ALS-7165: Update table name to include dataset id

hms-dbmi · Sep 4, 2024 · eeb971b · eeb971b
1 parent 9d0a260
commit eeb971b
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Showing 3 changed files with 19 additions and 11 deletions.
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
@@ -2,7 +2,6 @@
 
 import org.apache.avro.Schema;
 import org.apache.avro.SchemaBuilder;
-import org.apache.avro.file.Codec;
 import org.apache.avro.file.CodecFactory;
 import org.apache.avro.file.DataFileWriter;
 import org.apache.avro.generic.GenericData;
@@ -21,10 +20,15 @@
 
 public class PfbWriter implements ResultWriter {
 
+    public static final String PATIENT_TABLE_PREFIX = "pic-sure-";
     private Logger log = LoggerFactory.getLogger(PfbWriter.class);
 
     private final Schema metadataSchema;
     private final Schema nodeSchema;
+
+    private final String queryId;
+
+    private final String patientTableName;
     private SchemaBuilder.FieldAssembler<Schema> entityFieldAssembler;
 
     private List<String> fields;
@@ -35,8 +39,10 @@ public class PfbWriter implements ResultWriter {
 
     private static final Set<String> SINGULAR_FIELDS = Set.of("patient_id");
 
-    public PfbWriter(File tempFile) {
-        file = tempFile;
+    public PfbWriter(File tempFile, String queryId) {
+        this.file = tempFile;
+        this.queryId = queryId;
+        this.patientTableName = formatFieldName(PATIENT_TABLE_PREFIX + queryId);
         entityFieldAssembler = SchemaBuilder.record("entity")
                 .namespace("edu.harvard.dbmi")
                 .fields();
@@ -58,7 +64,7 @@ public PfbWriter(File tempFile) {
     @Override
     public void writeHeader(String[] data) {
         fields = Arrays.stream(data.clone()).map(this::formatFieldName).collect(Collectors.toList());
-        SchemaBuilder.FieldAssembler<Schema> patientRecords = SchemaBuilder.record("patientData")
+        SchemaBuilder.FieldAssembler<Schema> patientRecords = SchemaBuilder.record(patientTableName)
                 .fields();
 
         fields.forEach(field -> {
@@ -163,7 +169,7 @@ public void writeMultiValueEntity(Collection<List<List<String>>> entities) {
 
             GenericRecord entityRecord = new GenericData.Record(entitySchema);
             entityRecord.put("object", patientData);
-            entityRecord.put("name", "patientData");
+            entityRecord.put("name", patientTableName);
             entityRecord.put("id", patientId);
 
             try {

diff --git a/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java b/processing/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/processing/io/PfbWriterTest.java
@@ -7,6 +7,7 @@
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.UUID;
 
 import static org.junit.jupiter.api.Assertions.*;
 
@@ -15,7 +16,7 @@ public class PfbWriterTest {
 
     @Test
     public void writeValidPFB() {
-        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"));
+        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString());
 
         pfbWriter.writeHeader(new String[] {"patient_id", "\\demographics\\age\\", "\\phs123\\stroke\\"});
         List<List<String>> nullableList = new ArrayList<>();
@@ -38,21 +39,21 @@ public void writeValidPFB() {
 
     @Test
     public void formatFieldName_spacesAndBackslashes_replacedWithUnderscore() {
-        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"));
+        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString());
         String formattedName = pfbWriter.formatFieldName("\\Topmed Study Accession with Subject ID\\\\");
         assertEquals("_Topmed_Study_Accession_with_Subject_ID__", formattedName);
     }
 
     @Test
     public void formatFieldName_startsWithDigit_prependUnderscore() {
-        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"));
+        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString());
         String formattedName = pfbWriter.formatFieldName("123Topmed Study Accession with Subject ID\\\\");
         assertEquals("_123Topmed_Study_Accession_with_Subject_ID__", formattedName);
     }
 
     @Test
     public void formatFieldName_randomGarbage_replaceWithUnderscore() {
-        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"));
+        PfbWriter pfbWriter = new PfbWriter(new File("target/test-result.avro"), UUID.randomUUID().toString());
         String formattedName = pfbWriter.formatFieldName("$$$my garbage @vro var!able nam#");
         assertEquals("___my_garbage__vro_var_able_nam_", formattedName);
     }

diff --git a/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java b/service/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/service/QueryService.java
@@ -135,17 +135,18 @@ private AsyncResult initializeResult(Query query) throws ClassNotFoundException,
 				throw new RuntimeException("UNSUPPORTED RESULT TYPE");
 		}
 
+		String queryId = UUIDv5.UUIDFromString(query.toString()).toString();
 		ResultWriter writer;
         if (ResultType.DATAFRAME_PFB.equals(query.getExpectedResultType())) {
-            writer = new PfbWriter(File.createTempFile("result-" + System.nanoTime(), ".avro"));
+            writer = new PfbWriter(File.createTempFile("result-" + System.nanoTime(), ".avro"), queryId);
         } else {
             writer = new CsvWriter(File.createTempFile("result-" + System.nanoTime(), ".sstmp"));
         }
 
 		AsyncResult result = new AsyncResult(query, p, writer)
 				.setStatus(AsyncResult.Status.PENDING)
 				.setQueuedTime(System.currentTimeMillis())
-				.setId(UUIDv5.UUIDFromString(query.toString()).toString());
+				.setId(queryId);
 		query.setId(result.getId());
 		results.put(result.getId(), result);
 		return result;