Fixed bug when using aggregate mapping from resources folder (#98)

EBIvariation · Feb 28, 2017 · 3225152 · 3225152
1 parent 6056c72
commit 3225152
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Showing 4 changed files with 10 additions and 12 deletions.
diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AggregatedVcfLineMapper.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/AggregatedVcfLineMapper.java
@@ -21,6 +21,7 @@
 import uk.ac.ebi.eva.commons.models.data.Variant;
 import uk.ac.ebi.eva.utils.FileUtils;
 
+import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.List;
 import java.util.Properties;
@@ -49,7 +50,7 @@ public AggregatedVcfLineMapper(String fileId, String studyId, VariantSource.Aggr
 
         Properties mappings = null;
         if(mappingFilePath!=null){
-            mappings = FileUtils.getPropertiesFile(mappingFilePath);
+            mappings = FileUtils.getPropertiesFile(new FileInputStream(mappingFilePath));
         }
 
         switch (aggregation) {

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfEVSFactory.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfEVSFactory.java
@@ -16,14 +16,11 @@
  */
 package uk.ac.ebi.eva.pipeline.io.mappers;
 
-import org.opencb.biodata.models.variant.VariantSource;
-
 import uk.ac.ebi.eva.commons.models.data.Variant;
 import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry;
 import uk.ac.ebi.eva.commons.models.data.VariantStats;
 import uk.ac.ebi.eva.utils.FileUtils;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.Properties;
 import java.util.Set;
@@ -68,7 +65,7 @@ public VariantVcfEVSFactory(Properties tagMap) {
     @Override
     protected void loadDefaultMappings() {
         try {
-            loadMappings(FileUtils.getPropertiesFile(FileUtils.getResource(EVS_MAPPING_FILE).getAbsolutePath()));
+            loadMappings(FileUtils.getPropertiesFile(FileUtils.getResourceAsStream(EVS_MAPPING_FILE)));
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactory.java b/src/main/java/uk/ac/ebi/eva/pipeline/io/mappers/VariantVcfExacFactory.java
@@ -17,14 +17,12 @@
 package uk.ac.ebi.eva.pipeline.io.mappers;
 
 import org.opencb.biodata.models.feature.Genotype;
-import org.opencb.biodata.models.variant.VariantSource;
 
 import uk.ac.ebi.eva.commons.models.data.Variant;
 import uk.ac.ebi.eva.commons.models.data.VariantSourceEntry;
 import uk.ac.ebi.eva.commons.models.data.VariantStats;
 import uk.ac.ebi.eva.utils.FileUtils;
 
-import java.io.File;
 import java.io.IOException;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -80,7 +78,7 @@ public VariantVcfExacFactory(Properties tagMap) {
     @Override
     protected void loadDefaultMappings() {
         try {
-            loadMappings(FileUtils.getPropertiesFile(FileUtils.getResource(EXAC_MAPPING_FILE).getAbsolutePath()));
+            loadMappings(FileUtils.getPropertiesFile(FileUtils.getResourceAsStream(EXAC_MAPPING_FILE)));
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

diff --git a/src/main/java/uk/ac/ebi/eva/utils/FileUtils.java b/src/main/java/uk/ac/ebi/eva/utils/FileUtils.java
@@ -22,7 +22,6 @@
 import uk.ac.ebi.eva.pipeline.io.GzipLazyResource;
 
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
@@ -66,10 +65,13 @@ public static File getResource(String resourcePath) {
         return new File(FileUtils.class.getResource(resourcePath).getFile());
     }
 
-    public static Properties getPropertiesFile(String propertiesFilePath) throws IOException {
-        InputStream input = new FileInputStream(propertiesFilePath);
+    public static InputStream getResourceAsStream(String resourcePath) {
+        return FileUtils.class.getResourceAsStream(resourcePath);
+    }
+
+    public static Properties getPropertiesFile(InputStream propertiesInputStream) throws IOException {
         Properties properties = new Properties();
-        properties.load(input);
+        properties.load(propertiesInputStream);
         return properties;
     }
 }