Improve exception handling

Also start IGV after loading variants, this way there is no leftover process after shutdown.
MarWoes · Dec 22, 2017 · 43331ab · 43331ab
1 parent dfc32fe
commit 43331ab
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Showing 13 changed files with 66 additions and 35 deletions.
diff --git a/src/main/java/de/imi/marw/viper/api/TableReaderMultiplexer.java b/src/main/java/de/imi/marw/viper/api/TableReaderMultiplexer.java
@@ -22,6 +22,8 @@
 import de.imi.marw.viper.variants.table.TableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
 import de.imi.marw.viper.variants.table.VcfTableReader;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 
 /**
  *
@@ -38,7 +40,7 @@ public TableReaderMultiplexer(ViperServerConfig config) {
     }
 
     @Override
-    public VariantTable readTable(String fileName) {
+    public VariantTable readTable(String fileName) throws FileNotFoundException, IOException {
 
         if (fileName.endsWith(".vcf")) {
             return vcfReader.readTable(fileName);

diff --git a/src/main/java/de/imi/marw/viper/api/ViperServer.java b/src/main/java/de/imi/marw/viper/api/ViperServer.java
@@ -30,6 +30,8 @@
 import de.imi.marw.viper.variants.table.VariantTable;
 import de.imi.marw.viper.visualization.IGVVisualizer;
 import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Paths;
 import spark.Spark;
@@ -46,6 +48,7 @@ public class ViperServer {
     private final Gson gson;
     private final VariantClusterBuilder clusterer;
     private VariantTableCluster variantTableCluster;
+    private boolean sparkInitDone;
 
     private IGVVisualizer igv;
 
@@ -54,32 +57,41 @@ public ViperServer(ViperServerConfig config) {
         this.config = config;
         this.gson = new GsonBuilder().serializeNulls().create();
         this.clusterer = new VariantClusterBuilder(config.getBreakpointTolerance(), !config.isClusteringEnabled());
+        this.sparkInitDone = false;
     }
 
-    public void start() {
+    public void start() throws FileNotFoundException, IOException {
+
+        this.variantTableCluster = this.loadVariants();
 
         this.igv = this.setupIGV();
         this.igv.start();
 
-        this.variantTableCluster = this.loadVariants();
-
         this.igv.awaitStartup();
 
         this.setupRoutes();
 
         awaitInitialization();
+
     }
 
     public void stop() {
-        this.igv.shutdown();
-        Spark.stop();
+
+        if (this.igv != null) {
+            this.igv.shutdown();
+        }
+
+        if (this.sparkInitDone) {
+            Spark.stop();
+        }
+
     }
 
     public ViperServerConfig getConfig() {
         return this.config;
     }
 
-    private VariantTableCluster loadVariants() {
+    private VariantTableCluster loadVariants() throws FileNotFoundException, IOException {
         TableReaderMultiplexer reader = new TableReaderMultiplexer(config);
 
         VariantTable unclusteredTable = reader.readTable(config.getAnalysisFile());
@@ -102,6 +114,8 @@ private void setupRoutes() {
         setupTableApi();
 
         init();
+
+        this.sparkInitDone = true;
     }
 
     private void setupTableApi() {

diff --git a/src/main/java/de/imi/marw/viper/main/Main.java b/src/main/java/de/imi/marw/viper/main/Main.java
@@ -58,17 +58,26 @@ public static void main(String[] args) {
             configFileName = "config.json";
         }
 
+        ViperServer server = null;
+
         try {
 
             ViperServerConfig config = loadConfig(configFileName);
 
-            ViperServer server = new ViperServer(config);
+            server = new ViperServer(config);
             server.start();
 
         } catch (FileNotFoundException ex) {
             Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
+            System.err.println("[ERROR] File not found. Make sure your configuration paths are set correctly.");
         } catch (IOException ex) {
             Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
+        } finally {
+
+            if (server != null) {
+                server.stop();
+            }
+
         }
     }
 }
diff --git a/src/main/java/de/imi/marw/viper/variants/table/CsvTableReader.java b/src/main/java/de/imi/marw/viper/variants/table/CsvTableReader.java
@@ -20,6 +20,7 @@
 
 import de.imi.marw.viper.util.Util;
 import de.imi.marw.viper.variants.VariantPropertyType;
+import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.Reader;
@@ -182,7 +183,7 @@ private List<List<Object>> parseVariantCalls(String[] colNames, List<String[]> c
     }
 
     @Override
-    public VariantTable readTable(String fileName) {
+    public VariantTable readTable(String fileName) throws FileNotFoundException, IOException {
         try (Reader reader = new FileReader(fileName)) {
 
             List<String[]> rawStrings = new ArrayList<>();
@@ -208,11 +209,7 @@ public VariantTable readTable(String fileName) {
 
             return new VariantTable(parsedCalls, Arrays.asList(header), Arrays.asList(types));
 
-        } catch (IOException ex) {
-            Logger.getLogger(CsvTableReader.class.getName()).log(Level.SEVERE, null, ex);
         }
-
-        return null;
     }
 
