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Updated jomezarr API #42

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Updated jomezarr API #42

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6 changes: 3 additions & 3 deletions modules/HortaTracer/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -78,12 +78,12 @@
<dependency>
<groupId>org.aind</groupId>
<artifactId>jomezarr</artifactId>
<version>1.3.2</version>
<version>1.3.3</version>
</dependency>
<dependency>
<groupId>com.bc.zarr</groupId>
<groupId>dev.zarr</groupId>
<artifactId>jzarr</artifactId>
<version>0.3.9</version>
<version>0.4.2</version>
</dependency>
<dependency>
<groupId>edu.ucar</groupId>
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8 changes: 4 additions & 4 deletions modules/HortaTracer/src/main/java/org/janelia/horta/blocks/OmeZarrBlockTileSource.java
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@ public OmeZarrBlockTileSource init(String localPath, OmeZarrReaderProgressObserv

this.reader = null;

omeZarrGroup = OmeZarrGroup.open(Paths.get(localPath));
omeZarrGroup = OmeZarrGroupFactory.open(Paths.get(localPath));

return init(progressObserver, completionObserver);
}
Expand All @@ -82,20 +82,20 @@ public OmeZarrBlockTileSource init(TmSample sample, OmeZarrReaderProgressObserve

this.reader = new OmeZarrJadeReader(FileMgr.getFileMgr().getStorageService(), this.sampleOmeZarrTilesBaseDir);

omeZarrGroup = OmeZarrGroup.open(new JadeZarrStoreProvider("", reader));
omeZarrGroup = OmeZarrGroupFactory.open(new JadeZarrStoreProvider("", reader));

return init(progressObserver, completionObserver);
}

private OmeZarrBlockTileSource init(OmeZarrReaderProgressObserver progressObserver, OmeZarrReaderCompletionObserver completionObserver) {
cachedThreadPool.submit(() -> {
int datasetCount = omeZarrGroup.getAttributes().getMultiscales()[0].getDatasets().size();
int datasetCount = omeZarrGroup.getDatasetCount();

boolean haveExtents = false;

for (int idx = datasetCount - 1; idx >= 0; idx--) {
try {
OmeZarrDataset dataset = omeZarrGroup.getAttributes().getMultiscales()[0].getDatasets().get(idx);
OmeZarrDataset dataset = omeZarrGroup.getDataset(idx);

if (this.reader != null) {
dataset.setExternalZarrStore(new JadeZarrStoreProvider(dataset.getPath(), reader));
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41 changes: 7 additions & 34 deletions modules/HortaTracer/src/main/java/org/janelia/horta/omezarr/JadeZarrStoreProvider.java
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Original file line number Diff line number Diff line change
@@ -1,57 +1,30 @@
package org.janelia.horta.omezarr;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.util.TreeSet;
import java.util.stream.Stream;

import org.aind.omezarr.zarr.ExternalZarrStore;

public class JadeZarrStoreProvider extends ExternalZarrStore {

private final OmeZarrJadeReader reader;

public JadeZarrStoreProvider(String prefix, OmeZarrJadeReader reader)
{
public JadeZarrStoreProvider(String prefix, OmeZarrJadeReader reader) {
super(prefix);

this.reader = reader;
}

@Override
public InputStream getInputStream(String s) throws IOException {
return reader.getInputStream(prefix.length() > 0 ? prefix + File.separator + s :s);
}

@Override
public OutputStream getOutputStream(String s) throws IOException {
return null;
}

@Override
public void delete(String s) throws IOException {

public ExternalZarrStore cloneWithPrefix(String prefix) {
return new JadeZarrStoreProvider(prefix, reader);
}

@Override
public TreeSet<String> getArrayKeys() throws IOException {
return null;
}

@Override
public TreeSet<String> getGroupKeys() throws IOException {
return null;
}

@Override
public TreeSet<String> getKeysEndingWith(String s) throws IOException {
return null;
public boolean exists(String s) {
return reader.exists(!prefix.isEmpty() ? prefix + File.separator + s : s);
}

@Override
public Stream<String> getRelativeLeafKeys(String s) throws IOException {
return null;
public InputStream getInputStream(String s) {
return reader.getInputStream(!prefix.isEmpty() ? prefix + File.separator + s : s);
}
}
16 changes: 11 additions & 5 deletions modules/HortaTracer/src/main/java/org/janelia/horta/omezarr/OmeZarrJadeReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,28 +38,34 @@ public String getBasePath() {
return this.basePath;
}

public boolean exists(String location) {
final Path path = Paths.get(getBasePath(), location);
String relativePath = storageLocation.getRelativePath(path.toString().replace("\\", "/"));
return jadeStorage.exists(storageLocation,relativePath);
}

public InputStream getInputStream(String location) {
final Path path = Paths.get(basePath, location);
final Path path = Paths.get(getBasePath(), location);
String relativePath = storageLocation.getRelativePath(path.toString().replace("\\", "/"));
return jadeStorage.getContent(storageLocation, relativePath);
}

public InputStream getAttributesStream() {
final Path path = Paths.get(basePath, attributesFile);
final Path path = Paths.get(getBasePath(), attributesFile);
String relativePath = storageLocation.getRelativePath(path.toString().replace("\\", "/"));
return jadeStorage.getContent(storageLocation, relativePath);
}

public String[] list(final String pathName) throws IOException {
log.trace("list " + pathName);
final Path path = Paths.get(basePath, pathName);
final Path path = Paths.get(getBasePath(), pathName);
String relativePath = storageLocation.getRelativePath(path.toString());

try (Stream<StorageObject> stream = jadeStorage.getChildren(storageLocation, relativePath).stream()) {
return stream
.filter(a -> a.isCollection())
.filter(StorageObject::isCollection)
.map(a -> path.relativize(Paths.get(a.getAbsolutePath())).toString())
.toArray(n -> new String[n]);
.toArray(String[]::new);
} catch (StorageObjectNotFoundException e) {
throw new RuntimeException(e);
}
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