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Merge pull request #12 from virtualcell/Plugin-With-S3-Service
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Plugin with s3 service
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@AvocadoMoon
AvocadoMoon authored Nov 16, 2023
2 parents 3386674 + 8b3c1a0 commit 29e56f1
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Showing 3 changed files with 126 additions and 58 deletions.
166 changes: 117 additions & 49 deletions src/main/java/org/vcell/vcellfiji/N5ImageHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,53 +31,113 @@
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.List;


/*
Able to open N5 files locally, display the datasets that can be chosen from it, and open the datasets within ImageJ.
Flow of operations is select an N5 file, get dataset list, select a dataset and then open it.
http://vcellapi-beta.cam.uchc.edu:8088/test/test.n5
*/

@Plugin(type = Command.class, menuPath = "Plugins>VCell>N5 Dataset Viewer")
public class N5ImageHandler implements Command{
public class N5ImageHandler implements Command, ActionListener {
private VCellGUI vGui;
private File selectedLocalFile;
private AmazonS3 s3Client;
private String bucketName;

private String s3ObjectKey;
private SwingWorker<ArrayList<String>, ArrayList<String>> n5DatasetListUpdater;
@Override
public void actionPerformed(ActionEvent e) {
enableCriticalButtons(false);

if(e.getSource() == vGui.localFileDialog){
n5DatasetListUpdater= new SwingWorker<ArrayList<String>, ArrayList<String>>() {
@Override
protected ArrayList<String> doInBackground() throws Exception {
selectedLocalFile = vGui.localFileDialog.getSelectedFile();
ArrayList<String> n5DataSetList = getN5DatasetList();
publish(n5DataSetList);
return null;
}

@Override
protected void done() {
enableCriticalButtons(true);
}

@Override
protected void process(List<ArrayList<String>> chunks) {
displayN5Results(chunks.get(0));
}
};
n5DatasetListUpdater.execute();
}

else if (e.getSource() == vGui.okayButton) {
SwingWorker swingWorker = new SwingWorker() {
@Override
protected Object doInBackground() throws Exception {
try{
loadN5Dataset(vGui.datasetList.getSelectedValue());
return null;
}
catch (IOException ex){
return null;
}
}

@Override
protected void done() {
enableCriticalButtons(true);
}
};
swingWorker.execute();
}
// https://stackoverflow.com/questions/16937997/java-swingworker-thread-to-update-main-gui
// Why swing updating does not work

else if (e.getSource() == vGui.remoteFileSelection.submitS3Info){
n5DatasetListUpdater= new SwingWorker<ArrayList<String>, ArrayList<String>>() {
@Override
protected ArrayList<String> doInBackground() throws Exception {
createS3Client(vGui.remoteFileSelection.getS3URL(), vGui.remoteFileSelection.returnCredentials(), vGui.remoteFileSelection.returnEndpoint());
ArrayList<String> list = getS3N5DatasetList();
publish(list);
return null;
}

@Override
protected void done() {
enableCriticalButtons(true);
}

@Override
protected void process(List<ArrayList<String>> chunks) {
displayN5Results(chunks.get(0));
}
};
n5DatasetListUpdater.execute();
}
}

private void enableCriticalButtons(boolean enable) {
vGui.remoteFileSelection.submitS3Info.setEnabled(enable);
vGui.okayButton.setEnabled(enable);
vGui.LocalFiles.setEnabled(enable);
vGui.remoteFiles.setEnabled(enable);
}

@Override
public void run() {
this.vGui = new VCellGUI();
this.vGui.localFileDialog.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
selectedLocalFile = vGui.localFileDialog.getSelectedFile();
displayN5Results(getN5DatasetList());
}
});
this.vGui.localFileDialog.addActionListener(this);

this.vGui.okayButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try{
loadN5Dataset(vGui.datasetList.getSelectedValue());
}
catch (IOException ex){
return;
}
}
});

this.vGui.remoteFileSelection.submitS3Info.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
createS3Client(vGui.remoteFileSelection.getS3URL(), vGui.remoteFileSelection.returnCredentials(), vGui.remoteFileSelection.returnEndpoint());
ArrayList<String> list = getS3N5DatasetList();
displayN5Results(list);
}
});
this.vGui.okayButton.addActionListener(this);

this.vGui.remoteFileSelection.submitS3Info.addActionListener(this);
}

public ArrayList<String> getN5DatasetList(){
Expand All @@ -97,9 +157,7 @@ public ArrayList<String> getN5DatasetList(){
}

public void displayN5Results(ArrayList<String> datasetList){
SwingUtilities.invokeLater(() ->{
this.vGui.updateDatasetList(datasetList);
});
this.vGui.updateDatasetList(datasetList);
}


