eu.fbk.knowledgestore.tool.TestGenerator Maven / Gradle / Ivy
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A collection of command line tools for interacting with a KnowledgeStore server,
including benchmarking tools to create and perform a performance test of KS
retrieval methods as well as a tool for dumping the contents of a KS instance
to RDF files.
package eu.fbk.knowledgestore.tool;
import java.io.BufferedReader;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.Writer;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Random;
import java.util.Set;
import java.util.concurrent.atomic.AtomicReference;
import javax.annotation.Nullable;
import com.google.common.base.Charsets;
import com.google.common.base.Joiner;
import com.google.common.base.Preconditions;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import org.openrdf.query.BindingSet;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.fbk.knowledgestore.OperationException;
import eu.fbk.knowledgestore.Session;
import eu.fbk.knowledgestore.client.Client;
import eu.fbk.knowledgestore.data.Handler;
import eu.fbk.knowledgestore.data.Stream;
import eu.fbk.knowledgestore.internal.CommandLine;
import eu.fbk.knowledgestore.internal.Util;
import eu.fbk.rdfpro.util.IO;
import eu.fbk.rdfpro.util.Tracker;
public final class TestGenerator {
private static final Logger LOGGER = LoggerFactory.getLogger(TestGenerator.class);
private static final Random RANDOM = new Random(System.currentTimeMillis());
private final Dictionary dictionary;
private final String url;
private final String username;
private final String password;
private final int mixes;
private final File outputFile;
private final Query[] queries;
public static void main(final String[] args) {
try {
final CommandLine cmd = CommandLine
.parser()
.withName("ks-test-generator")
.withHeader(
"Generates the request mixes for the test, by querying the "
+ "KnowledgeStore. Generator parameters and queries are "
+ "supplied in a .properties file. Output data is written "
+ "to a .tsv file.")
.withOption("c", "config", "the configuration file", "FILE",
CommandLine.Type.FILE_EXISTING, true, false, true)
.withFooter(
"Configuration parameters may be overridden by supplying additional "
+ "property=value\narguments on the command line.")
.withLogger(LoggerFactory.getLogger("eu.fbk.knowledgestore")).parse(args);
final File configFile = cmd.getOptionValue("c", File.class);
final Properties config = new Properties();
try (InputStream configStream = IO.read(configFile.getAbsolutePath())) {
config.load(configStream);
}
for (final String arg : cmd.getArgs(String.class)) {
final int index = arg.indexOf('=');
if (index > 0) {
final String name = arg.substring(0, index);
final String value = arg.substring(index + 1);
config.setProperty(name, value);
}
}
new TestGenerator(config, configFile.getParentFile()).run();
} catch (final Throwable ex) {
CommandLine.fail(ex);
}
}
public TestGenerator(final Properties properties, @Nullable final File basePath) {
// Create a global dictionary for mapping values to codes and back
this.dictionary = new Dictionary();
// Get base path
final Path base = (basePath != null ? basePath : new File(System.getProperty("user.dir")))
.toPath();
// Parse server URL, username and password
this.url = TestUtil.read(properties, "test.url", String.class);
this.username = TestUtil.read(properties, "test.username", String.class, null);
this.password = TestUtil.read(properties, "test.password", String.class, null);
LOGGER.info("SUT: {}{}", this.url,
this.username == null && this.password == null ? " (anonymous access)"
: " (authenticated access)");
// Parse number of mixes to generate and output file
this.mixes = TestUtil.read(properties, "test.mixes", Integer.class, 0);
this.outputFile = base.resolve(
Paths.get(TestUtil.read(properties, "test.out", String.class))).toFile();
LOGGER.info("{} mix(es) to be written to {}", this.mixes,
this.outputFile.getAbsolutePath());
// Parse queries
final List allQueries = Query.create(properties, basePath);
final List enabledQueries = Lists.newArrayList();
final Set enabledNames = Sets.newLinkedHashSet(Arrays.asList(TestUtil.read(
