Better error message for non-numeric token in GSEA file.

mikekucera · mikekucera · commit 14611faec1ae · 2023-11-08T15:41:40.000-05:00
Refs #509
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentException.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentException.java
@@ -3,17 +3,14 @@
 @SuppressWarnings("serial")
 public class ParseGSEAEnrichmentException extends RuntimeException {
 	
-	public ParseGSEAEnrichmentException(String message, Throwable cause) {
-		super(message, cause);
-	}
-
-	public ParseGSEAEnrichmentException(String message) {
-		super(message);
-	}
+	private final String nonParsableToken;
 
-	public ParseGSEAEnrichmentException(Throwable cause) {
+	public ParseGSEAEnrichmentException(Throwable cause, String nonParsableToken) {
 		super(cause);
+		this.nonParsableToken = nonParsableToken;
 	}
 
-	
+	public String getNonParseableToken() {
+		return nonParsableToken;
+	}
 }
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentResults.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/ParseGSEAEnrichmentResults.java
@@ -132,21 +132,21 @@ private double parseDouble(String token) {
 		try {
 			return Double.parseDouble(token);
 		} catch(NumberFormatException e) {
-			if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1 && token.trim().equals("---")) {
+			if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1) {
 				return 1;
 			}
-			throw new ParseGSEAEnrichmentException(e);
+			throw new ParseGSEAEnrichmentException(e, token);
 		}
 	}
 	
 	private int parseInt(String token) {
 		try {
 			return Integer.parseInt(token);
 		} catch(NumberFormatException e) {
-			if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1 && token.trim().equals("---")) {
+			if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1) {
 				return 1;
 			}
-			throw new ParseGSEAEnrichmentException(e);
+			throw new ParseGSEAEnrichmentException(e, token);
 		}
 	}
 	
diff --git a/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/EMDialogTaskRunner.java b/EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/EMDialogTaskRunner.java
@@ -73,7 +73,8 @@ private void runImpl(TaskErrorStrategies strategies) {
 				}
 			} 
 			else if(e instanceof ParseGSEAEnrichmentException) {
-				boolean retry = promptForGSEAParseRetry();
+				String token = ((ParseGSEAEnrichmentException)e).getNonParseableToken();
+				boolean retry = promptForGSEAParseRetry(token);
 				if(retry) {
 					runImpl(strategies.with(ParseGSEAEnrichmentStrategy.REPLACE_WITH_1));
 				}
@@ -123,16 +124,18 @@ private boolean promptForMissingGenesetRetry(Collection<String> names) {
 		});
 	}
 	
-	private boolean promptForGSEAParseRetry() {
+	private boolean promptForGSEAParseRetry(String badToken) {
 		return prompt(dialog -> {
-			String title = "A GSEA enrichment file contained the characters '---' where a numeric value should be. "
-					+ "This is a known bug in some versions of GSEA.";
+			String title = "A GSEA enrichment file contained the characters '" + badToken + "' where a numeric value should be. ";
+			if(badToken.trim().equals("---"))
+				title += "This is a known bug in some versions of GSEA.";
 			
 			dialog.addSection(List.of(), title, IconManager.ICON_WARNING);
 			
 			String bottomMessage = "<html>Click 'Cancel' to stop the creation of the EnrichmentMap network. You may choose to update "
-					+ "your version of GSEA, or manually replace the occurrances of '---' with numeric values. <br>"
-					+ "Click 'Continue' to create the network with the current files. All instances of '---' in the enrichment file will be treated as the value 1.</html>";
+					+ "your version of GSEA, or manually replace the occurrances of '" + badToken + "' with numeric values. <br>"
+					+ "Click 'Continue' to create the network with the current files. All instances of '" + badToken + "' in the "
+					+ "enrichment file will be treated as the value 1.</html>";
 			dialog.addSection(List.of(), bottomMessage, null);
 		});
 	}
@@ -143,9 +146,9 @@ private boolean promptForUnsortedRanksRetry(String ranksFileName) {
 			
 			dialog.addSection(List.of(), title, IconManager.ICON_WARNING);
 			
-			String bottomMessage = "<html>Click 'Cancel' to stop the creation of the EnrichmentMap network. You may choose to provide "
+			String bottomMessage = "<html>Click <b>'Cancel'</b> to stop the creation of the EnrichmentMap network. You may choose to provide "
 					+ "sorted rank files instead. <br>"
-					+ "Click 'Continue' to create the network with the current files.</html>";
+					+ "Click <b>'Continue'</b> to create the network with the current files.</html>";
 			dialog.addSection(List.of(), bottomMessage, null);
 		});
 	}

Original file line number	Diff line number	Diff line change
`@@ -132,21 +132,21 @@ private double parseDouble(String token) {`
`132`	`132`	`try {`
`133`	`133`	`return Double.parseDouble(token);`
`134`	`134`	`} catch(NumberFormatException e) {`
`135`		`- if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1 && token.trim().equals("---")) {`
	`135`	`+ if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1) {`
`136`	`136`	`return 1;`
`137`	`137`	`}`
`138`		`- throw new ParseGSEAEnrichmentException(e);`
	`138`	`+ throw new ParseGSEAEnrichmentException(e, token);`
`139`	`139`	`}`
`140`	`140`	`}`
`141`	`141`
`142`	`142`	`private int parseInt(String token) {`
`143`	`143`	`try {`
`144`	`144`	`return Integer.parseInt(token);`
`145`	`145`	`} catch(NumberFormatException e) {`
`146`		`- if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1 && token.trim().equals("---")) {`
	`146`	`+ if(strategy == ParseGSEAEnrichmentStrategy.REPLACE_WITH_1) {`
`147`	`147`	`return 1;`
`148`	`148`	`}`
`149`		`- throw new ParseGSEAEnrichmentException(e);`
	`149`	`+ throw new ParseGSEAEnrichmentException(e, token);`
`150`	`150`	`}`
`151`	`151`	`}`
`152`	`152`