 }
diff --git a/src/main/java/de/imi/marw/viper/variants/table/TableReader.java b/src/main/java/de/imi/marw/viper/variants/table/TableReader.java
@@ -18,10 +18,13 @@
  */
 package de.imi.marw.viper.variants.table;
 
+import java.io.FileNotFoundException;
+import java.io.IOException;
+
 /**
  *
  * @author marius
  */
 public interface TableReader {
-    VariantTable readTable(String fileName);
+    VariantTable readTable(String fileName) throws FileNotFoundException, IOException;
 }
diff --git a/src/main/java/de/imi/marw/viper/variants/table/VariantTable.java b/src/main/java/de/imi/marw/viper/variants/table/VariantTable.java
@@ -275,7 +275,7 @@ private String getSingleColumnValue(List call, String column) {
     private void checkDataIntegrity() {
 
         if (Arrays.stream(MANDATORY_FIELDS).anyMatch((mandatory) -> !columnNames.contains(mandatory))) {
-            throw new IllegalArgumentException("Data must contain all mandatory columns");
+            throw new IllegalArgumentException("Variant call tables must contain all mandatory columns: " + Arrays.toString(VariantTable.MANDATORY_FIELDS) + ". Make sure you use the correct delimiter.");
         }
 
         if (types.size() != columnNames.size()) {

diff --git a/src/test/java/de/imi/marw/viper/test/api/APITest.java b/src/test/java/de/imi/marw/viper/test/api/APITest.java
@@ -60,7 +60,7 @@ private String readFromFile(String testResourceFileName) throws IOException {
     }
 
     @BeforeClass
-    public static void setUp() {
+    public static void setUp() throws IOException {
 
         ViperServerConfig conf = new ViperServerConfig();
         conf.setAnalysisFile(TestUtil.getResourceFile("examples.csv"));

diff --git a/src/test/java/de/imi/marw/viper/test/filtering/FilterTest.java b/src/test/java/de/imi/marw/viper/test/filtering/FilterTest.java
@@ -26,6 +26,7 @@
 import de.imi.marw.viper.variants.filters.StringFilter;
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.HashSet;
@@ -39,7 +40,7 @@
  */
 public class FilterTest {
 
-    private VariantTable loadData() {
+    private VariantTable loadData() throws IOException {
         CsvTableReader reader = new CsvTableReader(';', ",");
         VariantTable table = reader.readTable(TestUtil.getResourceFile("examples-filtering.csv"));
 
@@ -58,7 +59,7 @@ private void checkIDs(VariantTable table, String... expectedIdsAfterFiltering) {
     }
 
     @Test
-    public void numericFiltersWorkingCorrectly() {
+    public void numericFiltersWorkingCorrectly() throws IOException {
 
         VariantTable table = loadData();
 
@@ -79,7 +80,7 @@ public void numericFiltersWorkingCorrectly() {
     }
 
     @Test
-    public void numericCollectionFilterWorkingCorrectly() {
+    public void numericCollectionFilterWorkingCorrectly() throws IOException {
 
         VariantTable table = loadData();
 
@@ -100,7 +101,7 @@ public void numericCollectionFilterWorkingCorrectly() {
     }
 
     @Test
-    public void stringFilterWorkingCorrectly() {
+    public void stringFilterWorkingCorrectly() throws IOException {
 
         VariantTable table = loadData();
 
@@ -120,7 +121,7 @@ public void stringFilterWorkingCorrectly() {
     }
 
     @Test
-    public void stringCollectionFilterWorkingCorrectly() {
+    public void stringCollectionFilterWorkingCorrectly() throws IOException {
 
         VariantTable table = loadData();
 
@@ -144,7 +145,7 @@ public void stringCollectionFilterWorkingCorrectly() {
     }
 
     @Test
-    public void multipleFiltersWorkingCorrectly() {
+    public void multipleFiltersWorkingCorrectly() throws IOException {
 
         VariantTable table = loadData();
 

diff --git a/src/test/java/de/imi/marw/viper/test/variants/CallStringifierTest.java b/src/test/java/de/imi/marw/viper/test/variants/CallStringifierTest.java
@@ -22,6 +22,7 @@
 import de.imi.marw.viper.variants.table.CallStringifier;
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 import static org.junit.Assert.assertEquals;
@@ -34,7 +35,7 @@
 public class CallStringifierTest {
 
     @Test
-    public void callsAreCorrectlyTurnedIntoStrings() {
+    public void callsAreCorrectlyTurnedIntoStrings() throws IOException {
 
         CallStringifier callStringifier = new CallStringifier(",");
 

diff --git a/src/test/java/de/imi/marw/viper/test/variants/CsvTableReaderTest.java b/src/test/java/de/imi/marw/viper/test/variants/CsvTableReaderTest.java
@@ -22,6 +22,7 @@
 import de.imi.marw.viper.variants.VariantPropertyType;
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -46,7 +47,7 @@ private <T> Collection<T> coll(T... vals) {
     }
 
     @Test
-    public void correctlyReadsSmallExample() {
+    public void correctlyReadsSmallExample() throws IOException {
 
         CsvTableReader reader = new CsvTableReader(';', ",");
 
