Add Mainzelliste support

pom.xml

@@ -68,5 +68,11 @@
             <artifactId>mainzelliste-client</artifactId>
             <version>2.1.0</version>
         </dependency>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.9.0</version>
+        </dependency>
+
     </dependencies>
 </project>

src/docker/adt2fhir.properties

@@ -1,3 +1,5 @@
 file_path=/adt2fhir/clinical_data
-store_path=http://host.docker.internal:8080/fhir
-identifier_system=http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS
+store_path=http://host.docker.internal:8090/fhir
+identifier_system=http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS
+mainzelliste_url=http://host.docker.internal:8080
+mainzelliste_apikey=pleaseChangeMe

src/main/java/de/samply/adt2fhir/Adt2fhir.java

@@ -47,7 +47,9 @@ public static void main(String[] args) throws TransformerConfigurationException,
         System.out.print("initialize transformers... ");
         final TransformerFactoryImpl factory = (TransformerFactoryImpl) TransformerFactory.newInstance("net.sf.saxon.TransformerFactoryImpl", null);
         net.sf.saxon.Configuration saxonConfig = factory.getConfiguration();
-        ((Processor) saxonConfig.getProcessor()).registerExtensionFunction(new PatientPseudonymizer());
+        PatientPseudonymizer patientPseudonymizer = new PatientPseudonymizer();
+        patientPseudonymizer.setConfigReader(configReader);
+        ((Processor) saxonConfig.getProcessor()).registerExtensionFunction(patientPseudonymizer);
         ((Processor) saxonConfig.getProcessor()).registerExtensionFunction(new UniqueIdGenerator());
 
         final Transformer ADT2singleADTtransformer = factory.newTransformer(new StreamSource(Adt2fhir.class.getClassLoader().getResourceAsStream("toSinglePatients.xsl")));
@@ -95,9 +97,9 @@ private static void processXmlFiles (String inputData, Transformer transformer,
         else {
             int counter=1;
             for (File inputFile : listOfFiles) {
-                System.out.println("\u001B[AFile "+counter+" of "+listOfFiles.length);
-                counter+=1;
                 if (inputFile.isFile() & inputFile.getName().toLowerCase().endsWith(".xml")) {
+                    System.out.println("\u001B[AFile "+counter+" of "+(listOfFiles.length-1));
+                    counter+=1;
                     if (transformer ==null){
                         try {
                             postToFhirStore(inputFile, httppost);
@@ -109,17 +111,19 @@ private static void processXmlFiles (String inputData, Transformer transformer,
                     }
                     else {
                         //System.out.print("processing file " + inputFile.getName() + "...");
-                        String combinedADTfile = null;
+                        String inputXml = null;
                         try {
-                            combinedADTfile = new String(Files.readAllBytes(Paths.get(String.valueOf(inputFile))), StandardCharsets.UTF_8);
+                            inputXml = new String(Files.readAllBytes(Paths.get(String.valueOf(inputFile))), StandardCharsets.UTF_8);
                         } catch (IOException e) {
                             counter-=1;
                             System.out.print("ERROR - reading: problem with file " + inputFile);
                             e.printStackTrace();
                         }
                         try {
-                            String xmlResult = applyXslt(combinedADTfile, transformer);
+                            transformer.setParameter("customPrefix", inputFile.getName());
+                            String xmlResult = applyXslt(inputXml, transformer);
                             if(transformWrittenResults){
+                                transformer2.setParameter("customPrefix", inputFile.getName());
                                 applyXslt(xmlResult, transformer2);
                                 inputFile.deleteOnExit();
                             }

src/main/java/de/samply/adt2fhir/ConfigReader.java

@@ -8,6 +8,8 @@ public class ConfigReader {
     public String file_path;
     public String store_path;
     public String identifier_system;
+    public String mainzelliste_url;
+    public String mainzelliste_apikey;
 
     public void init() throws IOException {
         try {
@@ -31,6 +33,8 @@ public void init() throws IOException {
             this.file_path = prop.getProperty("file_path");
             this.store_path = prop.getProperty("store_path");
             this.identifier_system = prop.getProperty("identifier_system");
+            this.mainzelliste_url = prop.getProperty("mainzelliste_url");
+            this.mainzelliste_apikey = prop.getProperty("mainzelliste_apikey");
         } catch (IOException e) {
             e.printStackTrace();
         }
@@ -45,4 +49,8 @@ public String getStore_path() {
     public String getIdentifier_system() {
         return identifier_system;
     }
+    public String getMainzelliste_url() { return mainzelliste_url; }
+    public String getMainzelliste_apikey() {
+        return mainzelliste_apikey;
+    }
 }

src/main/java/de/samply/adt2fhir/PatientPseudonymizer.java

@@ -1,10 +1,14 @@
 package de.samply.adt2fhir;
 