properties, "test.queries", String.class).split("\\s*[,]\\s*")));
for (final String name : enabledNames) {
boolean added = false;
for (final Query query : allQueries) {
if (query.name.equals(name)) {
enabledQueries.add(query);
added = true;
break;
}
}
Preconditions.checkArgument(added, "Unknown query " + name);
}
this.queries = enabledQueries.toArray(new Query[enabledQueries.size()]);
LOGGER.info("{} queries enabled ({} defined): {}", enabledQueries.size(),
allQueries.size(), Joiner.on(", ").join(enabledQueries));
}
@SuppressWarnings("resource")
public void run() throws IOException, OperationException {
Client client = null;
Session session = null;
try {
// Obtain a session
client = Client.builder(this.url).compressionEnabled(true).validateServer(false)
.build();
session = client.newSession(this.username, this.password);
// Read schema and tuples from input files
final List> fileVars = Lists.newArrayList();
final List> fileTuples = Lists.newArrayList();
for (int i = 0; i < this.queries.length; ++i) {
final List vars = Lists.newArrayList();
final List tuples = Lists.newArrayList();
final File file = this.queries[i].download(session);
read(file, vars, tuples, this.dictionary);
fileVars.add(vars);
fileTuples.add(tuples);
}
// Compute output schema and mappings from file to output schema
final int[][] fileMappings = new int[this.queries.length][]; // m_ij -> var j file i
final List outputVars = Lists.newArrayList();
for (int i = 0; i < fileVars.size(); ++i) {
boolean insidePrefix = true;
fileMappings[i] = new int[fileVars.get(i).size()];
for (int j = 0; j < fileMappings[i].length; ++j) {
final String var = fileVars.get(i).get(j);
int index = outputVars.indexOf(var);
if (index < 0) {
insidePrefix = false;
index = outputVars.size();
outputVars.add(var);
} else if (!insidePrefix) {
throw new IllegalArgumentException("Variable " + var + " of query "
+ this.queries[i] + " matches var in previous files "
+ "but is preceded by newly intruduced variable ");
}
fileMappings[i][j] = index;
}
}
LOGGER.info("Output schema: ({})", Joiner.on(", ").join(outputVars));
// Use a tracker to display the progress of the operation
final Tracker tracker = new Tracker(LOGGER, null, //
"Generated %d tuples (%d tuple/s avg)", //
"Generated %d tuples (%d tuple/s, %d tuple/s avg)");
tracker.start();
// Generate a set of (unique) joined tuples, of the size specified
int numFailures = 0;
int numDuplicates = 0;
final Set outputTuples = Sets.newLinkedHashSet();
final int[] outputCodes = new int[outputVars.size()];
outer: while (outputTuples.size() < this.mixes) {
Arrays.fill(outputCodes, 0);
for (int i = 0; i < fileTuples.size(); ++i) {
if (!pick(fileTuples.get(i), fileMappings[i], outputCodes)) {
++numFailures;
continue outer;
}
}
if (outputTuples.add(Tuple.create(outputCodes))) {
tracker.increment();
} else {
++numDuplicates;
}
}
// Signal completion
tracker.end();
// Log number of failures and number of duplicate tuples during generation
LOGGER.info("Tuple generation statistics: {} attempts failed, {} duplicates",
numFailures, numDuplicates);
// Write resulting tuples
write(this.outputFile, outputVars, outputTuples, this.dictionary);
} finally {
// Release session
Util.closeQuietly(session);
Util.closeQuietly(client);
}
}
private static boolean pick(final List tuples, final int[] mappings,
final int[] outputCodes) {
final int numVariables = mappings.length;
final int numTuples = tuples.size();
// The a-priori range where to pick the tuple is the full tuples list
int start = 0;
int end = tuples.size();
// Check if range can be constrained based on codes previously assigned (i.e., join)
boolean constrained = false;
final int[] searchCodes = new int[numVariables];
for (int i = 0; i < numVariables; ++i) {
final int code = outputCodes[mappings[i]];
if (code != 0) {
searchCodes[i] = code;
constrained = true;
}
}
// If range can be constrained, build a 'search' tuple whose first codes are given by
// variables previously assigned, and remaining variables are zero; then do binary search
// followed by a scan for matching tuples to determine the range
if (constrained) {
final Tuple searchTuple = Tuple.create(searchCodes);
