diff --git a/pom.xml b/pom.xml
index 7ee65b0..7aa747c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,23 +4,23 @@
uk.ac.ebi.pride.toolsuite
submission-tool-validator
submission-tool-validator
- 1.0.5
+ 1.0.6
jar
UTF-8
1.0.2
- 2.0.28
+ 2.0.32
1.2.0
2.3.1
- 1.3.18
+ 1.3.23
2.0.6
1.0.7
- cpdetector
+ net.sourceforge.cpdetector
cpdetector
${cpdetector.version}
@@ -45,6 +45,10 @@
org.slf4j
slf4j-log4j12
+
+ uk.ac.ebi.pride
+ px-submission-core
+
net.sourceforge.cpdetector
diff --git a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/SubmissionToolValidator.java b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/SubmissionToolValidator.java
index 01199c9..69ecaff 100644
--- a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/SubmissionToolValidator.java
+++ b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/SubmissionToolValidator.java
@@ -1,7 +1,7 @@
package uk.ac.ebi.pride.toolsuite.px_validator;
+import lombok.extern.slf4j.Slf4j;
import org.apache.commons.cli.*;
-import org.apache.log4j.Logger;
import uk.ac.ebi.pride.toolsuite.px_validator.utils.IReport;
import java.io.File;
@@ -14,9 +14,9 @@
*
* @author ypriverol
*/
+@Slf4j
public class SubmissionToolValidator {
- private static final Logger log = Logger.getLogger(SubmissionToolValidator.class);
/**
* Main class that gets run. Parses command line arguments, starts either the converter or validation operations.
diff --git a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/Validator.java b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/Validator.java
index 4d11460..36f49a3 100644
--- a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/Validator.java
+++ b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/Validator.java
@@ -1,8 +1,8 @@
package uk.ac.ebi.pride.toolsuite.px_validator;
+import lombok.extern.slf4j.Slf4j;
import org.apache.commons.cli.CommandLine;
-import org.apache.log4j.Logger;
import uk.ac.ebi.pride.toolsuite.px_validator.utils.*;
import uk.ac.ebi.pride.toolsuite.px_validator.validators.MzIdValidator;
import uk.ac.ebi.pride.toolsuite.px_validator.validators.MzTabValidator;
@@ -21,10 +21,9 @@
*
* @author ypriverol
*/
+@Slf4j
public class Validator {
- private static final Logger log = Logger.getLogger(Validator.class);
-
/**
* This class parses the command line arguments and beings the file validation.
diff --git a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/Utility.java b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/Utility.java
index c1cb156..88c8392 100644
--- a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/Utility.java
+++ b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/utils/Utility.java
@@ -2,8 +2,8 @@
import com.google.common.io.Files;
import de.mpc.pia.intermediate.PeptideSpectrumMatch;
+import lombok.extern.slf4j.Slf4j;
import org.apache.commons.io.FileUtils;
-import org.apache.log4j.Logger;
import uk.ac.ebi.jmzidml.model.mzidml.FileFormat;
import uk.ac.ebi.jmzidml.model.mzidml.SpectraData;
import uk.ac.ebi.pride.utilities.util.Triple;
@@ -15,8 +15,8 @@
import java.util.Iterator;
import java.util.List;
+@Slf4j
public class Utility {
- private static final Logger log = Logger.getLogger(Utility.class);
public static final String ARG_VALIDATION = "v";
public static final String ARG_CONVERSION = "c";
diff --git a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/PXFileValidator.java b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/PXFileValidator.java
index 78a8b67..e6b6876 100644
--- a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/PXFileValidator.java
+++ b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/PXFileValidator.java
@@ -2,6 +2,7 @@
import org.apache.commons.cli.CommandLine;
import uk.ac.ebi.pride.data.exception.SubmissionFileException;
+
import uk.ac.ebi.pride.data.io.SubmissionFileParser;
import uk.ac.ebi.pride.data.model.Submission;
import uk.ac.ebi.pride.data.validation.SubmissionValidator;
@@ -44,8 +45,7 @@ public IReport validate(){
for(ValidationMessage message: submissionValidator.getMessages()){
report.addException(new IOException(message.getMessage()), message.getType());
}
-
- } catch (SubmissionFileException e) {
+ } catch (SubmissionFileException | IOException e) {
report.addException(e, ValidationMessage.Type.ERROR);
}