Java tutorial
/* * Copyright 2010-2015 Glencoe Software, Inc. All rights reserved. * Use is subject to license terms supplied in LICENSE.txt */ package integration; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertNull; import static org.testng.AssertJUnit.assertTrue; import static org.testng.AssertJUnit.fail; import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; import java.util.Collections; import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import java.util.UUID; import ome.formats.OMEROMetadataStoreClient; import ome.formats.importer.IObservable; import ome.formats.importer.IObserver; import ome.formats.importer.ImportCandidates; import ome.formats.importer.ImportConfig; import ome.formats.importer.ImportContainer; import ome.formats.importer.ImportEvent; import ome.formats.importer.ImportLibrary; import ome.formats.importer.OMEROWrapper; import ome.formats.importer.util.ErrorHandler; import ome.io.nio.SimpleBackOff; import ome.services.blitz.repo.path.FsFile; import omero.ApiUsageException; import omero.RLong; import omero.RType; import omero.ServerError; import omero.rtypes; import omero.api.IAdminPrx; import omero.api.IQueryPrx; import omero.api.IUpdatePrx; import omero.api.ServiceFactoryPrx; import omero.cmd.CmdCallbackI; import omero.cmd.Delete2; import omero.cmd.Delete2Response; import omero.cmd.DoAll; import omero.cmd.DoAllRsp; import omero.cmd.ERR; import omero.cmd.HandlePrx; import omero.cmd.OK; import omero.cmd.Request; import omero.cmd.Response; import omero.cmd.State; import omero.cmd.Status; import omero.grid.RepositoryMap; import omero.grid.RepositoryPrx; import omero.model.BooleanAnnotation; import omero.model.BooleanAnnotationI; import omero.model.ChannelBinding; import omero.model.CommentAnnotation; import omero.model.CommentAnnotationI; import omero.model.Dataset; import omero.model.DatasetAnnotationLink; import omero.model.DatasetAnnotationLinkI; import omero.model.Detector; import omero.model.DetectorAnnotationLink; import omero.model.DetectorAnnotationLinkI; import omero.model.Experiment; import omero.model.Experimenter; import omero.model.ExperimenterGroup; import omero.model.ExperimenterGroupI; import omero.model.ExperimenterI; import omero.model.FileAnnotation; import omero.model.FileAnnotationI; import omero.model.Fileset; import omero.model.FilesetI; import omero.model.IObject; import omero.model.Image; import omero.model.ImageAnnotationLink; import omero.model.ImageAnnotationLinkI; import omero.model.Instrument; import omero.model.InstrumentAnnotationLink; import omero.model.InstrumentAnnotationLinkI; import omero.model.LightSource; import omero.model.LightSourceAnnotationLink; import omero.model.LightSourceAnnotationLinkI; import omero.model.LongAnnotation; import omero.model.LongAnnotationI; import omero.model.MapAnnotation; import omero.model.MapAnnotationI; import omero.model.NamedValue; import omero.model.OriginalFile; import omero.model.OriginalFileAnnotationLink; import omero.model.OriginalFileAnnotationLinkI; import omero.model.Permissions; import omero.model.PermissionsI; import omero.model.Pixels; import omero.model.Plate; import omero.model.PlateAcquisition; import omero.model.PlateAcquisitionAnnotationLink; import omero.model.PlateAcquisitionAnnotationLinkI; import omero.model.PlateAnnotationLink; import omero.model.PlateAnnotationLinkI; import omero.model.Project; import omero.model.ProjectAnnotationLink; import omero.model.ProjectAnnotationLinkI; import omero.model.QuantumDef; import omero.model.RenderingDef; import omero.model.Screen; import omero.model.ScreenAnnotationLink; import omero.model.ScreenAnnotationLinkI; import omero.model.TagAnnotation; import omero.model.TagAnnotationI; import omero.model.TermAnnotation; import omero.model.TermAnnotationI; import omero.model.Well; import omero.model.WellAnnotationLink; import omero.model.WellAnnotationLinkI; import omero.model.WellSample; import omero.sys.EventContext; import omero.sys.ParametersI; import org.apache.commons.lang.StringUtils; import org.testng.Assert; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import com.google.common.collect.Lists; /** * Base test for integration tests. * * @since Beta4.2 */ public class AbstractServerTest extends AbstractTest { /** Performs the move as data owner. */ public static final int MEMBER = 100; /** Performs the move as group owner. */ public static final int GROUP_OWNER = 101; /** Performs the move as group owner. */ public static final int ADMIN = 102; /** Identifies the <code>system</code> group. */ public String SYSTEM_GROUP = "system"; /** Identifies the <code>user</code> group. */ public String USER_GROUP = "user"; /** Identifies the <code>guest</code> group. */ public String GUEST_GROUP = "guest"; /** Scaling factor used for CmdCallbackI loop timings. */ protected long scalingFactor; /** The client object, this is the entry point to the Server. */ protected omero.client client; /** A root-client object. */ protected omero.client root; /** Helper reference to the <code>Service factory</code>. */ protected ServiceFactoryPrx factory; /** Helper reference to the <code>Service factory</code>. */ protected ServiceFactoryPrx factoryEncrypted; /** Helper reference to the <code>IQuery</code> service. */ protected IQueryPrx iQuery; /** Helper reference to the <code>IUpdate</code> service. */ protected IUpdatePrx iUpdate; /** Helper reference to the <code>IAdmin</code> service. */ protected IAdminPrx iAdmin; /** Reference to the importer store. */ protected OMEROMetadataStoreClient importer; /** Helper class creating mock object. */ protected ModelMockFactory mmFactory; /** the managed repository directory for the user from test class setup **/ private String userFsDir = null; /** * {@link omero.client} instances which are created via the newUser* * methods. These will be forcefully closed at the end of the test. * "new omero.client(...)" should be strictly avoided except for in the * method {@link #newOmeroClient()}. * * @see #newUserAndGroup(Permissions) * @see #newUserAndGroup(String) * @see #newUserInGroup() * @see #newUserInGroup(EventContext) * @see #newUserInGroup(ExperimenterGroup) */ private final Set<omero.client> clients = new HashSet<omero.client>(); /** * Sole location where {@link omero.client#client()} or any other * {@link omero.client} constructor should be called. */ protected omero.client newOmeroClient() { omero.client client = new omero.client(); // OK clients.add(client); return client; } /** * Creates a client for the root user. * * @return See above. * @throws Exception * Thrown if an error occurred. */ protected omero.client newRootOmeroClient() throws Exception { omero.client client = newOmeroClient(); client.createSession("root", rootpass); return client; } /** * Initializes the various services. * * @throws Exception * Thrown if an error occurred. */ @Override @BeforeClass(alwaysRun = true) protected void setUp() throws Exception { // administrator client omero.client tmp = newOmeroClient(); rootpass = tmp.getProperty("omero.rootpass"); root = newRootOmeroClient(); tmp.