Python BlitzGateway.getObject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 getObject [as 别名]
    def test_canDoAction(self, func):
        """
        Test if canEdit returns appropriate flag
        """

        client, user = self.new_client_and_user()

        image = self.make_image()
        share_id = self.create_share(
            objects=[image], description="description", experimenters=[user])
        share = self.sf.getShareService()
        assert len(share.getContents(share_id)) == 1

        # test action by member
        user_conn = BlitzGateway(client_obj=client)
        # user CANNOT see image if not in share
        assert None == user_conn.getObject("Image", image.id.val)
        # activate share
        user_conn.SERVICE_OPTS.setOmeroShare(share_id)
        assert False == getattr(user_conn.getObject("Image",
                                                    image.id.val), func)()

        # test action by owner
        owner_conn = BlitzGateway(client_obj=self.client)
        # owner CAN do action on the object when not in share
        assert True == getattr(owner_conn.getObject("Image",
                                                    image.id.val), func)()
        # activate share
        owner_conn.SERVICE_OPTS.setOmeroShare(share_id)
        # owner CANNOT do action on the object when in share
        assert False == getattr(owner_conn.getObject("Image",
                                                     image.id.val), func)()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
    def testFakeImport(self):

        # TODO: should likely be in the "fs" namespace
        req = omero.cmd.OriginalMetadataRequest()

        client = self.new_client()
        rsp = self.fullImport(client) # Note: fake test produces no metadata!
        image = rsp.objects[0]

        req.imageId = image.id.val

        gateway = BlitzGateway(client_obj=client)

        # Load via the gateway
        image = gateway.getObject("Image", image.id.val)
        assert 3 ==  len(image.loadOriginalMetadata())

        # Load via raw request
        handle = client.sf.submit(req)
        try:
            gateway._waitOnCmd(handle, failonerror=True)
            rsp = handle.getResponse()
            assert dict ==  type(rsp.globalMetadata)
            assert dict ==  type(rsp.seriesMetadata)
        finally:
            handle.close()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv[1:])
    if not args.out_file:
        args.out_file = "map_screen_%d.tsv" % args.screen_id
    passwd = getpass.getpass()
    conn = BlitzGateway(
        args.user, passwd, host=args.host, port=args.port, group=args.group
    )
    conn.connect()
    screen = conn.getObject("Screen", args.screen_id)
    print "writing to %s" % args.out_file
    print "SCREEN: %s" % screen.name
    with open(args.out_file, "w") as fo:
        fo.write("PLATE\tSERIES\tWELL\tFIELD\tImageID\tWellID\n")
        for p in screen.listChildren():
            rows = []
            print "  plate: %s" % p.name
            for w in p.listChildren():
                n_fields = sum(1 for _ in w.listChildren())
                for i in xrange(n_fields):
                    img = w.getImage(i)
                    well_tag = "%s%02d" % (LETTERS[w.row], w.column + 1)
                    rows.append((
                        p.name, img.getSeries(), well_tag, i + 1, img.id, w.id
                    ))
            rows.sort(key=itemgetter(1))
            rows.sort()
            for r in rows:
                fo.write("%s\t%d\t%s\t%d\t%d\t%d\n" % r)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
def create_containers(cli, dataset, project=None):
    """
    Creates containers with names provided if they don't exist already.
    Returns Dataset ID.
    """
    sessionId = cli._event_context.sessionUuid
    conn = BlitzGateway()
    conn.connect(sUuid = sessionId)
    params = omero.sys.Parameters()
    params.theFilter = omero.sys.Filter()
    params.theFilter.ownerId = wrap(conn.getUser().getId())

    d = None
    prId = None
    if project is not None:
        p = conn.getObject("Project", attributes={'name': project}, params=params)
        if p is None:
            print "Creating Project:", project
            p = omero.model.ProjectI()
            p.name = wrap(project)
            prId = conn.getUpdateService().saveAndReturnObject(p).id.val
        else:
            print "Using Project:", project, p
            prId = p.getId()
            # Since Project already exists, check children for Dataset
            for c in p.listChildren():
                if c.getName() == dataset:
                    d = c

    if d is None:
        d = conn.getObject("Dataset", attributes={'name': dataset}, params=params)

    if d is None:
        print "Creating Dataset:", dataset
        d = omero.model.DatasetI()
        d.name = wrap(dataset)
        dsId = conn.getUpdateService().saveAndReturnObject(d).id.val
        if prId is not None:
            print "Linking Project-Dataset..."
            link = omero.model.ProjectDatasetLinkI()
            link.child = omero.model.DatasetI(dsId, False)
            link.parent = omero.model.ProjectI(prId, False)
            conn.getUpdateService().saveObject(link)
    else:
        print "Using Dataset:", dataset, d
        dsId = d.getId()
    return dsId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [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 getObject [as 别名]
    def ls(self, args):
        """List all the original files contained in a fileset"""
        client = self.ctx.conn(args)
        gateway = BlitzGateway(client_obj=client)
        gateway.SERVICE_OPTS.setOmeroGroup("-1")
        fileset = gateway.getObject("Fileset", args.fileset.id.val)

        defaultdict(list)
        for ofile in fileset.listFiles():
            print ofile.path + ofile.name