start = Collections.binarySearch(tuples, searchTuple);
if (start < 0) {
start = -start - 1; // in case exact match not found
}
if (start >= numTuples || !tuples.get(start).matches(searchTuple)) {
return false; // if range is empty or cannot join
}
end = start + 1;
while (end < numTuples && tuples.get(end).matches(searchTuple)) {
++end;
}
}
// Pick a random index inside the allowed range and use that tuple to augment output
final int chosenIndex = start + RANDOM.nextInt(end - start);
final Tuple chosenTuple = tuples.get(chosenIndex);
for (int i = 0; i < numVariables; ++i) {
final int slot = mappings[i];
final int oldValue = outputCodes[slot];
final int newValue = chosenTuple.get(i);
if (oldValue != 0 && newValue != oldValue) {
throw new Error("Join error: " + chosenTuple + " - "
+ Arrays.toString(outputCodes) + " (search: "
+ Arrays.toString(searchCodes) + "; start " + start + "; end " + end + ")");
}
outputCodes[mappings[i]] = chosenTuple.get(i);
}
// Return true upon success
return true;
}
private static void read(final File file, final List vars, final List tuples,
final Dictionary dictionary) throws IOException {
// Read the file specified, populating the supplied vars and tuples list
try (final BufferedReader reader = new BufferedReader(IO.utf8Reader(IO.buffer(IO.read(file
.getAbsolutePath()))))) {
// Read variables
for (final String token : reader.readLine().split("\t")) {
vars.add(token.trim().substring(1));
}
// Use a tracker to show the progress of the operation
final Tracker tracker = new Tracker(LOGGER, null, //
"Parsed " + file.getAbsolutePath() + " (" + Joiner.on(", ").join(vars)
+ "): %d tuples (%d tuple/s avg)", //
"Parsed %d tuples (%d tuple/s, %d tuple/s avg)");
tracker.start();
// Read data tuples, mapping values to codes using the dictionary
int lineNum = 0;
String line;
final int[] codes = new int[vars.size()];
while ((line = reader.readLine()) != null) {
try {
++lineNum;
final String[] tokens = line.split("\t");
for (int j = 0; j < codes.length; ++j) {
codes[j] = dictionary.codeFor(tokens[j]);
}
tuples.add(Tuple.create(codes));
tracker.increment();
} catch (final Throwable ex) {
LOGGER.warn("Ignoring invalid line " + lineNum + " of file " + file + " - "
+ ex.getMessage() + " [" + line + "]");
}
}
// Signal completion
tracker.end();
// Sort read tuples
Collections.sort(tuples);
}
}
private static void write(final File file, final List vars,
final Collection tuples, final Dictionary dictionary) throws IOException {
// Use a tracker to show the progress of the operation
final Tracker tracker = new Tracker(LOGGER, null, //
"Written " + file.getAbsolutePath() + " (" + Joiner.on(", ").join(vars)
+ "): %d tuples (%d tuple/s avg)", //
"Written %d tuples (%d tuple/s, %d tuple/s avg)");
tracker.start();
// Write to the file specified one line at a time
final int numVars = vars.size();
try (Writer writer = IO.utf8Writer(IO.buffer(IO.write(file.getAbsolutePath())))) {
// Start writing the header line: ?v1 ?v2 ...
for (int i = 0; i < numVars; ++i) {
if (i > 0) {
writer.write("\t");
}
writer.write("?");
writer.write(vars.get(i));
}
writer.write("\n");
// Write data lines
for (final Tuple tuple : tuples) {
for (int i = 0; i < numVars; ++i) {
if (i > 0) {
writer.write("\t");
}
writer.write(dictionary.stringFor(tuple.get(i)));
}
writer.write("\n");
tracker.increment();
}
}
// Signal completion
tracker.end();
}
private static class Query {
private final String name;
private final File file;
private final String string;
public Query(final String name, final File file, final String string) {
this.name = name;
this.file = file;
this.string = string;
}
public File download(final Session session) throws IOException, OperationException {
if (!this.file.exists()) {
final AtomicReference writerToClose = new AtomicReference(null);
final Tracker tracker = new Tracker(LOGGER, null, //
"Evaluated query " + this.name + ": %d tuples (%d tuple/s avg)", //
"Evaluating query " + this.name
+ ": %d tuples (%d tuple/s, %d tuple/s avg)");
tracker.start();
try (Stream stream = session.sparql(this.string).timeout(3600 * 1000L)
.execTuples()) {
stream.toHandler(new Handler() {
private Writer writer = null;