__del__(); scalingFactor = 500; final String timeoutString = System.getProperty("omero.test.timeout"); if (StringUtils.isNotBlank(timeoutString)) { try { scalingFactor = Long.valueOf(timeoutString); } catch (NumberFormatException e) { log.warn("Problem setting 'omero.test.timeout' to: {}. " + "Defaulting to {}.", timeoutString, scalingFactor); } } final EventContext ctx = newUserAndGroup("rw----"); this.userFsDir = ctx.userName + "_" + ctx.userId + FsFile.separatorChar; SimpleBackOff backOff = new SimpleBackOff(); long newScalingFactor = (long) backOff.getScalingFactor() * backOff.getCount(); if (newScalingFactor > scalingFactor) { scalingFactor = newScalingFactor; } } /** * Closes the session. * * @throws Exception * Thrown if an error occurred. */ @Override @AfterClass public void tearDown() throws Exception { for (omero.client c : clients) { if (c != null) { c.__del__(); } } } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserAndGroup(String perms, boolean owner) throws Exception { return newUserAndGroup(new PermissionsI(perms), owner); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserAndGroup(String perms) throws Exception { return newUserAndGroup(new PermissionsI(perms), false); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserAndGroup(Permissions perms, boolean owner) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); String uuid = UUID.randomUUID().toString(); ExperimenterGroup g = new ExperimenterGroupI(); g.setName(omero.rtypes.rstring(uuid)); g.setLdap(omero.rtypes.rbool(false)); g.getDetails().setPermissions(perms); g = new ExperimenterGroupI(rootAdmin.createGroup(g), false); return newUserInGroup(g, owner); } /** * Changes the permissions of the group. * * @param perms * The permissions level. * @param groupId * The identifier of the group to handle. * @throws Exception * Thrown if an error occurred. */ protected void resetGroupPerms(String perms, long groupId) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); ExperimenterGroup g = rootAdmin.getGroup(groupId); g.getDetails().setPermissions(new PermissionsI(perms)); rootAdmin.updateGroup(g); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenter. @ * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(Permissions perms, long experimenterId) throws Exception { return newGroupAddUser(perms, Arrays.asList(experimenterId), false); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenter. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(Permissions perms, long experimenterId, boolean owner) throws Exception { return newGroupAddUser(perms, Arrays.asList(experimenterId), owner); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterIds * The identifier of the experimenters. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(Permissions perms, List<Long> experimenterIds, boolean owner) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); String uuid = UUID.randomUUID().toString(); ExperimenterGroup g = new ExperimenterGroupI(); g.setName(omero.rtypes.rstring(uuid)); g.setLdap(omero.rtypes.rbool(false)); g.getDetails().setPermissions(perms); g = new ExperimenterGroupI(rootAdmin.createGroup(g), false); return addUsers(g, experimenterIds, owner); } protected ExperimenterGroup addUsers(ExperimenterGroup g, List<Long> experimenterIds, boolean owner) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); g = rootAdmin.getGroup(g.getId().getValue()); Iterator<Long> i = experimenterIds.iterator(); List<Experimenter> l = new ArrayList<Experimenter>(); while (i.hasNext()) { Experimenter e = rootAdmin.getExperimenter(i.next()); rootAdmin.addGroups(e, Arrays.asList(g)); l.add(e); } if (owner && l.size() > 0) { rootAdmin.addGroupOwners(g, l); } return g; } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenters. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(String perms, List<Long> experimenterIds, boolean owner) throws Exception { return newGroupAddUser(new PermissionsI(perms), experimenterIds, owner); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenters. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(String perms, List<Long> experimenterIds) throws Exception { return newGroupAddUser(new PermissionsI(perms), experimenterIds, false); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenter. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(String perms, long experimenterId) throws Exception { return newGroupAddUser(new PermissionsI(perms), experimenterId); } /** * Creates a new group and experimenter and returns the event context. * * @param perms * The permissions level. * @param experimenterId * The identifier of the experimenter. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected ExperimenterGroup newGroupAddUser(String perms, long experimenterId, boolean owner) throws Exception { return newGroupAddUser(new PermissionsI(perms), experimenterId, owner); } /** * Creates a new user in the current group. * * @return */ protected EventContext newUserInGroup() throws Exception { EventContext ec = client.getSession().getAdminService().getEventContext(); return newUserInGroup(ec); } /** * Takes the {@link EventContext} from another user and creates a new user * in the same group as that user is currently logged in to. * * @param previousUser * The context of the previous user. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserInGroup(EventContext previousUser) throws Exception { return newUserInGroup(previousUser, false); } /** * Takes the {@link EventContext} from another user and creates a new user * in the same group as that user is currently logged in to. * * @param previousUser * The context of the previous user. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserInGroup(EventContext previousUser, boolean owner) throws Exception { ExperimenterGroup eg = new ExperimenterGroupI(previousUser.groupId, false); return newUserInGroup(eg, owner); } /** * Creates a new user in the specified group. * * @param group * The group to add the user to. * @param owner * Pass <code>true</code> to indicate that the new user is an * owner of the group, <code>false</code> otherwise. * @return The context. * @throws Exception * Thrown if an error occurred. */ protected EventContext newUserInGroup(ExperimenterGroup group, boolean owner) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); group = rootAdmin.getGroup(group.getId().getValue()); String uuid = UUID.randomUUID().toString(); Experimenter e = new ExperimenterI(); e.setOmeName(omero.rtypes.rstring(uuid)); e.setFirstName(omero.rtypes.rstring("integration")); e.setLastName(omero.rtypes.rstring("tester")); e.setLdap(omero.rtypes.rbool(false)); long id = newUserInGroupWithPassword(e, group, uuid); e = rootAdmin.getExperimenter(id); rootAdmin.addGroups(e, Arrays.asList(group)); if (owner) { rootAdmin.addGroupOwners(group, Arrays.asList(e)); } omero.client client = newOmeroClient(); client.createSession(uuid, uuid); return init(client); } /** * Creates the specified user in the specified groups. Also adds the user * to the default user group. Requires a password. * * @param experimenter The pre-populated Experimenter object. * @param groups The target groups. * @param password The user password. * @return long The created user ID. */ protected long newUserInGroupWithPassword(Experimenter experimenter, List<ExperimenterGroup> groups, String password) throws Exception { IAdminPrx rootAdmin = root.getSession().getAdminService(); ExperimenterGroup userGroup = rootAdmin.lookupGroup(USER_GROUP); return rootAdmin.createExperimenterWithPassword(experimenter, omero.rtypes.rstring(password), userGroup, groups); } /** * Creates the specified user in the specified group. Also adds the user * to the default user group. Requires a password. * * @param experimenter The pre-populated Experimenter object. * @param group The target group. * @param password The user password. * @return long The created user ID. */ protected long newUserInGroupWithPassword(Experimenter experimenter, ExperimenterGroup group, String password) throws Exception { return newUserInGroupWithPassword(experimenter, Lists.newArrayList(group), password); } /** * Create a fileset with a template prefix appropriate for the user created * by {@link #setUp()}. Does not access the OMERO API or persist the new * fileset. * * @return a new fileset */ protected Fileset newFileset() { final Fileset fileset = new FilesetI(); fileset.setTemplatePrefix( omero.rtypes.rstring(this.userFsDir + System.currentTimeMillis() + FsFile.separatorChar)); return fileset; } /** * Logs in the user. * * @param g * The group to log into. * @throws Exception * Thrown if an error occurred. */ protected EventContext loginUser(ExperimenterGroup g) throws Exception { EventContext ec = iAdmin.getEventContext(); omero.client client = newOmeroClient(); client.createSession(ec.userName, ec.userName); client.getSession().setSecurityContext(new ExperimenterGroupI(g.getId(), false)); return init(client); } /** * Logs in the user. * * @param ownerEc * The context of the user. * @throws Exception * Thrown if an error occurred. */ protected void loginUser(EventContext ownerEc) throws Exception { omero.client client = newOmeroClient(); client.createSession(ownerEc.userName, ownerEc.userName); init(client); } /** * Creates a new {@link omero.client} for root based on the current group. */ protected void logRootIntoGroup() throws Exception { EventContext ec = iAdmin.getEventContext(); logRootIntoGroup(ec); } /** * Creates a new {@link omero.client} for root based on the * {@link EventContext} */ protected void logRootIntoGroup(EventContext ec) throws Exception { logRootIntoGroup(ec.groupId); } /** * Creates a new {@link omero.client} for root based on the group * identifier. */ protected void logRootIntoGroup(long groupId) throws Exception { omero.client rootClient = newRootOmeroClient(); rootClient.getSession().setSecurityContext(new ExperimenterGroupI(groupId, false)); init(rootClient); } /** * Makes the current user an owner of the current group. */ protected void makeGroupOwner() throws Exception { EventContext ec = client.getSession().getAdminService().getEventContext(); IAdminPrx rootAdmin = root.getSession().getAdminService(); rootAdmin.setGroupOwner(new ExperimenterGroupI(ec.groupId, false), new ExperimenterI(ec.userId, false)); disconnect(); init(ec); // Create new session with the added privileges } /** * Saves the current client before calling {@link #clean()} and returns it * to the user. */ protected omero.client disconnect() throws Exception { omero.client oldClient = client; client = null; clean(); return oldClient; } /** * If {@link #client} is non-null, destroys the client and nulls all fields * which were set on creation. */ protected void clean() throws Exception { if (importer != null) { importer.closeServices(); importer = null; } if (client != null) { client.__del__(); } client = null; } /** */ protected EventContext init(EventContext ec) throws Exception { omero.client c = newOmeroClient(); factoryEncrypted = c.createSession(ec.userName, ec.userName); return init(c); } /** * Resets the client and return the event context. * * @param client * The client to handle. * @return The event context to handle. * @throws Exception */ protected EventContext init(omero.client client) throws Exception { clean(); this.client = client; factory = client.getSession(); iQuery = factory.getQueryService(); iUpdate = factory.getUpdateService(); iAdmin = factory.getAdminService(); mmFactory = new ModelMockFactory(factory.getPixelsService()); importer = new OMEROMetadataStoreClient(); importer.initialize(factory); return iAdmin.getEventContext(); } /** * Compares the passed rendering definitions. * * @param def1 * The first rendering definition to handle. * @param def2 * The second rendering definition to handle. * @throws Exception * Thrown if an error occurred. */ protected void compareRenderingDef(RenderingDef def1, RenderingDef def2) throws Exception { assertNotNull(def1); assertNotNull(def2); assertTrue(def1.getDefaultZ().getValue() == def2.getDefaultZ().getValue()); assertTrue(def1.getDefaultT().getValue() == def2.getDefaultT().getValue()); assertTrue(def1.getModel().getValue().getValue().equals(def2.getModel().getValue().getValue())); QuantumDef