ALS-4751: Clean up excepetion handling, per checkmarx

hms-dbmi · Jul 12, 2023 · 7b7165f · 7b7165f
1 parent a3e90ab
commit 7b7165f
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Showing 22 changed files with 115 additions and 183 deletions.
diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java
@@ -100,7 +100,7 @@ public BucketIndexBySample(VariantStore variantStore, String storageDir) throws
 									}
 								});
 							} catch (IOException e) {
-								log.error("Error getting bucket", e);
+								throw new UncheckedIOException(e);
 							}
 
 							// For each patient set the patientBucketCharMask entry to 0 or 1 if they have a variant in the bucket.
@@ -149,7 +149,7 @@ public void run() {
 			}catch(NumberFormatException e) {
 				log.error("NFE caught for " + patientId, e);
 			} catch (IOException e) {
-				log.error("Error writing patient bucket masks", e);
+				throw new UncheckedIOException(e);
 			}
 			processedPatients[0] += 1;
 		});
@@ -178,9 +178,9 @@ public Collection<String> filterVariantSetForPatientSet(Set<String> variantSet,
 			try {
 				return patientBucketMasks.get(patientNum);
 			} catch (IOException e) {
-				log.error("Error getting mask for patient", e);
+				throw new UncheckedIOException(e);
 			}
-			return _defaultMask;
+			//return _defaultMask;
 		}).collect(Collectors.toList());
 		for(BigInteger patientMask : patientBucketmasksForSet) {
 			patientBucketMask = patientMask.or(patientBucketMask);

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java
@@ -1,10 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
-import java.io.Serializable;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -64,7 +60,7 @@ public TreeMap<Float, TreeSet<String>> buildContinuousValuesMap(FileBackedByteIn
 							continuousValueMap.put(DoubleValue, currentValues);
 							setMinAndMax(DoubleValue);
 						}catch(NumberFormatException e3) {
-							System.out.println("Unable to parse value : " + value.trim());
+							log.info("Unable to parse value : " + value.trim());
 						}
 					}
 				}
@@ -117,7 +113,7 @@ public void buildIndex(TreeMap<Float, TreeSet<String>> continuousValueMap) {
 								gzos.close();
 								compressed = baos.toByteArray();
 							} catch (IOException e) {
-								log.error("Error writing range map", e);
+								throw new UncheckedIOException(e);
 							}
 							return compressed;
 						})
@@ -176,9 +172,9 @@ private TreeMap<Double, TreeSet<String>> retrieveRangeMap(Range<Double> range) {
 				){
 			continousValueMap = (TreeMap<Double, TreeSet<String>>)ois.readObject();
 		} catch (IOException e) {
-			log.error("Error reading range map from file", e);
+			throw new UncheckedIOException(e);
 		} catch (ClassNotFoundException e) {
-			log.error("Error deserializing range map", e);
+			throw new RuntimeException(e);
 		}
 		return continousValueMap;
 	}

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
@@ -86,8 +86,7 @@ public Map<String, int[]> countVariants() {
 								|| masks.heterozygousNoCallMask != null || masks.homozygousNoCallMask != null ? 1 : 0;
 					}));
 				} catch (IOException e) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
+					throw new UncheckedIOException(e);
 				}
 			});
 		}
@@ -137,8 +136,7 @@ public void open() {
 				try {
 					fbbis.open();
 				} catch (FileNotFoundException e) {
-					// TODO Auto-generated catch block
-					e.printStackTrace();
+					throw new UncheckedIOException(e);
 				}
 			}
 		}));

diff --git a/...va/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java b/...va/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java
@@ -1,7 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype.util;
 
 import java.io.FileInputStream;
-import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.ObjectInputStream;
@@ -20,40 +19,27 @@
 public class HideAnnotationCategoryValue {
 	protected static LoadingCache<String, PhenoCube<?>> store;
 
-	protected static TreeMap<String, ColumnMeta> metaStoreSource;
-
 	protected static TreeSet<Integer> allIds;
 
-	public static void main(String[] args) throws ClassNotFoundException, FileNotFoundException, IOException {
+	public static void main(String[] args) throws ClassNotFoundException, IOException {
 		String infoStoreToModify = args[0];
 		String valueToScrub = args[1];
 
