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Add a flatgeobuf submodule (#881)
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* Move support for flatgeobuf in a dedicated submodule

* Add an API that supports reading and writing flatbuffers and domain objects corresponding to flatbuffers

* Make picocli and jackson insensitive with enums
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@bchapuis
bchapuis committed Jun 27, 2024
1 parent 8716d53 commit 933ca83
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Showing 27 changed files with 3,788 additions and 324 deletions.
1 change: 0 additions & 1 deletion baremaps-cli/src/license/override.properties
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Expand Up @@ -142,7 +142,6 @@ org.postgresql--postgresql--42.7.2=BSD 2-Clause License
org.reactivestreams--reactive-streams--1.0.4=MIT License
org.roaringbitmap--RoaringBitmap--1.0.1=Apache License 2.0
org.slf4j--slf4j-api--2.0.12=MIT License
org.wololo--flatgeobuf--3.26.2=ISC License
org.xerial--sqlite-jdbc--3.45.1.0=The Apache Software License, Version 2.0
org.xerial.thirdparty--nestedvm--1.0=Apache License 2.0
org.yaml--snakeyaml--2.2=Apache License 2.0
7 changes: 5 additions & 2 deletions baremaps-cli/src/main/java/org/apache/baremaps/cli/Baremaps.java
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Expand Up @@ -68,9 +68,12 @@ public static void main(String... args) {
}

// Execute the command
CommandLine cmd = new CommandLine(new Baremaps()).setUsageHelpLongOptionsMaxWidth(30)
CommandLine commandLine = new CommandLine(new Baremaps())
.setCaseInsensitiveEnumValuesAllowed(true)
.setUsageHelpLongOptionsMaxWidth(30)
.addMixin("options", new Options());
cmd.execute(args);

commandLine.execute(args);
}

@Override
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8 changes: 4 additions & 4 deletions baremaps-core/pom.xml
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Expand Up @@ -82,6 +82,10 @@ limitations under the License.
<groupId>org.apache.baremaps</groupId>
<artifactId>baremaps-data</artifactId>
</dependency>
<dependency>
<groupId>org.apache.baremaps</groupId>
<artifactId>baremaps-flatgeobuf</artifactId>
</dependency>
<dependency>
<groupId>org.apache.baremaps</groupId>
<artifactId>baremaps-geoparquet</artifactId>
Expand Down Expand Up @@ -142,10 +146,6 @@ limitations under the License.
<groupId>org.postgresql</groupId>
<artifactId>postgresql</artifactId>
</dependency>
<dependency>
<groupId>org.wololo</groupId>
<artifactId>flatgeobuf</artifactId>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
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213 changes: 73 additions & 140 deletions baremaps-core/src/main/java/org/apache/baremaps/storage/flatgeobuf/FlatGeoBufDataTable.java
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Expand Up @@ -17,7 +17,6 @@

package org.apache.baremaps.storage.flatgeobuf;

import com.google.flatbuffers.FlatBufferBuilder;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.ByteOrder;
Expand All @@ -26,18 +25,14 @@
import java.nio.file.StandardOpenOption;
import java.util.Iterator;
import java.util.NoSuchElementException;
import java.util.Objects;
import org.apache.baremaps.data.collection.DataCollection;
import org.apache.baremaps.data.storage.DataRow;
import org.apache.baremaps.data.storage.DataSchema;
import org.apache.baremaps.data.storage.DataStoreException;
import org.apache.baremaps.data.storage.DataTable;
import org.locationtech.jts.geom.*;
import org.wololo.flatgeobuf.Constants;
import org.wololo.flatgeobuf.GeometryConversions;
import org.wololo.flatgeobuf.HeaderMeta;
import org.wololo.flatgeobuf.PackedRTree;
import org.wololo.flatgeobuf.generated.Feature;
import org.wololo.flatgeobuf.generated.GeometryType;
import org.apache.baremaps.data.storage.*;
import org.apache.baremaps.data.storage.DataColumn.Type;
import org.apache.baremaps.flatgeobuf.FlatGeoBuf;
import org.apache.baremaps.flatgeobuf.FlatGeoBufReader;
import org.apache.baremaps.flatgeobuf.FlatGeoBufWriter;
import org.apache.baremaps.flatgeobuf.PackedRTree;

/**
* A {@link DataTable} that stores rows in a flatgeobuf file.
Expand All @@ -54,8 +49,18 @@ public class FlatGeoBufDataTable implements DataTable {
* @param file the path to the flatgeobuf file
*/
public FlatGeoBufDataTable(Path file) {
this(file, readSchema(file));
}

