package com.github.celldynamics.quimp.omero;
   
   import java.io.Closeable;
   import java.io.File;
   import java.io.FileInputStream;
   import java.io.FileOutputStream;
   import java.io.IOException;
   import java.net.URISyntaxException;
   import java.nio.ByteBuffer;
  import java.nio.file.Path;
  import java.nio.file.Paths;
  import java.util.ArrayList;
  import java.util.Arrays;
  import java.util.Collection;
  import java.util.Iterator;
  import java.util.List;
  import java.util.Map;
  import java.util.Properties;
  import java.util.concurrent.ExecutionException;
  
  import org.apache.commons.io.FilenameUtils;
  import org.scijava.Context;
  import org.scijava.io.IOService;
  import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import com.github.celldynamics.quimp.QuimpException;
  
  import Glacier2.CannotCreateSessionException;
  import Glacier2.PermissionDeniedException;
  import edu.emory.mathcs.backport.java.util.Collections;
  import loci.formats.in.DefaultMetadataOptions;
  import loci.formats.in.MetadataLevel;
  import net.imagej.Dataset;
  import net.imagej.omero.DefaultOMEROSession;
  import net.imagej.omero.OMEROLocation;
  import net.imagej.omero.OMEROService;
  import ome.formats.OMEROMetadataStoreClient;
  import ome.formats.importer.ImportCandidates;
  import ome.formats.importer.ImportConfig;
  import ome.formats.importer.ImportLibrary;
  import ome.formats.importer.OMEROWrapper;
  import ome.formats.importer.cli.ErrorHandler;
  import ome.formats.importer.cli.LoggingImportMonitor;
  import omero.ServerError;
  import omero.client;
  import omero.api.IMetadataPrx;
  import omero.api.RawFileStorePrx;
  import omero.gateway.Gateway;
  import omero.gateway.SecurityContext;
  import omero.gateway.exception.DSAccessException;
  import omero.gateway.exception.DSOutOfServiceException;
  import omero.gateway.facility.BrowseFacility;
  import omero.gateway.facility.DataManagerFacility;
  import omero.gateway.model.DatasetData;
  import omero.gateway.model.FileAnnotationData;
  import omero.gateway.model.ImageData;
  import omero.gateway.model.ProjectData;
  import omero.model.Annotation;
  import omero.model.ChecksumAlgorithm;
  import omero.model.ChecksumAlgorithmI;
  import omero.model.FileAnnotation;
  import omero.model.FileAnnotationI;
  import omero.model.Image;
  import omero.model.ImageAnnotationLink;
  import omero.model.ImageAnnotationLinkI;
  import omero.model.OriginalFile;
  import omero.model.OriginalFileI;
  import omero.model.enums.ChecksumAlgorithmSHA1160;
  import omero.sys.ParametersI;
  
  /**
   * Provide access to Omero.
   * 
   * @author p.baniukiewicz
   *
   */
  public class OmeroBrowser implements Closeable {
    private static final String NAMESPACE = "QCONF";
    static final Logger LOGGER = LoggerFactory.getLogger(OmeroBrowser.class.getName());
    static final int DEF_PORT = 4064;
  
    private Gateway gateway = null;
    private SecurityContext ctx;
    private String user;
    private String host;
    private String pass;
    private client client;
    private DefaultOMEROSession ds;
    OMEROService os;
    Context context;
    private int port;
  
    /**
     * Initialise browser.
     * 
     * <p>Do not open connection. Use {@link #connect()} instead.
     * 
     * @param user omero user name
    * @param pass omero password
    * @param host host
    * @param port port, see {@link #DEF_PORT}
    */
   public OmeroBrowser(String user, String pass, String host, int port) {
     this.port = port;
     this.host = host;
     this.user = user;
     this.pass = pass;
   }
 
