Merge pull request #5616 from openmicroscopy/next_infra

Re-integrate next_infra into develop

components/blitz/resources/omero/Constants.ice

@@ -163,6 +163,11 @@ module omero {
 
     };
 
+    /**
+     * Log levels used by {@link RawAccessRequest}'s {@code log} command for {@code path}.
+     **/
+    enum LogLevel { Trace, Debug, Info, Warn, Error };
+
     /**
      * Namespaces for the {@link omero.api.IMetadata} interface.
      **/

components/blitz/resources/omero/Repositories.ice

@@ -540,6 +540,7 @@ module omero {
          * testing and diagnosis rather than actual client
          * functionality.
          **/
+        ["deprecate:Not intended for use by production clients. Functionality to be moved from Ice to microservices."]
         class RawAccessRequest extends omero::cmd::Request {
             string repoUuid;
             string command;

components/blitz/src/ome/formats/importer/ImportConfig.java

@@ -1,14 +1,10 @@
 /*
- *   $Id$
- *
  *   Copyright 2009-2016 Glencoe Software, Inc. All rights reserved.
  *   Use is subject to license terms supplied in LICENSE.txt
  */
 
 package ome.formats.importer;
 
-import static omero.rtypes.rstring;
-
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.File;
@@ -348,6 +344,7 @@ public void configureDebug(String levelString) {
          setLevel("ome.services.blitz", level);
          setLevel("ome.system", level);
          setLevel("loci", level);
+         setLevel("org.scijava.nativelib", level);
      }
 
      private void setLevel(String loggerName, Level level) {

components/blitz/src/ome/formats/importer/ImportLibrary.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2005-2016 University of Dundee & Open Microscopy Environment.
+ * Copyright (C) 2005-2018 University of Dundee & Open Microscopy Environment.
  * All rights reserved.
  *
  * This program is free software; you can redistribute it and/or modify
@@ -496,6 +496,13 @@ public List<Pixels> importImage(final ImportContainer container, int index,
                 return Collections.emptyList();
             }
         }
+        final IObject target = container.getTarget();
+        if (target != null && !target.getDetails().getPermissions().canLink()) {
+            /* stop this import before file upload commences */
+            final String message = "Cannot link to target";
+            log.error(message);
+            throw new IllegalArgumentException(message);
+        }
         final ImportProcessPrx proc = createImport(container);
         final String[] srcFiles = container.getUsedFiles();
         final List<String> checksums = new ArrayList<String>();

components/blitz/src/ome/services/blitz/repo/RawAccessRequestI.java

@@ -23,6 +23,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.google.common.base.Joiner;
+import com.google.common.collect.ImmutableMap;
+
 import Ice.Current;
 
 import ome.io.nio.FileBuffer;
@@ -36,6 +39,7 @@
 import omero.cmd.IRequest;
 import omero.cmd.Response;
 import omero.cmd.Unknown;
+import omero.constants.LogLevel;
 import omero.grid.InternalRepositoryPrx;
 import omero.grid.RawAccessRequest;
 import omero.grid.RepositoryException;
@@ -52,13 +56,24 @@ public class RawAccessRequestI extends RawAccessRequest implements IRequest {
     private static final long serialVersionUID = -303948503984L;
 
     private static Logger log = LoggerFactory.getLogger(RawAccessRequestI.class);
+    private static Logger logCmd = LoggerFactory.getLogger(log.getName() + " log cmd");
+
+    private static ImmutableMap<String, LogLevel> logLevels;
 
     private final Registry reg;
 
     protected Helper helper;
 
     protected InternalRepositoryPrx repo;
 
