fix: invalid FHIR id for Bundle and DiagnosticReport

diz-unimr · Jul 31, 2024 · 673d29c · 673d29c
1 parent 58493b1
commit 673d29c
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Showing 3 changed files with 46 additions and 5 deletions.
diff --git a/src/main/java/de/unimarburg/diz/labtofhir/mapper/MiiLabReportMapper.java b/src/main/java/de/unimarburg/diz/labtofhir/mapper/MiiLabReportMapper.java
@@ -81,8 +81,8 @@ public Bundle apply(LaboratoryReport report) {
         Bundle bundle = new Bundle();
         try {
 
-            // set meta information
-            bundle.setId(report.getReportIdentifierValue());
+            // set meta information (with valid id)
+            bundle.setId(report.getValidReportId());
             bundle.setType(BundleType.TRANSACTION);
 
             processMetaResults(report)

diff --git a/src/main/java/de/unimarburg/diz/labtofhir/model/LaboratoryReport.java b/src/main/java/de/unimarburg/diz/labtofhir/model/LaboratoryReport.java
@@ -90,16 +90,28 @@ public void setResource(DiagnosticReport resource) {
     }
 
     private void sanitizeIdentifierValue(DiagnosticReport resource) {
-        var identifierValue = resource.getIdentifierFirstRep().getValue();
+        var identifierValue = resource.getIdentifierFirstRep()
+            .getValue();
         var idPart =
             StringUtils.substringAfterLast(identifierValue, "SWISSLAB_");
         if (StringUtils.isNotBlank(idPart)) {
-            resource.getIdentifierFirstRep().setValue(idPart);
+            resource.getIdentifierFirstRep()
+                .setValue(idPart);
         }
     }
 
     public String getReportIdentifierValue() {
-        return resource.getIdentifierFirstRep().getValue();
+        return resource.getIdentifierFirstRep()
+            .getValue();
+    }
+
+    @SuppressWarnings("checkstyle:MagicNumber")
+    public String getValidReportId() {
+        // replace invalid characters with "-"
+        var replaced =
+            getReportIdentifierValue().replaceAll("[^A-Za-z0-9\\-\\.]", "-");
+        // max 64 characters
+        return replaced.substring(0, Math.min(replaced.length(), 64));
     }
 
     public String getMetaCode() {

diff --git a/src/test/java/de/unimarburg/diz/labtofhir/model/LaboratoryReportTests.java b/src/test/java/de/unimarburg/diz/labtofhir/model/LaboratoryReportTests.java
@@ -19,4 +19,33 @@ void setResourceStripsIdentifierPrefix() {
 
         assertThat(labReport.getReportIdentifierValue()).isEqualTo(expectedId);
     }
+
+    @Test
+    void getValidReportIdReplacesInvalidCharacters() {
+        var source = new DiagnosticReport().addIdentifier(
+            new Identifier().setValue("SWISSLAB_20240710_123456"));
+        var expectedId = "20240710-123456";
+
+        var labReport = new LaboratoryReport();
+        labReport.setResource(source);
+
+        assertThat(labReport.getValidReportId()).isEqualTo(expectedId);
+    }
+
+    @Test
+    void getValidReportIdTrimsByMaxLength() {
+        var source =
+            new DiagnosticReport().addIdentifier(new Identifier().setValue(
+                // 70 characters
+                "111111111122222222223333333333444444444455555555556666666666"
+                    + "7777777777"));
+        // only 64 characters are valid
+        var expectedId =
+            "1111111111222222222233333333334444444444555555555566666666667777";
+
+        var labReport = new LaboratoryReport();
+        labReport.setResource(source);
+
+        assertThat(labReport.getValidReportId()).isEqualTo(expectedId);
+    }
 }