s/prepareImport/importFileset/ and add importPaths

Simplified method for clients which do not have access
to Bio-Formats and the ImportLibrary for filling out
the Fileset and ImportSettings objects. This prevents
a good deal of cut-n-paste but also reduces functionality.

components/blitz/resources/omero/Repositories.ice

@@ -296,13 +296,13 @@ module omero {
 
             /**
              * [ImportSettings] which are provided by the
-             * client on the call to [ManagedRepository::prepareImport].
+             * client on the call to [ManagedRepository::importFileset].
              **/
              ImportSettings settings;
 
             /**
              * [ImportLocation] which is calculated during
-             * the call to [ManagedRepository::prepareImport].
+             * the call to [ManagedRepository::importFileset].
              **/
              ImportLocation location;
 
@@ -342,7 +342,17 @@ module omero {
              * overwritten or interfering with one another, a new directory
              * may be created for the current session.
              **/
-            ImportProcess* prepareImport(omero::model::Fileset fs, ImportSettings settings) throws ServerError;
+            ImportProcess* importFileset(omero::model::Fileset fs, ImportSettings settings) throws ServerError;
+
+            /**
+             * For clients without access to Bio-Formats, the simplified
+             * []importPaths] method allows passing solely the absolute
+             * path of the files to be uploaded (no directories) and all
+             * configuration happens server-side. Much of the functionality
+             * provided via [omero::model::Fileset] and [omero::grid::ImportSettings]
+             * is of course lost.
+             **/
+            ImportProcess* importPaths(omero::api::StringSet filePaths) throws ServerError;
 
             /**
              * List imports that are currently running in this importer.

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

@@ -55,8 +55,8 @@ public class ImportContainer
     private IObject target;
 
 	public ImportContainer(File file,
-			IObject target,
-			Double[] userPixels, String reader, String[] usedFiles, Boolean isSPW)
+            IObject target,
+            Double[] userPixels, String reader, String[] usedFiles, Boolean isSPW)
 	{
 		this.file = file;
 		this.target = target;

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

@@ -80,10 +80,10 @@ public class ImportLibrary implements IObservable
 
     /** 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";
-    
+
     private final ArrayList<IObserver> observers = new ArrayList<IObserver>();
 
     private final OMEROMetadataStoreClient store;
@@ -140,7 +140,7 @@ 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.
      */
@@ -213,7 +213,7 @@ public ImportProcessPrx createImport(final ImportContainer container)
         final ImportSettings settings = new ImportSettings();
         final Fileset fs = new FilesetI();
         container.fillData(new ImportConfig(), settings, fs);
-        return repo.prepareImport(fs, settings);
+        return repo.importFileset(fs, settings);
 
     }
 

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

@@ -121,7 +121,7 @@ public void ice_exception(Exception ex) {
 
     /**
      * The import location as defined by the managed repository during
-     * prepareImport. Never null.
+     * importFileset. Never null.
      */
     private final ImportLocation location;
 

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

@@ -41,6 +41,7 @@
 import Ice.Current;
 
 import ome.formats.importer.ImportConfig;
+import ome.formats.importer.ImportContainer;
 import ome.services.blitz.impl.ServiceFactoryI;
 
 import omero.ServerError;
@@ -51,9 +52,11 @@
 import omero.grid._ManagedRepositoryTie;
 import omero.model.Fileset;
 import omero.model.FilesetEntry;
+import omero.model.FilesetI;
 import omero.model.FilesetJobLink;
 import omero.model.FilesetVersionInfo;
 import omero.model.FilesetVersionInfoI;
+import omero.model.IObject;
 import omero.model.IndexingJobI;
 import omero.model.Job;
 import omero.model.MetadataImportJob;
@@ -126,7 +129,7 @@ public Ice.Object tie() {
      *
      * @FIXME For the moment only the top-level directory is being incremented.
      */
-    public ImportProcessPrx prepareImport(Fileset fs, ImportSettings settings,
+    public ImportProcessPrx importFileset(Fileset fs, ImportSettings settings,
             Ice.Current __current) throws omero.ServerError {
 
         if (fs == null || fs.sizeOfUsedFiles() < 1) {
@@ -161,6 +164,25 @@ public ImportProcessPrx prepareImport(Fileset fs, ImportSettings settings,
         return createImportProcess(fs, location, settings, __current);
     }
 
+    public ImportProcessPrx importPaths(List<String> paths,
+            Ice.Current __current) throws ServerError {
+
+        if (paths == null || paths.size() < 1) {
+            throw new omero.ApiUsageException(null, null, "No paths provided");
+        }
+
+        final ImportContainer container = new ImportContainer(
+                null /*file*/, null /*target*/, null /*userPixels*/,
+                "Unknown" /*reader*/, paths.toArray(new String[0]),
+                false /*spw*/);
+
+        final ImportSettings settings = new ImportSettings();
+        final Fileset fs = new FilesetI();
+        container.fillData(new ImportConfig(), settings, fs);
+
+        return importFileset(fs, settings, __current);
+    }
+
     public List<ImportProcessPrx> listImports(Ice.Current __current) throws omero.ServerError {
 
         final List<Long> filesetIds = new ArrayList<Long>();

components/blitz/test/ome/services/blitz/test/ManagedRepositoryITest.java

@@ -136,7 +136,7 @@ public void testBasicImportExample() throws Exception {
         Fileset fs = new FilesetI();
         ic.fillData(new ImportConfig(), settings, fs);
 
-        ImportProcessPrx i = repo.prepareImport(fs, settings, curr());
+        ImportProcessPrx i = repo.importFileset(fs, settings, curr());
         assertNotNull(i);
 
         upload(i.getUploader(0));

components/tools/OmeroJava/test/integration/ManagedRepositoryTest.java

@@ -26,14 +26,14 @@
 import omero.model.OriginalFile;
 import omero.sys.EventContext;
 
-/** 
+/**
 * Collections of tests for the <code>ManagedRepository</code> service.
 *
 * @author Colin Blackburn &nbsp;&nbsp;&nbsp;&nbsp;
 * <a href="mailto:[email protected]">[email protected]</a>
 */
 @Test(groups = {"integration", "fs"})
-public class ManagedRepositoryTest 
+public class ManagedRepositoryTest
    extends AbstractServerTest
 {
 
@@ -67,7 +67,7 @@ public void setRepo() throws Exception {
 	 */
 	void assertFileExists(String message, String path)
 	        throws ServerError
-	{   
+	{
 	    assertTrue(message + path, repo.fileExists(path));
 	}
 
@@ -77,9 +77,9 @@ void assertFileExists(String message, String path)
 	 */
 	void assertFileDoesNotExist(String message, String path)
 	        throws ServerError
-	{  
+	{
 	    assertFalse(message + path, repo.fileExists(path));
-	}  
+	}
 
 	/**
 	 * Construct a path from its elements
@@ -96,7 +96,7 @@ String buildPath(String[] pathElements)
 	}
 
 	// Primarily to get code compiling during the major refactoring
-	ImportLocation prepareImport(List<String> srcPaths) {
+	ImportLocation importFileset(List<String> srcPaths) {
 	    fail("NYI");
 	    return null;
 	}
@@ -128,30 +128,30 @@ public void testGetCurrentRepoDirSimple()
 	    srcPaths.add(buildPath(src));
 	    String[] dest = {uniquePath, file1};
 	    destPath = buildPath(dest);
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 		assertContains(data.usedFiles.get(0), destPath);
 		touch(uploadUsedFile(data, data.usedFiles.get(0)));
-        
+
         // Different file that should go in existing directory
 	    src[1] = file2;
 	    srcPaths.set(0, buildPath(src));
 	    dest[1] = file2;
 	    destPath = buildPath(dest);
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 		assertContains(data.usedFiles.get(0), destPath);
 		touch(uploadUsedFile(data, data.usedFiles.get(0)));
 
         // Same file that should go in new directory
 	    dest[0] = uniquePath + "-1";
 	    destPath = buildPath(dest);
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 		assertContains(data.usedFiles.get(0), destPath);
 		touch(uploadUsedFile(data, data.usedFiles.get(0)));
 
         // Same file again that should go in new directory
 	    dest[0] = uniquePath + "-2";
 	    destPath = buildPath(dest);
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 		assertContains(data.usedFiles.get(0), destPath);
 	}
 
@@ -162,9 +162,9 @@ public void testGetCurrentRepoDirSimple()
 	 * @throws Exception Thrown if an error occurred.
 	 */
 	@Test
-	public void testGetCurrentRepoDirMultipleFiles() 
+	public void testGetCurrentRepoDirMultipleFiles()
 	        throws Exception
-	{   
+	{
 	    List<String> srcPaths = new ArrayList<String>();
 	    List<String> destPaths = new ArrayList<String>();
 
