Feature/optional sample id linkage (#57)

* feature: add pseudonym id option * refactor: make ID parameters properties not env * fix: make MAINZELLISTE_EXTERNAL_ID default true - backward compatibility --------- Co-authored-by: Pierre Delpy <[email protected]>
samply · Dec 12, 2024 · 3351fd8 · 3351fd8
1 parent a729766
commit 3351fd8
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Showing 5 changed files with 44 additions and 27 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -19,9 +19,11 @@ ENV FILE_PATH="/obds2fhir/clinical_data" \
     LOG_LEVEL="INFO" \
     MAINZELLISTE_URL="http://host.docker.internal:8080" \
     MAINZELLISTE_APIKEY="" \
+    MAINZELLISTE_EXTERNAL_ID="true" \
     IDTYPE="" \
     SALT="createLocalCustomSalt" \
     SSL_CERTIFICATE_VALIDATION="true" \
     ADD_DEPARTMENTS="false" \
     WAIT_FOR_CONNECTION="false" \
-    KEEP_INTERNAL_ID="false"
+    KEEP_INTERNAL_ID="false" \
+    USE_PSEUDONYM="false"
diff --git a/src/main/java/de/samply/obds2fhir/Obds2fhir.java b/src/main/java/de/samply/obds2fhir/Obds2fhir.java
@@ -198,10 +198,12 @@ public static void initializeTransformers(boolean pseudonymizeFlag) {
             ADT2SinglePatientTransformer.setParameter("filepath", System.getenv().getOrDefault("FILE_PATH",""));
             oBDS2MDSTransformer = factory.newTransformer(new StreamSource(Obds2fhir.class.getClassLoader().getResourceAsStream("oBDS2MDS_FHIR.xsl")));
             oBDS2MDSTransformer.setParameter("add_department", System.getenv().getOrDefault("ADD_DEPARTMENTS","false"));
-            oBDS2MDSTransformer.setParameter("keep_internal_id", System.getenv().getOrDefault("KEEP_INTERNAL_ID","false"));
+            oBDS2MDSTransformer.setParameter("keep_internal_id", System.getProperty("KEEP_INTERNAL_ID", "false"));
+            oBDS2MDSTransformer.setParameter("use_pseudonym", System.getProperty("USE_PSEUDONYM", "false"));
             ADT2MDSTransformer = factory.newTransformer(new StreamSource(Obds2fhir.class.getClassLoader().getResourceAsStream("ADT2MDS_FHIR.xsl")));
             ADT2MDSTransformer.setParameter("add_department", System.getenv().getOrDefault("ADD_DEPARTMENTS","false"));
-            ADT2MDSTransformer.setParameter("keep_internal_id", System.getenv().getOrDefault("KEEP_INTERNAL_ID","false"));
+            ADT2MDSTransformer.setParameter("keep_internal_id", System.getProperty("KEEP_INTERNAL_ID", "false"));
+            ADT2MDSTransformer.setParameter("use_pseudonym", System.getProperty("USE_PSEUDONYM", "false"));
             MDS2FHIRTransformer = factory.newTransformer(new StreamSource(Obds2fhir.class.getClassLoader().getResourceAsStream("MDS2FHIR.xsl")));
             MDS2FHIRTransformer.setParameter("filepath", System.getenv().getOrDefault("FILE_PATH",""));
             MDS2FHIRTransformer.setParameter("identifier_system", System.getenv().getOrDefault("IDENTIFIER_SYSTEM","http://dktk.dkfz.de/fhir/onco/core/CodeSystem/PseudonymArtCS"));

diff --git a/src/main/java/de/samply/obds2fhir/PatientPseudonymizer.java b/src/main/java/de/samply/obds2fhir/PatientPseudonymizer.java
@@ -172,7 +172,9 @@ private HttpPost createHttpPost (String prename, String surname, String formerna
         if (!birthmonth.equals("empty")) idat.add(new BasicNameValuePair("Geburtsmonat", birthmonth));
         if (!birthyear.equals("empty")) idat.add(new BasicNameValuePair("Geburtsjahr", birthyear));
         if (!gender.equals("empty")) idat.add(new BasicNameValuePair("Geschlecht", gender));
-        if (!identifier.equals("empty")) idat.add(new BasicNameValuePair("locallyUniqueId", identifier));
+        if (!identifier.equals("empty") && Boolean.parseBoolean(System.getProperty("MAINZELLISTE_EXTERNAL_ID", "true"))) {
+            idat.add(new BasicNameValuePair("locallyUniqueId", identifier));
+        }
         idat.add(new BasicNameValuePair("sureness", "true"));
         logger.debug("Posting IDAT to Mainzelliste: " +
                         "Vorname - " + preprocessIDAT(prename, ".", "*") +

