com.actelion.research.orbit.imageprovider.ImageProviderOmero Maven / Gradle / Ivy
/*
* Orbit, a versatile image analysis software for biological image-based quantification.
* Copyright (C) 2009 - 2017 Actelion Pharmaceuticals Ltd., Gewerbestrasse 16, CH-4123 Allschwil, Switzerland.
*
* 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 3 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, see hints = new ConcurrentHashMap<>();
public static final ConcurrentHashMap projectGroupMap = new ConcurrentHashMap<>();
public static final ConcurrentHashMap datasetGroupMap = new ConcurrentHashMap<>();
public static final ConcurrentHashMap rdfGroupMap = new ConcurrentHashMap<>();
public static final ConcurrentHashMap metaGroupMap = new ConcurrentHashMap<>();
private static final int INC = 16 * 1024;
private String omeroUser = "";
private String omeroPassword = "";
private String omeroUserScaleout = "";
private String omeroPasswordScaleout = "";
private String host = "localhost";
private int port = 4064;
private int webport = 8080;
private transient GatewayAndCtx gatewayAndCtx = new GatewayAndCtx();
protected int searchLimit = 1000;
protected boolean listAllSeries = true;
protected int selectedSeries = 0;
protected final Map> metaHashRDF = new ConcurrentHashMap<>();
protected final Map> metaHashRawData = new ConcurrentHashMap<>();
private boolean onlyOwnerObjects = false; // show/edit only objects owned by current user (otherwise show/edit all with read/write access)
private String configFile = "OrbitOmero.properties";
private boolean useSSL = false;
public ImageProviderOmero() {
Properties props = new Properties();
props.put("OmeroHost", host);
props.put("OmeroPort", String.valueOf(port));
props.put("OmeroWebPort", String.valueOf(webport));
props.put("UseSSL", String.valueOf(useSSL));
props.put("SearchLimit", String.valueOf(searchLimit));
props.put("OmeroUserScaleout", "");
props.put("OmeroPasswordScaleout", "");
String userDir = System.getProperty("user.dir");
String userHome = System.getProperty("user.home");
try {
boolean loaded = false;
log.info("searching for " + configFile + " in current directory (" + userDir + ")");
File config = new File(userDir + File.separator + configFile);
if (config.exists()) {
props.load(new FileInputStream(config));
log.info("using config file: " + config.getAbsolutePath());
loaded = true;
}
if (!loaded)
log.info("searching for " + configFile + " in user home (" + userHome + ")");
config = new File(userHome + File.separator + configFile);
if (!config.exists()) {
File configTemplate = new File(userHome + File.separator + configFile + ".template");
try {
props.store(new FileOutputStream(configTemplate), "Orbit Omero Config");
} catch (Exception e) {
log.warn("error saving Omero config template to: " + configTemplate.getAbsolutePath());
}
} else {
if (!loaded) {
props.load(new FileInputStream(config));
log.info("using config file: " + config.getAbsolutePath());
}
}
host = props.getProperty("OmeroHost");
port = Integer.parseInt(props.getProperty("OmeroPort"));
webport = Integer.parseInt(props.getProperty("OmeroWebPort"));
useSSL = Boolean.parseBoolean(props.getProperty("UseSSL"));
searchLimit = Integer.parseInt(props.getProperty("SearchLimit"));
omeroUserScaleout = props.getProperty("OmeroUserScaleout");
omeroPasswordScaleout = props.getProperty("OmeroPasswordScaleout");
} catch (Exception e) {
log.error("error loading omero config file", e);
}
log.info("Omero host: " + host);
log.info("Omero port: " + port);
log.info("Omero web port: " + webport);
log.info("Omero use SSL: " + useSSL);
log.info("Search limit: " + searchLimit);
log.info("Omero User Scaleout: " + omeroUserScaleout);
boolean connectionOk = false;
try {
SocketChannel socketChannel = SocketChannel.open();
socketChannel.configureBlocking(true);
connectionOk = socketChannel.connect(new InetSocketAddress(host, port));
socketChannel.close();
} catch (Exception e) {
connectionOk = false;
}
if (!connectionOk) {
String p1 = userDir + File.separator + configFile;
String p2 = userHome + File.separator + configFile;
throw new IllegalStateException("Cannot connect to Omero server.\nTried to connect on " + host + ":" + port + ".\nFor a different host/port please modify either\n" + p1 + " (priority) or\n" + p2 + ".\n(You can rename and use "+p1+".template)");
}
}
public void clearMetaRDFHash() {
metaHashRDF.clear();
}
public void clearMetaRawDataHash() {
metaHashRawData.clear();
}
protected Parameters getParameterRead() throws DSOutOfServiceException {
if (onlyOwnerObjects) {
long userId = gatewayAndCtx.getGateway().getLoggedInUser().getId();
ParametersI param = new ParametersI();
param.exp(omero.rtypes.rlong(userId));
return param;
} else {
return null;
}
}
protected Parameters getParameterWrite() throws DSOutOfServiceException {
return null;
}
/**
* returns the ownerId if onlyOwnerObjects is true, -1 otherwise (-1 is used for "all projects/datasets")
*
* @return long id of the owner
*/
protected long getOwnerId() throws DSOutOfServiceException {
return onlyOwnerObjects ? gatewayAndCtx.getGateway().getLoggedInUser().getId() : -1;
}
@Override
public List LoadRawDataByBioLabJournal(String elb) throws Exception {
return loadRawDataDatasets(elb);
}
/**
* Loads a Dataset by id
* Without transmitting the owner id because all datasets (with read-right) should be loaded.
*
* @param rawDataId
* @return RawData
* @throws Exception
*/
@Override
public RawData LoadRawData(int rawDataId) throws Exception {
long group = getDatasetGroup((long)rawDataId);
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Collection datasets = browse.getDatasets(getGatewayAndCtx().getCtx(group), /*getOwnerId(),*/ Collections.singleton((long) rawDataId));
if (datasets != null && datasets.size() > 0) {
return createRawDataDataset(datasets.iterator().next(),group);
} else {
return null;
}
}
/**
* Updates a Dataset
* Without transmitting the owner id because all datasets (with write-right) should be updated.
*
* @param rd the rawData object to update
* @return boolean true/false
* @throws Exception
*/
@Override
public boolean UpdateRawData(RawData rd) throws Exception {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
long group = getDatasetGroup(rd.getRawDataId());
if (rd instanceof RawDataProject) {
Collection projects = browse.getProjects(gatewayAndCtx.getCtx(group), /*getOwnerId(),*/ Collections.singleton((long) rd.getRawDataId()));
if (projects == null || projects.size() == 0)
throw new IllegalArgumentException("project with id " + rd.getRawDataId() + " not found");
ProjectData project = projects.iterator().next();
project.setName(rd.getBioLabJournal());
project.setDescription(rd.getDescription());
dm.updateObject(gatewayAndCtx.getCtx(group), project.asProject(), getParameterWrite());
return true;
} else if (rd instanceof RawDataDataset) {
Collection datasets = browse.getDatasets(gatewayAndCtx.getCtx(group), /*getOwnerId(),*/ Collections.singleton((long) rd.getRawDataId()));
if (datasets == null || datasets.size() == 0)
throw new IllegalArgumentException("dataset with id " + rd.getRawDataId() + " not found");
DatasetData dataset = datasets.iterator().next();
dataset.setName(rd.getBioLabJournal());
dataset.setDescription(rd.getDescription());
dm.updateObject(gatewayAndCtx.getCtx(group), dataset.asDataset(), getParameterWrite());
return true;
} else {
throw new IllegalArgumentException("RawData object must be instance of RawDataProject or RawDataDataset, but is " + rd.getClass().getName());
}
}
@Override
public boolean UpdateRawDataFile(RawDataFile rdf) throws Exception {
long group = getRdfGroup(rdf);
BrowseFacility browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
ImageData image = browse.getImage(gatewayAndCtx.getCtx(group), rdf.getRawDataFileId());
image.setName(rdf.getFileName());
dm.updateObject(gatewayAndCtx.getCtx(group), image.asImage(), getParameterWrite());
return true;
}
@Override
public RawDataFile LoadRawDataFile(int rdfId) throws Exception {
long group = getImageGroup((long)rdfId);
BrowseFacility browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
ImageData image = browse.getImage(gatewayAndCtx.getCtx(group), rdfId);
return createRawDataFile(image,group);
}
@Override
public List LoadRawDataFiles(int rawDataId) throws Exception {
return loadRdfList(rawDataId, -1);
}
@Override
public List LoadRawDataFiles(int rawDataId, int limit) throws Exception {
return loadRdfList(rawDataId, limit);
}
/**
* Load raw data files which are assigned to a dataset. Filetypes are currently ignored but might be used as filter in future.
*
* @param rawDataId
* @param fileTypes (currently ignored)
* @param limit
* @return List
* @throws Exception
*/
@Override
public List LoadRawDataFiles(int rawDataId, List fileTypes, int limit) throws Exception {
return loadRdfList(rawDataId, limit);
}
/**
* Search for raw data files. andMode is currently ignored.
*
* @param search
* @param andMode (currently ignored)
* @return List
* @throws Exception
*/
@Override
public List LoadRawDataFilesSearch(String search, boolean andMode) throws Exception {
return LoadRawDataFilesSearchGeneric("%" + search + "%", searchLimit);
}
/**
* Search for raw data files. andMode and fileTypes are currently ignored.
*
* @param search
* @param andMode (currently ignored)
* @param limit search limit (set < 0 to ignore)
* @param fileTypes currently ignored
* @return List
* @throws Exception
*/
@Override
public List LoadRawDataFilesSearch(String search, boolean andMode, int limit, List fileTypes) throws Exception {
return LoadRawDataFilesSearchGeneric("%" + search + "%", limit);
}
@Override
public List LoadRawDataFilesByFilenameStart(String search, boolean andMode, int searchLimit, List fileTypes, String orderHint) throws Exception {
return LoadRawDataFilesSearchGeneric("%" + search, searchLimit);
}
@Override
public List LoadRawDataFilesSearchFast(String search, int limit, List fileTypes) throws Exception {
return LoadRawDataFilesSearchGeneric("%" + search + "%", limit);
}
public List LoadRawDataFilesSearchGeneric(String search, int limit) throws Exception {
List rdfList = new ArrayList<>();
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
String query_string = "select i from Image i where UPPER(name) like :search";
ParametersI p = new ParametersI();
p.add("search", rstring(search.toUpperCase()));
p.page(0, limit);
for (RawData rdGroup: loadGroups()) {
long group = rdGroup.getRawDataId();
List results = gatewayAndCtx.getGateway().getQueryService(gatewayAndCtx.getCtx(group)).findAllByQuery(query_string, p);
for (IObject result : results) {
Image image = (Image) result;
ImageData imageData = browse.getImage(getGatewayAndCtx().getCtx(group), image.getId().getValue());
if (imageData.getSeries() == selectedSeries || listAllSeries) {
rdfList.add(createRawDataFile(imageData,group));
}
}
}
Collections.sort(rdfList, new Comparator() {
@Override
public int compare(RawDataFile o1, RawDataFile o2) {
return o1.getFileName().compareTo(o1.getFileName());
}
});
return rdfList;
}
@Override
public List LoadRawDataFilesByPlateName(String plateName, int plateBatch) throws Exception {
log.error("plate access is currently not supported");
return new ArrayList<>();
}
@Override
public List browseImages(Object parent) throws Exception {
return null;
}
@Override
public boolean useCustomBrowseImagesDialog() {
return false;
}
private String getWebserviceBase() {
//return useSSL?"https://":"http://"+host+":"+webport;
return "http://" + host + ":" + webport;
}
/**
* Returns the url of the image specified by the rdf.
*
* @param rdf
* @return URL
* e.g. http://localhost:8080/webgateway/render_image/5
* http://root:omero@localhost:8080/webgateway/render_image/5
* see https://www.openmicroscopy.org/site/support/omero5.2/developers/Web/WebGateway.html
* Authentification does currently not work. User has to be logged in already, e.g. via Omero web interace.
* Maybe username:password@ can be used?
*
*/
@Override
public URL getRawDataFileUrl(RawDataFile rdf) {
try {
return new URL(getWebserviceBase() + "/webgateway/render_image/" + rdf.getRawDataFileId());
} catch (Exception e) {
return null;
}
}
/**
* Returns the url of the image specified by the rdf.
*
* @param rdf
* @param level currently not taken into account!
* @return URL
*/
@Override
public URL getRawDataFileUrl(RawDataFile rdf, int level) {
try {
return new URL(getWebserviceBase() + "/webgateway/render_image/" + rdf.getRawDataFileId()); // TODO: level
} catch (MalformedURLException e) {
return null;
}
}
@Override
public URL getRawDataFileThumbnailUrl(RawDataFile rdf) {
try {
return new URL(getWebserviceBase() + "/webgateway/render_thumbnail/" + rdf.getRawDataFileId() + "/200/150"); // width=200, height=150
} catch (MalformedURLException e) {
return null;
}
}
public BufferedImage getThumbnail(RawDataFile rdf) throws Exception {
long group = getRdfGroup(rdf);
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
ImageData imageData = browse.getImage(getGatewayAndCtx().getCtx(group), rdf.getRawDataFileId());
ThumbnailStorePrx store = gatewayAndCtx.getGateway().getThumbnailService(gatewayAndCtx.getCtx(group));
PixelsData pixels = imageData.getDefaultPixels();
store.setPixelsId(pixels.getId());
byte[] array = store.getThumbnailByLongestSide(omero.rtypes.rint(RawUtilsCommon.THUMBNAIL_WIDTH));
ByteArrayInputStream stream = new ByteArrayInputStream(array);
BufferedImage thumbnail = ImageIO.read(stream);
store.close();
return thumbnail;
}
/**
* The idea is to get the filesetid of the image and query series 1 image for the fileset.
* However, I don't know how to query a fileset in Omero. Thus all images for the same dataset are
* queried and the image with same filesetid and series 1 is returned.
*
* It is also not clear which series means overview. I assume 1.
*/
@Override
public BufferedImage getOverviewImage(RawDataFile rdf) throws Exception {
try {
long group = getRdfGroup(rdf);
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
ImageData oriImage = browse.getImage(getGatewayAndCtx().getCtx(group), rdf.getRawDataFileId());
long fileSetId = oriImage.getFilesetId();
Collection images = browse.getImagesForDatasets(getGatewayAndCtx().getCtx(group), Collections.singleton((long) rdf.getRawDataId()));
Iterator j = images.iterator();
ImageData image;
ImageData overview = null;
while (j.hasNext()) {
image = j.next();
if (image.getFilesetId() == fileSetId && image.getSeries() == 1) {
overview = image;
}
}
if (overview != null) return new OmeroImage(overview.getId(), 0, getGatewayAndCtx()).getBufferedImage();
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
@Override
public IOrbitImage createOrbitImage(RawDataFile rdf, int level) throws Exception {
long imageId = rdf.getRawDataFileId();
long group = getImageGroupCached(imageId);
boolean useCache = true;
OrbitImageBioformatsOmero oi = new OrbitImageBioformatsOmero("omeroorbit:iid="+rdf.getRawDataFileId(),level,0, useCache, gatewayAndCtx,imageId, group);
return oi;
}
@Override
public AbstractOrbitTree createOrbitTree() {
return new JOrbitTreeOmero(this, "Omero", Arrays.asList(new TreeNodeGroup(this, null), new TreeNodeProject(this, null), new TreeNodeDataset(this, null)));
}
@Override
public boolean authenticateUser(String username, String password) {
LoginCredentials cred = new LoginCredentials();
cred.getServer().setHostname(host);
cred.getServer().setPort(port);
cred.setEncryption(useSSL);
cred.getUser().setUsername(username);
cred.getUser().setPassword(password);
//Logger omeroLogger = new SimpleLogger();
Logger omeroLogger = new Slf4jWrapper(log);
Gateway gateway = new Gateway(omeroLogger);
omeroUser = username;
omeroPassword = password;
try {
getGatewayAndCtx().reset();
ExperimenterData user = gateway.connect(cred);
omeroUser = username;
omeroPassword = password;
getGatewayAndCtx().reset();
return true;
} catch (DSOutOfServiceException e) {
log.warn("login failed with username: " + username);
return false;
} finally {
try {
if (gateway.isConnected()) gateway.disconnect();
} catch (Exception e) {
}
}
}
/**
* Technical user authentification for scaleout clients.
*
* @return login success/failure
*/
public boolean authenticateUserScaleout() {
omeroUser = omeroUserScaleout;
omeroPassword = omeroPasswordScaleout;
return authenticateUser(omeroUser, omeroPassword);
}
;
@Override
public ConcurrentHashMap getHints() {
return hints;
}
@Override
public IFileListCellRenderer getFileListCellRenderer() {
return new FileListCellRendererOmero();
}
@Override
public void logUsage(String username, String method) {
log.info("user: " + username + " :: method: " + method);
}
@Override
public boolean enforceLoginDialogAtStartup() {
return true;
}
private GatewayAndCtx getGatewayAndCtx() throws DSOutOfServiceException {
return gatewayAndCtx;
}
public List loadProjects(int group) {
List rdList = new ArrayList<>();
if (omeroUser != null && omeroUser.length() > 0) {
try {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Collection projects = browse.getProjects(gatewayAndCtx.getCtx(group), getOwnerId());
Iterator i = projects.iterator();
ProjectData project;
while (i.hasNext()) {
project = i.next();
rdList.add(createRawDataProject(project,group));
}
} catch (Exception e) {
e.printStackTrace();
}
// add additional project for datasets not in a project
RawData rd = new RawData();
rd.setRawDataId(-1);
rd.setBioLabJournal("unassigned");
rd.setDescription("datasets not assigned to a project");
rd.setReferenceDate(new Date());
rd.setModifyDate(new Date());
rdList.add(rd);
Collections.sort(rdList, new Comparator() {
@Override
public int compare(RawData o1, RawData o2) {
return o1.getBioLabJournal().compareTo(o2.getBioLabJournal());
}
});
}
return rdList;
}
public List loadGroups() {
List rdList = new ArrayList<>();
if (omeroUser != null && omeroUser.length() > 0) {
try {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Set groups = browse.getAvailableGroups(gatewayAndCtx.getCtx(), gatewayAndCtx.getGateway().getLoggedInUser());
for (GroupData group: groups) {
rdList.add(createRawDataGroup(group));
}
} catch (Exception e) {
e.printStackTrace();
}
Collections.sort(rdList, new Comparator() {
@Override
public int compare(RawData o1, RawData o2) {
return o1.getBioLabJournal().compareTo(o2.getBioLabJournal());
}
});
}
return rdList;
}
public List getGroups() {
List rdGroups = loadGroups();
List groupList = new ArrayList<>(rdGroups.size());
for (RawData rd: rdGroups) {
groupList.add((long) rd.getRawDataId());
}
return groupList;
}
public List loadRawDataDatasets(RawData projectRD) {
List rdList = new ArrayList<>();
if (omeroUser != null && omeroUser.length() > 0) {
try {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Collection projects;
if (projectRD != null && projectRD.getRawDataId() > 0) {
long group = getProjectGroup((long)projectRD.getRawDataId());
projects = browse.getProjects(gatewayAndCtx.getCtx(group), getOwnerId(), Collections.singleton((long) projectRD.getRawDataId()));
Iterator i = projects.iterator();
ProjectData project;
Iterator j;
DatasetData dataset;
while (i.hasNext()) {
project = i.next();
Set datasets = project.getDatasets();
j = datasets.iterator();
while (j.hasNext()) {
dataset = j.next();
rdList.add(createRawDataDataset(dataset,group));
}
}
} // datasets not assigned to projects (call all projects before calling this method without(=-1) projectID!)
else {
for (RawData groupRd: loadGroups()) {
long group = groupRd.getRawDataId();
HashSet loadedDatasetIDs = new HashSet<>();
projects = browse.getProjects(gatewayAndCtx.getCtx(group), getOwnerId()); // load all projects
Iterator i = projects.iterator();
ProjectData project;
Iterator j;
DatasetData dataset;
while (i.hasNext()) {
project = i.next();
Set datasets = project.getDatasets();
j = datasets.iterator();
while (j.hasNext()) {
dataset = j.next();
loadedDatasetIDs.add(dataset.getId());
}
}
// now load all datasets and keep the ones not in a project -> really bad...
Collection datasets = browse.getDatasets(gatewayAndCtx.getCtx(group), getOwnerId());
for (DatasetData dataset2 : datasets) {
if (!loadedDatasetIDs.contains(dataset2.getId())) {
rdList.add(createRawDataDataset(dataset2,group));
}
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
Collections.sort(rdList, new Comparator() {
@Override
public int compare(RawData o1, RawData o2) {
return o1.getBioLabJournal().compareTo(o2.getBioLabJournal());
}
});
}
return rdList;
}
/**
* Loads a list of raw datasets. Filter is optional and can be used to filter the results (case-insensitive).
*
* @param filter case-insensitive filter
* @return list of raw datasets.
*/
private List loadRawDataDatasets(String filter) {
List rdList = new ArrayList<>();
for (RawData groupRd: loadGroups()) {
long group = groupRd.getRawDataId();
try {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Collection datasets = browse.getDatasets(gatewayAndCtx.getCtx(group), getOwnerId());
Iterator i = datasets.iterator();
DatasetData dataset;
while (i.hasNext()) {
dataset = i.next();
if (filter == null || filter.length() == 0 || dataset.getName().toLowerCase().contains(filter.toLowerCase())) {
rdList.add(createRawDataDataset(dataset,group));
}
}
Collections.sort(rdList, new Comparator() {
@Override
public int compare(RawData o1, RawData o2) {
return o1.getBioLabJournal().compareTo(o2.getBioLabJournal());
}
});
} catch (Exception e) {
e.printStackTrace();
}
}
return rdList;
}
/**
* @param rawDataId
* @param limit set < 0 for no limit
* @return list of raw data files contained by the dataset
*/
private List loadRdfList(final int rawDataId, final int limit) {
return loadRdfList(rawDataId, limit, listAllSeries);
}
/**
* @param rawDataId
* @param limit set < 0 for no limit
* @return list of raw data files contained by the dataset
*/
private List loadRdfList(final int rawDataId, final int limit, boolean listAllSeries) {
long group = getDatasetGroup((long)rawDataId);
List rdfList = new ArrayList<>();
try {
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
Collection images = browse.getImagesForDatasets(getGatewayAndCtx().getCtx(group), Collections.singleton((long) rawDataId));
Iterator j = images.iterator();
ImageData image;
int cnt = 0;
while (j.hasNext()) {
image = j.next();
//System.out.println(image.getName()+" / index: "+ image.getSeries());
if (image.getSeries() == selectedSeries || listAllSeries) {
if (limit < 0 || cnt++ > limit) break;
rdfList.add(createRawDataFile(image,group));
}
}
Collections.sort(rdfList, new Comparator() {
@Override
public int compare(RawDataFile o1, RawDataFile o2) {
return o1.getFileName().compareTo(o2.getFileName());
}
});
} catch (Exception e) {
e.printStackTrace();
}
return rdfList;
}
@Override
public void close() throws IOException {
if (gatewayAndCtx != null) {
try {
if (gatewayAndCtx.getGateway().isConnected())
gatewayAndCtx.getGateway().disconnect();
log.info("Omero gateway closed");
} catch (Exception e) {
e.printStackTrace();
}
}
}
public class GatewayAndCtx {
transient Gateway gateway = null;
transient SecurityContext ctx = null;
LoginCredentials cred;
public GatewayAndCtx() {
}
public synchronized SecurityContext getCtx() throws DSOutOfServiceException {
getGateway();
return ctx;
}
public synchronized SecurityContext getCtx(long group) throws DSOutOfServiceException {
getGateway();
return new SecurityContext(group);
}
public synchronized Gateway getGateway() throws DSOutOfServiceException {
if (gateway == null) {
// TODO: authenticate in grid mode???
cred = new LoginCredentials();
cred.getServer().setHostname(host);
cred.getServer().setPort(port);
cred.setApplicationName("Orbit");
cred.getUser().setUsername(omeroUser);
cred.getUser().setPassword(omeroPassword);
//cred.setCompression(0.8f);
SimpleLogger simpleLogger = new SimpleLogger();
gateway = new Gateway(simpleLogger);
ExperimenterData user = gateway.connect(cred);
ctx = new SecurityContext(user.getGroupId()); // default group
log.info("Omero server version: " + gateway.getServerVersion());
} else {
if (!gateway.isConnected()/*||!gateway.isAlive(ctx)*/) {
gateway.connect(cred);
ExperimenterData user = gateway.connect(cred); // needed?
ctx = new SecurityContext(user.getGroupId());
}
}
return gateway;
}
/**
* e.g. if switch user
*/
public void reset() {
gateway = null;
}
}
// bean creation
protected RawDataFile createRawDataFile(ImageData image, long group) {
int rawDataId = 0; //loadRawDataId((int)image.getId());
try {
ParametersI param = new ParametersI();
param.addIds(Collections.singleton(image.getId()));
List list = gatewayAndCtx.getGateway().getQueryService(gatewayAndCtx.getCtx(group)).findAllByQuery("select l from DatasetImageLink as l left outer join fetch l.parent where l.child.id =:ids ", param);
if (list != null && list.size() > 0) {
DatasetI dataset = (DatasetI) ((DatasetImageLinkI) list.get(0)).getParent();
rawDataId = (int) dataset.getId().getValue();
}
} catch (Exception e) {
e.printStackTrace();
}
return createRawDataFile(image, rawDataId, group);
}
protected RawDataFile createRawDataFile(ImageData image, int rawDataId, long group) {
RawDataFile rdf = new RawDataFile();
rdf.setRawDataId(rawDataId);
rdf.setRawDataFileId((int) image.getId());
rdf.setReferenceDate(image.getCreated() != null ? image.getCreated() : new Date());
rdf.setModifyDate(image.getUpdated());
rdf.setFileName(image.getName());
rdf.setUserId(experimenterToString(image.getOwner()));
String ending = RawUtilsCommon.getExtension(image.getName());
String format = image.getFormat().toLowerCase();
System.out.println("ending: " + ending + " format: " + image.getFormat());
switch (ending) {
case "jpg":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_JPG);
break;
case "jpeg":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_JPG);
break;
case "jp2":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_JPEG2000);
break;
case "tif":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_TIFF);
break;
case "tiff":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_TIFF);
break;
case "png":
rdf.setFileType(RawUtilsCommon.DATA_TYPE_IMAGE_PNG);
break;
}
System.out.println("type: " + rdf.getFileType());
rdfGroupMap.put(image.getId(),group);
return rdf;
}
protected RawDataProject createRawDataProject(ProjectData project, long group) {
RawDataProject rd = new RawDataProject();
rd.setRawDataId((int) project.getId());
rd.setReferenceDate(project.getCreated() != null ? project.getCreated() : new Date());
rd.setModifyDate(project.getUpdated());
rd.setBioLabJournal(project.getName());
rd.setDescription(project.getDescription());
rd.setUserId(experimenterToString(project.getOwner()));
projectGroupMap.put(project.getId(),group);
return rd;
}
protected RawDataGroup createRawDataGroup(GroupData group) {
RawDataGroup rd = new RawDataGroup();
rd.setRawDataId((int) group.getId());
rd.setReferenceDate(group.getCreated() != null ? group.getCreated() : new Date());
rd.setModifyDate(group.getUpdated());
rd.setBioLabJournal(group.getName());
rd.setDescription(group.getDescription());
rd.setUserId(experimenterToString(group.getOwner()));
return rd;
}
protected RawDataDataset createRawDataDataset(DatasetData dataset, long group) {
RawDataDataset rd = new RawDataDataset();
rd.setRawDataId((int) dataset.getId());
rd.setReferenceDate(dataset.getCreated() != null ? dataset.getCreated() : new Date());
rd.setModifyDate(dataset.getUpdated());
rd.setBioLabJournal(dataset.getName());
rd.setDescription(dataset.getDescription());
rd.setUserId(experimenterToString(dataset.getOwner()));
datasetGroupMap.put(dataset.getId(),group);
return rd;
}
public String experimenterToString(ExperimenterData experimenterData) {
if (experimenterData == null) return "";
try {
IAdminPrx admin = getGatewayAndCtx().getGateway().getAdminService(gatewayAndCtx.getCtx());
Experimenter experimenter = admin.getExperimenter(experimenterData.getId());
if (experimenter != null) {
String username = experimenter.getOmeName().getValue(); // is omeName == username ???
if (log.isTraceEnabled())
log.trace("username: " + username);
return username;
}
} catch (Exception e) {
e.printStackTrace();
}
return "";
}
/**
* just for testing
*
* @param bi
*/
private static void DisplayImage(final BufferedImage bi) {
JFrame frame = new JFrame("Image Data");
frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
frame.setSize(bi.getWidth(), bi.getHeight());
JPanel pane = new JPanel() {
@Override
protected void paintComponent(Graphics g) {
super.paintComponent(g);
g.drawImage(bi, 0, 0, null);
}
};
frame.add(pane);
frame.setLocationRelativeTo(null);
frame.setVisible(true);
}
// Meta Data
@Override
public synchronized List LoadRawMetasByRawDataFile(int rdfId) throws Exception {
if (metaHashRDF.containsKey(rdfId)) {
Map metaMap = metaHashRDF.get(rdfId);
List rmList = new ArrayList<>(metaMap.size());
for (String key : metaMap.keySet()) {
RawMeta rm = metaMap.get(key).clone(); // because the name will be manipulated later
rmList.add(rm);
}
return rmList;
} else {
RawMetaFactoryFile rmff = new RawMetaFactoryFile(rdfId, new Date(), gatewayAndCtx.getGateway().getLoggedInUser().getUserName());
RawDataFile rdf = LoadRawDataFile(rdfId);
long group = getRdfGroup(rdf);
List rmList = new ArrayList<>();
rmList.add(rmff.createMetaStr("User", rdf.getUserId()));
rmList.add(rmff.createMetaStr("Filename", rdf.getFileName()));
rmList.add(rmff.createMetaInt("Filesize", (int) rdf.getFileSize()));
rmList.add(rmff.createMetaInt("Omero ID", rdf.getRawDataFileId()));
if (rdf.getReferenceDate() != null)
rmList.add(rmff.createMetaDate("Create Date", rdf.getReferenceDate()));
if (rdf.getModifyDate() != null)
rmList.add(rmff.createMetaDate("Update Date", rdf.getModifyDate()));
MetadataFacility metaData = getGatewayAndCtx().getGateway().getFacility(MetadataFacility.class);
List cd = metaData.getChannelData(gatewayAndCtx.getCtx(group), rdfId);
for (ChannelData channelData : cd) {
rmList.add(rmff.createMetaStr("Channel." + RawUtilsCommon.STR_META_CHANNEL + " " + channelData.getId(), channelData.getName() + " (" + channelData.getChannelLabeling() + ")"));
}
// annotations
IMetadataPrx proxy = gatewayAndCtx.getGateway().getMetadataService(gatewayAndCtx.getCtx(group));
List nsToInclude = new ArrayList();
//nsToInclude.add(NAME_SPACE_TO_SET);
List nsToExclude = new ArrayList();
// FileAnnotation.class.getName()
// TextAnnotation
// TagAnnotation
List annotations = proxy.loadSpecifiedAnnotations(TagAnnotation.class.getName(), nsToInclude, nsToExclude, getParameterRead());
StringBuilder tagBuilder = new StringBuilder();
for (Annotation annotation : annotations) {
tagBuilder.append(((TagAnnotationI) annotation).getTextValue().getValue() + " ");
}
String tags = tagBuilder.toString();
if (tags.length() > 0)
rmList.add(rmff.createMetaStr("Tags", tagBuilder.toString()));
List commentAnnotation = proxy.loadSpecifiedAnnotations(CommentAnnotation.class.getName(), nsToInclude, nsToExclude, getParameterRead());
for (Annotation annotation : commentAnnotation) {
rmList.add(rmff.createMetaStr("Comments." + annotation.getDetails().getOwner().getFirstName().getValue() + " " + annotation.getDetails().getOwner().getLastName().getValue(), ((CommentAnnotationI) annotation).getTextValue().getValue()));
}
//DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
// metaData
nsToInclude = new ArrayList<>();
nsToInclude.add(ORBIT_METADATA_NAMESPACE);
nsToExclude = new ArrayList<>();
List metaDataannotations = proxy.loadSpecifiedAnnotationsLinkedTo(MapAnnotationI.class.getName(), nsToInclude, nsToExclude, Image.class.getName(), Collections.singletonList((long) rdfId), getParameterRead()).get((long) rdfId);
if (metaDataannotations != null) {
for (Annotation metaDataannotation : metaDataannotations) {
if (metaDataannotation instanceof MapAnnotationI) {
MapAnnotationI anno = (MapAnnotationI) metaDataannotation;
RawMeta rm = rmff.createMetaStr(anno.getName().getValue(), anno.getMapValueAsMap().get(anno.getName().getValue()));
rm.setRawMetaId((int) anno.getId().getValue());
log.debug("meta loaded: " + rm + " id: " + rm.getRawMetaId());
rmList.add(rm);
//dm.deleteObject(gatewayAndCtx.getCtx(),anno);
}
}
}
// image dims and resolution
BrowseFacility browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
PixelsData imageData = browse.getImage(gatewayAndCtx.getCtx(group), rdfId).getDefaultPixels();
rmList.add(rmff.createMetaInt(RawUtilsCommon.STR_META_IMAGE_IMAGEWIDTH, imageData.getSizeX()));
rmList.add(rmff.createMetaInt(RawUtilsCommon.STR_META_IMAGE_IMAGEHEIGHT, imageData.getSizeY()));
Length mupp = imageData.getPixelSizeX(UnitsLength.MICROMETER);
if (mupp != null)
rmList.add(rmff.createMetaDouble(RawUtilsCommon.STR_META_IMAGE_SCALE, mupp.getValue())); // TODO: pixel size for x and y (and z)
// cache entries
Map metaMap = new HashMap<>();
for (RawMeta rm : rmList) {
metaMap.put(rm.getName(), rm);
}
metaHashRDF.put(rdfId, metaMap);
return rmList;
}
}
@Override
public synchronized List LoadRawMetasByRawDataFileAndName(int rdfId, String name) throws Exception {
if (!metaHashRDF.containsKey(rdfId)) {
LoadRawMetasByRawDataFile(rdfId);
}
List rmList = new ArrayList<>(1);
RawMeta rm = metaHashRDF.get(rdfId).get(name);
if (rm != null)
rmList.add(rm.clone());
return rmList;
}
@Override
public List LoadRawMetasByRawData(int rdId) throws Exception {
if (metaHashRawData.containsKey(rdId)) {
Map metaMap = metaHashRawData.get(rdId);
List rmList = new ArrayList<>(metaMap.size());
for (String key : metaMap.keySet()) {
RawMeta rm = metaMap.get(key).clone(); // because the name will be manipulated later
rmList.add(rm);
}
return rmList;
} else {
RawMetaFactoryData rmfd = new RawMetaFactoryData(rdId, new Date(), gatewayAndCtx.getGateway().getLoggedInUser().getUserName());
List rmList = new ArrayList<>();
RawData rd = LoadRawData(rdId);
if (rd.getBioLabJournal() != null)
rmList.add(rmfd.createMetaStr("Dataset", rd.getBioLabJournal()));
rmList.add(rmfd.createMetaStr("User", rd.getUserId()));
if (rd.getReferenceDate() != null)
rmList.add(rmfd.createMetaDate("Create Date", rd.getReferenceDate()));
if (rd.getModifyDate() != null)
rmList.add(rmfd.createMetaDate("Update Date", rd.getModifyDate()));
if (rd.getDescription() != null)
rmList.add(rmfd.createMetaStr("Description", rd.getDescription()));
if (rd.getComment() != null)
rmList.add(rmfd.createMetaStr("Comment", rd.getComment()));
rmList.add(rmfd.createMetaInt("Dataset ID", rd.getRawDataId()));
// cache entries
Map metaMap = new HashMap<>();
for (RawMeta rm : rmList) {
metaMap.put(rm.getName(), rm);
}
metaHashRawData.put(rdId, metaMap);
return rmList;
}
}
@Override
public List LoadRawMetasByRawDataAndName(int rawDataId, String name) throws Exception {
if (!metaHashRawData.containsKey(rawDataId)) {
LoadRawMetasByRawData(rawDataId);
}
List rmList = new ArrayList<>(1);
RawMeta rm = metaHashRawData.get(rawDataId).get(name);
if (rm != null)
rmList.add(rm.clone());
return rmList;
}
// annotations
@Override
public int InsertRawAnnotation(RawAnnotation rawAnnotation) throws Exception {
//ROIData roi = new ROIData();
//PointData pd = new PointData();
long group = getImageGroup(rawAnnotation.getRawDataFileId());
// fist version: save as attached file
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
String name = rawAnnotation.getDescription();
String path = ORBIT_PATH;
String fileMimeType = ORBIT_ANNOTATION_MIMETYPE;
//String namespace = fileMimeType+"/"+rawAnnotation.getRawAnnotationType(); // would be nice, but we can't query with a wildcard later, so we use a standard namespace
String namespace = ANNOTATION_NAMESPACE;
if (rawAnnotation.getRawDataFileId() < 0) namespace = ANNOTATION_NOFILE_NAMESPACE;
//create the original file object.
OriginalFile originalFile = new OriginalFileI();
originalFile.setName(omero.rtypes.rstring(name));
originalFile.setPath(omero.rtypes.rstring(path));
originalFile.setSize(omero.rtypes.rlong(rawAnnotation.getData().length));
final ChecksumAlgorithm checksumAlgorithm = new ChecksumAlgorithmI();
checksumAlgorithm.setValue(omero.rtypes.rstring(ChecksumAlgorithmSHA1160.value));
originalFile.setHasher(checksumAlgorithm);
originalFile.setMimetype(omero.rtypes.rstring(fileMimeType));
//Now we save the originalFile object
originalFile = (OriginalFile) dm.saveAndReturnObject(gatewayAndCtx.getCtx(group), originalFile);
// upload the byte array
originalFile = storeOriginalFile(rawAnnotation, originalFile);
//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.
FileAnnotation fa = new FileAnnotationI();
fa.setFile(originalFile);
fa.setDescription(omero.rtypes.rstring(rawAnnotation.getDescription()));
fa.setNs(omero.rtypes.rstring(namespace));
//save the file annotation.
fa = (FileAnnotation) dm.saveAndReturnObject(gatewayAndCtx.getCtx(group), fa);
//now link the image and the annotation
if (rawAnnotation.getRawDataFileId() >= 0) { // otherwise it's a non file specific annotation
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
ImageData image = browse.getImage(gatewayAndCtx.getCtx(group), rawAnnotation.getRawDataFileId());
ImageAnnotationLink link = new ImageAnnotationLinkI();
link.setChild(fa);
link.setParent(image.asImage());
//save the link back to the server.
link = (ImageAnnotationLink) dm.saveAndReturnObject(gatewayAndCtx.getCtx(group), link);
// to attach to a Dataset use DatasetAnnotationLink;
}
// set the id the the rawAnnotation object and return the id
rawAnnotation.setRawAnnotationId((int) fa.getId().getValue());
log.debug("rawAnnotation inserted: " + rawAnnotation);
return rawAnnotation.getRawAnnotationId();
}
@Override
public boolean UpdateRawAnnotation(RawAnnotation rawAnnotation) throws Exception {
long group = getImageGroup(rawAnnotation.getRawDataFileId());
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
FileAnnotation annotation = (FileAnnotation) loadAnnotation(rawAnnotation.getRawAnnotationId());
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
String name = rawAnnotation.getDescription();
String path = ORBIT_PATH;
String fileMimeType = ORBIT_ANNOTATION_MIMETYPE;
String namespace = ANNOTATION_NAMESPACE;
if (rawAnnotation.getRawDataFileId() < 0) namespace = ANNOTATION_NOFILE_NAMESPACE;
//save the original file object.
OriginalFile originalFile = annotation.getFile();
originalFile.setName(omero.rtypes.rstring(name));
originalFile.setPath(omero.rtypes.rstring(path));
originalFile.setSize(omero.rtypes.rlong(rawAnnotation.getData().length));
final ChecksumAlgorithm checksumAlgorithm = new ChecksumAlgorithmI();
checksumAlgorithm.setValue(omero.rtypes.rstring(ChecksumAlgorithmSHA1160.value));
originalFile.setHasher(checksumAlgorithm);
originalFile.setMimetype(omero.rtypes.rstring(fileMimeType));
//Now we update the originalFile object
originalFile = (OriginalFile) dm.updateObject(gatewayAndCtx.getCtx(group), originalFile, getParameterWrite());
if (log.isTraceEnabled())
log.trace("original file updated: " + originalFile);
// upload the byte array
originalFile = storeOriginalFile(rawAnnotation, originalFile);
//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.
FileAnnotation fa = annotation; // update existing annotation
fa.setFile(originalFile);
fa.setDescription(omero.rtypes.rstring(rawAnnotation.getDescription()));
fa.setNs(omero.rtypes.rstring(namespace)); // The name space you have set to identify the file annotation.
//save the file annotation.
fa = (FileAnnotation) dm.updateObject(gatewayAndCtx.getCtx(group), fa, getParameterWrite()); // id should be the same afterwards
//rawAnnotation.setRawAnnotationId((int) fa.getId().getValue());
log.debug("rawAnnotation updated: " + rawAnnotation);
return (int) fa.getId().getValue() == rawAnnotation.getRawAnnotationId();
}
private OriginalFile storeOriginalFile(RawAnnotation rawAnnotation, OriginalFile originalFile) throws DSOutOfServiceException, ServerError, IOException {
long group = getImageGroup(rawAnnotation.getRawDataFileId());
RawFileStorePrx rawFileStore = gatewayAndCtx.getGateway().getRawFileService(gatewayAndCtx.getCtx(group));
rawFileStore.setFileId(originalFile.getId().getValue());
ByteArrayOutputStream bos = new ByteArrayOutputStream();
ObjectOutputStream oos = new ObjectOutputStream(bos);
oos.writeObject(rawAnnotation);
oos.flush();
oos.close();
bos.flush();
bos.close();
InputStream stream = new ByteArrayInputStream(bos.toByteArray());
long pos = 0;
int rlen;
byte[] buf = new byte[INC];
ByteBuffer bbuf;
while ((rlen = stream.read(buf)) > 0) {
rawFileStore.write(buf, pos, rlen);
pos += rlen;
bbuf = ByteBuffer.wrap(buf);
bbuf.limit(rlen);
}
stream.close();
originalFile = rawFileStore.save();
rawFileStore.close();
return originalFile;
}
private Annotation loadAnnotation(int rawAnnotationId) throws Exception {
long group = getAnnotationGroup(rawAnnotationId);
Annotation annotation = null;
IMetadataPrx proxy = gatewayAndCtx.getGateway().getMetadataService(gatewayAndCtx.getCtx(group));
List annotations = proxy.loadAnnotation(Collections.singletonList((long) rawAnnotationId));
if (annotations == null || annotations.size() == 0) {
throw new Exception("annotation with id " + rawAnnotationId + " not found");
} else {
if (annotations.size() > 1) {
log.warn("more than one annotations found for id " + rawAnnotationId + " but only the first will be used");
}
annotation = annotations.get(0);
}
return annotation;
}
private List loadAnnotations(Collection annotations) throws Exception {
FileAnnotationData fa;
List rawAnnotations = new ArrayList<>(annotations.size());
RawFileStorePrx store = null;
long lastGroup = -2;
for (Annotation annotation : annotations) {
long group = getAnnotationGroup(annotation.getId().getValue());
if (group!=lastGroup) {
if (store!=null) {
try {
store.close();
} catch (Exception e) {}
}
store = gatewayAndCtx.getGateway().getRawFileService(gatewayAndCtx.getCtx(group));
lastGroup = group;
}
ByteArrayOutputStream stream = new ByteArrayOutputStream();
OriginalFile of;
if (annotation instanceof FileAnnotation) {
fa = new FileAnnotationData((FileAnnotation) annotation);
//The id of te original file
//of = getOriginalFile(fa.getFileID());
store.setFileId(fa.getFileID());
int offset = 0;
long size = store.size();
try {
for (offset = 0; (offset + INC) < size; ) {
stream.write(store.read(offset, INC));
offset += INC;
}
} finally {
stream.write(store.read(offset, (int) (size - offset)));
stream.close();
}
}
byte[] data = stream.toByteArray();
ByteArrayInputStream bis = new ByteArrayInputStream(data);
ObjectInputStream ois = new ObjectInputStream(bis);
try {
Object obj = ois.readObject();
RawAnnotation ra = (RawAnnotation) obj;
ra.setRawAnnotationId((int) annotation.getId().getValue());
rawAnnotations.add(ra);
} catch (ClassNotFoundException e) {
log.warn("class for deserialization not found: " + e.getMessage());
} catch (InvalidClassException ice) {
log.warn("invalid class exception");
}
finally {
ois.close();
bis.close();
}
}
if (store!=null) {
try {
store.close();
} catch (Exception e) {}
}
return rawAnnotations;
}
@Override
public RawAnnotation LoadRawAnnotation(int rawAnnotationId) throws Exception {
Annotation annotation = loadAnnotation(rawAnnotationId);
List rawAnnotations = loadAnnotations(Collections.singleton(annotation));
if (rawAnnotations == null || rawAnnotations.size() == 0)
throw new Exception("annotation with id " + rawAnnotationId + " not found");
return rawAnnotations.get(0);
}
@Override
public List LoadRawAnnotationsByRawDataFile(int rdfID) throws Exception {
long group = getImageGroup(rdfID);
IMetadataPrx proxy = gatewayAndCtx.getGateway().getMetadataService(gatewayAndCtx.getCtx(group));
List nsToInclude = new ArrayList();
nsToInclude.add(ANNOTATION_NAMESPACE);
List nsToExclude = new ArrayList();
List annotations = proxy.loadSpecifiedAnnotationsLinkedTo(FileAnnotation.class.getName(), nsToInclude, nsToExclude, Image.class.getName(), Collections.singletonList((long) rdfID), getParameterRead()).get((long) rdfID);
if (log.isTraceEnabled() && annotations != null)
log.trace("#annotations: " + annotations.size());
if (annotations == null || annotations.size() == 0) {
return new ArrayList<>();
}
return loadAnnotations(annotations);
}
@Override
public List LoadRawAnnotationsByRawDataFile(int rdfID, int rawAnnotationType) throws Exception {
List rawAnnotations = LoadRawAnnotationsByRawDataFile(rdfID);
List filtered = new ArrayList<>(rawAnnotations.size());
// TODO: better query correct types
for (RawAnnotation rawAnnotation : rawAnnotations) {
if (rawAnnotation.getRawAnnotationType() == rawAnnotationType) {
filtered.add(rawAnnotation);
}
}
return filtered;
}
@Override
public List LoadRawAnnotationsByType(int rawAnnotationType) throws Exception {
String namespace = ANNOTATION_NAMESPACE;
if (rawAnnotationType == RawAnnotation.ANNOTATION_TYPE_MODEL) namespace = ANNOTATION_NOFILE_NAMESPACE;
List annotations = new ArrayList<>();
for (long group: getGroups()) {
IMetadataPrx proxy = gatewayAndCtx.getGateway().getMetadataService(gatewayAndCtx.getCtx(group));
List nsToInclude = new ArrayList();
nsToInclude.add(namespace);
List nsToExclude = new ArrayList();
annotations.addAll(proxy.loadSpecifiedAnnotations(FileAnnotation.class.getName(), nsToInclude, nsToExclude, getParameterRead())); // use parameter param to restrict annotations to user
if (log.isTraceEnabled() && annotations != null)
log.trace("group "+group+ " #annotations: " + annotations.size());
}
if (annotations == null || annotations.size() == 0) {
return new ArrayList<>();
}
// TODO: better query correct types
List rawAnnotations = loadAnnotations(annotations);
List filtered = new ArrayList<>(rawAnnotations.size());
for (RawAnnotation rawAnnotation : rawAnnotations) {
if (rawAnnotation.getRawAnnotationType() == rawAnnotationType) {
filtered.add(rawAnnotation);
}
}
return filtered;
}
@Override
public boolean DeleteRawAnnotation(int rawAnnotationId) throws Exception {
long group = getAnnotationGroup(rawAnnotationId);
Annotation annotation = loadAnnotation(rawAnnotationId);
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
Delete2Response response = (Delete2Response) dm.deleteObject(gatewayAndCtx.getCtx(group), annotation);
return (response.deletedObjects.get("ome.model.annotations.FileAnnotation").size() > 0); // deleted one fileannotaiton (no id check here)
}
// Raw Meta
@Override
public int InsertRawMeta(RawMeta rm) throws Exception {
long group = getImageGroup(rm.getRawDataFileId());
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
MapAnnotationI anno = new MapAnnotationI();
anno.setNs(omero.rtypes.rstring(ORBIT_METADATA_NAMESPACE));
anno.setName(omero.rtypes.rstring(rm.getName()));
List kvList = new ArrayList<>(1);
kvList.add(new NamedValue(rm.getName(), rm.getValue()));
anno.setMapValue(kvList);
anno = (MapAnnotationI) dm.saveAndReturnObject(gatewayAndCtx.getCtx(group), anno);
rm.setRawMetaId((int) anno.getId().getValue());
log.debug("inserted meta data: " + rm);
// link to rawDataFile
BrowseFacility browse = getGatewayAndCtx().getGateway().getFacility(BrowseFacility.class);
ImageData image = browse.getImage(gatewayAndCtx.getCtx(group), rm.getRawDataFileId());
ImageAnnotationLink link = new ImageAnnotationLinkI();
link.setChild(anno);
link.setParent(image.asImage());
link = (ImageAnnotationLink) dm.saveAndReturnObject(gatewayAndCtx.getCtx(group), link);
clearMetaRDFHash();
return rm.getRawMetaId();
}
@Override
public boolean UpdateRawMeta(RawMeta rm) throws Exception {
if (rm.getRawMetaId() <= 0)
throw new IllegalArgumentException("RawMeta is not persistent, cannot update. RawMeta: " + rm);
long group = getImageGroup(rm.getRawDataFileId());
Annotation annotation = loadAnnotation(rm.getRawMetaId());
if (annotation instanceof MapAnnotationI) {
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
MapAnnotationI anno = (MapAnnotationI) annotation;
log.debug("update rawMeta annotation: " + anno);
anno.setName(omero.rtypes.rstring(rm.getName()));
List kvList = new ArrayList<>(1);
kvList.add(new NamedValue(rm.getName(), rm.getValue()));
anno.setMapValue(kvList);
anno = (MapAnnotationI) dm.updateObject(gatewayAndCtx.getCtx(group), anno, getParameterWrite());
clearMetaRDFHash();
return ((int) anno.getId().getValue()) == rm.getRawMetaId();
} else {
throw new IllegalArgumentException("annotation is not a MapAnnotationI, but is " + annotation.getClass().getName());
}
}
@Override
public boolean DeleteRawMeta(int rawMetaId) throws Exception {
if (rawMetaId <= 0)
throw new IllegalArgumentException("RawMeta is not persistent, cannot delete. RawMetaId: " + rawMetaId);
long group = getAnnotationGroup(rawMetaId);
Annotation annotation = loadAnnotation(rawMetaId);
if (annotation instanceof MapAnnotationI) {
DataManagerFacility dm = gatewayAndCtx.getGateway().getFacility(DataManagerFacility.class);
MapAnnotationI anno = (MapAnnotationI) annotation;
dm.delete(gatewayAndCtx.getCtx(group), anno);
log.debug("delete rawMeta annotation: " + anno);
} else {
throw new IllegalArgumentException("annotation is not a MapAnnotationI, but is " + annotation.getClass().getName());
}
return true;
}
@Override
public OrbitUser getOrbitUser(String username) {
OrbitUser user = new OrbitUser(username, "", "");
try {
ExperimenterData experimenter = getGatewayAndCtx().getGateway().getUserDetails(gatewayAndCtx.getCtx(), username);
user.setFirstName(experimenter.getFirstName());
user.setLastName(experimenter.getLastName());
} catch (DSOutOfServiceException e) {
e.printStackTrace();
log.error("cannot load user details", e);
}
return user;
}
public boolean isOnlyOwnerObjects() {
return onlyOwnerObjects;
}
public void setOnlyOwnerObjects(boolean onlyOwnerObjects) {
this.onlyOwnerObjects = onlyOwnerObjects;
}
public boolean isListAllSeries() {
return listAllSeries;
}
public void setListAllSeries(boolean listAllSeries) {
this.listAllSeries = listAllSeries;
}
public long getProjectGroup(long projectId) {
long group = -1;
if (projectGroupMap.containsKey(projectId)) {
group = projectGroupMap.get(projectId);
} else {
BrowseFacility browse = null;
try {
browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
} catch (Exception e) {
e.printStackTrace();
}
if (browse!=null) {
for (long g : getGroups()) {
ProjectData project = null;
try {
Collection projects = browse.getProjects(gatewayAndCtx.getCtx(g), Collections.singletonList(projectId));
if (projects != null && projects.size() > 0) {
project = projects.iterator().next();
}
} catch (Exception e) {
// do nothing here, just testing
}
if (project != null) { // correct group
group = g;
return group;
}
}
}
}
return group;
}
public long getDatasetGroup(long datasetId) {
long group = -1;
if (datasetGroupMap.containsKey(datasetId)) {
group = datasetGroupMap.get(datasetId);
} else {
BrowseFacility browse = null;
try {
browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
} catch (Exception e) {
e.printStackTrace();
}
if (browse!=null) {
for (long g : getGroups()) {
DatasetData dataset = null;
try {
Collection datasets = browse.getDatasets(gatewayAndCtx.getCtx(g), Collections.singletonList(datasetId));
if (datasets != null && datasets.size() > 0) {
dataset = datasets.iterator().next();
}
} catch (Exception e) {
// do nothing here, just testing
}
if (dataset != null) { // correct group
group = g;
datasetGroupMap.put(datasetId,group);
return group;
}
}
}
}
return group;
}
public long getRdfGroup(RawDataFile rdf) {
long group = -1;
if (rdfGroupMap.containsKey((long)rdf.getRawDataFileId())) {
group = rdfGroupMap.get((long)rdf.getRawDataFileId());
}
else if (datasetGroupMap.containsKey((long)rdf.getRawDataId())) {
group = getDatasetGroup((long) rdf.getRawDataId());
} else {
group = getImageGroup((long)rdf.getRawDataFileId());
}
return group;
}
public static long getImageGroupCached(long imageId) {
long group = -1;
if (rdfGroupMap.containsKey(imageId)) {
group = rdfGroupMap.get(imageId);
}
return group;
}
public long getImageGroup(long imageId) {
long group = -1;
if (rdfGroupMap.containsKey(imageId)) {
group = rdfGroupMap.get(imageId);
} else {
BrowseFacility browse = null;
try {
browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
} catch (Exception e) {
e.printStackTrace();
}
if (browse!=null) {
for (long g : getGroups()) {
ImageData image = null;
try {
browse = gatewayAndCtx.getGateway().getFacility(BrowseFacility.class);
image = browse.getImage(gatewayAndCtx.getCtx(g), imageId);
} catch (Exception e) {
// do nothing here, just testing
}
if (image != null) { // correct group
group = g;
rdfGroupMap.put(imageId,group);
return group;
}
}
}
}
return group;
}
public long getAnnotationGroup(long annotationId) {
long group = -1;
if (metaGroupMap.containsKey(annotationId)) {
group = metaGroupMap.get(annotationId);
} else {
for (long g : getGroups()) {
Annotation annotation = null;
try {
IMetadataPrx proxy = gatewayAndCtx.getGateway().getMetadataService(gatewayAndCtx.getCtx(g));
List annotations = proxy.loadAnnotation(Collections.singletonList(annotationId));
if (annotations!=null && annotations.size()>0) {
annotation = annotations.get(0);
}
} catch (Exception e) {
// do nothing here, just testing
}
if (annotation != null) { // correct group
group = g;
metaGroupMap.put(annotationId,group);
return group;
}
}
}
return group;
}
/**
* Only for debugging
* @param user
* @param pass
*/
protected void showOrbitTree(String user, String pass) {
boolean auth = authenticateUser(user, pass);
//boolean auth = ip.authenticateUser("root", "omero");
System.out.println("auth: "+auth);
AbstractOrbitTree tree = createOrbitTree();
tree.refresh();
JFrame frame = new JFrame("Omero");
frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
frame.add(tree);
frame.setBounds(0,0,500,700);
frame.setVisible(true);
RawUtilsCommon.centerComponent(frame);
}
public int getSelectedSeries() {
return selectedSeries;
}
public void setSelectedSeries(int selectedSeries) {
this.selectedSeries = selectedSeries;
}
public static void main(String[] args) throws Exception {
// just a demo
int id = 219; //219;
ImageProviderOmero ip = new ImageProviderOmero();
ip.authenticateUser("root","omero");
long group = ip.getImageGroup(id);
RawDataFile rdf = ip.LoadRawDataFile(id);
IOrbitImage image = ip.createOrbitImage(rdf,0);
System.out.println(image.getFilename());
System.out.println("isMultichan: "+((OmeroImage)image).isMultiChannel());
ip.close();
}
}