def screen_plate_run_well(self):
     """
     Returns a new OMERO Screen, linked Plate, linked Well, linked
     WellSample, linked Image populate by an
     L{test.integration.library.ITest} instance and
     linked PlateAcquisition with all required fields set.
     """
     screen = ScreenI()
     screen.name = rstring(self.uuid())
     plate = PlateI()
     plate.name = rstring(self.uuid())
     # Well A10 (will have two WellSamples)
     well_a = WellI()
     well_a.row = rint(0)
     well_a.column = rint(9)
     # Well A11 (will not have a WellSample)
     well_b = WellI()
     well_b.row = rint(0)
     well_b.column = rint(10)
     ws_a = WellSampleI()
     image_a = self.new_image(name=self.uuid())
     ws_a.image = image_a
     ws_b = WellSampleI()
     image_b = self.new_image(name=self.uuid())
     ws_b.image = image_b
     plate_acquisition = PlateAcquisitionI()
     plate_acquisition.plate = plate
     ws_a.plateAcquisition = plate_acquisition
     ws_b.plateAcquisition = plate_acquisition
     well_a.addWellSample(ws_a)
     well_a.addWellSample(ws_b)
     plate.addWell(well_a)
     plate.addWell(well_b)
     screen.linkPlate(plate)
     return self.update.saveAndReturnObject(screen)
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    def screen_plates(self, user1):
        """Return Screen with Plates and an orphaned Plate."""
        # Create and name all the objects
        screen = ScreenI()
        screen.name = rstring('screen')

        for i in range(5):
            plate1 = PlateI()
            plate1.name = rstring('Plate%s' % i)
            screen.linkPlate(plate1)

        # Create single orphaned Plate
        plate = PlateI()
        plate.name = rstring('plate')

        screen = get_update_service(user1).saveAndReturnObject(screen)
        plate = get_update_service(user1).saveAndReturnObject(plate)

