implemented outcome message filtering.

support more levels for debug logging.

cda-server/src/main/java/org/aktin/cda/etl/fhir/Binary.java

@@ -49,6 +49,7 @@ import org.aktin.cda.Validator;
 import org.aktin.cda.etl.fhir.SimplifiedOperationOutcome.IssueType;
 import org.aktin.cda.etl.fhir.SimplifiedOperationOutcome.Severity;
 import org.aktin.dwh.ImportSummary;
+import org.aktin.dwh.PreferenceKey;
 import org.w3c.dom.Document;
 
 @Path("Binary")
@@ -128,6 +129,33 @@ public class Binary implements ExternalInterface{
 	private DataSource serverErrorOutcome(Throwable e) throws XMLStreamException{
 		return outcomeToXML(SimplifiedOperationOutcome.error(e));
 	}
+
+	/**
+	 * Filter the operation outcome messages according to the configuration.
+	 * E.g. remove entries with level below a certain treshold
+	 * @param outcome outcome to filter
+	 */
+	private void filterOutcome(SimplifiedOperationOutcome outcome) {
+		String filter = prefs.get(PreferenceKey.importCdaFhirOutcomeLevel);
+		if( filter == null || filter.length() == 0 || filter.equals("all") ) {
+			return; // nothing to do
+		}
+		switch( filter ) {
+		case "info":
+			outcome.removeIssuesBelowSeverity(Severity.information);
+			break;
+		case "warning":
+			outcome.removeIssuesBelowSeverity(Severity.warning);
+			break;
+		case "error":
+			outcome.removeIssuesBelowSeverity(Severity.error);
+			break;
+		case "none":
+			outcome.removeAllIssues();
+			break;
+		}
+	}
+
 	@POST
 	public Response create(Source doc){
 		SimplifiedOperationOutcome outcome = new SimplifiedOperationOutcome();
@@ -226,14 +254,37 @@ public class Binary implements ExternalInterface{
 	}
 
 	private void tryDebugProcessing(Document cda, SimplifiedOperationOutcome outcome){
-		String debugDir = prefs.get("import.cda.debug.dir");
+		String debugDir = prefs.get(PreferenceKey.importCdaDebugDir);
 		if( debugDir == null || debugDir.length() == 0 ){
 			return; // nothing to do
 		}
-		String debugLevel = prefs.get("import.cda.debug.level");
-		if( debugLevel != null && debugLevel.equals("error") && outcome.getIssueCount() == 0 ){
-			// dump only documents with errors
-			return; // nothing to do
+		String debugLevel = prefs.get(PreferenceKey.importCdaDebugLevel);
+		if( debugLevel == null ) {
+			// unset debug level defaults to all documents
+			debugLevel = "all";
+		}
+		if( debugLevel.equals("none") ) {
+			// logging disables
+			return;
+		}
+		int[] counts = outcome.getDetailedCounts();
+		// add more severe messages to lesser ones
+		counts[1] += counts[0]; // warning logging also includes error logging
+		counts[2] += counts[1]; // info logging also includes error and warning logging
+		if( debugLevel.equals("all") ) {
+			// continue to store all documents
+		}else if( debugLevel.equals("error") && counts[0] == 0 ) {
+			// level is error but no errors occurred,
+			// skip this document
+			return;
+		}else if( debugLevel.equals("warning") && counts[1] == 0 ) {
+			// level is warning, but no warnings (or errors) occurred,
+			// skip document
+			return;
+		}else if( debugLevel.equals("info") && counts[2] == 0 ) {
+			// level is info, but no info message (or warnings/errors) occurred
+			// skip document
+			return;
 		}
 	
 		// XXX maybe extract patient id extension for name?
@@ -264,7 +315,7 @@ public class Binary implements ExternalInterface{
 				log.warning("Failed to configure indent for XML debug documents: "+e.getMessage());
 			}
 			copy.transform(src, new StreamResult(out));
-			// write errors in XML comment after content
+			// write messages in XML comment after content
 			out.write("\n\n<!-- OperationOutcome\n");
 			out.write(outcome.toString().replaceAll("<", "&lt;"));
 			out.write("\n-->\n");

cda-server/src/main/java/org/aktin/cda/etl/fhir/SimplifiedOperationOutcome.java

@@ -3,7 +3,10 @@ package org.aktin.cda.etl.fhir;
 import java.io.PrintWriter;
 import java.io.StringWriter;
 import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Set;
 
 import javax.activation.DataSource;
 import javax.xml.XMLConstants;
@@ -103,6 +106,29 @@ public class SimplifiedOperationOutcome {
 	public int getIssueCount(){
 		return issues.size();
 	}
+	/**
+	 * Retrieve detailed counts for debugging levels in the following order: errors, warnings, informational
+	 * @return array containing detailed counts for the outcome resource
+	 */
+	public int[] getDetailedCounts() {
+		int[] counts = new int[3];
+		for( Issue issue : issues ) {
+			switch( issue.severity ){
+			case error:
+			case fatal:
+				counts[0]++;
+				break;
+			case warning:
+				counts[1]++;
+				break;
+			case information:
+				counts[2]++;
+				break;
+			default:
+			}
+		}
+		return counts;
+	}
 	/**
 	 * Add an issue to the response
 	 * @param severity issue severity
@@ -134,6 +160,39 @@ public class SimplifiedOperationOutcome {
 		}
 		writer.writeEndElement();	
 	}
+
+	/**
+	 * Remove issues below a certain severity.
+	 * E.g. if the limit is {@code error} then warning and information messages are removed.
+	 * Limit of {@code information} has no effect, since no messages are below.}
+	 * To remove all issues, use {@link #removeAllIssues()}
+	 * @param severity. {@code null}
+	 */
+	public void removeIssuesBelowSeverity(Severity limit) {
+		Iterator<Issue> i = issues.iterator();
+		Set<Severity> forRemoval = new HashSet<>();
+		switch( limit ) {
+		case fatal:
+		case error:
+			forRemoval.add(Severity.warning);
+		case warning:
+			forRemoval.add(Severity.information);
+		case information:
+		default:
+		}
+		while( i.hasNext() ) {
+			Issue e = i.next();
+			if( forRemoval.contains(e.severity) ) {
+				i.remove();
+			}
+		}
+	}
+	/**
+	 * Remove all reported issues from the list.
+	 */
+	public void removeAllIssues() {
+		issues.clear();
+	}
 	/**
 	 * Generate the XML representation of the response
 	 *