate(String name, EcrMsgCaseAnswerDto in, POCDMT000

var element = out.getSection().getEntryArray(counter).getObservation().getValueArray(0);

XmlCursor cursor = element.newCursor();
cursor.toFirstAttribute();
cursor.insertAttributeWithValue(new QName(NAME_SPACE_URL, "type"), "TS");
TS ts = TS.Factory.newInstance();

var ot = cdaMapHelper.mapToTsType(in.getAnswerTxt()).toString();
cursor.insertAttributeWithValue("value", ot);
cursor.dispose();
ts.setValue(ot);
element.set(ts);
}

}
Expand Down Expand Up @@ -618,7 +615,7 @@ private MultiSelect mapToMultiSelect(EcrMsgCaseAnswerDto in,
out.getCode().setCodeSystem(CLINICAL_CODE_SYSTEM);
out.getCode().setCodeSystemName(CLINICAL_CODE_SYSTEM_NAME);
out.getCode().setDisplayName("Generic Repeating Questions Section");
out.getTitle().set(cdaMapHelper.mapToStringData("REPEATING QUESTIONS"));
out.getTitle().set(cdaMapHelper.mapToPCData("REPEATING QUESTIONS"));
int componentCounter = 0;
String dataType="DATE";
int questionGroupSeqNbr = 0;
Expand Down
4 changes: 2 additions & 2 deletions ...src/main/java/gov/cdc/dataingestion/nbs/ecr/service/helper/CdaInterviewMappingHelper.java
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@ public CdaInterviewMapper mapToInterviewTop(EcrSelectedRecord input, POCDMT00004
if (clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getTitle() == null) {
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().addNewTitle();
}
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getTitle().set(cdaMapHelper.mapToStringData("INTERVIEW SECTION"));
clinicalDocument.getComponent().getStructuredBody().getComponentArray(c).getSection().getTitle().set(cdaMapHelper.mapToPCData("INTERVIEW SECTION"));
}

POCDMT000040Component3 ot = clinicalDocument.getComponent().getStructuredBody().getComponentArray(c);
Expand Down Expand Up @@ -818,7 +818,7 @@ private void mapToInterviewObservationFieldP2Date(String name,
if(name.equals(COL_ANS_TXT) && !in.getAnswerTxt().isEmpty()){
var element = out.getEntryRelationshipArray(counter).getObservation().getValueArray(0);
XmlCursor cursor = element.newCursor();
cursor.setAttributeText(new QName(NAME_SPACE_URL, "type"), "TS");
cursor.setAttributeText(new QName(NAME_SPACE_URL, "xsi:type"), "TS");
cursor.setAttributeText(new QName("name"), value); // This is an assumption based on the original code

if(!in.getAnswerTxt().isEmpty()){
Expand Down
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