ALS-6511: Minor fixes and comments

hms-dbmi · Aug 13, 2024 · 37c739f · 37c739f
1 parent 93630c3
commit 37c739f
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Showing 3 changed files with 10 additions and 7 deletions.
diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/ResultStoreStream.java
@@ -45,8 +45,7 @@ public void appendResults(List<String[]> entries) {
 		writer.writeEntity(entries);
 	}
 	/**
-	 * A more compact method to append data to the temp file without making assumptions about the composition.
-	 * @param entries
+	 * Appending data to the writer that supports multiple values per patient/variable combination
 	 */
 	public void appendMultiValueResults(List<List<List<String>>> entries) {
 		writer.writeMultiValueEntity(entries);

diff --git a/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbResultStore.java b/...essing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbResultStore.java
diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriter.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriter.java
@@ -94,6 +94,10 @@ private boolean isSingularField(String field) {
         return SINGULAR_FIELDS.contains(field);
     }
 
+    /**
+     * Transforms our variable names to once that are valid avro fields. We replace invalid characters with underscores
+     * and add a leading underscore if the variable starts with a number
+     */
     protected String formatFieldName(String s) {
         String formattedFieldName = s.replaceAll("\\W", "_");
         if (Character.isDigit(formattedFieldName.charAt(0))) {
@@ -141,7 +145,11 @@ public void writeMultiValueEntity(Collection<List<List<String>>> entities) {
                 throw new IllegalArgumentException("Entity length much match the number of fields in this document");
             }
             GenericRecord patientData = new GenericData.Record(patientDataSchema);
+            String patientId = "";
             for(int i = 0; i < fields.size(); i++) {
+                if ("patient_id".equals(fields.get(i))) {
+                    patientId = (entity.get(i) != null && !entity.get(i).isEmpty()) ? entity.get(i).get(0) : "";
+                }
                 if (isSingularField(fields.get(i))) {
                     String entityValue = (entity.get(i) != null && !entity.get(i).isEmpty()) ? entity.get(i).get(0) : "";
                     patientData.put(fields.get(i), entityValue);
@@ -155,7 +163,7 @@ public void writeMultiValueEntity(Collection<List<List<String>>> entities) {
             GenericRecord entityRecord = new GenericData.Record(entitySchema);
             entityRecord.put("object", patientData);
             entityRecord.put("name", "patientData");
-            entityRecord.put("id", "192035");
+            entityRecord.put("id", patientId);
 
             try {
                 dataFileWriter.append(entityRecord);