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Add XML API to nNGM #239

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40 changes: 20 additions & 20 deletions src/main/java/de/samply/share/client/util/connector/CtsConnector.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.util.ResourceReferenceInfo;
import com.google.common.io.CharSource;
import com.mchange.rmi.NotAuthorizedException;
import de.samply.share.client.control.ApplicationBean;
import de.samply.share.client.crypt.Crypt;
Expand All @@ -19,6 +18,7 @@
import de.samply.share.client.util.xml.XmlUtils;
import de.samply.share.common.utils.SamplyShareUtils;
import jakarta.ws.rs.NotFoundException;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.net.MalformedURLException;
Expand Down Expand Up @@ -87,11 +87,11 @@ public CtsConnector() throws MalformedURLException {
* upload endpoint.
*
* @param bundleString the patient bundle as String.
* @throws IOException IOException
* @throws NotFoundException NotFoundException
* @throws NotAuthorizedException NotAuthorizedException
* @throws IOException IOException
* @throws NotFoundException NotFoundException
* @throws NotAuthorizedException NotAuthorizedException
* @throws MainzellisteConnectorException MainzellisteConnectorException
* @throws CtsConnectorException CtsConnectorException
* @throws CtsConnectorException CtsConnectorException
*/
public Response postFhirToCts(String bundleString, MediaType mediaType)
throws IOException,
Expand Down Expand Up @@ -159,16 +159,17 @@ private Bundle pseudonymiseBundle(String bundleString, MediaType mediaType)
* Pseudonymize any patient data in the bundle.
*
* @param xmlString the patient bundle which should be pseudonimised
* @return the pseudonimised bundle
* @return the pseudonimised xml
* @throws IOException IOException
* @throws ConfigurationException ConfigurationException
* @throws DataFormatException DataFormatException
*/
private Document pseudonymiseXml(String xmlString)
throws IOException, NotFoundException,
NotAuthorizedException, MainzellisteConnectorException, XmlPareException {
InputStream xmlInputStream = CharSource.wrap(xmlString)
.asByteSource(StandardCharsets.UTF_8).openStream();
byte[] bytes = xmlString.getBytes(StandardCharsets.UTF_8);
InputStream xmlInputStream = new ByteArrayInputStream(bytes);

Document xmlDocument;
xmlDocument = xmlUtils.domBuilder(xmlInputStream);
MainzellisteConnector mainzellisteConnector = ApplicationBean.getMainzellisteConnector();
Expand Down Expand Up @@ -235,7 +236,7 @@ private String cryptIds(Bundle bundle, boolean encrypt) throws CtsConnectorExcep
* @throws GeneralSecurityException GeneralSecurityException
*/
public static IIdType getEncryptedId(IIdType idType, boolean encrypt, Crypt crypt)
throws GeneralSecurityException {
throws GeneralSecurityException {
String id = idType.getIdPart();
if (id == null || "".equals(id)) {
logger.error("Reference or URL does not contain an ID of a resource " + idType.getValue());
Expand Down Expand Up @@ -287,21 +288,20 @@ public void closeResponse(CloseableHttpResponse response) {

/**
* Takes a stringified XML file, assumed to be containing identifying patient data (IDAT),
* replaces the IDAT with a pseudonym, and then sends the pseudonymized xml to the CTS data
* upload endpoint.
* replaces the IDAT with a pseudonym, and then sends the pseudonymized xml to the CTS data upload
* endpoint.
*
* @param xmlString the patient bundle as String.
* @throws IOException IOException
* @throws NotFoundException NotFoundException
* @throws NotAuthorizedException NotAuthorizedException
* @throws IOException IOException
* @throws NotFoundException NotFoundException
* @throws NotAuthorizedException NotAuthorizedException
* @throws MainzellisteConnectorException MainzellisteConnectorException
* @throws CtsConnectorException CtsConnectorException
* @throws CtsConnectorException CtsConnectorException
*/
public Response postXmlToCts(String xmlString)
throws IOException,
NotFoundException, NotAuthorizedException, XmlPareException,
MainzellisteConnectorException, CtsConnectorException {

