Using the CDK Validator now

egonw · Mar 23, 2011 · ba75780 · ba75780
1 parent 35295bb
commit ba75780
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Showing 5 changed files with 66 additions and 6 deletions.
diff --git a/jar/cdk-extra.jar b/jar/cdk-extra.jar
diff --git a/src/com/github/egonw/moldbvalid/ErrorHandler.java b/src/com/github/egonw/moldbvalid/ErrorHandler.java
@@ -12,28 +12,28 @@ public ErrorHandler(IReportHandler report) {
   }
 
   public void handleError(String message) {
-    report.handleError(":error", message);
+    report.handleError(":formatError", message);
   };
 
   public void handleError(String message,
     Exception exception)
   {
-    report.handleError(":error", message + "\n  -> " +
+    report.handleError(":formatError", message + "\n  -> " +
             exception.getMessage());
   };
 
   public void handleError(String message,
     int row, int colStart, int colEnd)
   {
-    report.handleError(":error", "location: " + row + ", " + 
+    report.handleError(":formatError", "location: " + row + ", " + 
       colStart + "-" + colEnd + ": " + message);
   };
 
   public void handleError(String message,
     int row, int colStart, int colEnd,
     Exception exception)
   {
-    report.handleError(":error", "location: " + row + ", " + 
+    report.handleError(":formatError", "location: " + row + ", " + 
       colStart + "-" + colEnd + ": " + message + " -> " +
       exception.getMessage());
   };

diff --git a/src/com/github/egonw/moldbvalid/IReportHandler.java b/src/com/github/egonw/moldbvalid/IReportHandler.java
@@ -2,6 +2,8 @@
 
 public interface IReportHandler {
 
+  public void setFile(String filename);
+
   public void setSubject(String subject);
 
   public void handleError(String type, String error);

diff --git a/src/com/github/egonw/moldbvalid/RDFN3Handler.java b/src/com/github/egonw/moldbvalid/RDFN3Handler.java
@@ -6,7 +6,8 @@ public class RDFN3Handler implements IReportHandler {
 
   private PrintStream output;
 
-  private String currentSubject = ":1";
+  private int counter = 0;
+  private String currentSubject = "";
 
   public RDFN3Handler(OutputStream output) {
     if (output instanceof PrintStream) {
@@ -16,8 +17,15 @@ public RDFN3Handler(OutputStream output) {
     }
   }
 
+  public void setFile(String filename) {
+    output.println(":file rdfs:label \"" + filename + "\" .");
+  }
+
   public void setSubject(String subject) {
+    this.counter++;
     this.currentSubject = subject;
+    output.println(":file :describes :mol" + counter + " .");
+    output.println(":mol" + counter + "  rdfs:label \"" + subject + "\" .");
   };
 
   public void handleError(String type, String error) {

diff --git a/src/com/github/egonw/moldbvalid/Validate.java b/src/com/github/egonw/moldbvalid/Validate.java
@@ -4,20 +4,59 @@
 import org.openscience.cdk.io.*;
 import org.openscience.cdk.io.iterator.*;
 import org.openscience.cdk.*;
+import org.openscience.cdk.atomtype.*;
+import org.openscience.cdk.exception.*;
 import org.openscience.cdk.nonotify.*;
 import org.openscience.cdk.io.IChemObjectReader.Mode;
+import org.openscience.cdk.validate.*;
 import java.io.*;
 
 public class Validate {
 
   IReportHandler handler;
+  ValidatorEngine validator;
 
   public Validate(IReportHandler handler) {
     this.handler = handler;
+    this.validator = new ValidatorEngine();
+    this.validator.addValidator(new CDKValidator());
+    this.validator.addValidator(new BasicValidator());
+    this.validator.addValidator(new AbstractValidator() {
+      CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(
+        DefaultChemObjectBuilder.getInstance()
+      );
+      public ValidationReport validateMolecule(IMolecule molecule) {
+        ValidationReport report = new ValidationReport();
+        try {
+          IAtomType[] types = matcher.findMatchingAtomType(molecule);
+          for (int i=0; i<types.length; i++) {
+            ValidationTest atError = new ValidationTest(
+              molecule.getAtom(i),
+              "The atom's type is not recognized."
+            );
+            System.out.println("type: " + types[i].getAtomTypeName());
+            if (types[i] == null) {
+              report.addError(atError);
+            } else {
+              report.addError(atError);
+            }
+          }
+        } catch (Exception exception) {
+          ValidationTest test = new ValidationTest(
+            molecule,
+            "Error while atom typing of molecule."
+          );
+          test.setDetails(exception.getMessage());
+          report.addCDKError(test);
+        }
+        return report;
+      }
+    });
   }
 
   public void validateFile(String fileName) throws Exception {
     ErrorHandler errorHandler = new ErrorHandler(this.handler);
+    handler.setFile(fileName);
 
     IteratingMDLReader iterator = new IteratingMDLReader(
       new FileReader(new File(fileName)),
@@ -28,7 +67,18 @@ public void validateFile(String fileName) throws Exception {
 
     while (iterator.hasNext()) {
       IMolecule mol = (IMolecule)iterator.next();
-      System.out.println("" + mol.getProperty(CDKConstants.TITLE));
+      handler.setSubject("" + mol.getProperty(CDKConstants.TITLE));
+      System.out.println("mol: " + mol.getProperty(CDKConstants.TITLE));
+      ValidationReport report = validator.validateMolecule(mol);
     }
   }
+
+  private void process(IReportHandler handler, ValidationReport report) {
+    for (ValidationTest test : report.getErrors())
+      handler.handleError(":error", test.getError());
+    for (ValidationTest test : report.getWarnings())
+      handler.handleError(":warning", test.getError());
+    for (ValidationTest test : report.getCDKErrors())
+      handler.handleError(":cdkError", test.getError());
+  }
 }