        # Add well to first plate
        plates = screen.linkedPlateList()
        plates.sort(cmp_name_insensitive)
        plate_id = plates[0].id.val
        well = WellI()
        well.column = rint(0)
        well.row = rint(0)
        well.plate = PlateI(plate_id, False)
        image = self.create_test_image(size_x=5,
                                       size_y=5,
                                       session=user1[0].getSession())
        ws = WellSampleI()
        ws.image = ImageI(image.id, False)
        ws.well = well
        well.addWellSample(ws)
        well = get_update_service(user1).saveAndReturnObject(well)
        return screen, plate
def screen_plate_run_well(request, itest, update_service):
    """
    Returns a new OMERO Screen, linked Plate, linked Well, linked WellSample,
    linked Image populate by an L{test.integration.library.ITest} instance and
    linked PlateAcquisition with all required fields set.
    """
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    # Well A10 (will have two WellSamples)
    well_a = WellI()
    well_a.row = rint(0)
    well_a.column = rint(9)
    # Well A11 (will not have a WellSample)
    well_b = WellI()
    well_b.row = rint(0)
    well_b.column = rint(10)
    ws_a = WellSampleI()
    image_a = itest.new_image(name=itest.uuid())
    ws_a.image = image_a
    ws_b = WellSampleI()
    image_b = itest.new_image(name=itest.uuid())
    ws_b.image = image_b
    plate_acquisition = PlateAcquisitionI()
    plate_acquisition.plate = plate
    ws_a.plateAcquisition = plate_acquisition
    ws_b.plateAcquisition = plate_acquisition
    well_a.addWellSample(ws_a)
    well_a.addWellSample(ws_b)
    plate.addWell(well_a)
    plate.addWell(well_b)
    screen.linkPlate(plate)
    return update_service.saveAndReturnObject(screen)
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def screen_plate(request, itest, update_service):
    """
    Returns a new OMERO Screen and linked Plate with required fields set.
    """
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    screen.linkPlate(plate)
    return update_service.saveAndReturnObject(screen)
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def screen_plate(request, itest, update_service):
    """
    Returns a new OMERO Screen and linked Plate with required fields set.
    """
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    screen.linkPlate(plate)
    return update_service.saveAndReturnObject(screen)
 def screen_plate(self):
     """
     Returns a new OMERO Screen and linked Plate with required fields set.
     """
     screen = ScreenI()
     screen.name = rstring(self.uuid())
     plate = PlateI()
     plate.name = rstring(self.uuid())
     screen.linkPlate(plate)
     return self.update.saveAndReturnObject(screen)
 def screen_plate_run(self):
     """
     Returns a new OMERO Screen, linked Plate, and linked PlateAcquisition
     with all required fields set.
     """
     screen = ScreenI()
     screen.name = rstring(self.uuid())
     plate = PlateI()
     plate.name = rstring(self.uuid())
     plate_acquisition = PlateAcquisitionI()
     plate.addPlateAcquisition(plate_acquisition)
     screen.linkPlate(plate)
     return self.update.saveAndReturnObject(screen)
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def screen_plate_run(request, itest, update_service):
    """
    Returns a new OMERO Screen, linked Plate, and linked PlateAcquisition
    with all required fields set.
    """
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    plate_acquisition = PlateAcquisitionI()
    plate.addPlateAcquisition(plate_acquisition)
    screen.linkPlate(plate)
    return update_service.saveAndReturnObject(screen)
 def create_screen(self, row_count, col_count):
     # TODO: remove 5.2 vs 5.3 compatibility
     try:
         plate = self.importPlates(plateRows=row_count,
                                   plateCols=col_count)[0]
     except AttributeError:
         plate = self.import_plates(plate_rows=row_count,
                                    plate_cols=col_count)[0]
     plate = self.set_name(plate, "Plate001")
     screen = ScreenI()
     screen.name = rstring("Screen001")
     screen.linkPlate(plate.proxy())
     return (self.client.sf.getUpdateService().saveAndReturnObject(screen),
             plate)
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 def create_screen(self, row_count, col_count):
     # TODO: remove 5.2 vs 5.3 compatibility
     try:
         plate = self.importPlates(plateRows=row_count,
                                   plateCols=col_count)[0]
     except AttributeError:
         plate = self.import_plates(plateRows=row_count,
                                    plateCols=col_count)[0]
     plate = self.set_name(plate, "Plate001")
     screen = ScreenI()
     screen.name = rstring("Screen001")
     screen.linkPlate(plate.proxy())
     return (self.client.sf.getUpdateService().saveAndReturnObject(screen),
             plate)
    def testChgrp11109(self):
        """
        Place a plate in a single screen and attempt to move it.
        """
        # One user in two groups
        client, user = self.new_client_and_user(perms=PRIVATE)
        admin = client.sf.getAdminService()
        target_grp = self.new_group([user], perms=PRIVATE)
        target_gid = target_grp.id.val
        admin.getEventContext()  # Refresh

        update = client.sf.getUpdateService()
        plate = PlateI()
        plate.name = rstring("testChgrp11109")
        screen = ScreenI()
        screen.name = rstring("testChgrp11109")
        link = screen.linkPlate(plate)
        link = update.saveAndReturnObject(link)

        # Now chgrp, should succeed
        chgrp = Chgrp2(
            targetObjects={"Plate": [link.child.id.val]}, groupId=target_gid)
        self.doSubmit(chgrp, client)

        # Check that the links have been destroyed
        query = client.sf.getQueryService()
        with pytest.raises(omero.ValidationException):
            query.get("ScreenPlateLink", link.id.val, {"omero.group": "-1"})
def screen_plate_well(request, itest, update_service):
    """
    Returns a new OMERO Screen, linked Plate and linked Well with required
    fields set.
    """
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    # Well A10
    well = WellI()
    well.row = rint(0)
    well.column = rint(9)
    plate.addWell(well)
    screen.linkPlate(plate)
    return update_service.saveAndReturnObject(screen)
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 def screen_plate_well(self):
     """
     Returns a new OMERO Screen, linked Plate and linked Well with required
     fields set.
     """
     screen = ScreenI()
     screen.name = rstring(self.uuid())
     plate = PlateI()
     plate.name = rstring(self.uuid())
     # Well A10
     well = WellI()
     well.row = rint(0)
     well.column = rint(9)
     plate.addWell(well)
     screen.linkPlate(plate)
     return self.update.saveAndReturnObject(screen)
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    def testChgrp11109(self):
        """
        Place a plate in a single screen and attempt to move it.
        """
        # One user in two groups
        client, user = self.new_client_and_user(perms=PRIVATE)
        admin = client.sf.getAdminService()
        target_grp = self.new_group([user], perms=PRIVATE)
        target_gid = target_grp.id.val
        admin.getEventContext()  # Refresh