Expand Down Expand Up @@ -172,38 +230,44 @@ public void loadN5Dataset(String selectedDataset) throws IOException {
public void createS3Client(String url, HashMap<String, String> credentials, HashMap<String, String> endpoint){
AmazonS3ClientBuilder s3ClientBuilder = AmazonS3ClientBuilder.standard();
URI uri = URI.create(url);
String defaultRegion = "site2-low";

if(credentials != null){
s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
}

// believe that it's a s3 URL
try{
AmazonS3URI s3URI = new AmazonS3URI(uri);
this.s3ObjectKey = s3URI.getKey();
this.bucketName = s3URI.getBucket();
defaultRegion = s3URI.getRegion();
if(s3URI.isPathStyle()){
s3ClientBuilder.withPathStyleAccessEnabled(true);
}
if(endpoint != null){
s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint.get("Endpoint"), endpoint.get("Region")));
this.s3Client = s3ClientBuilder.build();
return;
}
// if nothing is given, default user and return so that code after if statement does not execute
if(endpoint == null && credentials == null){
this.s3Client = AmazonS3ClientBuilder.standard().withRegion(s3URI.getRegion()).withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())).build();
return;
}
//creds not null, but region is
this.s3Client = s3ClientBuilder.withRegion(s3URI.getRegion()).build();
return;
}
// otherwise assume it is one of our URLs
// http://vcell:8000/bucket/object/object2
catch (IllegalArgumentException e){
String[] pathSubStrings = uri.getPath().split("/", 3);
this.s3ObjectKey = pathSubStrings[2];
this.bucketName = pathSubStrings[1];
}

if(credentials != null){
s3ClientBuilder.withCredentials(new AWSStaticCredentialsProvider(new BasicAWSCredentials(credentials.get("AccessKey"), credentials.get("SecretKey"))));
}
if(endpoint != null){
s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(endpoint.get("Endpoint"), endpoint.get("Region")));
s3ClientBuilder.withPathStyleAccessEnabled(true);
s3ClientBuilder.withEndpointConfiguration(new AwsClientBuilder.EndpointConfiguration(uri.getScheme() + "://" + uri.getAuthority(), "site2-low"));
this.s3Client = s3ClientBuilder.build();
return;
}
// if nothing is given, default user and return so that code after if statement does not execute
if(endpoint == null && credentials == null){
this.s3Client = AmazonS3ClientBuilder.standard().withRegion(defaultRegion).withCredentials(new AWSStaticCredentialsProvider(new AnonymousAWSCredentials())).build();
return;
}

//creds not null, but region is
this.s3Client = s3ClientBuilder.withRegion(defaultRegion).build();
}


Expand All @@ -228,4 +292,8 @@ public File getSelectedLocalFile() {
return selectedLocalFile;
}

public static void main(String[] args) {
N5ImageHandler n5ImageHandler = new N5ImageHandler();
n5ImageHandler.run();
}
}
4 changes: 2 additions & 2 deletions src/main/java/org/vcell/vcellfiji/UI/VCellGUI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@
import java.util.ArrayList;

public class VCellGUI extends JFrame {
private JButton LocalFiles;
public JButton LocalFiles;
public JPanel mainPanel;
private final JFrame jFrame;
public JFileChooser localFileDialog;
private JToolBar menuBar;
public JList<String> datasetList;
private JScrollPane resultsScrollPane;
private JButton remoteFiles;
public JButton remoteFiles;
public JButton okayButton;
public JCheckBox openVirtualCheckBox;

Expand Down
14 changes: 7 additions & 7 deletions src/test/java/org/vcell/vcellfiji/N5ImageHandlerTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -65,22 +65,22 @@ public void testS3Client() throws IOException {
credentials.put("AccessKey", "jj");
credentials.put("SecretKey", "jj");

final String s3ProxyURL = "/" + this.n5FileName;
final String s3ProxyURI = "http://localhost:4000/" + this.n5FileName;

N5ImageHandler n5ImageHandler = new N5ImageHandler();

// Environment variables are set in github actions VM

// n5ImageHandler.createS3Client(s3ProxyURL, null, null);
// this.remoteN5ImgPlusTests(n5ImageHandler);
n5ImageHandler.createS3Client(s3ProxyURI, null, null);
this.remoteN5ImgPlusTests(n5ImageHandler);

n5ImageHandler.createS3Client(s3ProxyURL, null, s3Endpoint);
n5ImageHandler.createS3Client(s3ProxyURI, null, s3Endpoint);
this.remoteN5ImgPlusTests(n5ImageHandler);

// n5ImageHandler.createS3Client(s3ProxyURL, credentials, null);
// this.remoteN5ImgPlusTests(n5ImageHandler);
n5ImageHandler.createS3Client(s3ProxyURI, credentials, null);
this.remoteN5ImgPlusTests(n5ImageHandler);

n5ImageHandler.createS3Client(s3ProxyURL, credentials, s3Endpoint);
n5ImageHandler.createS3Client(s3ProxyURI, credentials, s3Endpoint);
this.remoteN5ImgPlusTests(n5ImageHandler);
}

Expand Down

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