Python CLI.loadplugins方法代码示例

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
    def check(self):

        from omero.cli import CLI
        from omero.gateway import BlitzGateway

        cli = CLI()
        cli.loadplugins()
        cli.onecmd('login -q')

        try:
            gateway = BlitzGateway(client_obj=cli.get_client())
            for experiment in self.m["experiments"]:
                self.check_object(gateway, experiment, "Project")
            for experiment in self.m["screens"]:
                self.check_object(gateway, experiment, "Screen")
            if "map" in self.m:
                if self.m["experiments"]:
                    study_type = "Project"
                else:
                    study_type = "Screen"
                self.check_object(gateway, self.m, study_type)
        finally:
            if cli:
                cli.close()
            gateway.close()

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
def main():
    parser = Parser()
    parser.add_login_arguments()
    parser.add_argument("--orphans", action="store_true")
    parser.add_argument("--unknown", action="store_true")
    parser.add_argument("--search", action="store_true")
    parser.add_argument("--images", action="store_true")
    parser.add_argument("--copy-from", type=long, default=None)
    parser.add_argument("--copy-type", default="Image")
    parser.add_argument("--copy-to", type=long, default=None)
    parser.add_argument("screen", nargs="?")
    ns = parser.parse_args()

    cli = CLI()
    cli.loadplugins()
    client = cli.conn(ns)
    try:
        query = client.sf.getQueryService()
        if ns.orphans:
            orphans(query)
        elif ns.unknown:
            unknown(query)
        elif ns.search:
            search = client.sf.createSearchService()
            check_search(query, search)
        elif not ns.screen:
            stat_screens(query)
        else:
            if ns.copy_to:
                copy(client, ns.copy_from, ns.copy_type, ns.copy_to)
            else:
                for x in stat_plates(query, ns.screen, ns.images):
                    print x
    finally:
        cli.close()

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
 class T(Thread):
     def run(self, *args):
         pause = random.random()
         event.wait(pause)
         self.cli = CLI()
         self.cli.loadplugins()
         self.con = self.cli.controls["admin"]
         self.cmp = self.con.ctx

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
def as_stdout(path, readers=""):
        path = _to_list(path)
        readers = str(readers)
        cli = CLI()
        cli.loadplugins()
        if readers:
            cli.invoke(["import", "-l", readers, "-f"]+path)
        else:
            cli.invoke(["import", "-f"]+path)
        if cli.rv != 0:
            raise omero.InternalException(None, None, "'import -f' exited with a rc=%s. See console for more information" % cli.rv)

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
def main():
    parser = Parser()
    parser.add_login_arguments()
    parser.add_argument("file")
    parser.add_argument("object")
    ns = parser.parse_args()

    cli = CLI()
    cli.loadplugins()
    client = cli.conn(ns)
    try:
        screen_metadata(client, ns.file, ns.object)
    finally:
        cli.close()

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
    def status(self, args):
        self.ctx.invoke(["admin", "status", args.name])

    def stop(self, args):
        if self._isWindows():
            try:
                command = ["icegridnode", "--stop", "OMERO."+args.name]
                self.ctx.call(command)
                command = ["icegridnode", "--uninstall", "OMERO."+args.name]
                self.ctx.call(command)
            except NonZeroReturnCode, nzrc:
                self._handleNZRC(nzrc)
        else:
                pid = open(self._pid(), "r").readline()
                os.kill(int(pid), signal.SIGTERM)
                # command = ["icegridadmin"] + [self._intcfg()] + ["-c", "node
                # shutdown %s" % args.name]
                # self.ctx.call(command)

    def kill(self, args):
        pid = open(self._pid(), "r").readline()
        os.kill(int(pid), signal.SIGKILL)

try:
    register("node", NodeControl, HELP)
except NameError:
    if __name__ == "__main__":
        cli = CLI()
        cli.loadplugins()
        cli.invoke(sys.argv[1:])

# 需要导入模块: from omero.cli import CLI [as 别名]
# 或者: from omero.cli.CLI import loadplugins [as 别名]
def hrm_to_omero(conn, id_str, image_file):
    """Upload an image into a specific dataset in OMERO.

    In case we know from the suffix that a given file format is not supported
    by OMERO, the upload will not be initiated at all (e.g. for SVI-HDF5,
    having the suffix '.h5').

    The import itself is done by instantiating the CLI class, assembling the
    required arguments, and finally running cli.invoke(). This eventually
    triggers the importer() method defined in OMERO's Python bindings in
    <OMERO.server/lib/python/omero/plugins/import.py>, respectively (source)
    <openmicroscopy.git/components/tools/OmeroPy/src/omero/plugins/import.py>.

    Parameters
    ==========
    id_str: str - the ID of the target dataset in OMERO (e.g. "G:7:Dataset:23")
    image_file: str - the local image file including the full path

    Returns
    =======
    True in case of success, False otherwise.
    """
    if image_file.lower().endswith(('.h5', '.hdf5')):
        print 'ERROR: HDF5 files are not supported by OMERO!'
        return False
    # TODO I: group switching required!!
    _, gid, obj_type, dset_id = id_str.split(':')
    # we have to create the annotations *before* we actually upload the image
    # data itself and link them to the image during the upload - the other way
    # round is not possible right now as the CLI wrapper (see below) doesn't
    # expose the ID of the newly created object in OMERO (confirmed by J-M and
    # Sebastien on the 2015 OME Meeting):
    namespace = 'deconvolved.hrm'
    #### mime = 'text/plain'
    # extract the image basename without suffix:
    # TODO: is it [0-9a-f] or really [0-9a-z] as in the original PHP code?
    basename = re.sub(r'(_[0-9a-f]{13}_hrm)\..*', r'\1', image_file)
    comment = gen_parameter_summary(basename + '.parameters.txt')
    #### annotations = []
    #### # TODO: the list of suffixes should not be hardcoded here!
    #### for suffix in ['.hgsb', '.log.txt', '.parameters.txt']:
    ####     if not os.path.exists(basename + suffix):
    ####         continue
    ####     ann = conn.createFileAnnfromLocalFile(
    ####         basename + suffix, mimetype=mime, ns=namespace, desc=None)
    ####     annotations.append(ann.getId())
    # currently there is no direct "Python way" to import data into OMERO, so
    # we have to use the CLI wrapper for this:
    from omero.cli import CLI
    cli = CLI()
    cli.loadplugins()
    # NOTE: cli._client should be replaced with cli.set_client() when switching
    # to support for OMERO 5.1 and later only:
    cli._client = conn.c
    import_args = ["import"]
    import_args.extend(['-d', dset_id])
    if comment is not None:
        import_args.extend(['--annotation_ns', namespace])
        import_args.extend(['--annotation_text', comment])
    #### for ann_id in annotations:
    ####     import_args.extend(['--annotation_link', str(ann_id)])
    import_args.append(image_file)
    # print("import_args: " + str(import_args))
    try:
        cli.invoke(import_args, strict=True)
    except:
        print('ERROR: uploading "%s" to %s failed!' % (image_file, id_str))
        # print(import_args)
        return False
    return True