-import de.pseudonymisierung.mainzelliste.client.InvalidSessionException;
-import de.pseudonymisierung.mainzelliste.client.MainzellisteConnection;
-import de.pseudonymisierung.mainzelliste.client.MainzellisteNetworkException;
-import de.pseudonymisierung.mainzelliste.client.Session;
+import com.google.gson.Gson;
+import com.google.gson.JsonArray;
+import com.google.gson.JsonObject;
+import de.pseudonymisierung.mainzelliste.client.*;
+import java.io.*;
 import java.net.URISyntaxException;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
+import java.util.List;
 import net.sf.saxon.expr.XPathContext;
 import net.sf.saxon.lib.ExtensionFunctionCall;
 import net.sf.saxon.lib.ExtensionFunctionDefinition;
@@ -14,9 +18,20 @@
 import net.sf.saxon.value.SequenceType;
 import net.sf.saxon.value.StringValue;
 import org.apache.commons.codec.digest.DigestUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.message.BasicNameValuePair;
+import org.apache.http.protocol.HTTP;
+import org.apache.http.util.EntityUtils;
 
 public class PatientPseudonymizer extends ExtensionFunctionDefinition {
-
+    private String mainzelliste_url;
+    private String mainzelliste_apikey;
+    private boolean anonymize;
 
     @Override
     public net.sf.saxon.value.SequenceType[] getArgumentTypes() {
@@ -50,22 +65,63 @@ public Sequence call(XPathContext ctx, Sequence[] args) throws XPathException {
                 String surname = args[2].iterate().next().getStringValue();
                 String birthname = args[3].iterate().next().getStringValue();
                 String brithdate = args[4].iterate().next().getStringValue();
-//                output =  DigestUtils.sha256Hex(gender+prename+surname+birthname+brithdate);//TODO create patientlist call
-                // More Information on: https://github.com/medicalinformatics/mainzelliste-client
-                try {
-                    MainzellisteConnection mainzellisteConnection = new MainzellisteConnection("http://localhost:8080", "youReallyShouldChangeMe");
-                    Session session = mainzellisteConnection.createSession();
-                    String addPatientToken = session.getAddPatientToken(null, null);
-                } catch (MainzellisteNetworkException e) {
-
-                } catch (URISyntaxException e) {
 
-                } catch (InvalidSessionException e) {
-                    // create new session here
+                if (mainzelliste_url.isEmpty()) {
+                    output = DigestUtils.sha256Hex(gender + prename + surname + birthname + brithdate).substring(32);
+                } else {
+                    try {
+                        output=pseudonymizationCall(gender, prename, surname, birthname, brithdate);
+                    } catch (URISyntaxException | MainzellisteNetworkException | InvalidSessionException | IOException e) {
+                        e.printStackTrace();
+                    }
                 }
                 return StringValue.makeStringValue(output);
             }
 
