Python BlitzGateway.connect方法代码示例

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def run_as_program():
    """
    Testing function to allow the script to be called outside of the OMERO
    scripting environment. The connection details and image ID must be valid.
    """
    import getpass
    HOST = 'localhost'
    PORT = 4064
    USERNAME = raw_input("OMERO username: ")
    PASSWORD = getpass.getpass("OMERO password: ")
    h = raw_input("OMERO host (%s): " % HOST)
    if h:
        HOST = h
    p = raw_input("OMERO port (%d): " % PORT)
    if p:
        PORT = p

    conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
    conn.connect()
    conn.keepAlive()

    params = create_script_defaults()
    params[PARAM_DATATYPE] = 'Image'
    params[PARAM_IDS] = [51]
    # params[PARAM_DATATYPE] = 'Dataset'
    # params[PARAM_IDS] = [2]
    params[PARAM_UPLOAD_RESULTS] = True
    params[PARAM_EMAIL_RESULTS] = True
    params[PARAM_EMAIL] = ADMIN_EMAIL

    count = run(conn, params)

    if count >= 0:
        print ("Processed %d image%s" %
               (count, count != 1 and 's' or ''))

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
    def testChgrpAsync(self):
        """
        Try to reproduce "race condition" bugs seen in web #8037 (fails to reproduce)
        """
        image = self.image
        ctx = self.gateway.getAdminService().getEventContext()
        uuid = ctx.sessionUuid

        self.loginAsAdmin()
        gid = self.gateway.createGroup("chgrp-test-%s" % uuid, member_Ids=[ctx.userId], perms=COLLAB)
        self.loginAsAuthor()
        original_group = ctx.groupId
        self.assertNotEqual(None, self.gateway.getObject("Image", image.id))

        # Do the Chgrp
        rsp = self.doChange("Image", image.getId(), gid, return_complete=False)
        
        while rsp.getResponse() is None:
            # while waiting, try various things to reproduce race condition seen in web.
            img = self.gateway.getObject("Image", image.id)
            c = BlitzGateway()
            c.connect(sUuid=uuid)
            #self.gateway.setGroupForSession(gid)

        # Image should no-longer be available in current group
        self.assertEqual(None, self.gateway.getObject("Image", image.id), "Image should not be available in original group")

        # Switch to new group - confirm that image is there.
        self.gateway.setGroupForSession(gid)
        img = self.gateway.getObject("Image", image.id)
        self.assertNotEqual(None, img, "Image should be available in new group")
        self.assertEqual(img.getDetails().getGroup().id, gid, "Image group.id should match new group")

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
 def test_unicode_password(self):
     with pytest.raises(Ice.ConnectionRefusedException):
         gateway = BlitzGateway(
             username='user', passwd=u'ążźćółę',
             host='localhost', port=65535
         )
         gateway.connect()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def run_as_program():
    """
    Testing function to allow the script to be called outside of the OMERO
    scripting environment. The connection details and image ID must be valid.
    """
    import getpass
    HOST = 'localhost'
    PORT = 4064
    USERNAME = raw_input("OMERO username: ")
    PASSWORD = getpass.getpass("OMERO password: ")
    h = raw_input("OMERO host (%s): " % HOST)
    if h:
        HOST = h
    p = raw_input("OMERO port (%d): " % PORT)
    if p:
        PORT = p

    conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
    conn.connect()

    params = {}
    params[PARAM_IDS] = [1]
    params[PARAM_DATATYPE] = "Image"
    params[PARAM_ALL_IMAGES] = True
    params[PARAM_READABLE] = True

    (count, ok) = run(conn, params)

    print (summary(count, ok))

