Merge pull request #14 from sureshhewabi/master

updated PIA
bigbio · Dec 21, 2021 · 39ccedc · 39ccedc
2 parents 28dbb57 + 8ffb417
commit 39ccedc
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Showing 5 changed files with 16 additions and 13 deletions.
diff --git a/pom.xml b/pom.xml
@@ -4,23 +4,23 @@
     <groupId>uk.ac.ebi.pride.toolsuite</groupId>
     <artifactId>submission-tool-validator</artifactId>
     <name>submission-tool-validator</name>
-    <version>1.0.5</version>
+    <version>1.0.6</version>
     <packaging>jar</packaging>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <archive.repo.version>1.0.2</archive.repo.version>
-        <px.submission.core.version>2.0.28</px.submission.core.version>
+        <px.submission.core.version>2.0.32</px.submission.core.version>
         <javax.activation.version>1.2.0</javax.activation.version>
         <jaxb.api.version>2.3.1</jaxb.api.version>
-        <pia.version>1.3.18</pia.version>
+        <pia.version>1.3.23</pia.version>
         <uk.ac.ebi.pride.tools-jmzreader.version>2.0.6</uk.ac.ebi.pride.tools-jmzreader.version>
         <cpdetector.version>1.0.7</cpdetector.version>
     </properties>
 
     <dependencies>
         <dependency>
-            <groupId>cpdetector</groupId>
+            <groupId>net.sourceforge.cpdetector</groupId>
             <artifactId>cpdetector</artifactId>
             <version>${cpdetector.version}</version>
         </dependency>
@@ -45,6 +45,10 @@
                     <groupId>org.slf4j</groupId>
                     <artifactId>slf4j-log4j12</artifactId>
                 </exclusion>
+                <exclusion>
+                    <groupId>uk.ac.ebi.pride</groupId>
+                    <artifactId>px-submission-core</artifactId>
+                </exclusion>
                 <!--           exclude this as this fails to download from maven a lot. Instead include it separately-->
                 <exclusion>
                     <groupId>net.sourceforge.cpdetector</groupId>

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
@@ -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
@@ -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
@@ -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
@@ -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);
 
         }