/**
* Tests the deletion of an experimenter.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testDeleteExperimenter() throws Exception {
// First create a new user.
String uuid = UUID.randomUUID().toString();
Experimenter e = new ExperimenterI();
e.setOmeName(omero.rtypes.rstring(uuid));
e.setFirstName(omero.rtypes.rstring("user"));
e.setLastName(omero.rtypes.rstring("user"));
IAdminPrx svc = root.getSession().getAdminService();
// already tested
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(omero.rtypes.rstring(uuid));
g.getDetails().setPermissions(new PermissionsI("rw----"));
// create group.
svc.createGroup(g);
long id = svc.createUser(e, uuid);
e = svc.lookupExperimenter(uuid);
svc.deleteExperimenter(e);
ParametersI p = new ParametersI();
p.addId(id);
IQueryPrx query = root.getSession().getQueryService();
e =
(Experimenter)
query.findByQuery("select distinct e from Experimenter e where e.id = :id", p);
assertNull(e);
}
/**
* Tests the creation of a group with permission <code>rwrw--</code>.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testCreateGroupRWRW() throws Exception {
String uuid = UUID.randomUUID().toString();
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(omero.rtypes.rstring(uuid));
g.getDetails().setPermissions(new PermissionsI("rwrw--"));
IAdminPrx svc = root.getSession().getAdminService();
long id = svc.createGroup(g);
// Load the group
IQueryPrx query = root.getSession().getQueryService();
ParametersI p = new ParametersI();
p.addId(id);
ExperimenterGroup eg =
(ExperimenterGroup)
query.findByQuery("select distinct g from ExperimenterGroup g where g.id = :id", p);
assertNotNull(eg);
assertTrue(eg.getName().getValue().equals(uuid));
// test permissions
Permissions perms = eg.getDetails().getPermissions();
assertTrue(perms.isUserRead());
assertTrue(perms.isUserWrite());
assertTrue(perms.isGroupRead());
assertTrue(perms.isGroupWrite());
assertFalse(perms.isWorldRead());
assertFalse(perms.isWorldWrite());
}
/**
* Tests the default group of an experimenter.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testChangeDefaultGroup() throws Exception {
// Create 2 groups and add a user
String uuid1 = UUID.randomUUID().toString();
ExperimenterGroup g1 = new ExperimenterGroupI();
g1.setName(omero.rtypes.rstring(uuid1));
g1.getDetails().setPermissions(new PermissionsI("rw----"));
String uuid2 = UUID.randomUUID().toString();
ExperimenterGroup g2 = new ExperimenterGroupI();
g2.setName(omero.rtypes.rstring(uuid2));
g2.getDetails().setPermissions(new PermissionsI("rw----"));
IAdminPrx svc = root.getSession().getAdminService();
IQueryPrx query = root.getSession().getQueryService();
long id1 = svc.createGroup(g1);
long id2 = svc.createGroup(g2);
ParametersI p = new ParametersI();
p.addId(id1);
ExperimenterGroup eg1 =
(ExperimenterGroup)
query.findByQuery("select distinct g from ExperimenterGroup g where g.id = :id", p);
p = new ParametersI();
p.addId(id2);
ExperimenterGroup eg2 =
(ExperimenterGroup)
query.findByQuery("select distinct g from ExperimenterGroup g where g.id = :id", p);
Experimenter e = new ExperimenterI();
e.setOmeName(omero.rtypes.rstring(uuid1));
e.setFirstName(omero.rtypes.rstring("user"));
e.setLastName(omero.rtypes.rstring("user"));
List<ExperimenterGroup> groups = new ArrayList<ExperimenterGroup>();
// method tested elsewhere
ExperimenterGroup userGroup = svc.lookupGroup(USER_GROUP);
groups.add(eg1);
groups.add(eg2);
groups.add(userGroup);
long id = svc.createExperimenter(e, eg1, groups);
e = svc.lookupExperimenter(uuid1);
List<GroupExperimenterMap> links = e.copyGroupExperimenterMap();
assertTrue(groups.get(0).getId().getValue() == eg1.getId().getValue());
svc.setDefaultGroup(e, eg2);
e = svc.lookupExperimenter(uuid1);
links = e.copyGroupExperimenterMap();
groups = new ArrayList<ExperimenterGroup>();
for (GroupExperimenterMap link : links) {
groups.add(link.getParent());
}
assertTrue(groups.get(0).getId().getValue() == eg2.getId().getValue());
}
/**
* Tests the creation of a user using the <code>createUser</code> method.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testCreateUser() throws Exception {
String uuid = UUID.randomUUID().toString();
Experimenter e = new ExperimenterI();
e.setOmeName(omero.rtypes.rstring(uuid));
e.setFirstName(omero.rtypes.rstring("user"));
e.setLastName(omero.rtypes.rstring("user"));
IAdminPrx svc = root.getSession().getAdminService();
// already tested
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(omero.rtypes.rstring(uuid));
g.getDetails().setPermissions(new PermissionsI("rw----"));
long groupId = svc.createGroup(g);
long id = svc.createUser(e, uuid);
IQueryPrx query = root.getSession().getQueryService();
// Check if we have a user
ParametersI p = new ParametersI();
p.addId(id);
e =
(Experimenter)
query.findByQuery("select distinct e from Experimenter e where e.id = :id", p);
assertNotNull(e);
assertTrue(e.getOmeName().getValue().equals(uuid));
// check if we are in the correct group i.e. user and uuid
// now check if the user is in correct groups.