   /**
    * Connect to Omero.
    * 
    * <p>All fields provided to {@link #OmeroBrowser(String, String, String, int)} must contain
    * nonempty strings. Throw exception if connection unsuccessful.
    * 
    * @throws DSOutOfServiceException connection error
    * @throws QuimpException if any of fields: user/pass/host is empty or null
    * @throws URISyntaxException on Omero error
    * @throws CannotCreateSessionException on Omero error
    * @throws PermissionDeniedException on Omero error
    * @throws ServerError on Omero error
    */
   public void connect() throws DSOutOfServiceException, QuimpException, URISyntaxException,
           ServerError, PermissionDeniedException, CannotCreateSessionException {
     silentClose(); // close old connection
     LOGGER.debug("Opening connection:" + user + ", " + pass + ", " + host);
     if (user == null || user.isEmpty() || host == null || host.isEmpty() || pass == null
             || pass.isEmpty()) {
       throw new QuimpException("One of required fields is empty");
     }
     OMEROLocation credentials = new OMEROLocation(host, port, user, pass);
     context = new Context();
     os = context.getService(OMEROService.class);
     ds = new DefaultOMEROSession(credentials, os);
     client = ds.getClient();
     gateway = ds.getGateway();
     ctx = ds.getSecurityContext();
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see java.io.Closeable#close()
    */
   @Override
   public void close() throws IOException {
     silentClose();
   }
 
   /**
    * Close Omero without exception.
    */
   public void silentClose() {
     if (gateway != null) {
       ds.close();
       client.closeSession();
       gateway.disconnect();
       os.dispose();
       context.dispose();
       LOGGER.debug("Omero disconnected");
     }
   }
 
   /**
    * List projects.
    * 
    * @return list of projects for user.
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    * @throws ExecutionException on Omero error
    */
   public List<ProjectData> listProjects()
           throws DSOutOfServiceException, DSAccessException, ExecutionException {
     BrowseFacility browse = gateway.getFacility(BrowseFacility.class);
     return new ArrayList<ProjectData>(browse.getProjects(ctx));
   }
 
   /**
    * List datasets.
    * 
    * @return List of datasets for user.
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    * @throws ExecutionException on Omero error
    */
   public List<DatasetData> listDatasets()
           throws DSOutOfServiceException, DSAccessException, ExecutionException {
     BrowseFacility browse = gateway.getFacility(BrowseFacility.class);
     return new ArrayList<DatasetData>(browse.getDatasets(ctx));
   }
 
   /**
    * Open dataset.
    * 
    * @param name dataset name
    * @return images from dataset
    * @throws ExecutionException on Omero error
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    */
   public Collection<ImageData> openDataset(DatasetData name)
           throws ExecutionException, DSOutOfServiceException, DSAccessException {
     BrowseFacility browse = gateway.getFacility(BrowseFacility.class);
     List<Long> ida = new ArrayList<>();
     ida.add(name.getId());
     return browse.getImagesForDatasets(ctx, ida);
 
   }
 
   /**
    * Find dataset of specified name.
    * 
    * @param name name of dataset
    * @return dataset object
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    * @throws ExecutionException on Omero error
    */
   public DatasetData findDataset(String name)
           throws DSOutOfServiceException, DSAccessException, ExecutionException {
     for (DatasetData ds : listDatasets()) {
       if (ds.getName().equals(name)) {
         LOGGER.debug("Found dataset of name " + name + " (" + ds.toString() + ")");
         return ds;
       }
     }
     return null;
   }
 
   /**
    * Find dataset of specified id.
    * 
    * @param id id of dataset
    * @return dataset object
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    * @throws ExecutionException on Omero error
    */
   public DatasetData findDataset(Long id)
           throws DSOutOfServiceException, DSAccessException, ExecutionException {
     for (DatasetData ds : listDatasets()) {
       if (ds.getId() == id) {
         LOGGER.debug("Found dataset of id " + id + " (" + ds.toString() + ")");
         return ds;
       }
     }
     return null;
   }
 