+    static {
+        final ImmutableMap.Builder<String, LogLevel> builder = ImmutableMap.builder();
+        for (final LogLevel value : LogLevel.values()) {
+            builder.put(value.name().toLowerCase(), value);
+        }
+        logLevels = builder.build();
+    }
+
     public RawAccessRequestI(Registry reg) {
         this.reg = reg;
     }
@@ -247,6 +262,31 @@ public void local(AbstractRepositoryI abstractRepositoryI,
                 throw new omero.ApiUsageException(null, null,
                         "Command: " + command + " takes just one argument");
             }
+        } else if ("log".equals(command)) {
+            final LogLevel logLevel = path == null ? null : logLevels.get(path.toLowerCase());
+            if (logLevel == null) {
+                throw new omero.ApiUsageException(null, null,
+                        "Command: " + command + " requires path value of: " + Joiner.on(", ").join(logLevels.keySet()));
+            }
+            for (final String arg : args) {
+                switch (logLevel) {
+                case Trace:
+                    logCmd.trace(arg);
+                    break;
+                case Debug:
+                    logCmd.debug(arg);
+                    break;
+                case Info:
+                    logCmd.info(arg);
+                    break;
+                case Warn:
+                    logCmd.warn(arg);
+                    break;
+                case Error:
+                    logCmd.error(arg);
+                    break;
+                }
+            }
         } else {
             throw new omero.ApiUsageException(null, null,
                     "Unknown command: " + command);

components/blitz/src/omero/gateway/Gateway.java

@@ -30,6 +30,7 @@
 import java.util.Map;
 import java.util.ResourceBundle;
 import java.util.Set;
+import java.util.UUID;
 import java.util.concurrent.Callable;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
@@ -85,7 +86,6 @@
 import omero.gateway.util.PojoMapper;
 import Glacier2.CannotCreateSessionException;
 import Glacier2.PermissionDeniedException;
-import Ice.ConnectionRefusedException;
 import Ice.DNSException;
 import Ice.SocketException;
 
@@ -101,7 +101,7 @@
  * @since 5.1
  */
 
-public class Gateway {
+public class Gateway implements AutoCloseable {
 
     /** Property to indicate that a {@link Connector} has been created */
     public static final String PROP_CONNECTOR_CREATED = "PROP_CONNECTOR_CREATED";
@@ -141,7 +141,7 @@ public class Gateway {
 
     /** Property to indicate that a stateless service has been created */
     public static final String PROP_STATELESS_SERVICE_CREATED = "PROP_STATELESS_SERVICE_CREATED";
-
+    
     /** Reference to a {@link Logger} */
     private Logger log;
 
@@ -179,7 +179,7 @@ public class Gateway {
 
     /** Flag to indicate that executor threads should be shutdown on disconnect */
     private boolean executorShutdownOnDisconnect = false;
-    
+
     /**
      * Creates a new Gateway instance
      * @param log A {@link Logger}
@@ -400,15 +400,15 @@ public boolean isConnected() {
      * @param user
      *            The user to get the session ID for
      * @return See above
+     * @throws DSOutOfServiceException
+     *             If the connection is broken, or not logged in
      */
-    public String getSessionId(ExperimenterData user) {
-        try {
-            Connector c = getConnector(new SecurityContext(user.getGroupId()),
-                    false, false);
-            if (c != null) {
-                return c.getClient().getSessionId();
-            }
-        } catch (DSOutOfServiceException e) {
+    public String getSessionId(ExperimenterData user)
+            throws DSOutOfServiceException {
+        Connector c = getConnector(new SecurityContext(user.getGroupId()),
+                false, false);
+        if (c != null) {
+            return c.getClient().getSessionId();
         }
         return null;
     }
@@ -1030,38 +1030,35 @@ private client createSession(LoginCredentials c)
         }
         secureClient.setAgent(c.getApplicationName());
         ServiceFactoryPrx entryEncrypted = null;
-        boolean session = false;
-        ServiceFactoryPrx guestSession = null;
-        try {
-            // Check if it is a session first
-            guestSession = secureClient.createSession("guest", "guest");
-            guestSession.getSessionService().getSession(username);
-            session = true;
-        } catch (Throwable e) {
-            // thrown if it is not a session, session has expired, or
-            // the guest login doesn't exist on the server
-        }
-        finally {
-            if (guestSession != null) 
-                secureClient.closeSession();
-        }
-        try {
-            if (session) {
+
+        boolean connected = false;
+        if (isSessionID(username)) {
+            try {
                 entryEncrypted = secureClient.joinSession(username);
-            } else {
+                connected = true;
+            } catch (Exception e) {
+                // Although username looks like a session ID it apparently isn't
+                // one.
+                log.warn(this, new LogMessage("Could not join session "
+                        + username + " , trying username/password login next.",
+                        e));
+            }
+        }
+        if (!connected) {
+            try {
                 if (args != null) {
                     entryEncrypted = secureClient.createSession();
                 } else {
                     entryEncrypted = secureClient.createSession(c.getUser()
                             .getUsername(), c.getUser().getPassword());
                 }
+            } catch (Exception e1) {
+                // close the session again before passing on the exception
+                secureClient.closeSession();
+                throw e1;
             }
-        } 
-        catch (Exception e1) {
-            // close the session again before passing on the exception
-            secureClient.closeSession();
-            throw e1;
         }
+
         this.pcs.firePropertyChange(PROP_SESSION_CREATED, null,
                 secureClient.getSessionId());
         serverVersion = entryEncrypted.getConfigService().getVersion();
@@ -1099,6 +1096,23 @@ public void run() {
         return secureClient;
     }
 