q1 = def1.getQuantization(); QuantumDef q2 = def2.getQuantization(); assertNotNull(q1); assertNotNull(q2); assertTrue(q1.getBitResolution().getValue() == q2.getBitResolution().getValue()); assertTrue(q1.getCdStart().getValue() == q2.getCdStart().getValue()); assertTrue(q1.getCdEnd().getValue() == q2.getCdEnd().getValue()); List<ChannelBinding> channels1 = def1.copyWaveRendering(); List<ChannelBinding> channels2 = def2.copyWaveRendering(); assertNotNull(channels1); assertNotNull(channels2); assertTrue(channels1.size() == channels2.size()); Iterator<ChannelBinding> i = channels1.iterator(); ChannelBinding c1, c2; int index = 0; while (i.hasNext()) { c1 = i.next(); c2 = channels2.get(index); assertTrue(c1.getAlpha().getValue() == c2.getAlpha().getValue()); assertTrue(c1.getRed().getValue() == c2.getRed().getValue()); assertTrue(c1.getGreen().getValue() == c2.getGreen().getValue()); assertTrue(c1.getBlue().getValue() == c2.getBlue().getValue()); assertTrue(c1.getCoefficient().getValue() == c2.getCoefficient().getValue()); assertTrue(c1.getFamily().getValue().getValue().equals(c2.getFamily().getValue().getValue())); assertTrue(c1.getInputStart().getValue() == c2.getInputStart().getValue()); assertTrue(c1.getInputEnd().getValue() == c2.getInputEnd().getValue()); Boolean b1 = Boolean.valueOf(c1.getActive().getValue()); Boolean b2 = Boolean.valueOf(c2.getActive().getValue()); assertTrue(b1.equals(b2)); b1 = Boolean.valueOf(c1.getNoiseReduction().getValue()); b2 = Boolean.valueOf(c2.getNoiseReduction().getValue()); assertTrue(b1.equals(b2)); } } /** * Helper method to load the wells. * * @param plateID * The identifier of the plate. * @param pixels * Pass <code>true</code> to load the pixels, <code>false</code> * otherwise. * @return See above. * @throws Exception * Thrown if an error occurred. */ @SuppressWarnings("unchecked") protected List<Well> loadWells(long plateID, boolean pixels) throws Exception { StringBuilder sb = new StringBuilder(); ParametersI param = new ParametersI(); param.addLong("plateID", plateID); sb.append("select well from Well as well "); sb.append("left outer join fetch well.plate as pt "); sb.append("left outer join fetch well.wellSamples as ws "); sb.append("left outer join fetch ws.plateAcquisition as pa "); sb.append("left outer join fetch ws.image as img "); if (pixels) { sb.append("left outer join fetch img.pixels as pix "); sb.append("left outer join fetch pix.pixelsType as pixType "); } sb.append("where pt.id = :plateID"); return (List<Well>) (List<?>) iQuery.findAllByQuery(sb.toString(), param); } /** * Helper method to load a well sample with its well and plate intact (and * possibly a screen if one exists) for the given pixels. * * @param p * @return * @throws ServerError */ protected WellSample getWellSample(Pixels p) throws ServerError { long id = p.getImage().getId().getValue(); String sql = "select ws from WellSample as ws "; sql += "join fetch ws.well as w "; sql += "left outer join fetch ws.plateAcquisition as pa "; sql += "join fetch w.plate as p "; sql += "left outer join fetch p.screenLinks sl "; sql += "left outer join fetch sl.parent s "; sql += "where ws.image.id = :id"; ParametersI param = new ParametersI(); param.addId(id); List<IObject> results = iQuery.findAllByQuery(sql, param); assertTrue(results.size() == 1); WellSample ws = (WellSample) results.get(0); assertNotNull(ws); return ws; } /** * Helper method to load the Experiment which is is associated with the * pixels argument via Image. * * @param p * @return * @throws ServerError */ protected Experiment getExperiment(Pixels p) throws ServerError { long id = p.getImage().getId().getValue(); String sql = "select e from Image i "; sql += "join i.experiment e "; sql += "where i.id = :id"; ParametersI param = new ParametersI(); param.addId(id); List<IObject> results = iQuery.findAllByQuery(sql, param); assertTrue(results.size() == 1); Experiment e = (Experiment) results.get(0); assertNotNull(e); return e; } /** * @return a repository rooted at a directory named <q>ManagedRepository</q> * @throws ServerError if the repository map could not be retrieved */ protected RepositoryPrx getManagedRepository() throws ServerError { final RepositoryMap repos = factory.sharedResources().repositories(); int index = repos.descriptions.size(); while (--index >= 0) { if ("ManagedRepository".equals(repos.descriptions.get(index).getName().getValue())) { return repos.proxies.get(index); } } throw new RuntimeException("no managed repository"); } /** * Makes sure that the passed object exists. * * @param obj * The object to handle. * @throws Exception * Thrown if an error occurred. */ protected void assertExists(IObject obj) throws Exception { IObject copy = iQuery.find(obj.getClass().getSimpleName(), obj.getId().getValue()); assertNotNull(String.format("%s:%s", obj.getClass().getName(), obj.getId().getValue()) + " is missing!", copy); } protected void assertAllExist(IObject... obj) throws Exception { for (IObject iObject : obj) { assertExists(iObject); } } protected void assertAllExist(Iterable<? extends IObject> obj) throws Exception { for (IObject iObject : obj) { assertExists(iObject); } } protected void assertExists(String className, Long id) throws ServerError { assertAllExist(className, Collections.singletonList(id)); } protected void assertAllExist(String className, Collection<Long> ids) throws ServerError { final String hql = "SELECT COUNT(*) FROM " + className + " WHERE id IN (:ids)"; final List<List<RType>> results = iQuery.projection(hql, new ParametersI().addIds(ids)); final long count = ((RLong) results.get(0).get(0)).getValue(); Assert.assertEquals(count, ids.size()); } /** * Makes sure that the passed object does not exist. * * @param obj * The object to handle. * @throws Exception * Thrown if an error occurred. */ protected void assertDoesNotExist(IObject obj) throws Exception { IObject copy = iQuery.find(obj.getClass().getSimpleName(), obj.getId().getValue()); assertNull(String.format("%s:%s", obj.getClass().getName(), obj.getId().getValue()) + " still exists!", copy); } protected void assertNoneExist(IObject... obj) throws Exception { for (IObject iObject : obj) { assertDoesNotExist(iObject); } } protected void assertNoneExist(Iterable<? extends IObject> obj) throws Exception { for (IObject iObject : obj) { assertDoesNotExist(iObject); } } protected void assertDoesNotExist(String className, Long