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ALS-4751: Clean up excepetion handling, per checkmarx #70

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merged 3 commits into from
Jul 18, 2023
Merged

ALS-4751: Clean up excepetion handling, per checkmarx #70

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a3e90ab
ALS-4751: Remove e.printStackTrace instances, per checkmarx
ramari16 Jul 11, 2023
7b7165f
ALS-4751: Clean up excepetion handling, per checkmarx
ramari16 Jul 12, 2023
befa929
ALS-4751: Clean up excepetion handling, per checkmarx
ramari16 Jul 12, 2023
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10 changes: 5 additions & 5 deletions data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java
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Expand Up @@ -100,7 +100,7 @@ public BucketIndexBySample(VariantStore variantStore, String storageDir) throws
}
});
} catch (IOException e) {
e.printStackTrace();
throw new UncheckedIOException(e);
}

// For each patient set the patientBucketCharMask entry to 0 or 1 if they have a variant in the bucket.
Expand Down Expand Up @@ -135,7 +135,7 @@ public void run() {
try {
Thread.sleep(5 * 1000 * 60); //log a message every 5 minutes
} catch (InterruptedException e) {
e.printStackTrace();
log.error("Thread interrupted", e);
}
log.info("wrote " + processedPatients[0] + " patient bucket masks");
}
Expand All @@ -149,7 +149,7 @@ public void run() {
}catch(NumberFormatException e) {
log.error("NFE caught for " + patientId, e);
} catch (IOException e) {
e.printStackTrace();
throw new UncheckedIOException(e);
}
processedPatients[0] += 1;
});
Expand Down Expand Up @@ -178,9 +178,9 @@ public Collection<String> filterVariantSetForPatientSet(Set<String> variantSet,
try {
return patientBucketMasks.get(patientNum);
} catch (IOException e) {
e.printStackTrace();
throw new UncheckedIOException(e);
}
return _defaultMask;
//return _defaultMask;
}).collect(Collectors.toList());
for(BigInteger patientMask : patientBucketmasksForSet) {
patientBucketMask = patientMask.or(patientBucketMask);
Expand Down
20 changes: 8 additions & 12 deletions data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/CompressedIndex.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand All @@ -22,13 +18,16 @@
import com.google.common.collect.Range;

import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

public class CompressedIndex implements Serializable {

/**
*
*/
private static final long serialVersionUID = 5089713203903957829L;
private static final Logger log = LoggerFactory.getLogger(CompressedIndex.class);
public Float min = Float.MAX_VALUE, max = Float.MIN_VALUE;
private HashMap<Range<Float>, byte[]> compressedRangeMap;
private int valueCount;
Expand Down Expand Up @@ -61,7 +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());
}
}
}
Expand Down Expand Up @@ -114,8 +113,7 @@ public void buildIndex(TreeMap<Float, TreeSet<String>> continuousValueMap) {
gzos.close();
compressed = baos.toByteArray();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
throw new UncheckedIOException(e);
}
return compressed;
})
Expand Down Expand Up @@ -174,11 +172,9 @@ private TreeMap<Double, TreeSet<String>> retrieveRangeMap(Range<Double> range) {
){
continousValueMap = (TreeMap<Double, TreeSet<String>>)ois.readObject();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
throw new UncheckedIOException(e);
} catch (ClassNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
throw new RuntimeException(e);
}
return continousValueMap;
}
Expand Down
25 changes: 2 additions & 23 deletions data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantStore.java
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Expand Up @@ -58,25 +58,6 @@ public static VariantStore deserializeInstance(String genomicDataDirectory) thro
}
}

public ArrayList<String> listVariants() {
ArrayList<String> allVariants = new ArrayList<>();
for (String key : variantMaskStorage.keySet()) {
FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, VariantMasks>> storage = variantMaskStorage
.get(key);
storage.keys().stream().forEach((Integer bucket) -> {
try {
for (String variant : storage.get(bucket).keySet()) {
allVariants.add(variant);
}
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
});
}
return allVariants;
}

public Map<String, int[]> countVariants() {
HashMap<String, Integer> countOffsetMap = new HashMap<String, Integer>();
TreeMap<String, int[]> counts = new TreeMap<>();
Expand Down Expand Up @@ -105,8 +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);
}
});
}
Expand Down Expand Up @@ -156,8 +136,7 @@ public void open() {
try {
fbbis.open();
} catch (FileNotFoundException e) {
// TODO Auto-generated catch block
e.printStackTrace();
throw new UncheckedIOException(e);
}
}
}));
Expand Down
44 changes: 15 additions & 29 deletions ...va/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/util/HideAnnotationCategoryValue.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand All @@ -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();
}

}
15 changes: 4 additions & 11 deletions etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/DumpSourceCSV.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand Down Expand Up @@ -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();
Expand All @@ -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");
}
}
Expand Down
5 changes: 2 additions & 3 deletions ...n/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/FixCategoricalConcepts.java
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Expand Up @@ -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);
}
}

Expand Down Expand Up @@ -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("************************************************");
Expand Down
3 changes: 1 addition & 2 deletions etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RekeyDataset.java
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Expand Up @@ -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("************************************************");
Expand Down
5 changes: 2 additions & 3 deletions etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemapIds.java
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Expand Up @@ -124,7 +124,7 @@ private static void processRecord(final PhenoCube[] currentConcept, List<String>
store.allIds.add(patientId);
}
} catch (ExecutionException e) {
e.printStackTrace();
log.error("Error processing record", e);
}
}

Expand Down Expand Up @@ -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("************************************************");
Expand Down
1 change: 0 additions & 1 deletion ...ava/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RemoveConceptFromMetadata.java
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Expand Up @@ -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");
}
}
Expand Down
4 changes: 1 addition & 3 deletions ...rc/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/phenotype/util/RenameCategories.java
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Expand Up @@ -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);
}
});
}
Expand All @@ -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");
}
}
Expand Down
8 changes: 2 additions & 6 deletions etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand Down Expand Up @@ -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);
});
Expand Down
8 changes: 2 additions & 6 deletions etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java
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Original file line number Diff line number Diff line change
@@ -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;
Expand Down Expand Up @@ -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]);
Expand Down
3 changes: 2 additions & 1 deletion etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/phenotype/CSVLoader.java
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Expand Up @@ -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);
}
}
}
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