+    /**
+     * Checks if a String could be an ICE session ID.
+     * 
+     * @param s
+     *            The String to check
+     * @return <code>true</code> if it could be a session ID, <code>false</code>
+     *         otherwise.
+     */
+    private boolean isSessionID(String s) {
+        try {
+            UUID.fromString(s);
+        } catch (Exception e) {
+            return false;
+        }
+        return true;
+    }
+
     /**
      * Logs in a certain user
      * 
@@ -1220,7 +1234,9 @@ private void keepSessionAlive() throws DSOutOfServiceException {
             c = i.next();
             if (c.needsKeepAlive()) {
                 if (!c.keepSessionAlive()) {
-                    throw new DSOutOfServiceException("Network not available");
+                    // Session has died, e. g. due to server restart.
+                    // Remove connectors, so new ones will be created as requested.
+                    groupConnectorMap.removeAll(c.getGroupID());
                 }
             }
         }
@@ -1503,9 +1519,10 @@ public Connector getConnector(SecurityContext ctx, boolean recreate,
                             ConnectionStatus.NETWORK);
                 }
                 if (!c.keepSessionAlive()) {
-                    throw new DSOutOfServiceException(
-                            "Network down. Session not alive",
-                            ConnectionStatus.LOST_CONNECTION);
+                    // Session has died, e. g. due to server restart.
+                    // Remove connectors, so a new ones will be created.
+                    groupConnectorMap.removeAll(c.getGroupID());
+                    c = null;
                 }
             }
         }
@@ -1640,4 +1657,10 @@ private Connector createConnector(SecurityContext ctx, boolean permitNull)
         }
         return c;
     }
+
+    @Override
+    public void close() throws Exception {
+        if (connected)
+            disconnect();
+    }
 }

components/blitz/src/omero/gateway/JoinSessionCredentials.java

@@ -0,0 +1,69 @@
+/*
+ *------------------------------------------------------------------------------
+ *  Copyright (C) 2017 University of Dundee. All rights reserved.
+ *
+ *
+ *  This program is free software; you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation; either version 2 of the License, or
+ *  (at your option) any later version.
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License along
+ *  with this program; if not, write to the Free Software Foundation, Inc.,
+ *  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ *------------------------------------------------------------------------------
+ */
+package omero.gateway;
+
+import java.util.UUID;
+
+/**
+ * Holds all necessary information needed for joining an active OMERO server
+ * session
+ * 
+ * @author Dominik Lindner &nbsp;&nbsp;&nbsp;&nbsp; <a
+ *         href="mailto:d.lindner@dundee.ac.uk">d.lindner@dundee.ac.uk</a>
+ */
+public class JoinSessionCredentials extends LoginCredentials {
+
+    /**
+     * Creates a new instance
+     * 
+     * @param sessionId
+     *            The session ID
+     * @param host
+     *            The server hostname
+     */
+    public JoinSessionCredentials(String sessionId, String host) {
+        // simply set the session ID as username, everything else is
+        // handled in Gateway.createSession(LoginCredentials)
+        super(sessionId, "", host);
+
+        // Check that the sessionId is an UUID
+        UUID.fromString(sessionId);
+    }
+
+    /**
+     * Creates a new instance
+     * 
+     * @param sessionId
+     *            The session ID
+     * @param host
+     *            The server hostname
+     * @param port
+     *            The server port
+     */
+    public JoinSessionCredentials(String sessionId, String host, int port) {
+        // simply set the session ID as username, everything else is
+        // handled in Gateway.createSession(LoginCredentials)
+        super(sessionId, "", host, port);
+
+        // Check that the sessionId is an UUID
+        UUID.fromString(sessionId);
+    }
+}