From 4899a0694b6f34a1fba9eda9fb84f151e7d57c27 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Wed, 4 Aug 2010 17:56:04 +0000
Subject: [PATCH] add: a way to login to the openBIS server that doesn't leave
the user's password in the Matlab command history
SVN: 17344
---
screening/source/java/OpenBISML.java | 72 +++++-
.../plugin/screening/client/cli/Login.java | 221 ++++++++++++++++++
2 files changed, 286 insertions(+), 7 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
diff --git a/screening/source/java/OpenBISML.java b/screening/source/java/OpenBISML.java
index 4da3088323e..3ea9a7b234b 100644
--- a/screening/source/java/OpenBISML.java
+++ b/screening/source/java/OpenBISML.java
@@ -15,9 +15,11 @@
*/
import java.io.BufferedOutputStream;
+import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
+import java.io.FileReader;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
@@ -30,6 +32,7 @@ import java.util.Map;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.client.cli.Login;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorWithDescription;
@@ -43,8 +46,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageRef
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
- * Simple Matlab interface for openBIS for Screening. It is meant to be used in one Matlab
- * session at a time, i.e. it is <i>not</i> multi-threading safe.
+ * Simple Matlab interface for openBIS for Screening. It is meant to be used in one Matlab session
+ * at a time, i.e. it is <i>not</i> multi-threading safe.
* <p>
* While written in Java, the API is idiomatic for Matlab, i.e. values are returned as
* multi-dimensional arrays. For the <code>get...</code> and <code>load...</code> methods the first
@@ -66,6 +69,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
* OpenBISML.logout()
* </pre>
*
+ * <i>Note: using this login your password will end up in the Matlab command history. An alternative
+ * that avoids this is to call the
+ * {@link ch.systemsx.cisd.openbis.plugin.screening.client.cli.Login} class. Logging in on the
+ * console will grant this class access to the openBIS server.</i>
+ *
* @author Bernd Rinn
*/
public class OpenBISML
@@ -88,7 +96,7 @@ public class OpenBISML
{
// Not to be constructed.
}
-
+
//
// Versioning
//
@@ -97,14 +105,14 @@ public class OpenBISML
* The version of the API.
*/
public static final String VERSION = "1";
-
+
/**
- * The required version ("major.minor") of the screening API on the openBIS application server.
+ * The required version ("major.minor") of the screening API on the openBIS application server.
*/
public static final String REQUIRES_OPENBIS_AS_API = "1.2";
/**
- * The required version ("major.minor") of the screening API on the openBIS datastore server.
+ * The required version ("major.minor") of the screening API on the openBIS datastore server.
*/
public static final String REQUIRES_OPENBIS_DSS_API = "1.1";
@@ -132,6 +140,11 @@ public class OpenBISML
{
throw new RuntimeException("Login failed.");
}
+ init();
+ }
+
+ private static void init()
+ {
experiments = openbis.listExperiments();
experimentCodeToExperimentMap.clear();
for (ExperimentIdentifier e : experiments)
@@ -172,6 +185,10 @@ public class OpenBISML
return;
}
openbis.logout();
+ if (Login.OPENBIS_TOKEN_FILE.exists())
+ {
+ Login.OPENBIS_TOKEN_FILE.delete();
+ }
openbis = null;
}
@@ -944,7 +961,48 @@ public class OpenBISML
{
if (openbis == null)
{
- throw new RuntimeException("Not logged in.");
+ if (Login.OPENBIS_TOKEN_FILE.exists())
+ {
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new FileReader(Login.OPENBIS_TOKEN_FILE));
+ final String token = br.readLine();
+ br.close();
+ br = new BufferedReader(new FileReader(Login.OPENBIS_SERVER_URL_FILE));
+ final String serverUrl = br.readLine();
+ br.close();
+ br = null;
+ openbis = ScreeningOpenbisServiceFacadeFactory.tryCreate(token, serverUrl);
+ if (openbis == null)
+ {
+ throw new RuntimeException("Login failed.");
+ }
+ init();
+ } catch (IOException ex)
+ {
+ if (openbis == null)
+ {
+ throw new RuntimeException("Login failed.", ex);
+ }
+ } finally
+ {
+ if (br != null)
+ {
+ try
+ {
+ br.close();
+ } catch (IOException ex)
+ {
+ // Silence this.
+ }
+ }
+ }
+ }
+ if (openbis == null)
+ {
+ throw new RuntimeException("Not logged in.");
+ }
}
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
new file mode 100644
index 00000000000..a433b2c64ad
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/cli/Login.java
@@ -0,0 +1,221 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.client.cli;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.Closeable;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import org.apache.log4j.BasicConfigurator;
+import org.apache.log4j.varia.NullAppender;
+
+import jline.ConsoleReader;
+
+import ch.systemsx.cisd.args4j.Argument;
+import ch.systemsx.cisd.args4j.CmdLineParser;
+import ch.systemsx.cisd.args4j.Option;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.IScreeningOpenbisServiceFacade;
+import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacadeFactory;
+
+/**
+ * A class to provide a login on an openBIS screening server that can be used by the Matlab API.
