schema file from resource folder

bigbio · Apr 9, 2021 · a9ce931 · a9ce931
1 parent d23de57
commit a9ce931
Show file tree

Hide file tree

Showing 3 changed files with 1,856 additions and 7 deletions.
diff --git a/pom.xml b/pom.xml
@@ -12,7 +12,6 @@
         <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>
-        <ms.data.core.api.version>2.0.31-SNAPSHOT</ms.data.core.api.version>
         <javax.activation.version>1.2.0</javax.activation.version>
         <jaxb.api.version>2.3.1</jaxb.api.version>
         <pia.version>1.3.15</pia.version>
@@ -34,10 +33,6 @@
                     <groupId>org.slf4j</groupId>
                     <artifactId>slf4j-api</artifactId>
                 </exclusion>
-                <!--<exclusion>-->
-                    <!--<groupId>org.apache.logging.log4j</groupId>-->
-                    <!--<artifactId>log4j-slf4j-impl</artifactId>-->
-                <!--</exclusion>-->
                 <exclusion>
                     <groupId>ch.qos.logback</groupId>
                     <artifactId>logback-core</artifactId>
@@ -180,6 +175,10 @@
                     </execution>
                 </executions>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-resources-plugin</artifactId>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-jar-plugin</artifactId>

diff --git a/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/MzIdValidator.java b/src/main/java/uk/ac/ebi/pride/toolsuite/px_validator/validators/MzIdValidator.java
@@ -15,6 +15,7 @@
 import java.io.*;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
@@ -24,7 +25,7 @@ public class MzIdValidator implements Validator{
 
     private File file;
     private List<File> peakFiles;
-    private static final String MZID_SCHEMA = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/psi-pi/mzIdentML1.1.0.xsd";
+//    private static final String MZID_SCHEMA = "https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/psi-pi/mzIdentML1.1.0.xsd";
 
     public static Validator getInstance(CommandLine cmd) throws Exception {
         return new MzIdValidator(cmd);
@@ -86,7 +87,11 @@ private static IReport validateMzidSchema(File mzIdentML) {
         IReport report = new ResultReport();
         try (BufferedReader br = new BufferedReader(new FileReader(mzIdentML))) {
             GenericSchemaValidator genericValidator = new GenericSchemaValidator();
-            genericValidator.setSchema(new URI(MzIdValidator.MZID_SCHEMA));
+            URL url =  MzIdValidator.class.getClassLoader().getResource("mzIdentML1.1.0.xsd");
+            if (url == null || url.getPath().length() == 0) {
+                throw new IllegalStateException("MzIdentML1.1.0.xsd not found!");
+            }
+            genericValidator.setSchema(url.toURI());
             ErrorHandlerIface handler = new ValidationErrorHandler();
             genericValidator.setErrorHandler(handler);
             genericValidator.validate(br);