/*
* Licensed under the Apache License, Version 2.0 (the "License");
*
* You may not use this file except in compliance with the License.
*
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
*
* See the License for the specific language governing permissions and
* limitations under the License.
*
* Contributions from 2013-2017 where performed either by US government
* employees, or under US Veterans Health Administration contracts.
*
* US Veterans Health Administration contributions by government employees
* are work of the U.S. Government and are not subject to copyright
* protection in the United States. Portions contributed by government
* employees are USGovWork (17USC ยง105). Not subject to copyright.
*
* Contribution by contractors to the US Veterans Health Administration
* during this period are contractually contributed under the
* Apache License, Version 2.0.
*
* See: https://www.usa.gov/government-works
*
* Contributions prior to 2013:
*
* Copyright (C) International Health Terminology Standards Development Organisation.
* Licensed under the Apache License, Version 2.0.
*
*/
package sh.isaac.provider.identifier;
//~--- JDK imports ------------------------------------------------------------
import java.io.BufferedInputStream;
import java.io.BufferedOutputStream;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.Arrays;
import java.util.OptionalInt;
import java.util.concurrent.CopyOnWriteArrayList;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.locks.ReentrantLock;
import java.util.stream.IntStream;
//~--- non-JDK imports --------------------------------------------------------
import sh.isaac.api.collections.ConceptSequenceSet;
import sh.isaac.api.collections.NidSet;
//~--- classes ----------------------------------------------------------------
/**
* Created by kec on 12/18/14.
*/
public class ConcurrentSequenceIntMap {
/** The Constant SEGMENT_SIZE. */
private static final int SEGMENT_SIZE = 128000;
//~--- fields --------------------------------------------------------------
/** The lock. */
ReentrantLock lock = new ReentrantLock();
/** The sequence int list. */
CopyOnWriteArrayList<int[]> sequenceIntList = new CopyOnWriteArrayList<>();
/** The size. */
AtomicInteger size = new AtomicInteger(0);
//~--- constructors --------------------------------------------------------
/**
* Instantiates a new concurrent sequence int map.
*/
public ConcurrentSequenceIntMap() {
final int[] segmentArray = new int[SEGMENT_SIZE];
Arrays.fill(segmentArray, -1);
this.sequenceIntList.add(segmentArray);
}
//~--- methods -------------------------------------------------------------
/**
* Contains key.
*
* @param sequence the sequence
* @return true, if successful
*/
public boolean containsKey(int sequence) {
if (sequence < 0) {
sequence = sequence - Integer.MIN_VALUE;
}
final int segmentIndex = sequence / SEGMENT_SIZE;
final int indexInSegment = sequence % SEGMENT_SIZE;
if (segmentIndex >= this.sequenceIntList.size()) {
return false;
}
return this.sequenceIntList.get(segmentIndex)[indexInSegment] != 0;
}
/**
* Put.
*
* @param sequence the sequence
* @param value the value
* @return true, if successful
*/
public boolean put(int sequence, int value) {
if (sequence < 0) {
sequence = sequence - Integer.MIN_VALUE;
}
this.size.set(Math.max(sequence, this.size.get()));
final int segmentIndex = sequence / SEGMENT_SIZE;
if (segmentIndex >= this.sequenceIntList.size()) {
this.lock.lock();
try {
while (segmentIndex >= this.sequenceIntList.size()) {
final int[] segmentArray = new int[SEGMENT_SIZE];
Arrays.fill(segmentArray, -1);
this.sequenceIntList.add(segmentArray);
}
} finally {
this.lock.unlock();
}
}
final int indexInSegment = sequence % SEGMENT_SIZE;
this.sequenceIntList.get(segmentIndex)[indexInSegment] = value;
return true;
}
/**
* Read.
*
* @param folder the folder
* @throws IOException Signals that an I/O exception has occurred.