private List variables;
@SuppressWarnings("unchecked")
@Override
public void handle(final BindingSet bindings) throws Throwable {
if (this.writer == null) {
this.writer = IO.utf8Writer(IO.buffer(IO.write(Query.this.file
.getAbsolutePath())));
writerToClose.set(this.writer);
this.variables = stream.getProperty("variables", List.class);
for (int i = 0; i < this.variables.size(); ++i) {
this.writer.write(i > 0 ? "\t?" : "?");
this.writer.write(this.variables.get(i));
}
this.writer.write("\n");
}
if (bindings != null) {
this.writer.write(TestUtil.encode(this.variables, bindings));
this.writer.write("\n");
tracker.increment();
}
}
});
} finally {
final Writer writer = writerToClose.get();
if (writer != null) {
writer.flush();
Util.closeQuietly(writer);
try {
// TODO: remove this hack, necessary for giving gzip enough time to
// complete writing the file (the fix should be added to IO.write())
Thread.sleep(250);
} catch (InterruptedException ex) {
// ignore
}
}
}
tracker.end();
}
return this.file;
}
public static List create(final Properties properties, final File basePath) {
final List queries = Lists.newArrayList();
for (final Map.Entry entry : TestUtil.split(properties).entrySet()) {
final String name = entry.getKey();
final Properties props = entry.getValue();
final String filename = props.getProperty("file");
final String query = props.getProperty("query");
if (filename != null && query != null) {
final File file = basePath.toPath().resolve(Paths.get(filename)).toFile();
queries.add(new Query(name, file, query));
}
}
return queries;
}
@Override
public String toString() {
return this.name;
}
}
private static class Dictionary {
private static final int TABLE_SIZE = 32 * 1024 * 1024 - 1;
private static final int MAX_COLLISIONS = 1024;
private static final int BUFFER_BITS = 12;
private static final int BUFFER_SIZE = 1 << BUFFER_BITS;
private final int[] table;
private int[] list;
private final List buffers;
private int offset;
private int lastCode;
Dictionary() {
this.table = new int[Dictionary.TABLE_SIZE];
this.list = new int[1024];
this.buffers = Lists.newArrayList();
this.offset = BUFFER_SIZE;
this.lastCode = 0;
}
public int codeFor(final String string) {
final byte[] bytes = string.getBytes(Charsets.UTF_8);
int bucket = Math.abs(string.hashCode()) % TABLE_SIZE;
for (int i = 0; i < MAX_COLLISIONS; ++i) {
final int code = this.table[bucket];
if (code != 0) {
final int pointer = this.list[code - 1];
if (match(pointer, bytes)) {
return code;
}
} else {
final int pointer = store(bytes);
if (this.lastCode >= this.list.length) {
final int[] oldList = this.list;
this.list = Arrays.copyOf(oldList, this.list.length * 2);
}
this.list[this.lastCode++] = pointer;
this.table[bucket] = this.lastCode;
// if (lastCode % 100000 == 0) {
// System.out.println(buffers.size() * BUFFER_SIZE);
// }
return this.lastCode;
}
bucket = (bucket + 1) % TABLE_SIZE;
}
throw new Error("Max number of collisions exceeded - RDF vocabulary too large");
}
public String stringFor(final int code) {
final int pointer = this.list[code - 1];
return new String(load(pointer), Charsets.UTF_8);
}
private byte[] load(final int pointer) {
final int index = pointer >>> BUFFER_BITS - 2;
final int offset = pointer << 2 & BUFFER_SIZE - 1;
final byte[] buffer = this.buffers.get(index);
int end = offset;
while (buffer[end] != 0) {
++end;
}
return Arrays.copyOfRange(buffer, offset, end);
}
private int store(final byte[] bytes) {
if (this.offset + bytes.length + 1 > BUFFER_SIZE) {
this.buffers.add(new byte[BUFFER_SIZE]);
this.offset = 0;
}
final int index = this.buffers.size() - 1;
final int pointer = this.offset >> 2 | index << BUFFER_BITS - 2;
final byte[] buffer = this.buffers.get(index);
System.arraycopy(bytes, 0, buffer, this.offset, bytes.length);
this.offset += bytes.length;
buffer[this.offset++] = 0;
this.offset = this.offset + 3 & 0xFFFFFFFC;
return pointer;
}
private boolean match(final int pointer, final byte[] bytes) {
final int index = pointer >>> BUFFER_BITS - 2;
final int offset = pointer << 2 & BUFFER_SIZE - 1;
final byte[] buffer = this.buffers.get(index);
for (int i = 0; i < bytes.length; ++i) {