   /**
    * Find image of specified name in the dataset.
    * 
    * <p>If there is more than 1 image with specified name, then depending on
    * <tt>allowDuplicates</tt> the newest will be returned (true) or exception thrown (false).
    * 
    * @param imageName image name to look for
    * @param name dataset name
    * @param allowDuplicates if true newest image is returned if there is more than 1 image with
    *        imageName in the dataset, otherwise exception is thrown
    * @return found image object
    * 
    * @throws ExecutionException omero error
    * @throws DSOutOfServiceException omero error
    * @throws DSAccessException omero error
    * @throws QuimpException if there are multiple images with the same name and
    *         allowDuplicates==false
    */
   public ImageData findImage(String imageName, DatasetData name, boolean allowDuplicates)
           throws ExecutionException, DSOutOfServiceException, DSAccessException, QuimpException {
     ArrayList<ImageData> imgs = new ArrayList<>();
     for (ImageData im : openDataset(name)) {
       if (im.getName().equals(imageName)) {
         LOGGER.debug("Found image of name " + name + " (" + im.toString() + "), inserted: "
                 + im.getInserted());
         imgs.add(im);
       }
     }
     if (imgs.size() > 1 && allowDuplicates == false) {
       throw new QuimpException(
               "There are at least two images with name " + imageName + " in dataset");
     }
     if (imgs.size() == 0) {
       return null;
     }
     if (imgs.size() == 1) {
       return imgs.get(0);
     } else { // return newest
       Long now = System.currentTimeMillis(); // current time
       ArrayList<Long> deltas = new ArrayList<>(); // time from now for each file (with same name)
       for (ImageData im : imgs) { // check each file
         Long timeFile = im.getInserted().getTime(); // get upload time
         deltas.add(now - timeFile); // store difference from now
       }
       int closestInd = deltas.indexOf(Collections.min(deltas)); // index of smallest diff
       return imgs.get(closestInd); // file under this index
     }
 
   }
 
   /**
    * Find image of specified id in dataset.
    * 
    * @param imageId id to find
    * @param name dataset name
    * @return image object
    * @throws ExecutionException on Omero error
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    */
   public ImageData findImage(Long imageId, DatasetData name)
           throws ExecutionException, DSOutOfServiceException, DSAccessException {
     for (ImageData im : openDataset(name)) {
       if (im.getId() == imageId) {
         LOGGER.debug("Found image of id " + imageId + " (" + imageId.toString() + ")");
         return im;
       }
     }
     return null;
 
   }
 
   /**
    * Upload specified image to dataset.
    * 
    * @param pathsToImages list paths of images
    * @param name dataset name
    * @throws Exception on error
    */
   public void upload(String[] pathsToImages, DatasetData name) throws Exception {
     LOGGER.info("Trying to upload: " + Arrays.toString(pathsToImages));
     ImportConfig config = new ome.formats.importer.ImportConfig();
     config.email.set("");
     config.sendFiles.set(true);
     config.sendReport.set(false);
     config.contOnError.set(false);
     config.debug.set(true);
 
     config.hostname.set(host);
     config.port.set(port);
     config.username.set(user);
     config.password.set(pass);
     config.target.set("omero.model.Dataset:" + name.getId());
 
     OMEROMetadataStoreClient store;
     store = config.createStore();
     store.logVersionInfo(config.getIniVersionNumber());
     OMEROWrapper reader = new OMEROWrapper(config);
     ImportLibrary library = new ImportLibrary(store, reader);
 
     ErrorHandler handler = new ErrorHandler(config);
     library.addObserver(new LoggingImportMonitor());
 
     ImportCandidates candidates = new ImportCandidates(reader, pathsToImages, handler);
     reader.setMetadataOptions(new DefaultMetadataOptions(MetadataLevel.ALL));
     library.importCandidates(config, candidates);
 
     store.logout();
     LOGGER.info("Image uploaded");
 
   }
 
   /**
    * Upload attachment and attach it to image from dataset.
    * 
    * <p>Image is already in dataset.
    * 
    * @param imageName image name in dataset
    * @param pathToAttach path to attachment
    * @param name dataset name
    * @throws IOException on file error
    * @throws DSOutOfServiceException on Omero error
    * @throws DSAccessException on Omero error
    * @throws ServerError on Omero error
    * @throws ExecutionException on Omero error
    * @throws QuimpException on Omero error - no image in dataset
    */
   public void upload(String imageName, String pathToAttach, DatasetData name)
           throws IOException, DSOutOfServiceException, DSAccessException, ServerError,
           ExecutionException, QuimpException {
     LOGGER.info("Trying to upload attachement: " + pathToAttach + " to " + imageName);
 
     File file = new File(pathToAttach);
     String name1 = Paths.get(pathToAttach).getFileName().toString();
     String absolutePath = file.getAbsolutePath();
     String path = absolutePath.substring(0, absolutePath.length() - name1.length());
 
