Update some of the swagger docs.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/EMBuildCommandTask.java

@@ -82,65 +82,54 @@
  */
 public class EMBuildCommandTask extends AbstractTask {
 
-	@Tunable(description = "Analysis Type", groups = { "Analysis Type" }, gravity = 1.0)
-	public ListSingleSelection<String> analysisType = new ListSingleSelection<String>(method_GSEA, method_generic, method_Specialized);;
+	@Tunable(description = "Analysis Type")
+	public ListSingleSelection<String> analysisType = new ListSingleSelection<String>(method_GSEA, method_generic, method_Specialized);
 
-	@Tunable(description = "GMT", groups = { "User Input", "Gene Sets" }, gravity = 2.0, dependsOn = "analysisType=" + method_generic, 
-			params = "fileCategory=table;input=true", tooltip = "File specifying gene sets.\nFormat: geneset name <tab> description <tab> gene ...")
+	@Tunable(description = "Path to GMT File specifying gene sets. Format: geneset name <tab> description <tab> gene ...")
 	public File gmtFile;
 
 	//Dataset 1 Tunables
-	@Tunable(description = "Expression", groups = { "User Input", "Datasets", "Dataset 1" }, gravity = 3.0, params = "fileCategory=table;input=true", 
-			tooltip = "File with gene expression values.\nFormat: gene <tab> description <tab> expression value <tab> ...")
+	@Tunable(description = "Path to Expression File for Dataset 1 with gene expression values. Format: gene <tab> description <tab> expression value <tab> ...")
 	public File expressionDataset1;
 
-	@Tunable(description = "Enrichments", groups = { "User Input", "Datasets", "Dataset 1" }, gravity = 4.0, 
-			dependsOn = "analysisType=" + method_generic, params = "fileCategory=table;input=true", tooltip = "File specifying enrichment results.\n")
+	@Tunable(description = "Path to Enrichments File for Dataset 1 specifying enrichment results.")
 	public File enrichmentsDataset1;
 
-	@Tunable(description = "Enrichments 2", groups = { "User Input", "Datasets", "Dataset 1" }, gravity = 5.0, 
-			dependsOn = "analysisType=" + method_GSEA, params = "fileCategory=table;input=true", tooltip = "File specifying enrichment results.\n")
+	@Tunable(description = "Path to a second Enrichments File for Dataset 1 specifying enrichment results.")
 	public File enrichments2Dataset1;
 
-	@Tunable(description = "Ranks", groups = { "User Input", "Datasets", "Dataset 1", "Advanced" }, gravity = 6.0, params = "fileCategory=table;input=true", 
-			tooltip = "File specifying ranked genes.\nFormat: gene <tab> score or statistic")
+	@Tunable(description = "Path to a Ranks File for Dataset 1 specifying ranked genes. Format: gene <tab> score or statistic")
 	public File ranksDataset1;
 
-	@Tunable(description = "Classes", groups = { "User Input", "Datasets", "Dataset 1", "Advanced" }, gravity = 7.0, params = "fileCategory=table;input=true", 
-			tooltip = "File specifying the classes of each sample in expression file.\nformat: see GSEA website")
+	@Tunable(description = "Path to Classes File for Dataset 1 specifying the classes of each sample in expression file. Format: see GSEA website")
 	public File classDataset1;
 
-	@Tunable(description = "Phenotype1", groups = { "User Input", "Datasets", "Dataset 1", "Advanced" }, gravity = 8.0, tooltip = "Dataset1 phenotype/class")
+	@Tunable(description = "Phenotype 1 for Dataset 1")
 	public String phenotype1Dataset1;
 
-	@Tunable(description = "Phenotype2", groups = { "User Input", "Datasets", "Dataset 1", "Advanced" }, gravity = 9.0, tooltip = "Dataset1 phenotype/class")
+	@Tunable(description = "Phenotype 2 for Dataset 1")
 	public String phenotype2Dataset1;
 
 	//Dataset 2 Tunables
-	@Tunable(description = "Expression", groups = { "User Input", "Datasets", "Dataset 2" }, gravity = 10.0, 
-			params = "fileCategory=table;input=true;displayState=callapsed", tooltip = "File with gene expression values.\nFormat: gene <tab> description <tab> expression value <tab> ...")
+	@Tunable(description = "Path to Expression File for Dataset 2 with gene expression values. Format: gene <tab> description <tab> expression value <tab> ...")
 	public File expressionDataset2;
 
-	@Tunable(description = "Enrichments", groups = { "User Input", "Datasets", "Dataset 2" }, gravity = 11.0, 
-			dependsOn = "analysisType=" + method_generic, params = "fileCategory=table;input=true;displayState=callapsed", tooltip = "File specifying enrichment results.\n")
+	@Tunable(description = "Path to Enrichments File for Dataset 2 specifying enrichment results.")
 	public File enrichmentsDataset2;
 
