Import template

components/blitz/resources/omero/Constants.ice

@@ -168,6 +168,7 @@ module omero {
         const string NSFSRENAME = "openmicroscopy.org/omero/fs/rename";
         const string NSMEASUREMENT = "openmicroscopy.org/omero/measurement";
         const string NSAUTOCLOSE = "openmicroscopy.org/omero/import/autoClose";
+        const string NSTARGETTEMPLATE = "openmicroscopy.org/omero/import/targetTemplate";
         const string NSCOMPANIONFILE = "openmicroscopy.org/omero/import/companionFile";
         const string NSLOGFILE = "openmicroscopy.org/omero/import/logFile";
         const string NSFILETRANSFER = "openmicroscopy.org/omero/import/fileTransfer";

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

@@ -1923,8 +1923,8 @@ public <T extends IObject> T getTarget(Class<T> klass, long id)
     }
 
     /**
-     * @param projectId the ID of the project
-     * @return the project
+     * @param projectId
+     * @return project with given id
      */
     public Project getProject(long projectId)
     {

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

@@ -28,6 +28,8 @@
 
 import loci.formats.FormatTools;
 import ome.formats.OMEROMetadataStoreClient;
+import ome.formats.importer.targets.ImportTarget;
+import ome.formats.importer.targets.TargetBuilder;
 import ome.formats.importer.util.IniFileLoader;
 import ome.system.PreferenceContext;
 import ome.system.UpgradeCheck;
@@ -49,6 +51,12 @@ public class ImportConfig {
 
     private final static Logger log = LoggerFactory.getLogger(ImportConfig.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";
+
     /**
      * Delimiter used to encode multiple servers in one preferences value.
      */
@@ -111,9 +119,15 @@ public class ImportConfig {
     public final StrValue email;
     public final StrValue userSpecifiedName;
     public final StrValue userSpecifiedDescription;
+
+    @Deprecated
     public final StrValue targetClass;
+
+    @Deprecated
     public final LongValue targetId;
 
+    public final StrValue target;
+
     public final BoolValue debug;
     public final BoolValue contOnError;
     public final BoolValue sendReport;
@@ -253,6 +267,7 @@ public synchronized void load() {
         userSpecifiedDescription = new StrValue("userSpecifiedDescription", this);
         targetClass  = new StrValue("targetClass", this);
         targetId     = new LongValue("targetId", this, 0L);
+        target       = new StrValue("target", this);
 
         savedProject = new LongValue("savedProject", this, 0L);
         savedDataset = new LongValue("savedDataset", this, 0L);
@@ -1019,4 +1034,28 @@ public File get() {
             }
         }
     }
+
+    public ImportTarget getTarget() {
+        TargetBuilder builder = new TargetBuilder();
+        if (target.get() != null)
+        {
+            ImportTarget t = builder.parse(target.get()).build();
+            log.info("Using import target: {}", target);
+            return t;
+        }
+        if (DATASET_CLASS.equals(targetClass.get()))
+        {
+            return builder.parse(
+                    String.format("%s:%s", DATASET_CLASS, targetId.get()))
+                    .build();
+        }
+        else if (SCREEN_CLASS.equals(targetClass.get()))
+        {
+            return builder.parse(
+                    String.format("%s:%s", SCREEN_CLASS, targetId.get()))
+                    .build();
+        }
+        return null;
+    }
+
 }

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

@@ -32,8 +32,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import ome.formats.OMEROMetadataStoreClient;
-import ome.formats.importer.ImportEvent.FILESET_EXCLUSION;
 import ome.formats.importer.exclusions.FileExclusion;
+import ome.formats.importer.targets.ImportTarget;
 import ome.formats.importer.transfers.FileTransfer;
 import ome.formats.importer.transfers.TransferState;
 import ome.formats.importer.transfers.UploadFileTransfer;
@@ -67,6 +67,7 @@
 import omero.grid.ManagedRepositoryPrxHelper;
 import omero.grid.RepositoryMap;
 import omero.grid.RepositoryPrx;
+import omero.model.Annotation;
 import omero.model.ChecksumAlgorithm;
 import omero.model.Dataset;
 import omero.model.Fileset;
@@ -102,12 +103,6 @@ public class ImportLibrary implements IObservable
 {
     private static Logger log = LoggerFactory.getLogger(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";
-
     /* checksum provider factory for verifying file integrity in upload */
     private static final ChecksumProviderFactory checksumProviderFactory = new ChecksumProviderFactoryImpl();
 
