Python BlitzGateway.getGroupsMemberOf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 getGroupsMemberOf [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 getGroupsMemberOf [as 别名]
    def group_exists(self, user, group):
        if not self.user_exists(user):
            return False
        else:
            if group in self.known_users[user]:
                print "in Group:", group
                return True
        try:
            try:
                conn = BlitzGateway(user, "ome", host='localhost')
                conn.connect()
                groups = conn.getGroupsMemberOf()
            except:
                return False

            if group in [g.name for g in groups]:
                print "in Group:", group
                self.known_users[user].append(group)
                return True
            else:
                print "is not in Group:", group, "- ignoring."
                return False
        finally:
            conn.seppuku()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getGroupsMemberOf [as 别名]
    # conn.setSecure(True)         # <--------- Uncomment this


    # Current session details
    # =============================================================
    # By default, you will have logged into your 'current' group in OMERO. This
    # can be changed by switching group in the OMERO.insight or OMERO.web clients.

    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()

    print "Other Members of current group:"
    for exp in conn.listColleagues():
        print "   ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()

    print "Owner of:"
    for g in conn.listOwnedGroups():
        print "   ID:", g.getName(), " Name:", g.getId()

    # New in OMERO 5
    print "Admins:"
    for exp in conn.getAdministrators():

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getGroupsMemberOf [as 别名]
class Omg(object):
    """
    OMERO gateway that wraps Blitz gateway and CLI, intended for
    scripting and interactive work.

    Attributes
    ----------
    conn : Blitz gateway connection

    """

    def __init__(self, conn=None, user=None, passwd=None,
                 server=SERVER, port=PORT, skey=None):
        """
        Requires active Blitz connection OR username plus password or sesskey
        """
        if conn is None and (user is None or (passwd is None and skey is None)):
            raise ValueError("Bad parameters," + self.__init__.__doc__)
        if conn is not None:
            if conn.isConnected():
                self.conn = conn
            else:
                raise ValueError("Cannot initialize with closed connection!")
        else:
            if passwd is not None:
                self.conn = BlitzGateway(user, passwd, host=server, port=port)
                self.conn.connect()
            else:
                self.conn = BlitzGateway(user, host=server, port=port)
                self.conn.connect(skey)
        if self.conn.isConnected():
            self._server = self.conn.host
            self._port = self.conn.port
            self._user = self.conn.getUser().getName()
            self._key = self.conn.getSession().getUuid().getValue()
            print("Connected to {0} (port {1}) as {2}, session key={3}".format(
                  self._server, self._port, self._user, self._key))
        else:
            print("Failed to open connection :-(")

    def ls(self):
        """
        Print groups, then projects/datasets/images for current group.
        """
        print("Groups for {0}:-".format(self.conn.getUser().getName()))
        for gid, gname in self._ls_groups():
            print("  {0} ({1})".format(gname, str(gid)))
        curr_grp = self.conn.getGroupFromContext()
        gid, gname = curr_grp.getId(), curr_grp.getName()
        print("\nData for current group, {0} ({1}):-".format(gname, gid))
        for pid, pname in self._ls_projects():
            print("  Project: {0} ({1})".format(pname, str(pid)))
            for did, dname in self._ls_datasets(pid):
                print("    Dataset: {0} ({1})".format(dname, str(did)))
                for iid, iname in self._ls_images(did):
                    print("      Image: {0} ({1})".format(iname, str(iid)))
        # TODO, list orphaned Datasets and Images

    def _ls_groups(self):
        """list groups (id, name) this session is a member of"""
        groups = self.conn.getGroupsMemberOf()
        return [(group.getId(), group.getName()) for group in groups]

    def _ls_projects(self):
        """list projects (id, name) in the current session group"""
        projs = self.conn.listProjects(self.conn.getUserId())
        return [(proj.getId(), proj.getName()) for proj in projs]

    def _ls_datasets(self, proj_id):
        """list datasets (id, name) within the project id given"""
        dsets = self.conn.getObject("Project", proj_id).listChildren()
        return [(dset.getId(), dset.getName()) for dset in dsets]

    def _ls_images(self, dset_id):
        """list images (id, name) within the dataset id given"""
        imgs = self.conn.getObject("Dataset", dset_id).listChildren()
        return [(img.getId(), img.getName()) for img in imgs]

    def chgrp(self, group_id):
        """
        Change group for this session to the group_id given.
        """
        self.conn.setGroupForSession(group_id)

    def get(self, im_id, get_att=True):
        """
        Download the specified image as an OME-TIFF to current directory,
        with attachments also downloaded to folder: img_path + '_attachments'
        Return : path to downloaded image
        """
        img = self.conn.getObject("Image", oid=im_id)
        img_name = self._unique_name(img.getName(), im_id)
        img_path = os.path.join(os.getcwd(), img_name)
        img_file = open(str(img_path + ".ome.tiff"), "wb")
        fsize, blockgen = img.exportOmeTiff(bufsize=65536)
        for block in blockgen:
            img_file.write(block)
        img_file.close()
        fa_type = omero.model.FileAnnotationI
        attachments = [ann for ann in img.listAnnotations()
#.........这里部分代码省略.........

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getGroupsMemberOf [as 别名]
    if theT is not None:
        rect.theT = rint(theT)
    if label is not None:
        rect.textValue = wrap(label)
    rect.setRoi(roi)
    roi.addShape(rect)


# First, we want to make sure that every user has a tag(s) in every group
print "\n---- CREATING TAGS ----\n"
for exp in allUsers:
    username = exp.getOmeName()
    print username
    userConn = BlitzGateway(username, "ome")
    userConn.connect()
    for g in userConn.getGroupsMemberOf():
        if g.getName() == "user":
            continue
        print " ", g.getName()
        userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = rlong(exp.getId())
        tags = list( userConn.getObjects("TagAnnotation", params=params) )
        for i in range( TAG_COUNT-len(tags) ):
            t = TagAnnotationI()
            newTagVal = "%s_%s_TEST" % (username, g.getName())
            print "creating TAG:", newTagVal
            t.textValue = wrap(str(newTagVal))
            userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
        # for t in tags: