Merge pull request #200 from julianu/main

Dependencies and not existing file checks
medbioinf · Nov 30, 2023 · eaf8c0d · eaf8c0d
2 parents f066808 + 4ec1ce5
commit eaf8c0d
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Showing 2 changed files with 26 additions and 25 deletions.
diff --git a/pom.xml b/pom.xml
@@ -39,9 +39,10 @@
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 
-		<log4j2.version>2.20.0</log4j2.version>
-		<junit.version>4.13.1</junit.version>
-		<commons-collections.version>4.1</commons-collections.version>
+		<log4j2.version>2.22.0</log4j2.version>
+		<junit.version>4.13.2</junit.version>
+		<commons-collections.version>4.4</commons-collections.version>
+		<commons-text.version>1.11.0</commons-text.version>
 		<jmzidentml.version>1.2.11</jmzidentml.version>
 		<jmztab.version>3.0.8</jmztab.version>
 		<pride-mod.version>2.1.8</pride-mod.version>
@@ -51,24 +52,21 @@
 		<xtandem-parser.version>1.13.0</xtandem-parser.version>
 		<compomics-utilities.version>5.0.41</compomics-utilities.version>
 		<biojava-ontology.version>7.0.2</biojava-ontology.version>
-		<gson.version>2.8.9</gson.version>
-		<picocli.version>4.6.3</picocli.version>
+		<gson.version>2.10.1</gson.version>
+		<picocli.version>4.7.5</picocli.version>
 		<sqlite4java.version>1.0.392</sqlite4java.version>
-		<sqlite-jdbc.version>3.41.2.2</sqlite-jdbc.version>
+		<sqlite-jdbc.version>3.44.1.0</sqlite-jdbc.version>
 		<xercesImpl.version>2.12.2</xercesImpl.version>
+
+		<!-- override dependencies from some packages to avoid vulnarabilities  -->
+		<logback.version>1.4.13</logback.version>
+		<jackson-annotations.version>2.16.0</jackson-annotations.version>
+		<poi.version>5.2.5</poi.version>
 
 		<!-- these are "internal" dependencies, the jar files are delivered together with the source -->
 		<BaseLib.version>0.0.1-SNAPSHOT</BaseLib.version>
 		<CvtBaseLib.version>0.0.1-SNAPSHOT</CvtBaseLib.version>
 		<PDLibrary.version>0.0.1-SNAPSHOT</PDLibrary.version>
-
-		<!-- check for these dependencies the available KNIME deps. If these are ok, take them, even if they are older. -->
-		<commons-text.version>1.10.0</commons-text.version>
-
-		<!-- override dependencies from some packages to avoid vulnarabilities  -->
-		<logback.version>1.2.11</logback.version>
-		<jackson-annotations.version>2.13.3</jackson-annotations.version>
-		<poi.version>5.2.2</poi.version>
 	</properties>
 
 	<dependencies>

diff --git a/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java b/src/main/java/de/mpc/pia/intermediate/compiler/parser/InputFileParserFactory.java
@@ -1,9 +1,12 @@
 package de.mpc.pia.intermediate.compiler.parser;
 
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.log4j.Logger;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 
 import de.mpc.pia.intermediate.compiler.PIACompiler;
 import de.mpc.pia.intermediate.compiler.parser.searchengines.MascotDatFileParser;
@@ -14,10 +17,9 @@
 public class InputFileParserFactory {
 
     /** logger for this class */
-    private static final Logger LOGGER = Logger.getLogger(InputFileParserFactory.class);
+	private static final Logger LOGGER = LogManager.getLogger();
 
     public enum InputFileTypes {
-
         /**
          * the input file is a FASTA database file
          */
@@ -441,27 +443,28 @@ public static List<String> getAvailableTypeShorts() {
     public static boolean getDataFromFile(String name, String fileName,
             PIACompiler compiler, String additionalInfoFileName,
             String fileType) {
+
+    	if (!Files.exists(Path.of(fileName))) {
+    		LOGGER.error("'{}' does not exist, or is not accessible", fileName);
+    		return false;
+    	}
 
         if (fileType == null) {
             InputFileTypes type = getFileTypeByContent(fileName);
             if (type != null) {
-                LOGGER.info('\'' + fileName + "' seems to be a " +
-                        type.getFileTypeName()+" file");
+                LOGGER.info("'{}' seems to be a {} file", fileName, type.getFileTypeName());
                 return type.parseFile(name, fileName, compiler, additionalInfoFileName);
             }
 
-            LOGGER.error("File '" + fileName + "' could not be parsed, " +
-                    "fileType could not be guessed, please specify.");
+            LOGGER.error("File '{}' could not be parsed, fileType could not be guessed, please specify.", fileName);
         } else {
             InputFileTypes type = getFileTypeByShortName(fileType);
             if (type != null) {
-                LOGGER.info('\'' + fileName + "' should be a " +
-                        type.getFileTypeName()+" file");
+                LOGGER.info("'{}' should be a {} file", fileName, type.getFileTypeName());
                 return type.parseFile(name, fileName, compiler, additionalInfoFileName);
             }
 
-            LOGGER.error("File '" + fileName + "' could not be parsed, fileType '" +
-                    fileType + "' unknown.");
+            LOGGER.error("File '{}' could not be parsed, fileType '{}' unknown.", fileName, fileType);
         }
         return false;
     }