id) throws ServerError { assertNoneExist(className, Collections.singletonList(id)); } protected void assertNoneExist(String className, Collection<Long> ids) throws ServerError { final String hql = "SELECT COUNT(*) FROM " + className + " WHERE id IN (:ids)"; final List<List<RType>> results = iQuery.projection(hql, new ParametersI().addIds(ids)); final long count = ((RLong) results.get(0).get(0)).getValue(); Assert.assertEquals(count, 0); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param file * The file to import. * @param format * The format of the file to import. * @return The collection of imported pixels set. * @throws Exception * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(File file, String format) throws Throwable { return importFile(importer, file, format, false, null); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param file * The file to import. * @param format * The format of the file to import. * @return The collection of imported pixels set. * @throws Throwable * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(File file, String format, boolean metadata) throws Throwable { return importFile(importer, file, format, metadata, null); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param importer * The metadataStore to use. * @param file * The file to import. * @param format * The format of the file to import. * @return The collection of imported pixels set. * @throws Throwable * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(OMEROMetadataStoreClient importer, File file, String format) throws Throwable { return importFile(importer, file, format, false, null); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param importer * The metadataStore to use. * @param file * The file to import. * @param target * The container where to import the image. * @return The collection of imported pixels set. * @throws Throwable * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(File file, String format, IObject target) throws Throwable { return importFile(importer, file, format, false, target); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param importer * The metadataStore to use. * @param file * The file to import. * @param format * The format of the file to import. * @param metadata * Pass <code>true</code> to only import the metadata, * <code>false</code> otherwise. * @return The collection of imported pixels set. * @throws Throwable * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(OMEROMetadataStoreClient importer, File file, String format, boolean metadata) throws Throwable { return importFile(importer, file, format, metadata, null); } /** * Imports the specified OME-XML file and returns the pixels set if * successfully imported. * * @param importer * The metadataStore to use. * @param file * The file to import. * @param format * The format of the file to import. * @param metadata * Pass <code>true</code> to only import the metadata, * <code>false</code> otherwise. * @return The collection of imported pixels set. * @throws Throwable * Thrown if an error occurred while encoding the image. */ protected List<Pixels> importFile(OMEROMetadataStoreClient importer, File file, String format, boolean metadata, IObject target) throws Throwable { String[] paths = new String[1]; paths[0] = file.getAbsolutePath(); ImportConfig config = new ImportConfig(); OMEROWrapper reader = new OMEROWrapper(config); IObserver o = new IObserver() { public void update(IObservable importLibrary, ImportEvent event) { if (event instanceof ErrorHandler.EXCEPTION_EVENT) { Exception ex = ((ErrorHandler.EXCEPTION_EVENT) event).exception; if (ex instanceof RuntimeException) { throw (RuntimeException) ex; } else { throw new RuntimeException(ex); } } } }; ImportCandidates candidates = new ImportCandidates(reader, paths, o); ImportLibrary library = new ImportLibrary(importer, reader); library.addObserver(o); ImportContainer ic = candidates.getContainers().get(0); // new ImportContainer( // file, null, target, false, null, null, null, null); ic.setUserSpecifiedName(format); ic.setTarget(target); // ic = library.uploadFilesToRepository(ic); List<Pixels> pixels = library.importImage(ic, 0, 0, 1); assertNotNull(pixels); assertTrue(pixels.size() > 0); return pixels; } /** * Basic asynchronous delete command. Used in order to reduce the number of * places that we do the same thing in case the API changes. * * @param dc * The command to handle. * @throws ApiUsageException * @throws ServerError * @throws InterruptedException */ protected String delete(omero.client c, Delete2... dc) throws ApiUsageException, ServerError, InterruptedException { return delete(true, c, dc); } /** * Basic asynchronous delete command. Used in order to reduce the number of * places that we do the same thing in case the API changes. * * @param passes * Pass <code>true</code> to indicate that no error found in * report, <code>false</code> otherwise. * @param dc * The command to handle. * @param strict * whether or not the method should succeed. * @throws ApiUsageException * @throws ServerError * @throws InterruptedException */ protected String delete(boolean passes, omero.client c, Delete2... dc) throws ApiUsageException, ServerError, InterruptedException { callback(passes, c, dc); return "ok"; } /** * Asynchronous command for a single delete, this means a single report is * returned for testing. * * @param dc * The SINGLE command to handle. * @throws ApiUsageException * @throws ServerError * @throws InterruptedException */ protected Delete2Response singleDeleteWithReport(omero.client c, Delete2 dc) throws ApiUsageException, ServerError, InterruptedException { return deleteWithReports(c, dc)[0]; } /** * Asynchronous command for delete, report array is returned. * * @param dc * The command to handle. * @throws ApiUsageException * @throws ServerError * @throws InterruptedException */ private Delete2Response[] deleteWithReports(omero.client c, Delete2... dc) throws ApiUsageException, ServerError, InterruptedException { CmdCallbackI cb = callback(true, c, dc); // If the above passes, then we know it's not an ERR DoAllRsp all = (DoAllRsp) cb.getResponse(); Delete2Response[] reports = new Delete2Response[all.responses.size()]; for (int i = 0; i < reports.length; i++) { reports[i] = (Delete2Response) all.responses.get(i); } return reports; } /** * Create a single image with binary. * * After recent changes on the server to check for existing binary