 		String infoStoreFilename = "/opt/local/hpds/all/" + infoStoreToModify.trim();
-		try (
-				FileInputStream fis = new FileInputStream(infoStoreFilename);
-				GZIPInputStream gis = new GZIPInputStream(fis);
-				ObjectInputStream ois = new ObjectInputStream(gis)
-				){
-			FileBackedByteIndexedInfoStore infoStore = (FileBackedByteIndexedInfoStore) ois.readObject();
-			infoStore.getAllValues().keys().remove(valueToScrub);
-			try(
-					FileOutputStream fos = new FileOutputStream(infoStoreFilename);
-					GZIPOutputStream gos = new GZIPOutputStream(fos);
-					ObjectOutputStream oos = new ObjectOutputStream(gos);
-					){
-				oos.writeObject(infoStore);
-				oos.flush();oos.close();
-			}
-		} catch (FileNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (IOException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		} catch (ClassNotFoundException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
-		}
+
+		FileInputStream fis = new FileInputStream(infoStoreFilename);
+		GZIPInputStream gis = new GZIPInputStream(fis);
+		ObjectInputStream ois = new ObjectInputStream(gis);
+
+		FileBackedByteIndexedInfoStore infoStore = (FileBackedByteIndexedInfoStore) ois.readObject();
+		infoStore.getAllValues().keys().remove(valueToScrub);
+
+		FileOutputStream fos = new FileOutputStream(infoStoreFilename);
+		GZIPOutputStream gos = new GZIPOutputStream(fos);
+		ObjectOutputStream oos = new ObjectOutputStream(gos);
+
+		oos.writeObject(infoStore);
+		oos.flush();oos.close();
 	}
 
 }
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java
@@ -1,12 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.util;
 
-import java.io.ByteArrayInputStream;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.RandomAccessFile;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.Set;
 import java.util.TreeMap;
@@ -68,10 +62,10 @@ public static void main(String[] args) throws ClassNotFoundException, FileNotFou
 					cubeLines.add(line);
 				}
 				writer.printRecords(cubeLines);
-			}catch(ExecutionException e) {
-				e.printStackTrace();
+			} catch(ExecutionException e) {
+				throw new RuntimeException(e);
 			} catch (IOException e) {
-				e.printStackTrace();
+				throw new UncheckedIOException(e);
 			}
 		});
 		writer.flush();
@@ -90,7 +84,6 @@ protected static Object[] loadMetadata() {
 			Set<Integer> allIds = (TreeSet<Integer>) objectInputStream.readObject();
 			return new Object[] {metastoreScrubbed, allIds};
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			throw new RuntimeException("Could not load metastore");
 		} 
 	}

diff --git a/...n/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java b/...n/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java
@@ -125,7 +125,7 @@ private static void processRecord(final PhenoCube[] currentConcept, List<String>
 				store.allIds.add(Integer.parseInt(record.get(PATIENT_NUM)));
 			}
 		} catch (ExecutionException e) {
-			e.printStackTrace();
+			log.error("Error processing record", e);
 		}
 	}
 
@@ -174,10 +174,9 @@ protected static Object[] loadMetadata() {
 			Set<Integer> allIds = (TreeSet<Integer>) objectInputStream.readObject();
 			return new Object[] {metastoreScrubbed, allIds};
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			log.warn("************************************************");
 			log.warn("************************************************");
-			log.warn("Could not load metastore");
+			log.warn("Could not load metastore", e);
 			log.warn("If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service.");
 			log.warn("************************************************");
 			log.warn("************************************************");

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java
@@ -100,10 +100,9 @@ protected static Object[] loadMetadata() {
 			Set<Integer> allIds = (TreeSet<Integer>) objectInputStream.readObject();
 			return new Object[] {metastoreScrubbed, allIds};
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			log.warn("************************************************");
 			log.warn("************************************************");
-			log.warn("Could not load metastore");
+			log.warn("Could not load metastore", e);
 			log.warn("If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service.");
 			log.warn("************************************************");
 			log.warn("************************************************");

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java
@@ -177,10 +177,9 @@ protected static Object[] loadMetadata() {
 			Set<Integer> allIds = (TreeSet<Integer>) objectInputStream.readObject();
 			return new Object[] {metastoreScrubbed, allIds};
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			log.warn("************************************************");
 			log.warn("************************************************");
-			log.warn("Could not load metastore");
+			log.warn("Could not load metastore", e);
 			log.warn("If you meant to include phenotype data of any kind, please check that the file /opt/local/source/columnMeta.javabin exists and is readable by the service.");
 			log.warn("************************************************");
 			log.warn("************************************************");

diff --git a/...ava/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java b/...ava/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java
@@ -78,7 +78,6 @@ protected static TreeMap<String, ColumnMeta> removeMetadata(Path filePath) {
 
 			return metastore;
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			throw new RuntimeException("Could not load metastore");
 		} 
 	}

diff --git a/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java b/...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java
@@ -49,8 +49,7 @@ public static void main(String[] args) throws ClassNotFoundException, FileNotFou
 			try {
 				loadingStoreTarget.store.put(key, store.get(key));
 			} catch (ExecutionException e) {
-				// TODO Auto-generated catch block
-				e.printStackTrace();
+				throw new RuntimeException(e);
 			}
 		});
 	}
@@ -67,7 +66,6 @@ protected static Object[] loadMetadata() {
 			Set<Integer> allIds = (TreeSet<Integer>) objectInputStream.readObject();
 			return new Object[] {metastoreScrubbed, allIds};
 		} catch (IOException | ClassNotFoundException e) {
-			e.printStackTrace();
 			throw new RuntimeException("Could not load metastore");
 		} 
 	}

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java
@@ -1,9 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype;
 
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.ObjectInputStream;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.TreeSet;
 import java.util.concurrent.ConcurrentHashMap;
@@ -46,8 +43,7 @@ public static void main(String[] args) throws ClassNotFoundException, FileNotFou
 							}
 						}
 					} catch (IOException e) {
-						// TODO Auto-generated catch block
-						e.printStackTrace();
+						throw new UncheckedIOException(e);
 					}
 					System.out.println("Completed bucket : " + offsetBucket);
 				});

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java
@@ -1,9 +1,6 @@
 package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype;
 
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.ObjectInputStream;
+import java.io.*;
 import java.util.ArrayList;
 import java.util.TreeSet;
 import java.util.concurrent.ConcurrentHashMap;
@@ -34,8 +31,7 @@ public static void main(String[] args) throws ClassNotFoundException, FileNotFou
 						}
 
 					} catch (IOException e) {
-						// TODO Auto-generated catch block
-						e.printStackTrace();
+						throw new UncheckedIOException(e);
 					}
 				});
 				System.out.println(contig + "," + countOfVariants[0]);

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/CSVLoader.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/CSVLoader.java
@@ -106,7 +106,8 @@ private static void processRecord(final PhenoCube[] currentConcept, CSVRecord re
 				store.allIds.add(patientId);
 			}
 		} catch (ExecutionException e) {
-			e.printStackTrace();
+			// todo: do we really want to ignore this?
+			log.error("Error processing record", e);
 		}
 	}
 }
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/LoadingStore.java
@@ -54,20 +54,17 @@ public void onRemoval(RemovalNotification<String, PhenoCube> arg0) {
 							columnMeta.setMax(max);
 						}
 						ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
-						try {
-
-							ObjectOutputStream out = new ObjectOutputStream(byteStream);
-							out.writeObject(arg0.getValue());
-							out.flush();
-							out.close();
-						} catch (IOException e) {
-							e.printStackTrace();
-						}
+
+						ObjectOutputStream out = new ObjectOutputStream(byteStream);
+						out.writeObject(arg0.getValue());
+						out.flush();
+						out.close();
+
 						allObservationsStore.write(Crypto.encryptData(byteStream.toByteArray()));
 						columnMeta.setAllObservationsLength(allObservationsStore.getFilePointer());
 						metadataMap.put(columnMeta.getName(), columnMeta);
-					} catch (IOException e1) {
-						e1.printStackTrace();
+					} catch (IOException e) {
+						throw new UncheckedIOException(e);
 					}
 				}
 

diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SQLLoader.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/SQLLoader.java
@@ -20,12 +20,16 @@
 import edu.harvard.hms.dbmi.avillach.hpds.data.phenotype.PhenoCube;
 
 import org.apache.commons.io.IOUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.jdbc.core.JdbcTemplate;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.jdbc.datasource.DriverManagerDataSource;
 
 public class SQLLoader {
 
+	private static final Logger log = LoggerFactory.getLogger(SQLLoader.class);
+
 	private static final SimpleDateFormat ORACLE_DATE_FORMAT = new SimpleDateFormat("dd-MMM-yy");
 
 	static JdbcTemplate template;
@@ -157,8 +161,7 @@ public void processRow(ResultSet arg0) throws SQLException {
 		try {
 			Thread.sleep(5000);
 		} catch (InterruptedException e) {
-			// TODO Auto-generated catch block
-			e.printStackTrace();
+			log.error("Thread interrupted", e);
 		}
 //		stillProcessingRecords[0] = false;
 //		chunkWriteEx.shutdown();
@@ -223,11 +226,9 @@ private static void processRecord(final PhenoCube[] currentConcept, ResultSet ar
 				currentConcept[0].add(patientId, isAlpha ? value : Double.parseDouble(value), arg0.getDate(DATETIME));
 				store.allIds.add(patientId);
 			}
-		} catch (ExecutionException e) {
-			e.printStackTrace();
-		} catch (SQLException e2) {
-			// TODO Auto-generated catch block
-			e2.printStackTrace();
+		} catch (ExecutionException | SQLException e) {
+			// todo: do we really want to ignore these?
+			log.error("Exception processing record", e);
 		}
 	}
 }