Quick fix for adding new patient aliases to a Patient node (#593)

Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Feb 8, 2022 · bbdb78e · bbdb78e
1 parent e8259b3
commit bbdb78e
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Showing 2 changed files with 40 additions and 1 deletion.
diff --git a/model/src/main/java/org/mskcc/cmo/metadb/model/MetadbPatient.java b/model/src/main/java/org/mskcc/cmo/metadb/model/MetadbPatient.java
@@ -73,7 +73,14 @@ public void addMetaDbSample(MetadbSample metaDbSample) {
         metaDbSampleList.add(metaDbSample);
     }
 
+    /**
+     * Returns patient aliases list.
+     * @return List
+     */
     public List<PatientAlias> getPatientAliases() {
+        if (patientAliases == null) {
+            patientAliases = new ArrayList<>();
+        }
         return patientAliases;
     }
 
@@ -92,6 +99,24 @@ public void addPatientAlias(PatientAlias patientAlias) {
         patientAliases.add(patientAlias);
     }
 
+    /**
+     * Determines whether Patient has a patient alias matching the namespace provided.
+     * @param patientAlias
+     * @return Boolean
+     */
+    public Boolean hasPatientAlias(PatientAlias patientAlias) {
+        if (patientAliases == null) {
+            patientAliases = new ArrayList<>();
+            return Boolean.FALSE;
+        }
+        for (PatientAlias alias : patientAliases) {
+            if (alias.getNamespace().equalsIgnoreCase(patientAlias.getNamespace())) {
+                return Boolean.TRUE;
+            }
+        }
+        return Boolean.FALSE;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);

diff --git a/service/src/main/java/org/mskcc/cmo/metadb/service/impl/SampleServiceImpl.java b/service/src/main/java/org/mskcc/cmo/metadb/service/impl/SampleServiceImpl.java
@@ -3,12 +3,15 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import java.text.ParseException;
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.UUID;
 import org.mskcc.cmo.common.MetadbJsonComparator;
 import org.mskcc.cmo.metadb.model.MetadbPatient;
 import org.mskcc.cmo.metadb.model.MetadbRequest;
 import org.mskcc.cmo.metadb.model.MetadbSample;
+import org.mskcc.cmo.metadb.model.PatientAlias;
 import org.mskcc.cmo.metadb.model.SampleMetadata;
 import org.mskcc.cmo.metadb.model.web.PublishedMetadbSample;
 import org.mskcc.cmo.metadb.persistence.neo4j.MetadbSampleRepository;
@@ -66,9 +69,20 @@ public MetadbSample fetchAndLoadSampleDetails(MetadbSample sample) throws Except
             patientService.savePatientMetadata(patient);
             sample.setPatient(patient);
         } else {
+            // go through the new patient aliases and indicator for whether a
+            // new patient alias was added to the existing patient
+            Boolean patientUpdated = Boolean.FALSE;
+            for (PatientAlias pa : patient.getPatientAliases()) {
+                if (!existingPatient.hasPatientAlias(pa)) {
+                    existingPatient.addPatientAlias(pa);
+                    patientUpdated = Boolean.TRUE;
+                }
+            }
+            if (patientUpdated) {
+                patientService.savePatientMetadata(existingPatient);
+            }
             sample.setPatient(existingPatient);
         }
-
         return sample;
     }