data for * pixels, many resetDefaults methods tested below began returning null * since {@link omero.LockTimeout} exceptions were being thrown server-side. * By using omero.client.forEachTile, we can set the necessary data easily. * * @see ticket:5755 */ protected Image createBinaryImage() throws Exception { Image image = mmFactory.createImage(); image = (Image) iUpdate.saveAndReturnObject(image); return createBinaryImage(image); } /** * Create the binary data for the given image. */ protected Image createBinaryImage(Image image) throws Exception { Pixels pixels = image.getPrimaryPixels(); // Image List<Long> ids = new ArrayList<Long>(); ids.add(image.getId().getValue()); // method already tested // first write to the image omero.util.RPSTileLoop loop = new omero.util.RPSTileLoop(client.getSession(), pixels); loop.forEachTile(256, 256, new omero.util.TileLoopIteration() { public void run(omero.util.TileData data, int z, int c, int t, int x, int y, int tileWidth, int tileHeight, int tileCount) { data.setTile(new byte[tileWidth * tileHeight * 8], z, c, t, x, y, tileWidth, tileHeight); } }); // This block will change the updateEvent on the pixels // therefore we're going to reload the pixels. image.setPixels(0, loop.getPixels()); return image; } /** * Creates various sharable annotations i.e. TagAnnotation, TermAnnotation, * FileAnnotation * * @param parent1 * The object to link the annotation to. * @param parent2 * The object to link the annotation to if not null. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected List<Long> createSharableAnnotation(IObject parent1, IObject parent2) throws Exception { // Copying to a proxy to prevent issues with parent.annotationLinks // becoming stale on multiple copies. parent1 = parent1.proxy(); if (parent2 != null) { parent2 = parent2.proxy(); } // creation already tested in UpdateServiceTest List<Long> ids = new ArrayList<Long>(); TagAnnotation c = new TagAnnotationI(); c.setTextValue(omero.rtypes.rstring("tag")); c = (TagAnnotation) iUpdate.saveAndReturnObject(c); ids.add(c.getId().getValue()); TermAnnotation t = new TermAnnotationI(); t.setTermValue(omero.rtypes.rstring("term")); t = (TermAnnotation) iUpdate.saveAndReturnObject(t); ids.add(t.getId().getValue()); OriginalFile of = (OriginalFile) iUpdate.saveAndReturnObject(mmFactory.createOriginalFile()); assertNotNull(of); FileAnnotation f = new FileAnnotationI(); f.setFile(of); f = (FileAnnotation) iUpdate.saveAndReturnObject(f); ids.add(f.getId().getValue()); MapAnnotation ma = new MapAnnotationI(); List<NamedValue> values = new ArrayList<NamedValue>(); for (int i = 0; i < 3; i++) values.add(new NamedValue("name " + i, "value " + i)); ma.setMapValue(values); ma = (MapAnnotation) iUpdate.saveAndReturnObject(ma); ids.add(ma.getId().getValue()); List<IObject> links = new ArrayList<IObject>(); if (parent1 instanceof Image) { ImageAnnotationLink link = new ImageAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Image) parent1); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Image) parent1); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Image) parent1); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Image) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Image) parent2); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Image) parent2); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Image) parent2); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Image) parent2); links.add(link); } } else if (parent1 instanceof Project) { ProjectAnnotationLink link = new ProjectAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Project) parent1); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Project) parent1); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Project) parent1); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Project) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Project) parent2); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Project) parent2); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Project) parent2); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Project) parent2); links.add(link); } } else if (parent1 instanceof Dataset) { DatasetAnnotationLink link = new DatasetAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Dataset) parent1); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Dataset) parent1); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Dataset) parent1); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Dataset) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Dataset) parent2); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Dataset) parent2); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Dataset) parent2); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Dataset) parent2); links.add(link); } } else if (parent1 instanceof Plate) { PlateAnnotationLink link = new PlateAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Plate) parent1); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Plate) parent1); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Plate) parent1); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Plate) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Plate) parent2); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Plate) parent2); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Plate) parent2); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Plate) parent2); links.add(link); } } else if (parent1 instanceof Screen) { ScreenAnnotationLink link = new ScreenAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Screen) parent1); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Screen) parent1); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Screen) parent1); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Screen) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Screen) parent2); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Screen) parent2); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Screen) parent2); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Screen) parent2); links.add(link); } } else if (parent1 instanceof Well) { WellAnnotationLink link = new WellAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Well) parent1); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Well) parent1); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Well) parent1); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Well) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Well) parent2); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Well) parent2); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Well) parent2); links.add(link); link = new WellAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Well) parent2); links.add(link); } } else if (parent1 instanceof PlateAcquisition) { PlateAcquisitionAnnotationLink link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((PlateAcquisition) parent1); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((PlateAcquisition) parent1); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((PlateAcquisition) parent1); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((PlateAcquisition) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((PlateAcquisition) parent2); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((PlateAcquisition) parent2); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((PlateAcquisition) parent2); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((PlateAcquisition) parent2); links.add(link); } } else if (parent1 instanceof Detector) { DetectorAnnotationLink link = new DetectorAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); } } else if (parent1 instanceof Detector) { DetectorAnnotationLink link = new DetectorAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Detector) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Detector) parent2); links.add(link); } } else if (parent1 instanceof LightSource) { LightSourceAnnotationLink link = new LightSourceAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((LightSource) parent1); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((LightSource) parent1); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((LightSource) parent1); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((LightSource) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((LightSource) parent2); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((LightSource) parent2); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((LightSource) parent2); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((LightSource) parent2); links.add(link); } } else if (parent1 instanceof Instrument) { InstrumentAnnotationLink link = new InstrumentAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Instrument) parent1); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Instrument) parent1); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Instrument) parent1); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Instrument) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((Instrument) parent2); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((Instrument) parent2); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((Instrument) parent2); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((Instrument) parent2); links.add(link); } } else if (parent1 instanceof OriginalFile) { OriginalFileAnnotationLink link = new OriginalFileAnnotationLinkI(); link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((OriginalFile) parent1); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((OriginalFile) parent1); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((OriginalFile) parent1); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((OriginalFile) parent1); links.add(link); if (parent2 != null) { link.setChild(new TagAnnotationI(c.getId().getValue(), false)); link.setParent((OriginalFile) parent2); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new TermAnnotationI(t.getId().getValue(), false)); link.setParent((OriginalFile) parent2); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new FileAnnotationI(f.getId().getValue(), false)); link.setParent((OriginalFile) parent2); links.add(link); link = new OriginalFileAnnotationLinkI(); link.setChild(new MapAnnotationI(ma.getId().getValue(), false)); link.setParent((OriginalFile) parent2); links.add(link); } } else { throw new UnsupportedOperationException("Unknown parent type: " + parent1); } if (links.size() > 0) iUpdate.saveAndReturnArray(links); return ids; } /** * Creates various non sharable annotations. * * @param parent * The object to link the annotation to. * @param ns * The name space or <code>null</code>. * @return See above. * @throws Exception * Thrown if an error occurred. */ protected List<Long> createNonSharableAnnotation(IObject parent, String ns) throws Exception { // Copying to a proxy to prevent issues with parent.annotationLinks // becoming stale on multiple copies. parent = parent.proxy(); // creation already tested in UpdateServiceTest List<Long> ids = new ArrayList<Long>(); CommentAnnotation c = new CommentAnnotationI(); c.setTextValue(omero.rtypes.rstring("comment")); if (ns != null) c.setNs(omero.rtypes.rstring(ns)); c = (CommentAnnotation) iUpdate.saveAndReturnObject(c); LongAnnotation l = new LongAnnotationI(); l.setLongValue(omero.rtypes.rlong(1L)); if (ns != null) l.setNs(omero.rtypes.rstring(ns)); l = (LongAnnotation) iUpdate.saveAndReturnObject(l); BooleanAnnotation b = new BooleanAnnotationI(); b.setBoolValue(omero.rtypes.rbool(true)); if (ns != null) b.setNs(omero.rtypes.rstring(ns)); b = (BooleanAnnotation) iUpdate.saveAndReturnObject(b); ids.add(c.getId().getValue()); ids.add(l.getId().getValue()); ids.add(b.getId().getValue()); List<IObject> links = new ArrayList<IObject>(); if (parent instanceof Image) { ImageAnnotationLink link = new ImageAnnotationLinkI(); link.setChild(c); link.setParent((Image) parent); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(l); link.setParent((Image) parent); links.add(link); link = new ImageAnnotationLinkI(); link.setChild(b); link.setParent((Image) parent); links.add(link); } else if (parent instanceof Project) { ProjectAnnotationLink link = new ProjectAnnotationLinkI(); link.setChild(c); link.setParent((Project) parent); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(l); link.setParent((Project) parent); links.add(link); link = new ProjectAnnotationLinkI(); link.setChild(b); link.setParent((Project) parent); links.add(link); } else if (parent instanceof Dataset) { DatasetAnnotationLink link = new DatasetAnnotationLinkI(); link.setChild(c); link.setParent((Dataset) parent); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(l); link.setParent((Dataset) parent); links.add(link); link = new DatasetAnnotationLinkI(); link.setChild(b); link.setParent((Dataset) parent); links.add(link); } else if (parent instanceof