@@ -269,15 +264,22 @@ public boolean importCandidates(ImportConfig config, ImportCandidates candidates
             int numDone = 0;
             for (int index = 0; index < containers.size(); index++) {
                 ImportContainer ic = containers.get(index);
-                if (DATASET_CLASS.equals(config.targetClass.get()))
-                {
-                    ic.setTarget(store.getTarget(
-                            Dataset.class, config.targetId.get()));
-                }
-                else if (SCREEN_CLASS.equals(config.targetClass.get()))
-                {
-                    ic.setTarget(store.getTarget(
-                            Screen.class, config.targetId.get()));
+                ImportTarget target = config.getTarget();
+                if (target != null) {
+                    try {
+                        IObject obj = target.load(store, ic);
+                        if (!(obj instanceof Annotation)) {
+                            ic.setTarget(obj);
+                        } else {
+                            // This is likely a "post-processing" annotation
+                            // so that we don't have to resolve the target
+                            // until later.
+                            ic.getCustomAnnotationList().add((Annotation) obj);
+                        }
+                    } catch (Exception e) {
+                        log.error("Could not load target: {}", target);
+                        throw new RuntimeException("Failed to load target", e);
+                    }
                 }
 
                 if (config.checksumAlgorithm.get() != null) {
@@ -348,6 +350,7 @@ public ImportProcessPrx createImport(final ImportContainer container)
         notifyObservers(new ImportEvent.FILESET_UPLOAD_PREPARATION(
                 null, 0, usedFiles.length, null, null, null));
 
+        // Copied to ClientPathExclusion
         // TODO: allow looser sanitization according to server configuration
         final FilePathRestrictions portableRequiredRules =
                 FilePathRestrictionInstance.getFilePathRestrictions(FilePathRestrictionInstance.WINDOWS_REQUIRED,

components/blitz/src/ome/formats/importer/cli/CommandLineImporter.java

@@ -14,9 +14,9 @@
 import java.io.InputStreamReader;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.HashMap;
 
 import loci.formats.in.DefaultMetadataOptions;
 import loci.formats.in.MetadataLevel;
@@ -42,8 +42,6 @@
 import omero.grid.ImportProcessPrxHelper;
 import omero.model.Annotation;
 import omero.model.CommentAnnotationI;
-import omero.model.Dataset;
-import omero.model.Screen;
 
 import org.apache.commons.lang.time.StopWatch;
 import org.slf4j.Logger;
@@ -351,6 +349,7 @@ public static void usage() {
             + "  -l READER_FILE\t\t\tUse the list of readers rather than the default\n"
             + "  -d DATASET_ID\t\t\t\tOMERO dataset ID to import image into\n"
             + "  -r SCREEN_ID\t\t\t\tOMERO screen ID to import plate into\n"
+            + "  -T TARGET\t\t\t\ttarget for imports\n"
 
             + "  --report\t\t\t\tReport errors to the OME team\n"
             + "  --upload\t\t\t\tUpload broken files and log file (if any) with report. Required --report\n"
@@ -418,6 +417,7 @@ public static void advUsage() {
             + "  File exclusion:\n"
             + "  ---------------\n\n"
             + "    --exclude=filename      \tExclude files based on filename.\n\n"
+            + "    --exclude=clientpath    \tExclude files based on the original path.\n\n"
             + "\n"
             + "  e.g. $ bin/omero import -- --exclude=filename foo.tiff # First-time imports\n"
             + "       $ bin/omero import -- --exclude=filename foo.tiff # Second-time skips\n"
@@ -557,13 +557,16 @@ public static void main(String[] args) throws Exception {
         LongOpt exclude =
                 new LongOpt("exclude", LongOpt.REQUIRED_ARGUMENT, null, 20);
 
+        LongOpt target =
+                new LongOpt("target", LongOpt.REQUIRED_ARGUMENT, null, 21);
+
         LongOpt qaBaseURL = new LongOpt(
-                "qa-baseurl", LongOpt.REQUIRED_ARGUMENT, null, 21);
+                "qa-baseurl", LongOpt.REQUIRED_ARGUMENT, null, 22);
 