*/
public void read(File folder)
throws IOException {
this.sequenceIntList = null;
int segments = 1;
for (int segment = 0; segment < segments; segment++) {
try (DataInputStream in = new DataInputStream(new BufferedInputStream(new FileInputStream(new File(folder,
segment +
".sequence-int.map"))))) {
final int segmentSize = in.readInt();
segments = in.readInt();
if (this.sequenceIntList == null) {
this.sequenceIntList = new CopyOnWriteArrayList<>();
}
final int[] segmentArray = new int[segmentSize];
Arrays.fill(segmentArray, -1);
this.sequenceIntList.add(segmentArray);
for (int indexInSegment = 0; indexInSegment < segmentSize; indexInSegment++) {
this.sequenceIntList.get(segment)[indexInSegment] = in.readInt();
}
this.size.set(in.readInt());
}
}
}
/**
* Write.
*
* @param folder the folder
* @throws IOException Signals that an I/O exception has occurred.
*/
public void write(File folder)
throws IOException {
folder.mkdirs();
final int segments = this.sequenceIntList.size();
for (int segment = 0; segment < segments; segment++) {
try (DataOutputStream out = new DataOutputStream(new BufferedOutputStream(new FileOutputStream(new File(folder,
segment +
".sequence-int.map"))))) {
out.writeInt(SEGMENT_SIZE);
out.writeInt(segments);
final int[] segmentArray = this.sequenceIntList.get(segment);
for (int indexInSegment = 0; indexInSegment < SEGMENT_SIZE; indexInSegment++) {
out.writeInt(segmentArray[indexInSegment]);
}
out.writeInt(this.size.get());
}
}
}
//~--- get methods ---------------------------------------------------------
/**
* Gets the component nid stream.
*
* @return the component nid stream
*/
public IntStream getComponentNidStream() {
final int componentSize = this.size.get();
return IntStream.of(Integer.MIN_VALUE, componentSize + Integer.MIN_VALUE)
.filter((nid) -> {
final int i = nid - Integer.MIN_VALUE;
final int segmentIndex = i / SEGMENT_SIZE;
final int indexInSegment = i % SEGMENT_SIZE;
return this.sequenceIntList.get(segmentIndex)[indexInSegment] != 0;
});
}
/**
* Gets the component nids for concept nids.
*
* @param conceptSequenceSet the concept sequence set
* @return the component nids for concept nids
*/
public NidSet getComponentNidsForConceptNids(ConceptSequenceSet conceptSequenceSet) {
final NidSet conceptNids = NidSet.of(conceptSequenceSet);
final NidSet results = new NidSet();
final int componentSize = this.size.get();
for (int i = 0; i < componentSize; i++) {
final int segmentIndex = i / SEGMENT_SIZE;
final int indexInSegment = i % SEGMENT_SIZE;
if (this.sequenceIntList.get(segmentIndex)[indexInSegment] != 0) {
if (conceptNids.contains(this.sequenceIntList.get(segmentIndex)[indexInSegment])) {
results.add(i + Integer.MIN_VALUE);
}
}
}
return results;
}
/**
* Gets the components not set.
*
* @return the components not set
*/
public IntStream getComponentsNotSet() {
final int componentSize = this.size.get();
return IntStream.of(Integer.MIN_VALUE, componentSize + Integer.MIN_VALUE)
.filter((nid) -> {
final int i = nid - Integer.MIN_VALUE;
final int segmentIndex = i / SEGMENT_SIZE;
final int indexInSegment = i % SEGMENT_SIZE;
return this.sequenceIntList.get(segmentIndex)[indexInSegment] == 0;
});
}
/**
* Gets the.
*
* @param sequence the sequence
* @return the optional int
*/
public OptionalInt get(int sequence) {
if (sequence < 0) {
sequence = sequence - Integer.MIN_VALUE;
}
final int segmentIndex = sequence / SEGMENT_SIZE;
if (segmentIndex >= this.sequenceIntList.size()) {
return OptionalInt.empty();
}
final int indexInSegment = sequence % SEGMENT_SIZE;
final int returnValue = this.sequenceIntList.get(segmentIndex)[indexInSegment];
if (returnValue == -1) {
return OptionalInt.empty();
}
return OptionalInt.of(returnValue);
}
/**
* Gets the size.
*
* @return the size
*/
public int getSize() {
return this.size.get();
}
}