Figure scripts

README.txt

@@ -1,9 +1,5 @@
+For a quick start-up guide, see docs/QUICKSTART.txt
 
-For the impatient, see docs/QUICKSTART.txt
-
-For extensive information on installation and developing omero,
-please see the OMERO development Trac:
-
-  http://trac.openmicroscopy.org.uk/ome/wiki/OmeroInstall
-  http://trac.openmicroscopy.org.uk/ome/wiki/OmeroBuild
+Full developer documentation is available from http://www.openmicroscopy.org/site/support/omero4/developers/index.html
 
+If you are looking for something else, please refer to the main OME website http://www.openmicroscopy.org/site

build.xml

@@ -550,6 +550,7 @@ To get started using Eclipse, execute "./build.py build-dev" and import the top-
         <gitdescribe select="\2"> </gitdescribe>
 
         <exec executable="make" failonerror="true" dir="${sphinx.dir}">
+            <env key="SOURCE_BRANCH" value="v.${version.describe}"/>
             <env key="OMERO_RELEASE" value="${version.describe}"/>
             <arg line="clean html latexpdf"/>
         </exec>
@@ -885,7 +886,7 @@ omero.version=${omero.version}
     </target>
 
     <target name="webstart-sign">
-        <signjar alias="${jarsign.alias}" keystore="${jarsign.keystore}" storepass="${jarsign.storepass}" preservelastmodified="true">
+        <signjar alias="${jarsign.alias}" keystore="${jarsign.keystore}" storepass="${jarsign.storepass}" preservelastmodified="false">
             <path>
                 <fileset dir="${dist.dir}/lib/insight" includes="*.jar"/>
             </path>
@@ -899,7 +900,7 @@ omero.version=${omero.version}
         </apply>
     </target>
 
-    <target name="release-webstart" depends="init">
+    <target name="release-webstart" depends="init" description="Generates webstart jars under dist/lib/insight">
         <unzip src="components/insight/OUT/dist/OMERO.insight-${omero.version}.zip" dest="${dist.dir}/lib/insight">
             <patternset>
                 <include name="**/*.jar"/>

components/blitz/resources/omero/Constants.ice

@@ -160,6 +160,7 @@ module omero {
         const string NSCOMPANIONFILE = "openmicroscopy.org/omero/import/companionFile";
         const string NSEXPERIMENTERPHOTO = "openmicroscopy.org/omero/experimenter/photo";
         const string NSBULKANNOTATIONS = "openmicroscopy.org/omero/bulk_annotations";
+        const string NSOMETIFF = "openmicroscopy.org/omero/ome_tiff";
         //
         // omero.grid.Param.namespaces in Scripts.ice
         //

components/blitz/src/ome/formats/OMEROMetadataStoreClient.java

@@ -1510,15 +1510,11 @@ private File createSeriesMetadataFile(String suffix)
     }
 
     /**
-     * Populates archive flags on all images currently processed links
-     * relevant original metadata files as requested and performs graph logic
-     * to have the scafolding in place for later original file upload if
+     * Links relevant companion files for later original file upload if
      * we are of the HCS domain.
-     * @param archive Whether or not the user requested the original files to
-     * be archived.
      * @return A list of the temporary metadata files created on local disk.
      */
-    public List<File> setArchiveScreeningDomain(boolean archive)
+    public List<File> setArchiveScreeningDomain()
     {
 	List<File> metadataFiles = new ArrayList<File>();
 	String[] usedFiles = reader.getUsedFiles();
@@ -1529,55 +1525,34 @@ public List<File> setArchiveScreeningDomain(boolean archive)
 	formatString = formatString.replace("class loci.formats.in.", "");
 	formatString = formatString.replace("Reader", "");
 	LSID plateKey = new LSID(Plate.class, 0);
-		// Populate the archived flag on the image. This inadvertently
-		// ensures that an Image object (and corresponding container)
-		// exists.
+	// Set the archived flag to false as archiving is disabled for screens
 	for (int series = 0; series < reader.getSeriesCount(); series++)
 	{
 		LinkedHashMap<Index, Integer> imageIndexes =
 			new LinkedHashMap<Index, Integer>();
 		imageIndexes.put(Index.IMAGE_INDEX, series);
 		Image image = getSourceObject(Image.class, imageIndexes);
-		image.setArchived(toRType(archive));
+		image.setArchived(toRType(false));
 	}
-	// Create all original file objects for later population based on
-	// the existence or abscence of companion files and the archive
-	// flag. This increments the original file count by the number of
-	// files to actually be created.
+	// Create original file objects for later population for companion
+	// files. This increments the original file count by the
+	// number of files to actually be created.
 	int originalFileIndex = 0;
 	for (String usedFilename : usedFiles)
 	{
 		File usedFile = new File(usedFilename);
 		boolean isCompanionFile = companionFiles == null? false :
-			companionFiles.contains(usedFilename);
-		if (archive || isCompanionFile)
-		{
-			LinkedHashMap<Index, Integer> indexes =
+			    companionFiles.contains(usedFilename);
+		LinkedHashMap<Index, Integer> indexes =
 				new LinkedHashMap<Index, Integer>();
-			indexes.put(Index.ORIGINAL_FILE_INDEX, originalFileIndex);
-			if (isCompanionFile)
-			{
-				// PATH 1: The file is a companion file, create it,
-				// and increment the next original file's index.
-				String format = "Companion/" + formatString;
-				createOriginalFileFromFile(usedFile, indexes, format);
-				addCompanionFileAnnotationTo(plateKey, indexes,
-						                     originalFileIndex);
-				originalFileIndex++;
-			}
-			else
-			{
-				// PATH 2: We're archiving and the file is not a
-				// companion file, create it, and increment the next
-				// original file's index.
-				createOriginalFileFromFile(usedFile, indexes,
-						formatString);
-				LSID originalFileKey =
-					new LSID(OriginalFile.class, originalFileIndex);
-				addReference(plateKey, originalFileKey);
-				originalFileIndex++;
-			}
-		}
+		indexes.put(Index.ORIGINAL_FILE_INDEX, originalFileIndex);
+		// The file is a companion file, create it,
+		// and increment the next original file's index.
+		String format = "Companion/" + formatString;
+		createOriginalFileFromFile(usedFile, indexes, format);
+		addCompanionFileAnnotationTo(plateKey, indexes,
+		        originalFileIndex);
+		originalFileIndex++;
 	}
 	return metadataFiles;
     }

