Don't show EDB GMT warning if common GMT file provided. Fixes #220.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/DetailPanel.java

@@ -14,7 +14,7 @@ public interface DetailPanel {
 
 	String getIcon();
 
-	List<Message> validateInput();
+	List<Message> validateInput(MasterDetailDialogPage parent);
 
 	default DataSetParameters createDataSetParameters() { return null; };
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/EditCommonPanel.java

@@ -1,5 +1,7 @@
 package org.baderlab.csplugins.enrichmentmap.view.creation;
 
+import static com.google.common.base.Strings.isNullOrEmpty;
+
 import java.util.ArrayList;
 import java.util.List;
 
@@ -85,7 +87,7 @@ private void createContents() {
 
 
 	@Override
-	public List<Message> validateInput() {
+	public List<Message> validateInput(MasterDetailDialogPage parent) {
 		gmtText.hideError();
 		expressionsText.hideError();
 
@@ -106,6 +108,14 @@ public String getGmtFile() {
 	public String getExpressionFile() {
 		return expressionsText.getText();
 	}
+	
+	public boolean hasExpressionFile() {
+		return !isNullOrEmpty(getExpressionFile());
+	}
+	
+	public boolean hasGmtFile() {
+		return !isNullOrEmpty(getGmtFile());
+	}
 
 	public void reset() {
 		gmtText.setText("");

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/EditDataSetPanel.java

@@ -292,7 +292,7 @@ private void initialize(DataSetParameters initDataSet) {
 
 
 	@Override
-	public List<Message> validateInput() {
+	public List<Message> validateInput(MasterDetailDialogPage parent) {
 		List<Message> messages = new ArrayList<>();
 		if(nameText.isEmpty())
 			messages.add(Message.error("Name field is empty."));
@@ -313,10 +313,10 @@ public List<Message> validateInput() {
 		if(!classesText.emptyOrReadable())
 			messages.add(Message.error("Classes file path is not valid."));
 
-		if(gmtText.isReadable()) {
-			String parent = gmtText.getPath().getParent().getFileName().toString();
-			if("edb".equalsIgnoreCase(parent)) {
-				messages.add(Message.warn("Using GMT file from GSEA EDB directory. This GMT file has been filtered by "
+		if(gmtText.isReadable() && !parent.getCommonPanel().hasGmtFile()) {
+			String parentDir = gmtText.getPath().getParent().getFileName().toString();
+			if("edb".equalsIgnoreCase(parentDir)) {
+				messages.add(Message.warn("Using GMT file from EDB directory. This GMT file was filtered by "
 						+ "the expressions and may effect the universe size when adding signature gene sets."));
 			}
 		}		

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/MasterDetailDialogPage.java

@@ -347,11 +347,16 @@ public void allFinished(FinishStatus finishStatus) {
 		}
 	}
 
+	
+	public EditCommonPanel getCommonPanel() {
+		return commonPanel;
+	}
+	
 	private boolean validateInput() {
 		ErrorMessageDialog dialog = errorMessageDialogFactory.create(callback.getDialogFrame());
 
 		// Check if the user provided a global expression file, warn if there are also per-dataset expression files.
-		if(!isNullOrEmpty(commonPanel.getExpressionFile())) {
+		if(commonPanel.hasExpressionFile()) {
 			for(DataSetListItem item : dataSetListModel.toList()) {
 				DetailPanel panel = item.getDetailPanel();
 				if(panel instanceof EditDataSetPanel && !isNullOrEmpty(((EditDataSetPanel)panel).getExpressionFileName())) {
@@ -363,7 +368,7 @@ private boolean validateInput() {
 		}
 
 		// Check if the user provided a global gmt file, warn if there are also per-dataset gmt files.
-		if(!isNullOrEmpty(commonPanel.getGmtFile())) {
+		if(commonPanel.hasGmtFile()) {
 			for(DataSetListItem item : dataSetListModel.toList()) {
 				DetailPanel panel = item.getDetailPanel();
 				if(panel instanceof EditDataSetPanel && !isNullOrEmpty(((EditDataSetPanel)panel).getGMTFileName())) {
@@ -397,7 +402,7 @@ private boolean validateInput() {
 		// Check for input errors.
 		for(DataSetListItem item : dataSetListModel.toList()) {
 			DetailPanel panel = item.getDetailPanel();
-			List<Message> messages = panel.validateInput();
+			List<Message> messages = panel.validateInput(this);
 			if(!messages.isEmpty()) {
 				dialog.addSection(messages, panel.getDisplayName(), panel.getIcon());
 			}