if (buffer[offset + i] != bytes[i]) {
return false;
}
}
return true;
}
}
private static abstract class Tuple implements Comparable {
public static Tuple create(final int... codes) {
switch (codes.length) {
case 0:
return Tuple0.INSTANCE;
case 1:
return new Tuple1(codes[0]);
case 2:
return new Tuple2(codes[0], codes[1]);
case 3:
return new Tuple3(codes[0], codes[1], codes[2]);
case 4:
return new Tuple4(codes[0], codes[1], codes[2], codes[3]);
default:
return new TupleN(codes.clone());
}
}
public abstract int size();
public abstract int get(int index);
public boolean matches(final Tuple tuple) {
final int size = size();
for (int i = 0; i < size; ++i) {
final int expected = tuple.get(i);
if (expected != 0 && get(i) != expected) {
return false;
}
}
return true;
}
@Override
public int compareTo(final Tuple other) {
final int thisSize = size();
final int otherSize = other.size();
final int minSize = Math.min(thisSize, otherSize);
for (int i = 0; i < minSize; ++i) {
final int result = get(i) - other.get(i);
if (result != 0) {
return result;
}
}
return thisSize - otherSize;
}
@Override
public boolean equals(final Object object) {
if (object == this) {
return true;
}
if (!(object instanceof Tuple)) {
return false;
}
final Tuple other = (Tuple) object;
final int size = size();
if (other.size() != size) {
return false;
}
for (int i = 0; i < size; ++i) {
if (get(i) != other.get(i)) {
return false;
}
}
return true;
}
@Override
public int hashCode() {
final int size = size();
int hash = size;
for (int i = 0; i < size; ++i) {
hash = 37 * hash + get(i);
}
return hash;
}
@Override
public String toString() {
final int size = size();
final StringBuilder builder = new StringBuilder();
builder.append('(');
for (int i = 0; i < size; ++i) {
if (i > 0) {
builder.append(", ");
}
builder.append(get(i));
}
builder.append(')');
return builder.toString();
}
private static final class Tuple0 extends Tuple {
static final Tuple0 INSTANCE = new Tuple0();
@Override
public int size() {
return 0;
}
@Override
public int get(final int index) {
throw new IndexOutOfBoundsException("Invalid index " + index);
}
}
private static final class Tuple1 extends Tuple {
private final int code;
Tuple1(final int code) {
this.code = code;
}
@Override
public int size() {
return 1;
}
@Override
public int get(final int index) {
Preconditions.checkElementIndex(index, 1);
return this.code;
}
}
private static final class Tuple2 extends Tuple {
private final int code0;
private final int code1;
Tuple2(final int code0, final int code1) {
this.code0 = code0;
this.code1 = code1;
}
@Override
public int size() {
return 2;
}
@Override
public int get(final int index) {
Preconditions.checkElementIndex(index, 2);
return index == 0 ? this.code0 : this.code1;
}
}
private static final class Tuple3 extends Tuple {
private final int code0;
private final int code1;
private final int code2;
Tuple3(final int code0, final int code1, final int code2) {
this.code0 = code0;
this.code1 = code1;
this.code2 = code2;
}
@Override
public int size() {
return 3;
}
@Override
public int get(final int index) {
switch (index) {
case 0:
return this.code0;
case 1:
return this.code1;
case 2:
return this.code2;
default:
throw new IndexOutOfBoundsException("Index " + index + ", size 3");
}
}
}
private static final class Tuple4 extends Tuple {
private final int code0;
private final int code1;
private final int code2;
private final int code3;
Tuple4(final int code0, final int code1, final int code2, final int code3) {
this.code0 = code0;
this.code1 = code1;
this.code2 = code2;
this.code3 = code3;
}
@Override
public int size() {
return 4;
}
@Override
public int get(final int index) {
switch (index) {
case 0:
return this.code0;
case 1:
return this.code1;
case 2:
return this.code2;
case 3:
return this.code3;
default:
throw new IndexOutOfBoundsException("Index " + index + ", size 4");
}
}
}
private static final class TupleN extends Tuple {
private final int[] codes;
TupleN(final int[] codes) {
this.codes = codes;
}
@Override
public int size() {
return this.codes.length;
}
@Override
public int get(final int index) {
return this.codes[index];
}
}
}
}
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