throws IOException,
NotFoundException, NotAuthorizedException, XmlPareException,
MainzellisteConnectorException, CtsConnectorException {
Document pseudonymXmlDocument = pseudonymiseXml(xmlString);
String pseudonymXmlAsString = xmlUtils.xmlDocToString(pseudonymXmlDocument);
HttpEntity entity = new StringEntity(pseudonymXmlAsString, Consts.UTF_8);
Expand All @@ -314,7 +314,7 @@ public Response postXmlToCts(String xmlString)
response = httpClient.execute(httpPost);
int statusCode = response.getStatusLine().getStatusCode();
String message =
"CTS server response: statusCode:" + statusCode + "; response: " + response;
"CTS server response: statusCode:" + statusCode + "; response: " + response;
String responseBody = EntityUtils.toString(response.getEntity(), Consts.UTF_8);
if (responseBody != null && !responseBody.isEmpty()) {
message += ";body: " + responseBody;
Expand Down
22 changes: 17 additions & 5 deletions src/main/java/de/samply/share/client/util/connector/MainzellisteConnector.java
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Expand Up @@ -188,7 +188,7 @@ public Bundle getPatientFhirPseudonym(Bundle bundle)
/**
* prepare xml transaction to be sent to the edc system.
*
* @param xmlDoc xml tree.
* @param xmlDoc xml tree
* @return xmlDoc
* @throws NotFoundException Not Found Exception
* @throws NotAuthorizedException Not Authorized Exception
Expand Down Expand Up @@ -226,14 +226,26 @@ public Document getPatientXmlPseudonym(Document xmlDoc)
tokenNode.setTextContent(encryptedId.get(MAINZELLISTE_IDTYPE_ENC_ID).getAsString());
identifyingDataNode.appendChild(tokenNode);
} catch (ConflictException | MandatoryAttributeException
| IllegalArgumentException | XmlPareException e) {
| IllegalArgumentException | XmlPareException e) {
throw new MainzellisteConnectorException(e);
}
return xmlDoc;
}

private String concatenateDate(String year, String month, String day) {
return year + "-" + month + "-" + day;
protected String concatenateDate(String year, String month, String day) {
StringBuilder stringBuilder = new StringBuilder(10);
stringBuilder.append(year);
stringBuilder.append('-');
if (month.length() == 1) {
stringBuilder.append('0');
}
stringBuilder.append(month);
stringBuilder.append('-');
if (day.length() == 1) {
stringBuilder.append('0');
}
stringBuilder.append(day);
return stringBuilder.toString();
}


Expand Down Expand Up @@ -859,7 +871,7 @@ HumanName getPatientName(List<HumanName> nameList, HumanName.NameUse nameUse) {
/**
* validate a date.
*
* @param date date as String
* @param date date as String
* @param dateFormatter Date Time Formatter
* @return boolean
*/
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/de/samply/share/client/util/xml/XmlUtils.java
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Expand Up @@ -35,9 +35,9 @@ public class XmlUtils {
public static final String GEBURTSMONAT_ELEMENT = "geburtsmonat";
public static final String GEBURTSJAHR_ELEMENT = "geburtsjahr";
public static final String VERSICHERUNGSNUMMER_ELEMENT = "versicherungsnummer";
public static final String ADRESSEPLZ_ELEMENT = "adresseplz";
public static final String ADRESSESTADT_ELEMENT = "adressestadt";
public static final String ADRESSESTRASSE_ELEMENT = "adressestrasse";
public static final String ADRESSEPLZ_ELEMENT = "adresse.plz";
public static final String ADRESSESTADT_ELEMENT = "adresse.stadt";
public static final String ADRESSESTRASSE_ELEMENT = "adresse.strasse";
public static final String MEDICAL_DATA_ELEMENT = "medical-data";
public static final String TOKEN_ELEMENT = "token";
public static final String BIRTHDATE_ELEMENT = "birthdate";
Expand Down
26 changes: 26 additions & 0 deletions src/test/java/de/samply/share/client/util/connector/MainzellisteConnectorTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
package de.samply.share.client.util.connector;

import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.*;

import de.samply.share.client.util.connector.MainzellisteConnector;
import org.junit.jupiter.api.Test;

class MainzellisteConnectorTest {

@Test
void testConcatenateDate() {
MainzellisteConnector connectorMock = mock(
de.samply.share.client.util.connector.MainzellisteConnector.class);
String year = "2023";
String month = "4";
String day = "20";

String expectedDate = "2023-04-20";
when(connectorMock.concatenateDate(year, month, day)).thenCallRealMethod();
String actualDate = connectorMock.concatenateDate(year, month, day);

assertEquals(expectedDate, actualDate);

}
}