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); }