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
    def setup_method(self, method):
        super(MetadataTestBase, self).setup_method(method)
        self.name = self.uuid()
        self.image = self.importSingleImage(
            GlobalMetadata={'gmd-' + self.name: 'gmd-' + self.name})

        conn = BlitzGateway(client_obj=self.client)
        self.imageid = unwrap(self.image.getId())
        assert type(self.imageid) == long
        wrapper = conn.getObject("Image", self.imageid)
        self.md = Metadata(wrapper)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
def check_file_annotation(client, file_annotation,
                          parent_type="Image", link_count=0):
    """
    Check validity of file annotation. If hasFileAnnotation, check the size,
    name and number of objects linked to the original file.
    """
    assert file_annotation is not None
    id = file_annotation.getId().getValue()
    assert id > 0
    orig_file = file_annotation.getFile()
    assert orig_file.getSize().getValue() > 0
    assert orig_file.getName().getValue() is not None

    conn = BlitzGateway(client_obj=client)

    wrapper = conn.getObject("FileAnnotation", id)
    links = sum(1 for i in wrapper.getParentLinks(parent_type))
    conn.close()
    assert links == link_count

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
def checkFileAnnotation(self, fileAnnotation, hasFileAnnotation=True, parentType="Image", isLinked=True, client=None):
    """
    Check validity of file annotation. If hasFileAnnotation, check the size, name and number of objects linked to the original file.
    """
    if hasFileAnnotation:
        self.assertNotEqual(fileAnnotation,None)
        self.assertTrue(fileAnnotation.val._file._size._val>0)
        self.assertNotEqual(fileAnnotation.val._file._name._val,None)

        if client is None: client = self.root
        conn = BlitzGateway(client_obj = client)
        faWrapper = conn.getObject("FileAnnotation", fileAnnotation.val.id.val)
        nLinks = sum(1 for i in faWrapper.getParentLinks(parentType))
        if isLinked:
            self.assertEqual(nLinks,1)
        else:
            self.assertEqual(nLinks,0)
    else:
        self.assertEqual(fileAnnotation,None)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
    def user_exists(self, user):
        if user in self.known_users.keys():
            print "User:", user,
            return True
        try:
            try:
                conn = BlitzGateway("root", "omero", host='localhost')
                conn.connect()
                params = omero.sys.Parameters()
                params.theFilter = omero.sys.Filter()
                u = conn.getObject("Experimenter", attributes={'omeName': user}, params=params)
            except:
                print "Error getting user - ignoring."
                return False

            if u is None:
                print "User:", user, "does not exist - ignoring."
                return False
            else:
                print "User:", user,
                self.known_users[user] = []
                return True
        finally:
            conn.seppuku()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
# Create a connection
# =================================================================
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()


# Configuration
# =================================================================
imageId = 101


# Get the 'Fileset' for an Image
# =================================================================
# A Fileset is a collection of the original files imported to
# create an image or set of images in OMERO.
image = conn.getObject("Image", imageId)
fileset = image.getFileset()       # will be None for pre-FS images
fsId = fileset.getId()
# List all images that are in this fileset
for fsImage in fileset.copyImages():
    print fsImage.getId(), fsImage.getName()
# List original imported files
for origFile in fileset.listFiles():
    name = origFile.getName()
    path = origFile.getPath()
    print path, name


# Get Original Imported Files directly from the image
# =================================================================
# this will include pre-FS data IF images were archived on import

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
    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)
        output_dir = 'r%dc%d' % (row_num, col_num)
        full_output_dir = os.path.join(frame_dir, output_dir)
        makedirs_exist_ok(full_output_dir)
        # Get image object and a few of its useful attributes.

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [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 getObject [as 别名]
        # process the list of args above. Not scrictly necessary, but useful for more complex scripts
        scriptParams = {}
        for key in client.getInputKeys():
            if client.getInput(key):
                scriptParams[key] = client.getInput(key, unwrap=True) # unwrap rtypes to String, Integer etc

        print scriptParams    # handy to have inputs in the std-out log

        # wrap client to use the Blitz Gateway
        conn = BlitzGateway(client_obj=client)

        # do the editing...
        editedImgIds = editDescriptions(conn, scriptParams)

        # now handle the result, displaying message and returning image if appropriate
        if editedImgIds is None:
            message = "Script failed. See 'error' or 'info' for more details"
        else:
            if len(editedImgIds) == 1:
                img = conn.getObject("Image", editedImgIds[0])      # image-wrapper
                message = "One Image edited: %s" % img.getName()
                omeroImage = img._obj                               # omero.model object
                client.setOutput("Edited Image", robject(omeroImage))  # Insight will display 'View' link to image
            elif len(editedImgIds) > 1:
                message = "%s Images edited" % len(editedImgIds)
            else:
                message = "No images edited. See 'error' or 'info' for more details"

        client.setOutput("Message", rstring(message))    # Insight will display the 'Message' parameter
    finally:
        client.closeSession()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObject [as 别名]
def copy(client, copy_from, copy_type, copy_to):
    gateway = BlitzGateway(client_obj=client)
    print gateway.applySettingsToSet(copy_from, copy_type, [copy_to])
    gateway.getObject("Image", copy_to).getThumbnail(size=(96,), direct=False)