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv[1:])
    if not args.out_file:
        args.out_file = "map_screen_%d.tsv" % args.screen_id
    passwd = getpass.getpass()
    conn = BlitzGateway(
        args.user, passwd, host=args.host, port=args.port, group=args.group
    )
    conn.connect()
    screen = conn.getObject("Screen", args.screen_id)
    print "writing to %s" % args.out_file
    print "SCREEN: %s" % screen.name
    with open(args.out_file, "w") as fo:
        fo.write("PLATE\tSERIES\tWELL\tFIELD\tImageID\tWellID\n")
        for p in screen.listChildren():
            rows = []
            print "  plate: %s" % p.name
            for w in p.listChildren():
                n_fields = sum(1 for _ in w.listChildren())
                for i in xrange(n_fields):
                    img = w.getImage(i)
                    well_tag = "%s%02d" % (LETTERS[w.row], w.column + 1)
                    rows.append((
                        p.name, img.getSeries(), well_tag, i + 1, img.id, w.id
                    ))
            rows.sort(key=itemgetter(1))
            rows.sort()
            for r in rows:
                fo.write("%s\t%d\t%s\t%d\t%d\t%d\n" % r)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
    def create_containers(self, cli, project, dataset):
        """
        Creates containers with names provided if they don't exist already.
        Returns Dataset ID.
        """
        sessionId = cli._event_context.sessionUuid
        conn = BlitzGateway(host='localhost')
        conn.connect(sUuid = sessionId)
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = wrap(conn.getUser().getId())

        d = None
        dsId = None
        if project is not None:
            # We need to find or create a project
            # This is not nice but we really shouldn't be dealing with large numbers of objects here
            plist = list(conn.getObjects("Project", attributes={'name': project}, params=params))
            if len(plist) == 0:
                # Create project and dataset then link
                p = self.create_project(conn, project)
                d = self.create_dataset(conn, dataset)
                dsId = d.id.val
                self.link_dataset(conn, p.id.val, dsId)
            else:
                # Pick the first, it's as good as any
                p = plist[0]
                print "Using existing Project:", project
                # Since Project already exists check children for dataset
                for c in p.listChildren():
                    if c.getName() == dataset:
                        d = c
                        dsId = d.getId()

                # No existing child dataset so create one and link
                if d is None:
                    d = self.create_dataset(conn, dataset)
                    dsId = d.id.val
                    self.link_dataset(conn, p.getId(), dsId)
                else:
                    print "Using existing Dataset:", dataset
        else:
            # There may be more than one dataset with the same name
            # This is not nice but we really shouldn't be dealing with large numbers of objects here
            dlist = list(conn.getObjects("Dataset", attributes={'name': dataset}, params=params))
            if len(dlist) != 0:
                # We want one without a parent, the first will do
                for c in dlist:
                    if len(c.listParents()) == 0:
                        d = c
                        dsId = d.getId()
            if d is None:
                dsId = self.create_dataset(conn, dataset).id.val
            else:
                print "Using existing Dataset:", dataset

        return dsId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def connect_to_omero(user, password, host, port=4064):
    conn = BlitzGateway(user, password, host=host, port=port)
    print conn.connect()
    user = conn.getUser()
    print "Current user:"
    print "   ID:", user.getId()
    print "   Username:", user.getName()
    print "   Full Name:", user.getFullName()
    print "Member of:"
    for g in conn.getGroupsMemberOf():
        print "   ID:", g.getName(), " Name:", g.getId()
    group = conn.getGroupFromContext()
    print "Current group: ", group.getName()
    return conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def connect_to_omero(uname, passwd):
    conn = BlitzGateway(uname, passwd, host=HOST, port=PORT)
    connected = conn.connect()
    if not connected:
        sys.stderr.write("Error : Connection not available, please check your user name and password.\n")
        return None
    return conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def connect( server, port, username, password ): 
    '''
    Helper method that connects to an OMERO.searcher server.
    @param server
    @param port
    @param username
    @param password
    @returns connection
    '''
    
    try:
        conn = BlitzGateway( username, password, host=server, port=int(port))
        conn.connect()
        return conn
    except:
        return None

