Python BlitzGateway.getUserId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 getUserId [as 别名]
    def test_chgrp_new_container(self, dataset, credentials):
        """
        Performs a chgrp POST, polls the activities json till done,
        then checks that Dataset has moved to new group and has new
        Project as parent.
        """

        django_client = self.get_django_client(credentials)
        request_url = reverse('chgrp')
        projectName = "chgrp-project%s" % (self.uuid())
        data = {
            "group_id": self.group2.id.val,
            "Dataset": dataset.id.val,
            "new_container_name": projectName,
            "new_container_type": "project",
        }
        data = _csrf_post_response_json(django_client, request_url, data)
        expected = {"update": {"childless": {"project": [],
                                             "orphaned": False,
                                             "dataset": []},
                               "remove": {"project": [],
                                          "plate": [],
                                          "screen": [],
                                          "image": [],
                                          "dataset": [dataset.id.val]}}}
        assert data == expected

        activities_url = reverse('activities_json')

        data = _get_response_json(django_client, activities_url, {})

        # Keep polling activities until no jobs in progress
        while data['inprogress'] > 0:
            time.sleep(0.5)
            data = _get_response_json(django_client, activities_url, {})

        # individual activities/jobs are returned as dicts within json data
        for k, o in data.items():
            if hasattr(o, 'values'):    # a dict
                if 'report' in o:
                    print o['report']
                assert o['status'] == 'finished'
                assert o['job_name'] == 'Change group'
                assert o['to_group_id'] == self.group2.id.val

        # Dataset should now be in new group, contained in new Project
        conn = BlitzGateway(client_obj=self.client)
        userId = conn.getUserId()
        conn.SERVICE_OPTS.setOmeroGroup('-1')
        d = conn.getObject("Dataset", dataset.id.val)
        assert d is not None
        assert d.getDetails().group.id.val == self.group2.id.val
        p = d.getParent()
        assert p is not None
        assert p.getName() == projectName
        # Project owner should be current user
        assert p.getDetails().owner.id.val == userId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getUserId [as 别名]
    def test_chgrp_old_container(self, dataset, credentials):
        """
        Tests Admin moving user's Dataset to their Private group and
        linking it to an existing Project there.
        Bug from https://github.com/openmicroscopy/openmicroscopy/pull/3420
        """

        django_client = self.get_django_client(credentials)
        # user creates project in their target group
        project = ProjectI()
        projectName = "chgrp-target-%s" % self.client.getSessionId()
        project.name = rstring(projectName)
        ctx = {"omero.group": str(self.group2.id.val)}
        project = self.sf.getUpdateService().saveAndReturnObject(project, ctx)
        request_url = reverse('chgrp')

        data = {
            "group_id": self.group2.id.val,
            "Dataset": dataset.id.val,
            "target_id": "project-%s" % project.id.val,
        }
        data = _csrf_post_response_json(django_client, request_url, data)
        expected = {"update": {"childless": {"project": [],
                                             "orphaned": False,
                                             "dataset": []},
                               "remove": {"project": [],
                                          "plate": [],
                                          "screen": [],
                                          "image": [],
                                          "dataset": [dataset.id.val]}}}
        assert data == expected

        activities_url = reverse('activities_json')

        data = _get_response_json(django_client, activities_url, {})

        # Keep polling activities until no jobs in progress
        while data['inprogress'] > 0:
            time.sleep(0.5)
            data = _get_response_json(django_client, activities_url, {})

        # individual activities/jobs are returned as dicts within json data
        for k, o in data.items():
            if hasattr(o, 'values'):    # a dict
                if 'report' in o:
                    print o['report']
                assert o['status'] == 'finished'
                assert o['job_name'] == 'Change group'
                assert o['to_group_id'] == self.group2.id.val

        # Dataset should now be in new group, contained in Project
        conn = BlitzGateway(client_obj=self.client)
        userId = conn.getUserId()
        conn.SERVICE_OPTS.setOmeroGroup('-1')
        d = conn.getObject("Dataset", dataset.id.val)
        assert d is not None
        assert d.getDetails().group.id.val == self.group2.id.val
        p = d.getParent()
        assert p is not None
        assert p.getName() == projectName
        # Project owner should be current user
        assert p.getDetails().owner.id.val == userId
        assert p.getId() == project.id.val

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getUserId [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.........