From ee61540c5d359c0bd6fccab7bdbeb306989415c5 Mon Sep 17 00:00:00 2001
From: Jan Kozusznik <jan@kozusznik.cz>
Date: Wed, 22 Nov 2017 16:30:23 +0100
Subject: [PATCH] inspect size correctly
---
.../fiji/haas/CheckStatusOfHaaSWindow.java | 5 +-
.../haas/ui/CheckStatusOfHaaSController.java | 9 +++-
.../fiji/haas_java_client/HaaSClient.java | 17 +++---
.../cz/it4i/fiji/scpclient/ScpClient.java | 54 ++++++++++++++++++-
java-scpclient/src/test/java/TestSCP.java | 2 +-
5 files changed, 76 insertions(+), 11 deletions(-)
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java
index 00928d7f..b206ea2b 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java
@@ -16,12 +16,15 @@ public class CheckStatusOfHaaSWindow extends FXFrame<CheckStatusOfHaaSController
private Context context;
private CheckStatusOfHaaSController controller;
+
+ private Frame applicationFrame;
public CheckStatusOfHaaSWindow(Frame applicationFrame, Context context) {
super(applicationFrame,"/cz/it4i/fiji/haas/ui/CheckStatusOfHaaS.fxml");
this.context = context;
init(this::initController);
this.setResizable(false);
this.setTitle("Manage status of HaaS jobs");
+ this.applicationFrame = applicationFrame;
}
public void addJob(JobInfo job) {
@@ -31,7 +34,7 @@ public class CheckStatusOfHaaSWindow extends FXFrame<CheckStatusOfHaaSController
private void initController(CheckStatusOfHaaSController controller) {
this.controller = controller;
context.inject(controller);
- controller.init();
+ controller.init(applicationFrame);
}
}
diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java
index b8119d97..fa9f59dd 100644
--- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java
+++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java
@@ -1,11 +1,13 @@
package cz.it4i.fiji.haas.ui;
+import java.awt.Frame;
import java.util.function.Function;
import org.scijava.log.LogService;
import org.scijava.plugin.Parameter;
import cz.it4i.fiji.haas.JobManager.JobInfo;
+import javafx.application.Platform;
import javafx.event.ActionEvent;
import javafx.event.EventHandler;
import javafx.fxml.FXML;
@@ -24,6 +26,8 @@ public class CheckStatusOfHaaSController {
@FXML
private TableView<JobInfo> jobs;
+ private Frame root;
+
public CheckStatusOfHaaSController() {
}
@@ -32,13 +36,14 @@ public class CheckStatusOfHaaSController {
jobs.getItems().add(job);
}
- public void init() {
+ public void init(Frame root) {
initTable();
initMenu();
+ this.root = root;
}
private void downloadData(ActionEvent event) {
- jobs.getSelectionModel().getSelectedItem().downloadData(new ProgressDialog(null));
+ Platform.runLater(() -> jobs.getSelectionModel().getSelectedItem().downloadData(new ProgressDialog(root)));
}
private void initMenu() {
diff --git a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
index af64b4b3..9266e90f 100644
--- a/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
+++ b/haas-java-client/src/main/java/cz/it4i/fiji/haas_java_client/HaaSClient.java
@@ -254,8 +254,8 @@ public class HaaSClient {
try (ScpClient scpClient = getScpClient(ft)) {
String[] files = getFileTransfer().listChangedFilesForJob(jobId, getSessionID());
List<Long> fileSizes = getSizes(Arrays.asList(files).stream()
- .map(filename -> ft.getSharedBasepath() + "/" + filename).collect(Collectors.toList()),
- scpClient);
+ .map(filename -> "'" + ft.getSharedBasepath() + "/" + filename + "'").collect(Collectors.toList()),
+ scpClient, notifier);
final long totalFileSize = fileSizes.stream().mapToLong(i -> i.longValue()).sum();
int[] idx = { 0 };
final int[] totalDownloaded = { 0 };