        update = client.sf.getUpdateService()
        plate = PlateI()
        plate.name = rstring("testChgrp11109")
        screen = ScreenI()
        screen.name = rstring("testChgrp11109")
        link = screen.linkPlate(plate)
        link = update.saveAndReturnObject(link)

        # Now chgrp, should succeed
        chgrp = Chgrp2(targetObjects={"Plate": [link.child.id.val]},
                       groupId=target_gid)
        self.doSubmit(chgrp, client)

        # Check that the links have been destroyed
        query = client.sf.getQueryService()
        with pytest.raises(omero.ValidationException):
            query.get("ScreenPlateLink", link.id.val, {"omero.group": "-1"})
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def plates_runs(request, itest, update_service, names):
    """
    Returns a four new Plates, and two linked PlateAcquisitions with required
    fields set and with names that can be used to exercise sorting semantics.
    """
    plates = [PlateI(), PlateI(), PlateI(), PlateI()]
    for index, plate in enumerate(plates):
        plate.name = rstring(names[index])
        plate_acquisitions = [PlateAcquisitionI(), PlateAcquisitionI()]
        for plate_acquisition in plate_acquisitions:
            plate.addPlateAcquisition(plate_acquisition)
    # Non-orphaned Plate to catch issues with queries where non-orphaned
    # plates are included in the results.
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    screen.linkPlate(plate)
    update_service.saveAndReturnObject(screen)
    return update_service.saveAndReturnArray(plates)
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def plates_runs(request, itest, update_service, names):
    """
    Returns a four new Plates, and two linked PlateAcquisitions with required
    fields set and with names that can be used to exercise sorting semantics.
    """
    plates = [PlateI(), PlateI(), PlateI(), PlateI()]
    for index, plate in enumerate(plates):
        plate.name = rstring(names[index])
        plate_acquisitions = [PlateAcquisitionI(), PlateAcquisitionI()]
        for plate_acquisition in plate_acquisitions:
            plate.addPlateAcquisition(plate_acquisition)
    # Non-orphaned Plate to catch issues with queries where non-orphaned
    # plates are included in the results.
    screen = ScreenI()
    screen.name = rstring(itest.uuid())
    plate = PlateI()
    plate.name = rstring(itest.uuid())
    screen.linkPlate(plate)
    update_service.saveAndReturnObject(screen)
    return update_service.saveAndReturnArray(plates)
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    def testListParentsSPW(self):
        """Test listParents() for Image in WellSample"""

        client, exp = self.new_client_and_user()
        conn = BlitzGateway(client_obj=client)

        # setup SPW-WS-Img...
        s = ScreenI()
        s.name = wrap('ScreenA')
        p = PlateI()
        p.name = wrap('PlateA')
        s.linkPlate(p)
        w = WellI()
        w.column = wrap(0)
        w.row = wrap(0)
        p.addWell(w)
        s = client.sf.getUpdateService().saveAndReturnObject(s)
        p = s.linkedPlateList()[0]
        w = p.copyWells()[0]
        i = self.make_image(name="SPW listParents", client=client)
        ws = WellSampleI()
        ws.image = i
        ws.well = WellI(w.id.val, False)
        w.addWellSample(ws)
        ws = client.sf.getUpdateService().saveAndReturnObject(ws)

        # Traverse from Image -> Screen
        image = conn.getObject("Image", i.id.val)
        wellSample = image.listParents()[0]

        well = wellSample.listParents()[0]
        assert well.id == w.id.val

        plate = well.listParents()[0]
        assert plate.id == p.id.val

        screen = plate.listParents()[0]
        assert screen.id == s.id.val
        # Screen has no parent
        assert len(screen.listParents()) == 0