Python BlitzGateway.listProjects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 listProjects [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 listProjects [as 别名]
perm_string = str(group_perms)
permission_names = {
    'rw----': 'PRIVATE',
    'rwr---': 'READ-ONLY',
    'rwra--': 'READ-ANNOTATE',
    'rwrw--': 'READ-WRITE'}  # Not exposed in 4.4.0 clients
print "Permissions: %s (%s)" % (permission_names[perm_string], perm_string)


# By default, any query applies to ALL data that we can access in our Current
# group.
# This will be determined by group permissions e.g. in Read-Only or
# Read-Annotate groups, this will include other users' data See
# :doc:`/sysadmins/server-permissions`.

projects = conn.listProjects()      # may include other users' data
for p in projects:
    print p.getName(), "Owner: ", p.getDetails().getOwner().getFullName()
# Will return None if Image is not in current group
image = conn.getObject("Image", imageId)
print "Image: ", image


# 'Cross-group' querying, use '-1'
# ===============================
conn.SERVICE_OPTS.setOmeroGroup('-1')
image = conn.getObject("Image", imageId)     # Will query across all my groups
print "Image: ", image,
if image is not None:
    print "Group: ", image.getDetails().getGroup().getName(),
    print image.details.group.id.val    # access groupId without loading group

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import listProjects [as 别名]
        " " * indent,
        obj.OMERO_CLASS,
        obj.getId(),
        obj.getName(),
        obj.getOwnerOmeName())


# List all Projects available to the user currently logged in
# ===========================================================
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is False, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
    print_obj(project)
    for dataset in project.listChildren():
        print_obj(dataset, 2)
        for image in dataset.listChildren():
            print_obj(image, 4)


# Retrieve the datasets owned by the user currently logged in
# ===========================================================
# Here we create an omero.sys.ParametersI instance which we
# can use to filter the results that are returned. If we did
# not pass the params argument to getObjects, then all Datasets
# in the current group would be returned.
print "\nList Datasets:"
print "=" * 50

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import listProjects [as 别名]
    print """%s%s:%s  Name:"%s" (owner=%s)""" % (\
            " " * indent,
            obj.OMERO_CLASS,\
            obj.getId(),\
            obj.getName(),\
            obj.getOwnerOmeName())


# List all Projects available to me, and their Datasets and Images:
# =================================================================
# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is Fale, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
for project in conn.listProjects(only_owned=True):
    print_obj(project)
    for dataset in project.listChildren():
        print_obj(dataset, 2)
        for image in dataset.listChildren():
            print_obj(image, 4)


# Retrieve the datasets owned by the user currently logged in:
# =================================================================
# Here we create an omero.sys.ParametersI instance which we
# can use to filter the results that are returned. If we did
# not pass the params argument to getObjects, then all Datasets
# in the current group would be returned.
print "\nList Datasets:"
print "=" * 50