/**
* Constructs a table from a flatgeobuf file and a schema (used for writing).
*
* @param file the path to the flatgeobuf file
* @param schema the schema of the table
*/
public FlatGeoBufDataTable(Path file, DataSchema schema) {
this.file = file;
this.schema = readSchema(file);
this.schema = schema;
}

/**
Expand All @@ -65,27 +70,15 @@ public FlatGeoBufDataTable(Path file) {
* @return the schema of the table
*/
private static DataSchema readSchema(Path file) {
try (var channel = FileChannel.open(file, StandardOpenOption.READ)) {
try (var reader = new FlatGeoBufReader(FileChannel.open(file, StandardOpenOption.READ))) {
// try to read the schema from the file
var buffer = ByteBuffer.allocate(1 << 20).order(ByteOrder.LITTLE_ENDIAN);
HeaderMeta headerMeta = readHeaderMeta(channel, buffer);
return FlatGeoBufTypeConversion.asSchema(headerMeta);
var header = reader.readHeader();
return FlatGeoBufTypeConversion.asSchema(header);
} catch (IOException e) {
return null;
}
}

/**
* Constructs a table from a flatgeobuf file and a schema (used for writing).
*
* @param file the path to the flatgeobuf file
* @param schema the schema of the table
*/
public FlatGeoBufDataTable(Path file, DataSchema schema) {
this.file = file;
this.schema = schema;
}

/**
* {@inheritDoc}
*/
Expand All @@ -100,22 +93,13 @@ public DataSchema schema() {
@Override
public Iterator<DataRow> iterator() {
try {
var channel = FileChannel.open(file, StandardOpenOption.READ);
var reader = new FlatGeoBufReader(FileChannel.open(file, StandardOpenOption.READ));

var buffer = ByteBuffer.allocate(1 << 20).order(ByteOrder.LITTLE_ENDIAN);
HeaderMeta headerMeta = readHeaderMeta(channel, buffer);
channel.position(headerMeta.offset);

// skip the index
long indexOffset = headerMeta.offset;
long indexSize =
PackedRTree.calcSize((int) headerMeta.featuresCount, headerMeta.indexNodeSize);
channel.position(indexOffset + indexSize);

buffer.clear();
var header = reader.readHeader();
reader.skipIndex();

// create the feature stream
return new RowIterator(channel, headerMeta, schema, buffer);
return new RowIterator(reader, header, schema);
} catch (IOException e) {
throw new DataStoreException(e);
}
Expand All @@ -134,30 +118,14 @@ public void clear() {
*/
@Override
public long size() {
try (var channel = FileChannel.open(file, StandardOpenOption.READ)) {
var buffer = ByteBuffer.allocate(1 << 20).order(ByteOrder.LITTLE_ENDIAN);
HeaderMeta headerMeta = readHeaderMeta(channel, buffer);
return headerMeta.featuresCount;
try (var reader = new FlatGeoBufReader(FileChannel.open(file, StandardOpenOption.READ))) {
FlatGeoBuf.Header header = reader.readHeader();
return header.featuresCount();
} catch (IOException e) {
throw new DataStoreException(e);
}
}

/**
* Reads the header meta from a channel.
*
* @param channel the channel to read from
* @param buffer the buffer to use
* @return the header meta
* @throws IOException if an error occurs while reading the header meta
*/
private static HeaderMeta readHeaderMeta(SeekableByteChannel channel, ByteBuffer buffer)
throws IOException {
channel.read(buffer);
buffer.flip();
return HeaderMeta.read(buffer);
}

/**
* Writes a collection of rows to a flatgeobuf file.
*
Expand All @@ -166,68 +134,45 @@ private static HeaderMeta readHeaderMeta(SeekableByteChannel channel, ByteBuffer
*/
public void write(DataCollection<DataRow> features) throws IOException {
try (
var channel = FileChannel.open(file, StandardOpenOption.CREATE, StandardOpenOption.WRITE);
var outputStream = Channels.newOutputStream(channel)) {
outputStream.write(Constants.MAGIC_BYTES);

var bufferBuilder = new FlatBufferBuilder();

var headerMeta = new HeaderMeta();
headerMeta.geometryType = GeometryType.Unknown;
headerMeta.indexNodeSize = 16;
headerMeta.srid = 3857;
headerMeta.featuresCount = features.size();
headerMeta.name = schema.name();
headerMeta.columns = FlatGeoBufTypeConversion.asColumns(schema.columns());
HeaderMeta.write(headerMeta, outputStream, bufferBuilder);
var writer = new FlatGeoBufWriter(
FileChannel.open(file, StandardOpenOption.CREATE, StandardOpenOption.WRITE))) {