diff --git a/src/main/resources/ADT2MDS_FHIR.xsl b/src/main/resources/ADT2MDS_FHIR.xsl
@@ -13,6 +13,7 @@
     <xsl:strip-space elements="*"/>
     <xsl:param name="add_department" />
     <xsl:param name="keep_internal_id" />
+    <xsl:param name="use_pseudonym" />
 
     <xsl:template match="/ADT_GEKID/Menge_Patient">
         <Patienten>
@@ -24,7 +25,6 @@
         <xsl:choose>
             <xsl:when test="Patienten_Stammdaten/@Patient_ID!=''">
                 <Patient>
-                    <xsl:variable name="Patient_Id" select="if ($keep_internal_id=true()) then Patienten_Stammdaten/@Patient_ID else hash:hash(Patienten_Stammdaten/@Patient_ID,'','')"/>
                     <xsl:variable name="Geburtsdatum" select="Patienten_Stammdaten/xsi:Get-FHIR-date(Patienten_Geburtsdatum)"/>
                     <xsl:variable name="Geburtstag" select="string(replace($Geburtsdatum,'^\d{4}-\d{2}-(\d{2})$','$1'))"/>
                     <xsl:variable name="Geburtsmonat" select="string(replace($Geburtsdatum,'^\d{4}-(\d{2})-\d{2}$','$1'))"/>
@@ -38,6 +38,11 @@
                     xsi:ReplaceEmpty($Geburtsmonat),
                     xsi:ReplaceEmpty($Geburtsjahr),
                     xsi:ReplaceEmpty(Patienten_Stammdaten/@Patient_ID))"/>
+                    <xsl:variable name="Patient_Id" select="
+                        if ($use_pseudonym = true())
+                        then (if ($keep_internal_id = true()) then $Patient_Pseudonym else hash:hash($Patient_Pseudonym, '', ''))
+                        else (if ($keep_internal_id = true()) then Patienten_Stammdaten/@Patient_ID else hash:hash(Patienten_Stammdaten/@Patient_ID, '', ''))
+                    " />
                     <xsl:attribute name="Patient_ID" select="$Patient_Id"/>
                     <Geschlecht>
                         <xsl:value-of select="if (Patienten_Stammdaten/Patienten_Geschlecht = 'D') then 'S' else Patienten_Stammdaten/Patienten_Geschlecht" />

diff --git a/src/main/resources/oBDS2MDS_FHIR.xsl b/src/main/resources/oBDS2MDS_FHIR.xsl
@@ -13,41 +13,47 @@
     <xsl:strip-space elements="*"/>
     <xsl:param name="add_department" />
     <xsl:param name="keep_internal_id" />
+    <xsl:param name="use_pseudonym" />
 