     // create the original file object.
     OriginalFile originalFile = new OriginalFileI();
     originalFile.setName(omero.rtypes.rstring(name1));
     originalFile.setPath(omero.rtypes.rstring(path));
     originalFile.setSize(omero.rtypes.rlong(file.length()));
     final ChecksumAlgorithm checksumAlgorithm = new ChecksumAlgorithmI();
     checksumAlgorithm.setValue(omero.rtypes.rstring(ChecksumAlgorithmSHA1160.value));
     originalFile.setHasher(checksumAlgorithm);
     originalFile.setMimetype(omero.rtypes.rstring("application/octet-stream"));
     // Now we save the originalFile object
     DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
     originalFile = (OriginalFile) dm.saveAndReturnObject(ctx, originalFile);
 
     // Initialize the service to load the raw data
     RawFileStorePrx rawFileStore = gateway.getRawFileService(ctx);
 
     long inc = file.length();
     long pos = 0;
     int rlen;
     byte[] buf = new byte[(int) inc];
     ByteBuffer bbuf;
     // Open file and read stream
     try (FileInputStream stream = new FileInputStream(file)) {
       rawFileStore.setFileId(originalFile.getId().getValue());
       while ((rlen = stream.read(buf)) > 0) {
         rawFileStore.write(buf, pos, rlen);
         pos += rlen;
         bbuf = ByteBuffer.wrap(buf);
         bbuf.limit(rlen);
       }
       originalFile = rawFileStore.save();
     } finally {
       rawFileStore.close();
     }
     // now we have an original File in DB and raw data uploaded.
     // We now need to link the Original file to the image using
     // the File annotation object. That's the way to do it.
     FileAnnotation fa = new FileAnnotationI();
     fa.setFile(originalFile);
     // The description set above e.g. PointsModel
     fa.setDescription(omero.rtypes.rstring("PointsModel"));
     // The name space you have set to identify the file annotation.
     fa.setNs(omero.rtypes.rstring(NAMESPACE));
 
     // save the file annotation.
     fa = (FileAnnotation) dm.saveAndReturnObject(ctx, fa);
 
     // now link the image and the annotation
     ImageAnnotationLink link = new ImageAnnotationLinkI();
     link.setChild(fa);
     ImageData imageData = findImage(imageName, name, true);
     link.setParent(imageData.asImage());
     // save the link back to the server.
     link = (ImageAnnotationLink) dm.saveAndReturnObject(ctx, link);
     // o attach to a Dataset use DatasetAnnotationLink;
     LOGGER.info("Attachement uploaded");
 
   }
 
   /**
    * Download image and attachment.
    * 
    * @param image image with attachment (if no attachment only image is downloaded)
    * @param path path to file (should be not file name)
    * @throws DSOutOfServiceException on Omero error
    * @throws ServerError on Omero error
    * @throws DSAccessException on Omero error
    * @throws ExecutionException on Omero error
    * @throws IOException on file error
    * @throws URISyntaxException on Omero error
    * @throws PermissionDeniedException on Omero error
    * @throws CannotCreateSessionException on Omero error
    */
   public void download(ImageData image, Path path)
           throws DSOutOfServiceException, ServerError, DSAccessException, ExecutionException,
           IOException, URISyntaxException, PermissionDeniedException, CannotCreateSessionException {
 
     if (path.toFile().isFile()) {
       throw new IllegalArgumentException("Path must point to folder");
     }
 
     Dataset img = os.downloadImage(client, image.getId());
     IOService io = context.getService(IOService.class);
     Path imageFile = path.resolve(image.getName());
     io.save(img, imageFile.toString());
     long[] dim = new long[img.numDimensions()];
     img.dimensions(dim);
     LOGGER.info("Saved: " + imageFile.toString() + " : " + img.toString() + " dim: "
             + Arrays.toString(dim));
 
     long userId = gateway.getLoggedInUser().getId();
     List<String> nsToInclude = new ArrayList<String>();
     nsToInclude.add(NAMESPACE);
     List<String> nsToExclude = new ArrayList<String>();
     ParametersI param = new ParametersI();
     param.exp(omero.rtypes.rlong(userId)); // load the annotation for a given user.
     IMetadataPrx proxy = gateway.getMetadataService(ctx);
     List<Long> ids = new ArrayList<>();
     ids.add(image.getId());
     Map<Long, List<Annotation>> annotations =
             proxy.loadSpecifiedAnnotationsLinkedTo(FileAnnotation.class.getName(), nsToInclude,
                     nsToExclude, Image.class.getName(), ids, param);
     LOGGER.debug("Length: " + annotations.size());
     // for (Annotation a : annotations.get(image.getId())) {
     // if (a instanceof FileAnnotation) {
     // FileAnnotationData fa = new FileAnnotationData((FileAnnotation) a);
     // LOGGER.debug("id " + fa.getFileID());
     // }
     // }
 
