Merge pull request #4 from sureshhewabi/master

more validation output fields added

README.md

@@ -33,6 +33,8 @@ Validation an mzIdentML
 
 ```
 $ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid
+$ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid -peak /path/to/data/file.mgf 
+$ java -jar submission-tool-validator-{version}-bin.jar -v -mzid /path/to/data/file.mzid -peaks /path/to/data/file1.mgf##/path/to/data/file2.mgf
 ```
 
 

pom.xml

@@ -4,7 +4,7 @@
     <groupId>uk.ac.ebi.pride.toolsuite</groupId>
     <artifactId>submission-tool-validator</artifactId>
     <name>submission-tool-validator</name>
-    <version>1.0.0</version>
+    <version>1.0.2</version>
     <packaging>jar</packaging>
 
 

src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/Report.java

@@ -34,7 +34,9 @@ public String toString() {
         for(Map.Entry er: errors)
             error.append(er.getKey().toString()).append(" == Level Error: ").append(er.getValue()).append(" ==\n");
         if(errors.isEmpty()){
-            error.append("Errors found: None").append("\n");
+            error.append("Status : Valid").append("\n");
+        }else{
+            error.append("Status : Invalid").append("\n");
         }
         return error.toString();
     }

src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/ResultReport.java

@@ -5,10 +5,13 @@
  */
 public class ResultReport extends Report {
 
+    private String assayFile;
+    private long fileSize;
     private int numberOfProteins;
     private int numberOfPeptides;
     private int numberOfPSMs;
     private int numberOfPeakFiles;
+    private boolean isValidSchema = false;
 
     public ResultReport() {
 
@@ -30,11 +33,28 @@ public void setNumberOfPeakFiles(int numberOfPeakFiles) {
         this.numberOfPeakFiles = numberOfPeakFiles;
     }
 
+    public void setValidSchema(boolean validSchema) {
+        isValidSchema = validSchema;
+    }
+
+    public void setAssayFile(String assayFile) {
+        this.assayFile = assayFile;
+    }
+
+    public void setFileSize(long fileSize) {
+        this.fileSize = fileSize;
+    }
+
     @Override
     public String toString() {
-        return super.toString() + "Number of reported proteins : " + numberOfProteins + "\n" +
+        return super.toString() +
+                "Assay file : " + assayFile + "\n" +
+                "Assay file size: " + fileSize + "\n" +
+                "Valid Schema : " + isValidSchema + "\n" +
+                "Number of reported proteins : " + numberOfProteins + "\n" +
                 "Number of reported peptides : " + numberOfPeptides + "\n" +
                 "Number of reported PSMs : " + numberOfPSMs + "\n" +
                 "Number of peak files : " + numberOfPeakFiles + "\n";
+
     }
 }

src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/MzIdValidator.java

@@ -70,10 +70,13 @@ public IReport validate() {
         int numPSMs = piaCompiler.getNrPeptideSpectrumMatches();
         int numPeakFiles = spectrumFiles.size();
 
-        ((ResultReport) report).setNumberOfPeptides(numPeptides);
+        ((ResultReport) report).setAssayFile(file.getName());
+        ((ResultReport) report).setFileSize(file.getTotalSpace());
         ((ResultReport) report).setNumberOfProteins(numProteins);
+        ((ResultReport) report).setNumberOfPeptides(numPeptides);
         ((ResultReport) report).setNumberOfPSMs(numPSMs);
         ((ResultReport) report).setNumberOfPeakFiles(numPeakFiles);
+        ((ResultReport) report).setValidSchema(true);
         return report;
     }