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

@@ -457,8 +457,15 @@ protected ImportContainer singleFile(File file, ImportConfig config)
         } catch (MissingLibraryException mle)
         {
             safeUpdate(new ErrorHandler.MISSING_LIBRARY(path, mle, usedFiles, format));
-        } catch (Exception e)
+        } catch (Throwable t)
         {
+            Exception e = null;
+            if (t instanceof Exception) {
+                e = (Exception) t;
+            }
+            else {
+                e = new Exception(t);
+            }
             safeUpdate(new ErrorHandler.FILE_EXCEPTION(path, e, usedFiles, format));
         }
 

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

@@ -89,6 +89,12 @@ public class ImportLibrary implements IObservable
 {
     private static Log log = LogFactory.getLog(ImportLibrary.class);
 
+    /** The class used to identify the dataset target.*/
+    private static final String DATASET_CLASS = "omero.model.Dataset";
+
+    /** The class used to identify the screen target.*/
+    private static final String SCREEN_CLASS = "omero.model.Screen";
+
     /** Default arraybuf size for planar data transfer. (1MB) */
     public static final int DEFAULT_ARRAYBUF_SIZE = 1048576;
 
@@ -266,6 +272,9 @@ public void notifyObservers(ImportEvent event)
 
     /**
      * Primary user method for importing a number
+     * 
+     * @param config The configuration information.
+     * @param candidates Hosts information about the files to import.
      */
     public boolean importCandidates(ImportConfig config, ImportCandidates candidates)
     {
@@ -274,12 +283,12 @@ public boolean importCandidates(ImportConfig config, ImportCandidates candidates
             int numDone = 0;
             for (int index = 0; index < containers.size(); index++) {
                 ImportContainer ic = containers.get(index);
-                if (config.targetClass.get() == "omero.model.Dataset")
+                if (DATASET_CLASS.equals(config.targetClass.get()))
                 {
                     ic.setTarget(store.getTarget(
                             Dataset.class, config.targetId.get()));
                 }
-                else if (config.targetClass.get() == "omero.model.Screen")
+                else if (SCREEN_CLASS.equals(config.targetClass.get()))
                 {
                     ic.setTarget(store.getTarget(
                             Screen.class, config.targetId.get()));
@@ -289,6 +298,9 @@ else if (config.targetClass.get() == "omero.model.Screen")
                     importImage(ic, index, numDone, containers.size());
                     numDone++;
                 } catch (Throwable t) {
+                    notifyObservers(new ErrorHandler.INTERNAL_EXCEPTION(
+                        ic.getFile().toString(), new RuntimeException(t),
+                        ic.getUsedFiles(), ic.getReader()));
                     if (!config.contOnError.get()) {
                         log.info("Exiting on error");
                         return false;
@@ -527,7 +539,7 @@ public List<Pixels> importImage(ImportContainer container, int index,
             {
                 log.info("Reader is of HCS domain, disabling metafile.");
 
-                metadataFiles = store.setArchiveScreeningDomain(archive);
+                metadataFiles = store.setArchiveScreeningDomain();
             }
             else
             {

components/blitz/src/ome/formats/importer/util/IniFileLoader.java

@@ -151,7 +151,7 @@ public String getLogFile() {
      */
     public String getHomeUrl()
     {
-        return staticPref("General", "url", "http://www.openmicroscopy.org/site/support/omero4/products/feature-list");
+        return staticPref("General", "url", "http://www.openmicroscopy.org/site/products/omero/feature-list");
     }
 
     /**

components/blitz/src/omero/client.java

@@ -24,6 +24,7 @@
 import java.util.Properties;
 import java.util.Set;
 import java.util.UUID;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import ome.util.Utils;
 import omero.api.ClientCallback;
@@ -153,6 +154,17 @@ public void run() {
      */
     private volatile Resources __resources;
 
+    /**
+     * Whether or not remote calls are allowed during shutdown.
+     * If false (the default), then the instance will try to
+     * connect to the server and free any resources. Otherwise,
+     * a fastShutdown will take place. The most common reason
+     * to perform a fast shutdown is the loss of network
+     * connection. Calling "waitForShutdown" on the Ice stack
+     * without the proper connection will hang. (See #9673)
+     */
+    private AtomicBoolean fastShutdown = new AtomicBoolean(false);
+
     /**
      * @see #isSecure()
      */
@@ -370,6 +382,15 @@ private void init(Ice.InitializationData id) {
 
     }
 
+    /**
+     * Sets the {@link #fastShutdown} flag. By setting this
+     * to true, you will prevent proper clean up. This should
+     * only be used in the case of network loss (or similar).
+     */
+    public boolean setFastShutdown(boolean fastShutdown) {
+        return this.fastShutdown.getAndSet(fastShutdown);
+    }
+
     /**
      * Sets the {@link omero.model.Session#getUserAgent() user agent} string for
      * this client. Every session creation will be passed this argument. Finding
@@ -831,8 +852,9 @@ public void closeSession() {
             }
         }
 
+        final boolean fast = this.fastShutdown.get();
         try {
-            if (oldSf != null) {
+            if (oldSf != null && !fast) {
                 oldSf = ServiceFactoryPrxHelper.uncheckedCast(oldSf.ice_oneway());
             }
         } catch (Ice.ConnectionLostException cle) {
@@ -847,7 +869,9 @@ public void closeSession() {
             // ok. client is having network issues
         } finally {
             try {
-                oldIc.destroy();
+                if (oldIc != null && !fast) {
+                    oldIc.destroy();
+                }
             } finally {
                 CLIENTS.remove(this);
             }

components/blitz/src/pojos/ExperimenterData.java

@@ -298,4 +298,20 @@ public long getGroupId() {
     	return g.getId();
     }
 
+    /**
+     * Checks if supplied group id matches any group to which the current
+     * experimenter belongs to.
+     * @param long groupId
+     * @return bolean <code>true</code>/<code>false</code> depending if matching
+     *                id found
+     */
+    public boolean isMemberOfGroup(long groupId) {
+        for (GroupData group : this.getGroups()) {
+            if (group.getId() == groupId) {
+                return true;
+            }
+        }
+        return false;
+    }
+
 }

components/blitz/src/pojos/GroupData.java

@@ -9,7 +9,9 @@
 
 
 //Java imports
+import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
@@ -114,6 +116,9 @@ public class GroupData extends DataObject {
     /** The leaders of the group. */
     private Set leaders;
 
+    /** The users that belong to the group who are not owners.*/
+    private Set members;
+
     /** Creates a new instance. */
     public GroupData() {
         setDirty(true);
@@ -234,6 +239,32 @@ && asGroup().sizeOfGroupExperimenterMap() >= 0) {
     }
 
     /**
+     * Returns the list of experimenters that are not owners of the group.
+     * 
+     * @return See above.
+     */
+    public Set getMembersOnly() {
+    	Set leaders = getLeaders();
+    	Set experimenters = getExperimenters();
+    	if (leaders == null || leaders.size() == 0) return experimenters;
+    	if (experimenters == null || experimenters.size() == 0)
+    		return leaders;
+    	List<Long> ids = new ArrayList<Long>(leaders.size());
+    	Iterator i = leaders.iterator();
+    	while (i.hasNext()) {
+			ids.add(((ExperimenterData) i.next()).getId());
+		}
+    	Set members = new HashSet();
+    	i = experimenters.iterator();
+    	ExperimenterData exp;
+    	while (i.hasNext()) {
+    		exp = (ExperimenterData) i.next();
+			if (!ids.contains(exp.getId()))
+				members.add(exp);
+		}
+    	return members;
+    }
+     /**
      * Overridden to return the id of the object.
      * @see DataObject#getGroupId()
      */

components/common/src/ome/util/package.html

@@ -22,20 +22,6 @@
   object model</a>.
 </p>
 
-<h2>Related Documentation</h2>
-
-For more information, please see:
-<ul>
-  <li>
-    <a href="http://trac.openmicroscopy.org.uk/ome/wiki/FilterPattern">
-    wiki:FilterPattern</a>
-  </li>
-  <li>
-    <a href="http://trac.openmicroscopy.org.uk/ome/wiki/ModelMapping">
-    wiki:ModelMapping</a>
-  </li>
-</ul>
-
 <!-- Put @see and @since tags down here. -->
   @see ome.util.Filter
 </body>