-	@Tunable(description = "Enrichments 2", groups = { "User Input", "Datasets", "Dataset 2" }, gravity = 12.0, 
-			dependsOn = "analysisType=" + method_GSEA, params = "fileCategory=table;input=true;displayState=callapsed", tooltip = "File specifying enrichment results.\n")
+	@Tunable(description = "Path to a second Enrichments File for Dataset 2 specifying enrichment results.")
 	public File enrichments2Dataset2;
 
-	@Tunable(description = "Ranks", groups = { "User Input", "Datasets", "Dataset 2", "Advanced" }, gravity = 13.0, 
-			params = "fileCategory=table;input=true;displayState=callapsed", tooltip = "File specifying ranked genes.\nFormat: gene <tab> score or statistic")
+	@Tunable(description = "Path to Ranks File for Dataset 2 specifying ranked genes. Format: gene <tab> score or statistic")
 	public File ranksDataset2;
 
-	@Tunable(description = "Classes", groups = { "User Input", "Datasets", "Dataset 2", "Advanced" }, gravity = 14.0, 
-			params = "fileCategory=table;input=true;displayState=callapsed", tooltip = "File specifying the classes of each sample in expression file.\nformat: see GSEA website")
+	@Tunable(description = "Path to Classes File for Dataset 2 specifying the classes of each sample in expression file. format: see GSEA website")
 	public File classDataset2;
 
-	@Tunable(description = "Phenotype1", groups = { "User Input", "Datasets", "Dataset 2", "Advanced" }, gravity = 15.0, params = "displayState=callapsed", tooltip = "Dataset2 phenotype/class")
+	@Tunable(description = "Phenotype 1 for Dataset 2")
 	public String phenotype1Dataset2;
 
-	@Tunable(description = "Phenotype2", groups = { "User Input", "Datasets", "Dataset 2", "Advanced" }, gravity = 16.0, params = "displayState=callapsed", tooltip = "Dataset2 phenotype/class")
+	@Tunable(description = "Phenotype 2 for Dataset 2")
 	public String phenotype2Dataset2;
 
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/PAKnownSignatureCommandTask.java

@@ -55,7 +55,7 @@ public class PAKnownSignatureCommandTask extends AbstractTask {
 	@Tunable(description = "When 'hypergeomUniverseType' is USER_DEFINED, sets the value for N.")
 	public int userDefinedUniverseSize = 0;
 
-	@Tunable(description = "Name of the data set.")
+	@Tunable(description = "Name of the signature data set that will be created.")
 	public String name;
 
 	@ContainsTunables @Inject

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/FilterTunables.java

@@ -35,7 +35,7 @@ public class FilterTunables {
 	@Tunable(description = "Similarity Cutoff (value between 0 and 1). Edges with a similarity score lower than the one entered will not be included in the network.")
 	public Double similaritycutoff = 0.25;
 
-	@Tunable(description = "Similarity Coeffecient (value between 0 and 1). Used to choose the formula used to calculate the similarity score.")
+	@Tunable(description = "Used to choose the formula used to calculate the similarity score.")
 	public ListSingleSelection<String> coefficients;
 
 	@Tunable(description = "When coefficients=COMBINED this parameter is used to determine what percentage to use for JACCARD and OVERLAP when combining their value."

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/TableTunables.java

@@ -14,16 +14,16 @@ public class TableTunables {
 			longDescription = "If the prefix ```SUID:``` is used, the table corresponding the SUID will be returned. Example: \"galFiltered.sif default node\"")
 	public String table;
 
-	@Tunable(required=true)
+	@Tunable(required=true, description="Name of column that contains the names of the gene sets.")
 	public String nameColumn;
 
-	@Tunable(required=true)
+	@Tunable(required=true, description="Name of column that contains the list of genes.")
 	public String genesColumn;
 
-	@Tunable(required=true)
+	@Tunable(required=true, description="Name of column that contains p values.")
 	public String pvalueColumn;
 
-	@Tunable
+	@Tunable(description="Name of column that contains the gene set description (optional).")
 	public String descriptionColumn;
 
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/resolver/DataSetResolver.java

@@ -159,16 +159,6 @@ private static Optional<Path> findClosestMatch(Path p, List<Path> candidates) {
 
 		// Find closest match by using edit distance on file name;
 		Optional<Path> closest = candidates.stream().reduce(BinaryOperator.maxBy(Comparator.comparing(scores::get)));
-		
-		// There should be a threshold for considering the path a match
-		// MKTODO can this heuristic be improved?
-//		if(closest.isPresent()) {
-//			int score = scores.get(closest.get());
-//			if(score == 0) {
-//				return Optional.empty();
-//			}
-//		}
-		
 		return closest;
 	}
 
@@ -183,11 +173,7 @@ public static Type guessType(Path path) {
 			return Type.IGNORE;
 		}
 		if(Files.isDirectory(path)) {
-//			if(GSEAResolver.isGSEAResultsFolder(path)) {
-//				return Type.GSEA_FOLDER;
-//			} else {
-				return Type.IGNORE;
-//			}
+			return Type.IGNORE;
 		}
 
 		return guess(path);