         };
     }
+
+    private String pseudonymizationCall(String gender, String prename, String surname, String birthname, String brithdate) throws URISyntaxException, MainzellisteNetworkException, InvalidSessionException, IOException {
+        String pseudonym="";
+        String[] brithdateParts = brithdate.split("[.]");
+        MainzellisteConnection mainzellisteConnection = new MainzellisteConnection(mainzelliste_url, mainzelliste_apikey);
+        Session session = mainzellisteConnection.createSession();
+        AddPatientToken token = new AddPatientToken();
+        token.addIdType("pid");
+        String addPatientToken = session.getToken(token);
+        HttpPost httppost = new HttpPost(mainzelliste_url+"/patients?tokenId="+addPatientToken);
+        httppost.addHeader("content-type", "application/x-www-form-urlencoded");
+        httppost.addHeader("mainzellisteApiVersion", "3.2");
+        List<NameValuePair> idat = new ArrayList<NameValuePair>();
+        //idat.add(new BasicNameValuePair("gender", gender));
+        idat.add(new BasicNameValuePair("vorname", prename));
+        idat.add(new BasicNameValuePair("nachname", surname));
+        idat.add(new BasicNameValuePair("geburtsname", birthname));
+        idat.add(new BasicNameValuePair("geburtstag", brithdateParts[0]));
+        idat.add(new BasicNameValuePair("geburtsmonat", brithdateParts[1]));
+        idat.add(new BasicNameValuePair("geburtsjahr", brithdateParts[2]));
+        //idat.add(new BasicNameValuePair("plz", ""));
+        //idat.add(new BasicNameValuePair("ort", ""));
+        idat.add(new BasicNameValuePair("sureness", "true"));
+        httppost.setEntity(new UrlEncodedFormEntity(idat, HTTP.UTF_8));
+        CloseableHttpClient httpclient = HttpClients.createDefault();
+        HttpResponse response = httpclient.execute(httppost);
+        if (response.getStatusLine().getStatusCode()!=201) {
+            System.out.println("Error - Pseudonymization response: " +  response.getStatusLine().getStatusCode());
+        }
+        String responseBody = EntityUtils.toString(response.getEntity(), StandardCharsets.UTF_8);
+        httpclient.close();
+
+        JsonArray ids = new Gson ().fromJson(responseBody, JsonArray.class);
+        if(!ids.isEmpty()){
+            JsonObject id = ids.get(0).getAsJsonObject();
+            pseudonym=id.getAsJsonPrimitive("idString").getAsString();
+        }
+        return pseudonym;
+    }
+
+    public void setConfigReader (ConfigReader configReader){
+        this.mainzelliste_url=configReader.getMainzelliste_url();
+        this.mainzelliste_apikey=configReader.getMainzelliste_apikey();
+    }
 }

src/main/resources/MDS2FHIR.xsl

@@ -24,6 +24,7 @@
     <xsl:output omit-xml-declaration="yes" indent="yes" />
     <xsl:strip-space elements="*" />
     <xsl:param name="filepath" />
+    <xsl:param name="customPrefix" />
 
     <xsl:template match="/">
 
@@ -37,7 +38,7 @@
     <xsl:template match="Patient" mode="patient">
         <xsl:variable name="Patient_ID" select="@Patient_ID" />
         <xsl:variable name="Vitalstatus_ID" select="hash:hash($Patient_ID, 'vitalstatus', '')" />
-        <xsl:result-document href="file:{$filepath}/FHIR_Patients/Bundle_{$Patient_ID}.xml">
+        <xsl:result-document href="file:{$filepath}/FHIR_Patients/Bundle_{$customPrefix}{$Patient_ID}.xml">
         <Bundle xmlns="http://hl7.org/fhir">
             <id value="{generate-id()}" />
             <type value="transaction" />

src/main/resources/adt2fhir.properties

@@ -1,3 +1,5 @@
 file_path=changeMeToAbsolutePath/adt2fhir/clinical_data
-store_path=http://localhost:8080/fhir
-identifier_system=http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS
+store_path=http://localhost:8090/fhir
+identifier_system=http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS
+mainzelliste_url=http://localhost:8080
+mainzelliste_apikey=pleaseChangeMe

src/main/resources/toSinglePatients.xsl

@@ -10,10 +10,11 @@
     <xsl:output omit-xml-declaration="no" indent="yes"/>
     <xsl:strip-space elements="*"/>
     <xsl:param name="filepath" />
+    <xsl:param name="customPrefix" />
 
     <xsl:template match="/ADT_GEKID">
         <xsl:for-each select="Menge_Patient/Patient">
-            <xsl:result-document method="xml" href="file:{$filepath}/ADT_Patients/Patient_{Patienten_Stammdaten/@Patient_ID}.xml">
+            <xsl:result-document method="xml" href="file:{$filepath}/ADT_Patients/Patient_{$customPrefix}{Patienten_Stammdaten/@Patient_ID}.xml">
             <!--<xsl:result-document method="xml" href="Patient_{Patienten_Stammdaten/@Patient_ID}.xml">-->
                 <ADT_GEKID Schema_Version="2.2.1">
                     <xsl:copy-of select="/ADT_GEKID/@*" />