@@ -183,7 +183,7 @@ public void testGetCurrentRepoDirMultipleFiles()
 	    destPaths.add(buildPath(dest));
 	    dest[1] = file2;
 	    destPaths.add(buildPath(dest));
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -200,7 +200,7 @@ public void testGetCurrentRepoDirMultipleFiles()
 	    destPaths.set(0, buildPath(dest));
 	    dest[1] = file4;
 	    destPaths.set(1, buildPath(dest));
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -217,7 +217,7 @@ public void testGetCurrentRepoDirMultipleFiles()
 	    destPaths.set(0, buildPath(dest));
 	    dest[1] = file4;
 	    destPaths.set(1, buildPath(dest));
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -230,7 +230,7 @@ public void testGetCurrentRepoDirMultipleFiles()
 	    destPaths.set(0, buildPath(dest));
 	    dest[1] = file4;
 	    destPaths.set(1, buildPath(dest));
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -275,7 +275,7 @@ public void testGetCurrentRepoDirNested()
 	    dest[2] = subSubDir;
 	    dest = (String[]) ArrayUtils.add(dest,file3);
 	    destPaths.add(buildPath(dest));
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -292,7 +292,7 @@ public void testGetCurrentRepoDirNested()
 	    dest2[2] = subSubDir;
 	    dest2 = (String[]) ArrayUtils.add(dest2,file3);
 	    destPaths.add(buildPath(dest2));
-	    data = prepareImport(srcPaths);
+	    data = importFileset(srcPaths);
 	    assertTrue(data.usedFiles.size()==destPaths.size());
 	    for (int i=0; i<data.usedFiles.size(); i++) {
             assertContains(data.usedFiles.get(i), destPaths.get(i));
@@ -315,7 +315,7 @@ public void testDeleteUploadedFileSimple()
 
 	    String[] src = {uniquePath, file1};
 	    srcPaths.add(buildPath(src));
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 		touch(uploadUsedFile(data, data.usedFiles.get(0)));
 		for (String path : data.usedFiles) {
 		    assertFileExists("Upload failed. File does not exist: ", path);
@@ -344,7 +344,7 @@ public void testDeleteUploadedMultipleFilesSimple()
 	    srcPaths.add(buildPath(src));
 	    src[1] = file2;
 	    srcPaths.add(buildPath(src));
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 		for (String path : data.usedFiles) {
 		    touch(uploadUsedFile(data, path));
 		    assertFileExists("Upload failed. File does not exist: ", path);
@@ -373,7 +373,7 @@ public void testDeleteUploadedPartialFiles()
 	    srcPaths.add(buildPath(src));
 	    src[1] = file2;
 	    srcPaths.add(buildPath(src));
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 		touch(uploadUsedFile(data, data.usedFiles.get(0)));
 		assertFileExists("Upload failed. File does not exist: ", data.usedFiles.get(0));
 		assertFileDoesNotExist("Something wrong. File does exist!: ", data.usedFiles.get(1));
@@ -411,7 +411,7 @@ public void testDeleteUploadedMultipleFilesNested()
 	    src = (String[]) ArrayUtils.add(src,file3);
 	    srcPaths.add(buildPath(src));
 
-	    ImportLocation data = prepareImport(srcPaths);
+	    ImportLocation data = importFileset(srcPaths);
 		for (String path : data.usedFiles) {
 		    touch(uploadUsedFile(data, path));
 		    assertFileExists("Upload failed. File does not exist: ", path);
@@ -440,7 +440,7 @@ public void testDeleteUploadedMultipleSetsDeleteOneSet()
 	    srcPaths.add(buildPath(src));
 	    src[1] = file2;
 	    srcPaths.add(buildPath(src));
-	    ImportLocation data1 = prepareImport(srcPaths);
+	    ImportLocation data1 = importFileset(srcPaths);
 
 	    srcPaths.clear();
 	    file1 = UUID.randomUUID().toString() + ".dv";
@@ -449,7 +449,7 @@ public void testDeleteUploadedMultipleSetsDeleteOneSet()
 	    srcPaths.add(buildPath(src));
 	    src[1] = file2;
 	    srcPaths.add(buildPath(src));
-	    ImportLocation data2 = prepareImport(srcPaths);
+	    ImportLocation data2 = importFileset(srcPaths);
 
 		for (String path : data1.usedFiles) {
 		    touch(uploadUsedFile(data1, path));

components/tools/OmeroPy/test/integration/repository.py

@@ -429,14 +429,26 @@ def upload_folder(self, proc, folder):
                 rfs.close()
         return ret_val
 
-    def testSimpleImport(self):
+    def testImportFileset(self):
         client = self.new_client()
         mrepo = self.getManagedRepo(client)
         folder = self.create_test_dir()
         fileset = self.create_fileset(folder)
         settings = self.create_settings()
 
-        proc = mrepo.prepareImport(fileset, settings)
+        proc = mrepo.importFileset(fileset, settings)
+        self.assertImport(client, proc, folder)
+
+    def testImportPaths(self):
+        client = self.new_client()
+        mrepo = self.getManagedRepo(client)
+        folder = self.create_test_dir()
+        paths = folder.files()
+
+        proc = mrepo.importPaths(paths)
+        self.assertImport(client, proc, folder)
+
+    def assertImport(self, client, proc, folder):
         hashes = self.upload_folder(proc, folder)
         handle = proc.verifyUpload(hashes)
         cb = CmdCallbackI(client, handle)
@@ -447,6 +459,5 @@ def testSimpleImport(self):
         else:
             self.assertEquals(1, len(rsp.pixels))
 
-
 if __name__ == '__main__':
     unittest.main()