Fix #695 SeriesInstanceUID Modality Block

news/695-bugfix.md

@@ -0,0 +1 @@
+Fixes #695. Removes the checks preventing modality being specified with other extraction keys

src/applications/com.smi.applications.extractorcli/src/main/java/org/smi/extractorcl/Program.java

@@ -84,7 +84,7 @@ private static CommandLine ParseOptions(String[] args) throws ParseException {
 			Option        
 			.builder("m")
 			.argName("modality")
-			.desc("Extraction modality. Should only be specified if extracting at the Study level")
+			.desc("Extraction modality")
 			.hasArg()
 			.longOpt("modality")
 			.build());

src/applications/com.smi.applications.extractorcli/src/main/java/org/smi/extractorcl/fileUtils/ExtractMessagesCsvHandler.java

@@ -64,11 +64,6 @@ public ExtractMessagesCsvHandler(UUID extractionJobID, String projectID, String
 		_extractionModality = extractionModality;
 		_isIdentifiableExtraction = isIdentifiableExtraction;
 		_isNoFilterExtraction = isNoFilterExtraction;
-
-        // TODO(rkm 2020-01-30) Properly handle parsing of the supported modalities
-        if (_extractionModality != null && (!_extractionModality.equals("CT") && !_extractionModality.equals("MR"))) {
-			throw new IllegalArgumentException("Invalid value " + _extractionModality + " for extractionModality. Supported values are: CT, MR");
-		}
 	}
 
 	@Override
@@ -92,8 +87,6 @@ public void processHeader(String[] header) throws LineProcessingException, Illeg
 
 		if (_extractionKey == ExtractionKey.StudyInstanceUID && _extractionModality == null)
 			throw new IllegalArgumentException("Extracting by StudyInstanceUID, but extraction modality not set");
-		if (_extractionKey != ExtractionKey.StudyInstanceUID && _extractionModality != null)
-			throw new IllegalArgumentException("Extraction modality set, but extraction identifier is " + _extractionKey);
 
 		_logger.debug("extractionKey: " + _extractionKey);
 	}
@@ -177,8 +170,7 @@ public void sendMessages(boolean autoRun, int maxIdentifiersPerMessage) throws I
 		sb.append("    ExtractionKey:                         " + _extractionKey + System.lineSeparator());
 		sb.append("    IsIdentifiableExtraction:              " + _isIdentifiableExtraction + System.lineSeparator());
 		sb.append("    IsNoFilterExtraction:                  " + _isNoFilterExtraction + System.lineSeparator());
-		if (_extractionKey == ExtractionKey.StudyInstanceUID)
-			sb.append("    ExtractionModality:                    " + _extractionModality + System.lineSeparator());
+		sb.append("    ExtractionModality:                    " + _extractionModality + System.lineSeparator());
 		sb.append("    KeyValueCount:                         " + _identifierSet.size() + System.lineSeparator());
 		sb.append("    Number of ExtractionRequestMessage(s): " + split.size() + System.lineSeparator());
 		System.out.println(sb);

src/applications/com.smi.applications.extractorcli/src/test/java/org/smi/extractorcl/test/fileUtils/ExtractImagesCsvHandlerTest.java

@@ -250,14 +250,6 @@ public void testModalityRequirement() throws LineProcessingException {
 		// Yes, I know there's probably some way to do this with JUnit
 		boolean thrown = false;
 
-		try {
-			handler = new ExtractMessagesCsvHandler(uuid, "MyProjectID", "MyProjectFolder", "aaaaa",false,false,
-					extractRequestMessageProducerModel, extractRequestInfoMessageProducerModel);
-		} catch (IllegalArgumentException e) {
-			thrown = true;
-		}
-		assertTrue(thrown);
-
 		handler = new ExtractMessagesCsvHandler(uuid, "MyProjectID", "MyProjectFolder", null,false,false,
 				extractRequestMessageProducerModel, extractRequestInfoMessageProducerModel);
 

src/microservices/Microservices.CohortPackager/Execution/ExtractJobStorage/ExtractJobStore.cs

@@ -26,9 +26,9 @@ public void PersistMessageToStore(
         {
             Logger.Info($"Received new job info {message}");
 
-            // If KeyTag is StudyInstanceUID then ExtractionModality must be specified, otherwise must be null
-            if (message.KeyTag == "StudyInstanceUID" ^ !string.IsNullOrWhiteSpace(message.ExtractionModality))
-                throw new ApplicationException($"Invalid combination of KeyTag and ExtractionModality (KeyTag={message.KeyTag}, ExtractionModality={message.ExtractionModality}");
+            // If KeyTag is StudyInstanceUID then ExtractionModality must be specified
+            if (message.KeyTag == "StudyInstanceUID" && string.IsNullOrWhiteSpace(message.ExtractionModality))
+                throw new ApplicationException($"ExtractionModality must be specified when the extraction key is StudyInstanceUID");
 
             PersistMessageToStoreImpl(message, header);
         }

tests/microservices/Microservices.CohortPackager.Tests/Execution/ExtractJobStorage/ExtractJobStoreTest.cs

@@ -68,10 +68,6 @@ public void TestPersistMessageToStore_ExtractionRequestInfoMessage()
             message.KeyTag = "StudyInstanceUID";
             message.ExtractionModality = null;
             Assert.Throws<ApplicationException>(() => testExtractJobStore.PersistMessageToStore(message, mockHeader));
-
-            message.KeyTag = "SeriesInstanceUID";
-            message.ExtractionModality = "MR";
-            Assert.Throws<ApplicationException>(() => testExtractJobStore.PersistMessageToStore(message, mockHeader));
         }
 
         [Test]