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def create_containers(cli, dataset, project=None):
    """
    Creates containers with names provided if they don't exist already.
    Returns Dataset ID.
    """
    sessionId = cli._event_context.sessionUuid
    conn = BlitzGateway()
    conn.connect(sUuid = sessionId)
    params = omero.sys.Parameters()
    params.theFilter = omero.sys.Filter()
    params.theFilter.ownerId = wrap(conn.getUser().getId())

    d = None
    prId = None
    if project is not None:
        p = conn.getObject("Project", attributes={'name': project}, params=params)
        if p is None:
            print "Creating Project:", project
            p = omero.model.ProjectI()
            p.name = wrap(project)
            prId = conn.getUpdateService().saveAndReturnObject(p).id.val
        else:
            print "Using Project:", project, p
            prId = p.getId()
            # Since Project already exists, check children for Dataset
            for c in p.listChildren():
                if c.getName() == dataset:
                    d = c

    if d is None:
        d = conn.getObject("Dataset", attributes={'name': dataset}, params=params)

    if d is None:
        print "Creating Dataset:", dataset
        d = omero.model.DatasetI()
        d.name = wrap(dataset)
        dsId = conn.getUpdateService().saveAndReturnObject(d).id.val
        if prId is not None:
            print "Linking Project-Dataset..."
            link = omero.model.ProjectDatasetLinkI()
            link.child = omero.model.DatasetI(dsId, False)
            link.parent = omero.model.ProjectI(prId, False)
            conn.getUpdateService().saveObject(link)
    else:
        print "Using Dataset:", dataset, d
        dsId = d.getId()
    return dsId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def connect_to_omero():
	conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
	connected = conn.connect()
	if not connected:
		import sys
		sys.stderr.write("Error : Connection not available, please check your user name and password.\n")
		return None
	return conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def omero_login(user, passwd, host, port):
    """Establish the connection to an OMERO server.

    Parameters
    ==========
    user : str - OMERO user name (e.g. "demo_user_01")
    passwd : str - OMERO user password
    host : str - OMERO server hostname to connect to
    port : int - OMERO server port number (e.g. 4064)

    Returns
    =======
    conn : omero.gateway._BlitzGateway - OMERO connection object
    """
    conn = BlitzGateway(user, passwd, host=host, port=port, secure=True,
                        useragent="HRM-OMERO.connector")
    conn.connect()
    return conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def temporary_connection():
    temp_client = omero.client()
    omeroProperties = temp_client.getProperties().getPropertiesForPrefix('omero')
    # Configuration
    HOST = omeroProperties.get('omero.host', 'localhost')
    PORT = omeroProperties.get('omero.port', 4064)
    USERNAME = omeroProperties.get('omero.user')
    PASSWORD = omeroProperties.get('omero.pass')
    temp_conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
    connected = temp_conn.connect()
    return temp_client,temp_conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
def connect_base():
    """Establish the base connection to OMERO.

    Returns the connection in the context defined in localconfig.
    """
    # establish the base connection with an admin account
    su_conn = BlitzGateway(SU_USER, SU_PASS, host=HOST, port=PORT)
    if su_conn.connect() is False:
        raise RuntimeError('Connection to OMERO failed, check settings!')
    log.debug("Successfully connected to OMERO.")
    return su_conn

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import connect [as 别名]
    def create_screen(self, cli, screen):
        """
        Creates screen with name provided if it doesn't exist already.
        Returns Screen ID.
        """
        sessionId = cli._event_context.sessionUuid
        conn = BlitzGateway(host='localhost')
        conn.connect(sUuid = sessionId)
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = wrap(conn.getUser().getId())

        slist = list(conn.getObjects("Screen", attributes={'name': screen}, params=params))
        if len(slist) == 0:
            print "Creating Screen:", screen
            s = ScreenI()
            s.name = wrap(screen.encode('ascii','ignore'))
            scrId = conn.getUpdateService().saveAndReturnObject(s).id.val
        else:
            scrId = slist[0].getId()
            print "Using Screen:", screen

        return scrId