Python BlitzGateway.getQueryService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 getQueryService [as 别名]

#.........这里部分代码省略.........
        """
        downloads = []
        wdir = os.getcwd()
        proj_name = self.conn.getObject("Project", project_id).getName()
        proj_path = os.path.join(wdir, proj_name + "_P" + str(project_id))
        os.mkdir(proj_path)
        os.chdir(proj_path)
        for dset_id, dset_name in self._ls_datasets(project_id):
            downloads.extend(self.dget(dset_id))
        os.chdir(wdir)
        return downloads

    def put(self, filename, name=None, dataset=None):
        """
        Import filename using OMERO CLI, optionally with a specified name
        to a specified dataset (dataset_id).
        Return : OMERO image Id
        """
        cli = omero.cli.CLI()
        cli.loadplugins()
        import_args = ["import"]
        import_args.extend(["-s", str(self._server)])
        import_args.extend(["-k", str(self._key)])
        if dataset is not None:
            import_args.extend(["-d", str(dataset)])
        if name is not None:
            import_args.extend(["-n", str(name)])
        clio = "cli.out"
        clie = "cli.err"
        import_args.extend(["---errs=" + clie, "---file=" + clio, "--"])
        import_args.append(filename)
        cli.invoke(import_args, strict=True)
        pix_id = int(open(clio, 'r').read().rstrip())
        im_id = self.conn.getQueryService().get("Pixels", pix_id).image.id.val
        os.remove(clio)
        os.remove(clie)
        return im_id

    def describe(self, im_id, description):
        """
        Append to image description.
        """
        img = self.conn.getObject("Image", oid=im_id)
        old_description = img.getDescription() or ""
        img.setDescription(old_description + "\n" + description)
        img.save()

    def attach(self, im_id, attachments):
        """
        Attach a list of files to an image.
        """
        img = self.conn.getObject("Image", oid=im_id)
        for attachment in attachments.split():
            fann = self.conn.createFileAnnfromLocalFile(attachment)
            img.linkAnnotation(fann)
        img.save()

    # TODO: ls_tags() and tag() methods?

    def mkp(self, project_name, description=None):
        """
        Make new OMERO project in current group, returning the new project Id.
        """
        # see: omero/lib/python/omeroweb/webclient/controller/container.py
        proj = omero.model.ProjectI()
        proj.name = omero.rtypes.rstring(str(project_name))

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getQueryService [as 别名]
colors = []
for ch in image.getChannels():
    cNames.append(ch.getLabel())
    colors.append(ch.getColor().getRGB())


# Save channel names and colors
# =================================================================
print "Applying channel Names:", cNames, " Colors:", colors
for i, c in enumerate(newImg.getChannels()):
    lc = c.getLogicalChannel()
    lc.setName(cNames[i])
    lc.save()
    r, g, b = colors[i]
    # need to reload channels to avoid optimistic lock on update
    cObj = conn.getQueryService().get("Channel", c.id)
    cObj.red = rint(r)
    cObj.green = rint(g)
    cObj.blue = rint(b)
    cObj.alpha = rint(255)
    conn.getUpdateService().saveObject(cObj)
newImg.resetRDefs()  # reset based on colors above


# Apply pixel sizes from original image
# =================================================================
newPix = conn.getQueryService().get("Pixels", newImg.getPixelsId())

physicalSizeX = pixels.getPhysicalSizeX()
if physicalSizeX is not None:
    newPix.setPhysicalSizeX(rdouble(physicalSizeX))