@@ -280,8 +280,8 @@ public class HaaSClient {
public void dataTransfered(long bytesTransfered) {
totalDownloaded[0] += bytesTransfered;
fileDownloaded[0] += bytesTransfered;
- notifier.setCount((int) (totalDownloaded[0] >> 10), (int) (Math.max(totalFileSize,totalDownloaded[0]) >> 10));
- notifier.setItemCount((int) (fileDownloaded[0] >> 10), (int) ( Math.max(fileSizes.get(idx[0]),fileDownloaded[0]) >> 10));
+ notifier.setCount((int) (totalDownloaded[0] >> 10), (int) (totalFileSize>> 10));
+ notifier.setItemCount((int) (fileDownloaded[0] >> 10), (int) ( fileSizes.get(idx[0]) >> 10));
}
});
@@ -297,11 +297,16 @@ public class HaaSClient {
}
}
- private List<Long> getSizes(List<String> asList, ScpClient scpClient) throws JSchException, IOException {
+ private List<Long> getSizes(List<String> asList, ScpClient scpClient, ProgressNotifier notifier) throws JSchException, IOException {
List<Long> result = new LinkedList<>();
+
+ String item;
+ notifier.addItem(item = "Checking sizes");
for (String lfile : asList) {
- result.add(0l);//scpClient.size(lfile).get(0));
+ result.add(scpClient.size(lfile));
+ notifier.setItemCount(result.size(), asList.size());
}
+ notifier.itemDone(item);
return result;
}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java
index a979d645..8a69e78d 100644
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java
+++ b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java
@@ -247,7 +247,7 @@ public class ScpClient implements Closeable {
}
@SuppressWarnings("unchecked")
- public List<Long> size(String lfile) throws JSchException, IOException {
+ public List<Long> sizeByLs(String lfile) throws JSchException, IOException {
Session session = connectionSession();
// exec 'scp -f rfile' remotely
@@ -352,4 +352,56 @@ public class ScpClient implements Closeable {
session = null;
}
}
+
+ public long size(String lfile) throws JSchException, IOException {
+ Session session = connectionSession();
+
+ // exec 'scp -f rfile' remotely
+ String command = "scp -f " + lfile;
+ Channel channel = session.openChannel("exec");
+
+ try {
+ ((ChannelExec) channel).setCommand(command);
+
+ // get I/O streams for remote scp
+ try (OutputStream out = channel.getOutputStream(); InputStream in = channel.getInputStream()) {
+
+ channel.connect();
+
+ byte[] buf = new byte[getBufferSize()];
+
+ // send '\0'
+ buf[0] = 0;
+ out.write(buf, 0, 1);
+ out.flush();
+
+ while (true) {
+ int c = checkAck(in);
+ if (c != 'C') {
+ break;
+ }
+
+ // read '0644 '
+ in.read(buf, 0, 5);
+
+ long filesize = 0L;
+ while (true) {
+ if (in.read(buf, 0, 1) < 0) {
+ // error
+ break;
+ }
+ if (buf[0] == ' ')
+ break;
+ filesize = filesize * 10L + (long) (buf[0] - '0');
+ }
+ return filesize;
+
+ }
+ }
+
+ } finally {
+ channel.disconnect();
+ }
+ return -1;
+ }
}
diff --git a/java-scpclient/src/test/java/TestSCP.java b/java-scpclient/src/test/java/TestSCP.java
index bc70bc6d..5c20cd53 100644
--- a/java-scpclient/src/test/java/TestSCP.java
+++ b/java-scpclient/src/test/java/TestSCP.java
@@ -15,7 +15,7 @@ public class TestSCP {
try(ScpClient scp = new ScpClient("salomon.it4i.cz", "koz01", "/home/koz01/.ssh/it4i_rsa-np", null)) {
// System.out.println( scp.upload(
// Paths.get("/home/koz01/Work/vyzkumnik/fiji/work/aaa/spim-data/exampleSingleChannel(9).czi"), "'/home/koz01/exampleSingleChannel(9).czi'"));
- System.out.println( scp.size("/home/koz01/exampleSingleChannel(9).czi"));
+ System.out.println( scp.size("'/home/koz01/exampleSingleChannel(9).czi'"));
}
}
--
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