ExperimenterGroup userGroup = svc.lookupGroup(USER_GROUP);
List<Long> ids = new ArrayList<Long>();
ids.add(groupId);
ids.add(userGroup.getId().getValue());
p = new ParametersI();
p.addLongs("gids", ids);
List list =
(List)
query.findAllByQuery(
"select m "
+ "from GroupExperimenterMap as m "
+ "left outer join fetch m.child "
+ "left outer join fetch m.parent"
+ " where m.parent.id in (:gids)",
p);
assertNotNull(list);
Iterator i = list.iterator();
GroupExperimenterMap geMap;
int count = 0;
while (i.hasNext()) {
geMap = (GroupExperimenterMap) i.next();
if (geMap.getChild().getId().getValue() == id) count++;
}
assertTrue(count == 2);
}
/**
* Retrieve the log file.
*
* @param id The id of the file to load.
* @param session The OMERO session.
* @return See above.
* @throws Throwable Thrown if an error occurred while loading file.
*/
private File retrieveLogFile(Long id, ServiceFactoryPrx session) throws Throwable {
if (id == null) return null;
// dowload the file
StringBuffer buf = new StringBuffer();
buf.append("importLog_");
buf.append(id);
File logfile = File.createTempFile(buf.toString(), ".log");
logfile.deleteOnExit();
IQueryPrx svc = session.getQueryService();
ParametersI param = new ParametersI();
param.map.put("id", omero.rtypes.rlong(id));
OriginalFile of =
(OriginalFile) svc.findByQuery("select p from OriginalFile as p where p.id = :id", param);
if (of == null) return null;
final String path = logfile.getAbsolutePath();
RawFileStorePrx store = null;
try {
store = session.createRawFileStore();
store.setFileId(id);
} catch (Throwable e) {
store.close();
return null; // Never reached.
}
try {
long size = -1;
long offset = 0;
int INC = 262144;
FileOutputStream stream = new FileOutputStream(logfile);
try {
try {
size = store.size();
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();
}
} catch (Exception e) {
log.error("Cannot write log file", e);
if (stream != null) stream.close();
}
} catch (IOException e) {
log.error("Cannot write log file", e);
} finally {
store.close();
}
return logfile;
}
/**
* Tests the update of the details of the user currently logged in using the <code>
* updateExperimenter</code> method.
*
* @throws Exception Thrown if an error occurred.
*/
@Test(enabled = true)
public void testUpdateExperimenterByUserUsingUpdateExperimenter() throws Exception {
// First create a new user.
String uuid = UUID.randomUUID().toString();
Experimenter e = new ExperimenterI();
e.setOmeName(omero.rtypes.rstring(uuid));
e.setFirstName(omero.rtypes.rstring("user"));
e.setLastName(omero.rtypes.rstring("user"));
IAdminPrx svc = root.getSession().getAdminService();
// already tested
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(omero.rtypes.rstring(uuid));
g.getDetails().setPermissions(new PermissionsI("rw----"));
// create group.
svc.createGroup(g);
long id = svc.createUser(e, uuid);
IQueryPrx query = root.getSession().getQueryService();
ParametersI p = new ParametersI();
p.addId(id);
e =
(Experimenter)
query.findByQuery("select distinct e from Experimenter e where e.id = :id", p);
assertNotNull(e);
String name = "userModified";
// uuid = UUID.randomUUID().toString();
e.setOmeName(omero.rtypes.rstring(uuid));
e.setFirstName(omero.rtypes.rstring(name));
e.setLastName(omero.rtypes.rstring(name));
//
// owner logs in.
omero.client client = newOmeroClient();
client.createSession(uuid, uuid);
init(client);
iAdmin.updateExperimenter(e);
e =
(Experimenter)
query.findByQuery("select distinct e from Experimenter e where e.id = :id", p);
assertNotNull(e);
assertTrue(e.getOmeName().getValue().equals(uuid));
assertTrue(e.getFirstName().getValue().equals(name));
assertTrue(e.getLastName().getValue().equals(name));
}
/**
* Tests to make a user the owner of a group.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testSetOwner() throws Exception {
// First create a new user.
String uuid = UUID.randomUUID().toString();
Experimenter e = new ExperimenterI();
e.setOmeName(omero.rtypes.rstring(uuid));
e.setFirstName(omero.rtypes.rstring("user"));
e.setLastName(omero.rtypes.rstring("user"));
IAdminPrx svc = root.getSession().getAdminService();
// already tested
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(omero.rtypes.rstring(uuid));
g.getDetails().setPermissions(new PermissionsI("rw----"));
// create group.
long groupId = svc.createGroup(g);
g = svc.lookupGroup(uuid);
// create the user.
long expId = svc.createUser(e, uuid);
e = svc.lookupExperimenter(uuid);
// set the user as the group owner.
svc.setGroupOwner(g, e);
IQueryPrx query = root.getSession().getQueryService();
String sql = "select m from GroupExperimenterMap as m ";
sql += "left outer join fetch m.child as c ";
sql += "left outer join fetch m.parent as p ";
sql += "where ";
sql += "c.id = :expId ";
sql += " and p.id = :groupId";
ParametersI p = new ParametersI();
p.addLong("expId", expId);
p.addLong("groupId", groupId);
List l = (List) query.findAllByQuery(sql, p);
Iterator i = l.iterator();
GroupExperimenterMap map;
while (i.hasNext()) {
map = (GroupExperimenterMap) i.next();
assertTrue(map.getOwner().getValue());
}
}
@Override
protected void initFile(String id) throws FormatException, IOException {
LOGGER.debug("OmeroReader.initFile({})", id);
super.initFile(id);
if (!id.startsWith("omero:")) {
throw new IllegalArgumentException("Not an OMERO id: " + id);
}
// parse credentials from id string
LOGGER.info("Parsing credentials");
String address = server, user = username, pass = password;
int port = thePort;
long iid = -1;
final String[] tokens = id.substring(6).split("\n");
for (String token : tokens) {
final int equals = token.indexOf("=");
if (equals < 0) continue;
final String key = token.substring(0, equals);
final String val = token.substring(equals + 1);
if (key.equals("server")) address = val;
else if (key.equals("user")) user = val;
else if (key.equals("pass")) pass = val;
else if (key.equals("port")) {
try {
port = Integer.parseInt(val);
} catch (NumberFormatException exc) {
}
} else if (key.equals("session")) {
sessionID = val;
} else if (key.equals("groupName")) {
group = val;
} else if (key.equals("groupID")) {
groupID = new Long(val);
} else if (key.equals("iid")) {
try {
iid = Long.parseLong(val);
} catch (NumberFormatException exc) {
}
}
}
if (address == null) {
throw new FormatException("Invalid server address");
}
if (user == null && sessionID == null) {
throw new FormatException("Invalid username");
}
if (pass == null && sessionID == null) {
throw new FormatException("Invalid password");
}
if (iid < 0) {
throw new FormatException("Invalid image ID");
}
try {
// authenticate with OMERO server
LOGGER.info("Logging in");
client = new omero.client(address, port);
ServiceFactoryPrx serviceFactory = null;
if (user != null && pass != null) {
serviceFactory = client.createSession(user, pass);
} else {
serviceFactory = client.createSession(sessionID, sessionID);
}
if (!encrypted) {
client = client.createClient(false);
serviceFactory = client.getSession();
}
if (group != null || groupID != null) {
IAdminPrx iAdmin = serviceFactory.getAdminService();
IQueryPrx iQuery = serviceFactory.getQueryService();
EventContext eventContext = iAdmin.getEventContext();
ExperimenterGroup defaultGroup = iAdmin.getDefaultGroup(eventContext.userId);
if (!defaultGroup.getName().getValue().equals(group)
&& !new Long(defaultGroup.getId().getValue()).equals(groupID)) {
Experimenter exp = iAdmin.getExperimenter(eventContext.userId);
ParametersI p = new ParametersI();
p.addId(eventContext.userId);
List<IObject> groupList =
iQuery.findAllByQuery(
"select distinct g from ExperimenterGroup as g "
+ "join fetch g.groupExperimenterMap as map "
+ "join fetch map.parent e "
+ "left outer join fetch map.child u "
+ "left outer join fetch u.groupExperimenterMap m2 "
+ "left outer join fetch m2.parent p "
+ "where g.id in "
+ " (select m.parent from GroupExperimenterMap m "
+ " where m.child.id = :id )",
p);
Iterator<IObject> i = groupList.iterator();
ExperimenterGroup g = null;
boolean in = false;
while (i.hasNext()) {
g = (ExperimenterGroup) i.next();
if (g.getName().getValue().equals(group)
|| new Long(g.getId().getValue()).equals(groupID)) {
in = true;
groupID = g.getId().getValue();
break;
}
}
if (in) {
iAdmin.setDefaultGroup(exp, iAdmin.getGroup(groupID));
serviceFactory.setSecurityContext(new ExperimenterGroupI(groupID, false));
}
}
}
// get raw pixels store and pixels
store = serviceFactory.createRawPixelsStore();
final GatewayPrx gateway = serviceFactory.createGateway();
img = gateway.getImage(iid);
if (img == null) {
throw new FormatException(
"Could not find Image with ID=" + iid + " in group '" + group + "'.");
}
long pixelsId = img.getPixels(0).getId().getValue();
store.setPixelsId(pixelsId, false);
pix = gateway.getPixels(pixelsId);
final int sizeX = pix.getSizeX().getValue();
final int sizeY = pix.getSizeY().getValue();
final int sizeZ = pix.getSizeZ().getValue();
final int sizeC = pix.getSizeC().getValue();
final int sizeT = pix.getSizeT().getValue();
final String pixelType = pix.getPixelsType().getValue().getValue();
// populate metadata
LOGGER.info("Populating metadata");
core[0].sizeX = sizeX;
core[0].sizeY = sizeY;
core[0].sizeZ = sizeZ;
core[0].sizeC = sizeC;
core[0].sizeT = sizeT;
core[0].rgb = false;
core[0].littleEndian = false;
core[0].dimensionOrder = "XYZCT";
core[0].imageCount = sizeZ * sizeC * sizeT;
core[0].pixelType = FormatTools.pixelTypeFromString(pixelType);
RDouble x = pix.getPhysicalSizeX();
Double px = x == null ? null : x.getValue();
RDouble y = pix.getPhysicalSizeY();
Double py = y == null ? null : y.getValue();
RDouble z = pix.getPhysicalSizeZ();
Double pz = z == null ? null : z.getValue();
RDouble t = pix.getTimeIncrement();
Double time = t == null ? null : t.getValue();
RString imageName = img.getName();
String name = imageName == null ? null : imageName.getValue();
if (name != null) {
currentId = name;
} else {
currentId = "Image ID " + iid;
}
RString imgDescription = img.getDescription();
String description = imgDescription == null ? null : imgDescription.getValue();
RTime date = img.getAcquisitionDate();
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
store.setImageName(name, 0);
store.setImageDescription(description, 0);
if (date != null) {
store.setImageAcquisitionDate(
new Timestamp(DateTools.convertDate(date.getValue(), (int) DateTools.UNIX_EPOCH)), 0);
}
if (px != null && px > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(px), 0);
}
if (py != null && py > 0) {
store.setPixelsPhysicalSizeY(new PositiveFloat(py), 0);
}
if (pz != null && pz > 0) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(pz), 0);
}
if (time != null) {
store.setPixelsTimeIncrement(time, 0);
}
List<Channel> channels = pix.copyChannels();
for (int c = 0; c < channels.size(); c++) {
LogicalChannel channel = channels.get(c).getLogicalChannel();
RInt emWave = channel.getEmissionWave();
RInt exWave = channel.getExcitationWave();
RDouble pinholeSize = channel.getPinHoleSize();
RString cname = channel.getName();
Integer emission = emWave == null ? null : emWave.getValue();
Integer excitation = exWave == null ? null : exWave.getValue();
String channelName = cname == null ? null : cname.getValue();
Double pinhole = pinholeSize == null ? null : pinholeSize.getValue();
if (channelName != null) {
store.setChannelName(channelName, 0, c);
}
if (pinhole != null) {
store.setChannelPinholeSize(pinhole, 0, c);
}
if (emission != null && emission > 0) {
store.setChannelEmissionWavelength(new PositiveInteger(emission), 0, c);
}
if (excitation != null && excitation > 0) {
store.setChannelExcitationWavelength(new PositiveInteger(excitation), 0, c);
}
}
} catch (CannotCreateSessionException e) {
throw new FormatException(e);
} catch (PermissionDeniedException e) {
throw new FormatException(e);
} catch (ServerError e) {
throw new FormatException(e);
}
}