     <xsl:template match="/oBDS/Menge_Patient">
         <Patienten>
             <xsl:apply-templates select="node()| @*"/>
         </Patienten>
     </xsl:template>
+
     <xsl:template match="Patient">
         <Patient>
-            <xsl:variable name="Patient_Id" select="if ($keep_internal_id=true()) then @Patient_ID else hash:hash(@Patient_ID,'','')"/>
-            <xsl:attribute name="Patient_ID" select="$Patient_Id"/>
             <xsl:variable name="Geburtsdatum" select="Patienten_Stammdaten/Geburtsdatum"/>
             <xsl:variable name="Geburtstag" select="string(replace($Geburtsdatum,'\d\d\d\d\-\d\d\-(\d\d)$','$1'))"/>
             <xsl:variable name="Geburtsmonat" select="string(replace($Geburtsdatum,'\d\d\d\d\-(\d\d)\-\d\d$','$1'))"/>
             <xsl:variable name="Geburtsjahr" select="string(replace($Geburtsdatum,'(\d\d\d\d)\-\d\d\-\d\d$','$1'))"/>
-            <xsl:choose>
-                <xsl:when test="Patienten_Stammdaten/Geschlecht!='' and $Geburtsdatum!='' and Patienten_Stammdaten/Vornamen !='' and Patienten_Stammdaten/Nachname!=''">
-                    <DKTK_LOCAL_ID>
-                        <xsl:value-of select="hash:pseudonymize(
-                        xsi:ReplaceEmpty(Patienten_Stammdaten/Geschlecht),
-                        xsi:ReplaceEmpty(Patienten_Stammdaten/Vornamen),
-                        xsi:ReplaceEmpty(Patienten_Stammdaten/Nachname),
-                        xsi:ReplaceEmpty(Patienten_Stammdaten/Geburtsname),
-                        xsi:ReplaceEmpty($Geburtstag),
-                        xsi:ReplaceEmpty($Geburtsmonat),
-                        xsi:ReplaceEmpty($Geburtsjahr),
-                        xsi:ReplaceEmpty(@Patient_ID))"/>
-                    </DKTK_LOCAL_ID>
-                </xsl:when>
-                <xsl:otherwise>
-                    <xsl:message><xsl:value-of select="'Warn: Missing IDAT for Patient', @Patient_ID, ' !&#10;&#10;'"/></xsl:message>
-                </xsl:otherwise>
-            </xsl:choose>
-            <xsl:apply-templates select="Patienten_Stammdaten/Geschlecht | Patienten_Stammdaten/Geburtsdatum"/>
+            <xsl:variable name="Patient_Pseudonym">
+                <xsl:choose>
+                    <xsl:when test="Patienten_Stammdaten/Geschlecht!='' and $Geburtsdatum!='' and Patienten_Stammdaten/Vornamen !='' and Patienten_Stammdaten/Nachname!=''">
+                            <xsl:value-of select="hash:pseudonymize(
+                            xsi:ReplaceEmpty(Patienten_Stammdaten/Geschlecht),
+                            xsi:ReplaceEmpty(Patienten_Stammdaten/Vornamen),
+                            xsi:ReplaceEmpty(Patienten_Stammdaten/Nachname),
+                            xsi:ReplaceEmpty(Patienten_Stammdaten/Geburtsname),
+                            xsi:ReplaceEmpty($Geburtstag),
+                            xsi:ReplaceEmpty($Geburtsmonat),
+                            xsi:ReplaceEmpty($Geburtsjahr),
+                            xsi:ReplaceEmpty(@Patient_ID))"/>
+                    </xsl:when>
+                    <xsl:otherwise>
+                        <xsl:message><xsl:value-of select="'Warn: Missing IDAT for Patient', @Patient_ID, ' !&#10;&#10;'"/></xsl:message>
+                    </xsl:otherwise>
+                </xsl:choose>
+            </xsl:variable>
+            <xsl:variable name="Patient_Id" select="
+                if ($use_pseudonym = true())
+                then (if ($keep_internal_id = true()) then $Patient_Pseudonym else hash:hash($Patient_Pseudonym, '', ''))
+                else (if ($keep_internal_id = true()) then @Patient_ID else hash:hash(@Patient_ID, '', ''))
+            " />
+            <xsl:attribute name="Patient_ID" select="$Patient_Id"/>
+            <DKTK_LOCAL_ID><xsl:value-of select="$Patient_Pseudonym"/></DKTK_LOCAL_ID>
             <!--<DKTK_ID>TODO</DKTK_ID>-->
-
+            <xsl:apply-templates select="Patienten_Stammdaten/Geschlecht | Patienten_Stammdaten/Geburtsdatum"/>
             <Vitalstatus_Gesamt Vitalstatus_ID="{concat('vital', $Patient_Id)}">
                 <Datum_des_letztbekannten_Vitalstatus>
                     <xsl:value-of select="if (Patienten_Stammdaten/Vitalstatus_Datum != '') then 'Patienten_Stammdaten/Vitalstatus_Datum' else xsi:Datum_des_letztbekannten_Vitalstatus(Menge_Meldung)"/>