Plate) { PlateAnnotationLink link = new PlateAnnotationLinkI(); link.setChild(c); link.setParent((Plate) parent); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(l); link.setParent((Plate) parent); links.add(link); link = new PlateAnnotationLinkI(); link.setChild(b); link.setParent((Plate) parent); links.add(link); } else if (parent instanceof Screen) { ScreenAnnotationLink link = new ScreenAnnotationLinkI(); link.setChild(c); link.setParent((Screen) parent); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(l); link.setParent((Screen) parent); links.add(link); link = new ScreenAnnotationLinkI(); link.setChild(b); link.setParent((Screen) parent); links.add(link); } else if (parent instanceof Well) { WellAnnotationLink link = new WellAnnotationLinkI(); link.setChild(c); link.setParent((Well) parent); links.add(link); link = new WellAnnotationLinkI(); link.setChild(l); link.setParent((Well) parent); links.add(link); link = new WellAnnotationLinkI(); link.setChild(b); link.setParent((Well) parent); links.add(link); } else if (parent instanceof PlateAcquisition) { PlateAcquisitionAnnotationLink link = new PlateAcquisitionAnnotationLinkI(); link.setChild(c); link.setParent((PlateAcquisition) parent); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(l); link.setParent((PlateAcquisition) parent); links.add(link); link = new PlateAcquisitionAnnotationLinkI(); link.setChild(b); link.setParent((PlateAcquisition) parent); links.add(link); } else if (parent instanceof Detector) { DetectorAnnotationLink link = new DetectorAnnotationLinkI(); link.setChild(c); link.setParent((Detector) parent); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(l); link.setParent((Detector) parent); links.add(link); link = new DetectorAnnotationLinkI(); link.setChild(b); link.setParent((Detector) parent); links.add(link); } else if (parent instanceof Instrument) { InstrumentAnnotationLink link = new InstrumentAnnotationLinkI(); link.setChild(c); link.setParent((Instrument) parent); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(l); link.setParent((Instrument) parent); links.add(link); link = new InstrumentAnnotationLinkI(); link.setChild(b); link.setParent((Instrument) parent); links.add(link); } else if (parent instanceof LightSource) { LightSourceAnnotationLink link = new LightSourceAnnotationLinkI(); link.setChild(c); link.setParent((LightSource) parent); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(l); link.setParent((LightSource) parent); links.add(link); link = new LightSourceAnnotationLinkI(); link.setChild(b); link.setParent((LightSource) parent); links.add(link); } else { throw new UnsupportedOperationException("Unknown parent type: " + parent); } if (links.size() > 0) iUpdate.saveAndReturnArray(links); return ids; } /** * Create a new unpersisted experimenter with the given field values. * @param omeName an OME name * @param firstName a first name * @param lastName a last time * @return the new experimenter */ protected Experimenter createExperimenterI(String omeName, String firstName, String lastName) { final Experimenter experimenter = new ExperimenterI(); experimenter.setOmeName(rtypes.rstring(omeName)); experimenter.setFirstName(rtypes.rstring(firstName)); experimenter.setLastName(rtypes.rstring(lastName)); experimenter.setLdap(rtypes.rbool(false)); return experimenter; } /** * Modifies the graph. * * @param change * The object hosting information about data to modify. * @return See above. * @throws Exception */ protected Response doChange(Request change) throws Exception { return doChange(client, factory, change, true, null); } /** * Modifies the graph. * * @param change * The object hosting information about data to modify. * @return See above. * @throws Exception */ protected Response doChange(Request change, long groupID) throws Exception { return doChange(client, factory, change, true, groupID); } protected Response doChange(omero.client c, ServiceFactoryPrx f, Request change, boolean pass) throws Exception { return doChange(c, f, change, pass, null); } protected Response doAllChanges(omero.client c, ServiceFactoryPrx f, boolean pass, Request... changes) throws Exception { DoAll all = new DoAll(); all.requests = new ArrayList<Request>(); all.requests.addAll(Arrays.asList(changes)); return doChange(c, f, all, pass); } /** * * @param c * @param f * @param change * @param pass * @return * @throws Exception */ protected Response doChange(omero.client c, ServiceFactoryPrx f, Request change, boolean pass, Long groupID) throws Exception { final Map<String, String> callContext = new HashMap<String, String>(); if (groupID != null) { callContext.put("omero.group", "" + groupID); } final HandlePrx prx = f.submit(change, callContext); // assertFalse(prx.getStatus().flags.contains(State.FAILURE)); CmdCallbackI cb = new CmdCallbackI(c, prx); cb.loop(20, scalingFactor); return assertCmd(cb, pass); } protected CmdCallbackI callback(boolean passes, omero.client c, omero.cmd.Request... reqs) throws ApiUsageException, ServerError, InterruptedException { DoAll all = new DoAll(); all.requests = new ArrayList<omero.cmd.Request>(); for (omero.cmd.Request req : reqs) { all.requests.add(req); } HandlePrx handle = c.getSession().submit(all); CmdCallbackI cb = new CmdCallbackI(c, handle); cb.loop(10 * reqs.length, scalingFactor); // throws on timeout assertCmd(cb, passes); return cb; } protected Response assertCmd(CmdCallbackI cb, boolean pass) { Status status = cb.getStatus(); Response rsp = cb.getResponse(); assertNotNull(rsp); if (pass) { if (rsp instanceof ERR) { ERR err = (ERR) rsp; String name = err.getClass().getSimpleName(); fail(String.format("Found %s when pass==true: %s (%s) params=%s", name, err.category, err.name, err.parameters)); } assertFalse(status.flags.contains(State.FAILURE)); } else { if (rsp instanceof OK) { OK ok = (OK) rsp; fail(String.format("Found OK when pass==false: %s", ok)); } assertTrue(status.flags.contains(State.FAILURE)); } return rsp; } /** * Creates a new group with the specified permissions and sets the role of * the user. * * @param permissions * The permissions of the group. * @param userRole * The role of the user e.g. group owner. * @throws Exception * Thrown if an error occurred. */ protected void login(String permissions, int userRole) throws Exception { newUserAndGroup(permissions); switch (userRole) { case GROUP_OWNER: makeGroupOwner(); break; case ADMIN: logRootIntoGroup(); } } }