     if (annotations.get(image.getId()) != null) {
       Iterator<Annotation> j = annotations.get(image.getId()).iterator();
       Annotation annotation;
       FileAnnotationData fa;
       RawFileStorePrx store = gateway.getRawFileService(ctx);
       File qconfFile =
               path.resolve(FilenameUtils.removeExtension(image.getName()) + ".QCONF").toFile();
       int index = 0;
 
       int inc;
       try (FileOutputStream stream = new FileOutputStream(qconfFile)) {
         while (j.hasNext()) {
           annotation = j.next();
           if (annotation instanceof FileAnnotation && index == 0) {
             fa = new FileAnnotationData((FileAnnotation) annotation);
             // // The id of the original file
             // create the original file object.
             OriginalFile originalFile = new OriginalFileI();
             originalFile.setName(omero.rtypes.rstring(qconfFile.getName()));
             originalFile.setPath(omero.rtypes.rstring(qconfFile.getParent()));
             originalFile.setSize(omero.rtypes.rlong(fa.getFileSize()));
             final ChecksumAlgorithm checksumAlgorithm = new ChecksumAlgorithmI();
             checksumAlgorithm.setValue(omero.rtypes.rstring(ChecksumAlgorithmSHA1160.value));
             originalFile.setHasher(checksumAlgorithm);
             originalFile.setMimetype(omero.rtypes.rstring("application/octet-stream"));
             // Now we save the originalFile object
             DataManagerFacility dm = gateway.getFacility(DataManagerFacility.class);
             originalFile = (OriginalFile) dm.saveAndReturnObject(ctx, originalFile);
 
             store.setFileId(fa.getFileID());
             int offset = 0;
             inc = (int) fa.getFileSize();
             long size = originalFile.getSize().getValue();
             try {
               for (offset = 0; (offset + inc) < size;) {
                 stream.write(store.read(offset, inc));
                 offset += inc;
               }
             } finally {
               stream.write(store.read(offset, (int) (size - offset)));
               LOGGER.info("Saved: " + qconfFile.toString() + " from image " + image.getId());
             }
             index++;
           }
         }
       } finally {
         store.close();
       }
     } else {
       LOGGER.warn("There is no QCONF file attached to image [ " + image.getId() + "]");
     }
   }
 
   /**
    * Dummy tests.
    * 
    * @param args args
    */
   public static void main(String[] args) {
     String user;
     String pass;
     String host;
     Properties prop = new Properties();
     try (FileInputStream input = new FileInputStream(
             Paths.get(System.getProperty("user.home"), "omero.properties").toFile())) {
       prop.load(input);
       user = prop.getProperty("user");
       pass = prop.getProperty("pass");
       host = prop.getProperty("host");
     } catch (IOException ex) {
       ex.printStackTrace();
       return;
     }
 
     try (OmeroBrowsermero/OmeroBrowser.html#OmeroBrowser">OmeroBrowser client = new OmeroBrowser(user, pass, host, DEF_PORT)) {
       client.connect();
       LOGGER.debug("Projects:");
       client.listDatasets().stream().forEach(x -> LOGGER.debug("dataset " + x.getName()));
       // pick dataset
       DatasetData ds = client.findDataset("Q");
       // list images
       client.openDataset(ds).stream()
               .forEach(x -> LOGGER.debug("image: " + x.getName() + ": " + x.getId()));
 
       // client.upload(new String[] {
       // "src/test/Resources-static/ProtAnalysisTest/fluoreszenz-test.tif kept stack.tif" }, ds);
       // client.upload("fluoreszenz-test.tif kept stack.tif",
       // "src/test/Resources-static/ProtAnalysisTest/fluoreszenz-test.QCONF", ds);
       client.download(client.findImage(194021L, ds), Paths.get("./").toAbsolutePath());
 
       // client.downloadIJ_TEST(); // this or these above
 
     } catch (Exception e) {
       // TODO Auto-generated catch block
       e.printStackTrace();
     }
 
     // https://github.com/ome/minimal-omero-client/blob/master/src/main/java/com/example/SimpleConnection.java
     // https://docs.openmicroscopy.org/omero/5.4.10/developers/Java.html
 
   }
 
 }