+ *
+ * @author Bernd Rinn
+ */
+public class Login
+{
+ private final static File OPENBIS_DIR = new File(System.getProperty("user.home"), ".openbis");
+
+ public final static File OPENBIS_TOKEN_FILE = new File(OPENBIS_DIR, "session-token");
+
+ public final static File OPENBIS_USER_FILE = new File(OPENBIS_DIR, "user");
+
+ public final static File OPENBIS_SERVER_URL_FILE = new File(OPENBIS_DIR, "server");
+
+ private static class Parameters
+ {
+ private final CmdLineParser parser;
+
+ @Argument()
+ private final List<String> args = new ArrayList<String>();
+
+ @Option(name = "u", longName = "user")
+ private String user;
+
+ @Option(name = "s", longName = "server")
+ private String server;
+
+ Parameters(String[] args)
+ {
+ parser = new CmdLineParser(this);
+ try
+ {
+ parser.parseArgument(args);
+
+ if (server == null)
+ {
+ if (OPENBIS_SERVER_URL_FILE.exists())
+ {
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new FileReader(Login.OPENBIS_SERVER_URL_FILE));
+ server = br.readLine();
+ br.close();
+ } finally
+ {
+ closeQuietly(br);
+ }
+ } else
+ {
+ server = new ConsoleReader().readLine("Server URL: ");
+ }
+ }
+
+ if (user == null)
+ {
+ if (OPENBIS_USER_FILE.exists())
+ {
+ BufferedReader br = null;
+ try
+ {
+ br = new BufferedReader(new FileReader(OPENBIS_USER_FILE));
+ user = br.readLine();
+ br.close();
+ } finally
+ {
+ closeQuietly(br);
+ }
+ } else
+ {
+ user = new ConsoleReader().readLine("User: ");
+ }
+ }
+ } catch (final Exception ex)
+ {
+ throw new RuntimeException(ex.getMessage(), ex);
+ }
+ }
+
+ @SuppressWarnings("unused")
+ public List<String> getArgs()
+ {
+ return Collections.unmodifiableList(args);
+ }
+
+ public String getUser()
+ {
+ return user;
+ }
+
+ public String getServer()
+ {
+ return server;
+ }
+
+ }
+
+ private static void closeQuietly(Closeable closeable)
+ {
+ if (closeable != null)
+ {
+ try
+ {
+ closeable.close();
+ } catch (IOException ex)
+ {
+ // Silence this.
+ }
+ }
+ }
+
+ private static void write(String server, String user, String token)
+ {
+ BufferedWriter bw = null;
+ try
+ {
+ if (OPENBIS_DIR.exists() == false)
+ {
+ OPENBIS_DIR.mkdir();
+ }
+ bw = new BufferedWriter(new FileWriter(OPENBIS_SERVER_URL_FILE));
+ bw.write(server);
+ bw.close();
+ bw = new BufferedWriter(new FileWriter(OPENBIS_USER_FILE));
+ bw.write(user);
+ bw.close();
+ bw = new BufferedWriter(new FileWriter(OPENBIS_TOKEN_FILE));
+ bw.write(token);
+ } catch (Exception ex)
+ {
+ throw new RuntimeException(ex);
+ } finally
+ {
+ closeQuietly(bw);
+ }
+
+ }
+
+ public static void main(String[] args) throws IOException
+ {
+ BasicConfigurator.configure(new NullAppender());
+ try
+ {
+ final Parameters params = new Parameters(args);
+ if (params.getServer() == null)
+ {
+ throw new RuntimeException("Server not specified (give '-s').");
+ }
+ if (params.getUser() == null)
+ {
+ throw new RuntimeException("User not specified (give '-u').");
+ }
+ final String password =
+ new ConsoleReader().readLine("Password: ", Character.valueOf('*'));
+ if (password == null || password.length() == 0)
+ {
+ throw new RuntimeException("Password empty.");
+ }
+ final IScreeningOpenbisServiceFacade service =
+ ScreeningOpenbisServiceFacadeFactory.tryCreate(params.getUser(), password,
+ params.getServer());
+ if (service == null)
+ {
+ throw new RuntimeException("Login failed.");
+ }
+ final String token = service.getSessionToken();
+ write(params.getServer(), params.getUser(), token);
+ } catch (RuntimeException ex)
+ {
+ String msg = ex.getMessage();
+ if (msg == null && ex.getCause() != null)
+ {
+ msg = ex.getCause().getClass().getSimpleName() + ": " + ex.getMessage();
+ }
+ System.err.println(msg);
+ System.exit(1);
+ }
+ }
+
+}
--
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