schema.columns().stream()
.filter(c -> c.cardinality() == DataColumn.Cardinality.REQUIRED)
.forEach(c -> {
if (Objects.requireNonNull(c.type()) == Type.BINARY) {
throw new UnsupportedOperationException();
}
});

var header = new FlatGeoBuf.Header(
schema.name(),
null,
FlatGeoBuf.GeometryType.UNKNOWN,
false,
false,
false,
false,
FlatGeoBufTypeConversion.asColumns(schema.columns()),
features.size(),
2,
null,
null,
null,
null);

writer.writeHeader(header);

var indexSize =
(int) PackedRTree.calcSize((int) headerMeta.featuresCount, headerMeta.indexNodeSize);
(int) PackedRTree.calcSize((int) header.featuresCount(), header.indexNodeSize());

for (int i = 0; i < indexSize; i++) {
outputStream.write(0);
}
writer.writeIndexBuffer(ByteBuffer.allocate(indexSize).order(ByteOrder.LITTLE_ENDIAN));

var iterator = features.iterator();
while (iterator.hasNext()) {
var featureBuilder = new FlatBufferBuilder(4096);

var row = iterator.next();

var propertiesBuffer = ByteBuffer.allocate(1 << 20).order(ByteOrder.LITTLE_ENDIAN);
var properties = row.values().stream()
.filter(v -> !(v instanceof Geometry))
.toList();
for (int i = 0; i < properties.size(); i++) {
var column = headerMeta.columns.get(i);
var value = properties.get(i);
propertiesBuffer.putShort((short) i);
FlatGeoBufTypeConversion.writeValue(propertiesBuffer, column, value);
}
if (propertiesBuffer.position() > 0) {
propertiesBuffer.flip();
}
var propertiesOffset = org.wololo.flatgeobuf.generated.Feature
.createPropertiesVector(featureBuilder, propertiesBuffer);

var geometry = row.values().stream()
.filter(v -> v instanceof Geometry)
.map(Geometry.class::cast)
.findFirst();

var geometryOffset = geometry.isPresent()
? GeometryConversions.serialize(featureBuilder, geometry.get(), headerMeta.geometryType)
: 0;

var featureOffset =
org.wololo.flatgeobuf.generated.Feature.createFeature(featureBuilder, geometryOffset,
propertiesOffset, 0);
featureBuilder.finishSizePrefixed(featureOffset);

ByteBuffer data = featureBuilder.dataBuffer();
while (data.hasRemaining()) {
channel.write(data);
}
var feature = FlatGeoBufTypeConversion.asFeature(row);
writer.writeFeature(feature);
}
}
}
Expand All @@ -237,38 +182,36 @@ public void write(DataCollection<DataRow> features) throws IOException {
*/
public static class RowIterator implements Iterator<DataRow> {

private final HeaderMeta headerMeta;
private final FlatGeoBuf.Header header;

private final DataSchema schema;

private final SeekableByteChannel channel;

private final ByteBuffer buffer;
private final FlatGeoBufReader reader;

private long cursor = 0;

/**
* Constructs a row iterator.
*
* @param channel the channel to read from
* @param headerMeta the header meta
* @param reader the channel to read from
* @param header the header of the file
* @param schema the schema of the table
* @param buffer the buffer to use
*/
public RowIterator(SeekableByteChannel channel, HeaderMeta headerMeta,
DataSchema schema, ByteBuffer buffer) {
this.channel = channel;
this.headerMeta = headerMeta;
public RowIterator(
FlatGeoBufReader reader,
FlatGeoBuf.Header header,
DataSchema schema) {
this.reader = reader;
this.header = header;
this.schema = schema;
this.buffer = buffer;
}

/**
* {@inheritDoc}
*/
@Override
public boolean hasNext() {
return cursor < headerMeta.featuresCount;
return cursor < header.featuresCount();
}

/**
Expand All @@ -277,19 +220,9 @@ public boolean hasNext() {
@Override
public DataRow next() {
try {
channel.read(buffer);
buffer.flip();

var featureSize = buffer.getInt();
var row =
FlatGeoBufTypeConversion.asRow(headerMeta, schema, Feature.getRootAsFeature(buffer));

buffer.position(Integer.BYTES + featureSize);
buffer.compact();

var feature = reader.readFeature();
cursor++;

return row;
return FlatGeoBufTypeConversion.asRow(schema, feature);
} catch (IOException e) {
throw new NoSuchElementException(e);
}
Expand Down
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