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getQueryService [as 别名]
def run():
    """
    """
    dataTypes = [rstring("Plate")]

    client = scripts.client(
        "Manage_Plate_Acquisitions.py",
        "Add or remove PlateAcquisition(s) in a given Plate",

        scripts.String("Data_Type", optional=False, grouping="1",
                       description="The data type you want to work with.",
                       values=dataTypes,
                       default="Plate"),

        scripts.List("IDs", optional=False, grouping="2",
                     description="List of Plate IDs").ofType(rlong(0)),

        scripts.String("Mode", optional=False, grouping="3",
                       description="Select if you want to add or "
                                   "remove PlateAcquisitions",
                       values=[rstring("Add"), rstring("Remove")],
                       default="Add"),

        version="0.2",
        authors=["Niko Klaric"],
        institutions=["Glencoe Software Inc."],
        contact="[email protected]",
    )

    try:
        scriptParams = {}
        for key in client.getInputKeys():
            if client.getInput(key):
                scriptParams[key] = client.getInput(key, unwrap=True)

        connection = BlitzGateway(client_obj=client)
        updateService = connection.getUpdateService()
        queryService = connection.getQueryService()

        processedMessages = []

        for plateId in scriptParams["IDs"]:
            plateObj = connection.getObject("Plate", plateId)
            if plateObj is None:
                client.setOutput(
                    "Message",
                    rstring("ERROR: No Plate with ID %s" % plateId))
                return

            if scriptParams["Mode"] == "Add":
                plateAcquisitionObj = PlateAcquisitionI()
                plateAcquisitionObj.setPlate(PlateI(plateObj.getId(), False))

                wellGrid = plateObj.getWellGrid()
                for axis in wellGrid:
                    for wellObj in axis:
                        wellSampleList = wellObj.copyWellSamples()
                        plateAcquisitionObj.addAllWellSampleSet(wellSampleList)

                plateAcquisitionObj = updateService.saveAndReturnObject(
                    plateAcquisitionObj)
                plateAcquisitionId = plateAcquisitionObj.getId()._val

                processedMessages.append(
                    "Linked new PlateAcquisition with ID %d"
                    " to Plate with ID %d." % (plateAcquisitionId, plateId))
            else:
                params = ParametersI()
                params.addId(plateId)

                queryString = """
                    FROM PlateAcquisition AS pa
                    LEFT JOIN FETCH pa.wellSample
                    LEFT OUTER JOIN FETCH pa.annotationLinks
                        WHERE pa.plate.id = :id
                    """
                plateAcquisitionList = queryService.findAllByQuery(
                    queryString, params, connection.SERVICE_OPTS)
                if plateAcquisitionList:
                    updateList = []

                    for plate_acquisition in plateAcquisitionList:
                        for well_sample in plate_acquisition.copyWellSample():
                            well_sample.setPlateAcquisition(None)
                            updateList.append(well_sample)

                        updateService.saveArray(updateList)

                        plate_acquisition.clearWellSample()
                        plate_acquisition.clearAnnotationLinks()

                        plate_acquisition = updateService.saveAndReturnObject(
                            plate_acquisition)
                        updateService.deleteObject(plate_acquisition)

                processedMessages.append(
                    "%d PlateAcquisition(s) removed from Plate with ID %d." %
                    (len(plateAcquisitionList), plateId))

        client.setOutput("Message", rstring("No errors. %s" %
#.........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 getQueryService [as 别名]
HOST = config.get('OMERODetails', 'host')
PORT = config.getint('OMERODetails', 'port')
USERNAME = config.get('OMERODetails', 'username')
PASSWORD = config.get('OMERODetails', 'password')

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = conn.connect()

if not connected:
    import sys
    sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
    sys.exit(1)

session = conn.getSession()
queryService = conn.getQueryService()
params = Parameters()
ldapSearch = LDAPSearch(ldap_details)

# Check users
query = "from Experimenter"
experimenters = queryService.findAllByQuery(query, params)
print('Experimenters')

for experimenter in experimenters:

	output = '%s' %experimenter.omeName.getValue()
	if experimenter.email and experimenter.email.getValue().strip() != '':
		output = output + ', %s ' %experimenter.email.getValue()

	if len(ldapSearch.userSearch(experimenter.omeName.getValue())) == 1: