/**
* 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 <code>lookupGroup</code> method. Retrieves a specified group. Controls if the
* following groups exist: <code>system, user</code> and converts the group into the corresponding
* POJO.
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testLookupGroup() throws Exception {
IAdminPrx svc = root.getSession().getAdminService();
ExperimenterGroup group = svc.lookupGroup(USER_GROUP);
assertNotNull(group);
assertTrue(group.getName().getValue().equals(USER_GROUP));
GroupData data = new GroupData(group);
assertTrue(data.getId() == group.getId().getValue());
assertTrue(data.getName() == group.getName().getValue());
group = svc.lookupGroup(SYSTEM_GROUP);
assertNotNull(group);
assertTrue(group.getName().getValue().equals(SYSTEM_GROUP));
// Test the conversion into the corresponding POJO
data = new GroupData(group);
assertTrue(data.getId() == group.getId().getValue());
assertTrue(data.getName() == group.getName().getValue());
}
@Test(enabled = false)
public void testSudoCreatesUserAccountThroughIAdmin() throws Exception {
ExperimenterGroup g = new ExperimenterGroupI();
g.setName(rstring(UUID.randomUUID().toString()));
getSudoAdmin("ome").createGroup(g);
Experimenter e = new ExperimenterI();
e.setOmeName(rstring(UUID.randomUUID().toString()));
e.setFirstName(rstring("ticket:181"));
e.setLastName(rstring("ticket:199"));
e =
getSudoAdmin("ome")
.getExperimenter(getSudoAdmin("ome").createUser(e, g.getName().getValue()));
assertCanLogin(e.getOmeName().getValue(), "");
assertCanLogin(e.getOmeName().getValue(), "ome");
assertCanLogin(e.getOmeName().getValue(), "bob");
doesNotHaveSystemPrivileges(e);
}
/**
* Tests the adding and modifying of a user photo, specify all the exception thrown by ticket:1791
*
* @throws Exception Thrown if an error occurred.
*/
@Test
public void testUserPhoto() throws Exception {
IAdminPrx prx = root.getSession().getAdminService();
String uuid = UUID.randomUUID().toString();
// First create a user in two groups, one rwrw-- and one rwr---
ExperimenterGroup rwr = new ExperimenterGroupI();
rwr.setName(rstring(uuid));
rwr.getDetails().setPermissions(new PermissionsI("rwr---"));
long rwrID = prx.createGroup(rwr);
rwr = prx.getGroup(rwrID);
ExperimenterGroup rwrw = new ExperimenterGroupI();
rwrw.setName(rstring(UUID.randomUUID().toString()));
rwr.getDetails().setPermissions(new PermissionsI("rwrw--"));
long rwrwID = prx.createGroup(rwrw);
rwrw = prx.getGroup(rwrwID);
Experimenter e = new ExperimenterI();
e.setOmeName(rstring(uuid));
e.setFirstName(rstring(uuid));
e.setLastName(rstring(uuid));
long userID = prx.createUser(e, rwrw.getName().getValue());
e = prx.getExperimenter(userID);
prx.addGroups(e, Arrays.asList(rwr));
omero.client client = new omero.client(root.getPropertyMap());
try {
client.createSession(e.getOmeName().getValue(), "foo");
prx = client.getSession().getAdminService();
prx.uploadMyUserPhoto("/tmp/foto.jpg", "image/jpeg", new byte[] {1});
client.getSession().setSecurityContext(new ExperimenterGroupI(rwrID, false));
prx.uploadMyUserPhoto("/tmp/foto2.jpg", "image/jpeg", new byte[] {2});
} finally {
client.closeSession();
}
}
@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);
}
}