         LongOpt noStatsInfo =
-                new LongOpt("no-stats-info", LongOpt.NO_ARGUMENT, null, 22);
+                new LongOpt("no-stats-info", LongOpt.NO_ARGUMENT, null, 23);
         LongOpt noUpgradeCheck =
-                new LongOpt("no-upgrade-check", LongOpt.NO_ARGUMENT, null, 23);
+                new LongOpt("no-upgrade-check", LongOpt.NO_ARGUMENT, null, 24);
 
         // DEPRECATED OPTIONS
         LongOpt plateName = new LongOpt(
@@ -581,14 +584,14 @@ public static void main(String[] args) throws Exception {
         LongOpt annotationLinkDeprecated =
             new LongOpt("annotation_link", LongOpt.REQUIRED_ARGUMENT, null, 96);
 
-        Getopt g = new Getopt(APP_NAME, args, "cfl:s:u:w:d:r:k:x:n:p:h",
+        Getopt g = new Getopt(APP_NAME, args, "cfl:s:u:w:d:r:T:k:x:n:p:h",
                 new LongOpt[] { debug, report, upload, logs, email,
                                 name, description, noThumbnails,
                                 agent, annotationNamespace, annotationText,
                                 annotationLink, transferOpt, advancedHelp,
                                 checksumAlgorithm, minutesWait,
                                 closeCompleted, waitCompleted, autoClose,
-                                exclude, noStatsInfo,
+                                exclude, target, noStatsInfo,
                                 noUpgradeCheck, qaBaseURL,
                                 plateName, plateDescription,
                                 noThumbnailsDeprecated,
@@ -713,16 +716,21 @@ public static void main(String[] args) throws Exception {
                 }
                 break;
             }
+            case 'T':
             case 21: {
-                config.qaBaseURL.set(g.getOptarg());
+                config.target.set(g.getOptarg());
                 break;
             }
             case 22: {
+                config.qaBaseURL.set(g.getOptarg());
+                break;
+            }
+            case 23: {
                 log.info("Skipping minimum/maximum computation");
                 config.noStatsInfo.set(true);
                 break;
             }
-            case 23: {
+            case 24: {
                 log.info("Disabling upgrade check");
                 config.checkUpgrade.set(false);
                 break;
@@ -786,22 +794,18 @@ public static void main(String[] args) throws Exception {
             }
             case 'd': {
                 String datasetString = g.getOptarg();
-                if (datasetString.startsWith("Dataset:")) {
-                    datasetString = datasetString.substring(
-                            "Dataset:".length());
+                if (!datasetString.startsWith("Dataset:")) {
+                    datasetString = "Dataset:" + Long.valueOf(datasetString).toString();
                 }
-                config.targetId.set(Long.parseLong(datasetString));
-                config.targetClass.set(Dataset.class.getName());
+                config.target.set(datasetString);
                 break;
             }
             case 'r': {
                 String screenString = g.getOptarg();
-                if (screenString.startsWith("Screen:")) {
-                    screenString = screenString.substring(
-                            "Screen:".length());
+                if (!screenString.startsWith("Screen:")) {
+                    screenString = "Screen:" + Long.valueOf(screenString).toString();
                 }
-                config.targetId.set(Long.parseLong(screenString));
-                config.targetClass.set(Screen.class.getName());
+                config.target.set(screenString);
                 break;
             }
             case 'n': {

components/blitz/src/ome/formats/importer/exclusions/AbstractFileExclusion.java

@@ -42,7 +42,8 @@ public abstract class AbstractFileExclusion implements FileExclusion {
      * Enum of well-known {@link FileExclusion} names.
      */
     public enum Exclusion {
-        filename(FilenameExclusion.class);
+        filename(FilenameExclusion.class),
+        clientpath(ClientPathExclusion.class);
         Class<?> kls;
         Exclusion(Class<?> kls) {
             this.kls = kls;
@@ -82,4 +83,4 @@ protected String checksum(String filename, ChecksumAlgorithm checksumAlgorithm)
         return cp.checksumAsString();
     }
 
-}
+}