@@ -81,7 +82,7 @@ public void correctlyReadsSmallExample() {
     }
 
     @Test
-    public void correctlyReadsBiggerExample() {
+    public void correctlyReadsBiggerExample() throws IOException {
         CsvTableReader reader = new CsvTableReader(';', ",");
 
         VariantTable table = reader.readTable(TestUtil.getResourceFile("examples.csv"));
@@ -127,7 +128,7 @@ public void correctlyReadsBiggerExample() {
     }
 
     @Test
-    public void correctlyReadsEdgeCases() {
+    public void correctlyReadsEdgeCases() throws IOException {
         CsvTableReader reader = new CsvTableReader('\t', "_");
 
         VariantTable table = reader.readTable(TestUtil.getResourceFile("examples-edge-cases.csv"));
@@ -155,7 +156,7 @@ public void correctlyReadsEdgeCases() {
     }
 
     @Test
-    public void correctlyReadsEmptyTable() {
+    public void correctlyReadsEmptyTable() throws IOException {
 
         CsvTableReader reader = new CsvTableReader(';', ",");
 

diff --git a/src/test/java/de/imi/marw/viper/test/variants/ProgressManagerTest.java b/src/test/java/de/imi/marw/viper/test/variants/ProgressManagerTest.java
@@ -23,6 +23,7 @@
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.DecisionManager;
 import de.imi.marw.viper.variants.table.VariantTable;
+import java.io.IOException;
 import static org.junit.Assert.assertEquals;
 import org.junit.Test;
 
@@ -32,15 +33,15 @@
  */
 public class ProgressManagerTest {
 
-    private VariantTable loadData() {
+    private VariantTable loadData() throws IOException {
         VariantTable unclustered = new CsvTableReader(';', ",").readTable(TestUtil.getResourceFile("examples-unclustered.csv"));
         VariantTable clustered = new VariantClusterBuilder(5, false).clusterVariantTable(unclustered).getClusteredTable();
 
         return clustered;
     }
 
     @Test
-    public void progressIsProperlySavedAndLoaded() {
+    public void progressIsProperlySavedAndLoaded() throws IOException {
 
         VariantTable clustered1 = loadData();
         VariantTable clustered2 = loadData();

diff --git a/src/test/java/de/imi/marw/viper/test/variants/VariantTableClusterTest.java b/src/test/java/de/imi/marw/viper/test/variants/VariantTableClusterTest.java
@@ -23,6 +23,7 @@
 import de.imi.marw.viper.variants.VariantTableCluster;
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -42,7 +43,7 @@ private <T> Collection<T> coll(T... vals) {
     }
 
     @Test
-    public void variantsAreCorrectlyClustered() {
+    public void variantsAreCorrectlyClustered() throws IOException {
 
         CsvTableReader reader = new CsvTableReader(';', ",");
 

diff --git a/src/test/java/de/imi/marw/viper/test/variants/VcfTableReaderTest.java b/src/test/java/de/imi/marw/viper/test/variants/VcfTableReaderTest.java
@@ -23,6 +23,7 @@
 import de.imi.marw.viper.variants.table.CsvTableReader;
 import de.imi.marw.viper.variants.table.VariantTable;
 import de.imi.marw.viper.variants.table.VcfTableReader;
+import java.io.IOException;
 import java.util.List;
 import static org.junit.Assert.assertEquals;
 import org.junit.Test;
@@ -34,7 +35,7 @@
 public class VcfTableReaderTest {
 
     //TODO: check all combinations
-    private void checkVcfCorrectness(boolean simple, boolean excludeReferenceCalls, String targetVcf, String expectedFileName) {
+    private void checkVcfCorrectness(boolean simple, boolean excludeReferenceCalls, String targetVcf, String expectedFileName) throws IOException {
 
         CsvTableReader rd = new CsvTableReader(';', ",");
         CallStringifier strf = new CallStringifier(",");
@@ -54,28 +55,28 @@ private void checkVcfCorrectness(boolean simple, boolean excludeReferenceCalls,
     }
 
     @Test
-    public void allSimpleCallsCorrectlyLoaded() {
+    public void allSimpleCallsCorrectlyLoaded() throws IOException {
 
         checkVcfCorrectness(true, false, "examples.vcf", "vcf-import-simple-all.csv");
 
     }
 
     @Test
-    public void allNonRefCallsCorrectlyLoaded() {
+    public void allNonRefCallsCorrectlyLoaded() throws IOException {
 
         checkVcfCorrectness(true, true, "examples.vcf", "vcf-import-simple-nonref.csv");
 
     }
 
     @Test
-    public void allNonRefComplexCallsCorrectlyLoaded() {
+    public void allNonRefComplexCallsCorrectlyLoaded() throws IOException {
 
         checkVcfCorrectness(false, true, "examples.vcf", "vcf-import-complex-nonref.csv");
 
     }
 
     @Test
-    public void minimalVcfNonRefComplexCallsCorrectlyLoaded() {
+    public void minimalVcfNonRefComplexCallsCorrectlyLoaded() throws IOException {
 
         checkVcfCorrectness(false, false, "example-minimal.vcf", "vcf-import-minimal-complex-nonref.csv");