Python BlitzGateway.setGroupForSession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 setGroupForSession [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 setGroupForSession [as 别名]
conn = BlitzGateway(username, password, host=HOST, port=PORT)
connected = conn.connect()
if not connected:
    print >> sys.stderr, ("Error: Connection not available, please check your " "username and password.")
    sys.exit(1)
else:
    print "Login successful.\n"

# Set our default group so we can see the data.
# (I thought I had to do this, but now I am not sure it's needed.
# -JLM 2013/12/04)
try:
    group = next(g for g in conn.listGroups() if g.getName() == GROUP)
except StopIteration:
    print >> sys.stderr, "Error: could not find group '%s'" % GROUP
conn.setGroupForSession(group.getId())

# Get plate of interest.
# (ID 1552 is "RTK ligands induce differing FOXO3a translocation dynamics")
plate = conn.getObject("Plate", 1552)
# Get list of lists of well objects from the plate.
well_grid = plate.getWellGrid()

# Loop over all wells in the plate.
for (raw_row_num, row) in enumerate(well_grid):
    for (raw_col_num, well) in enumerate(row):
        # Fix up row and column numbers to match Pat's nomenclature.
        row_num = raw_row_num + 1
        col_num = raw_col_num + 2
        # Construct paths and create output directory. (I dislike this naming
        # format but it's what Pat has chosen. -JLM)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import setGroupForSession [as 别名]
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

# Suggests OMERO.cli commands to fix the idr0004 field-image mapping.
# author: [email protected]

from omero.gateway import BlitzGateway
from omero.rtypes import wrap
from omero.sys import ParametersI
import os

conn = BlitzGateway(
    os.environ.get('IDR_USER', 'root'),
    os.environ.get('IDR_PASSWORD', 'omero'),
    host=os.environ.get('IDR_HOST', 'localhost'))
conn.connect()
conn.setGroupForSession(3)  # Public

query_service = conn.getQueryService()

# Find the plates of idr0004.

query = """
SELECT child.id
  FROM ScreenPlateLink
  WHERE parent.name LIKE :name
"""

params = ParametersI()
params.add('name', wrap('idr0004-%'))

rows = query_service.projection(query, params)