Python builder.get_logger函数代码示例

        def deco(*a, **b):
            try:

                return func(*a, **b)

            except common.NotAllowed as ex:
                log = get_logger(_LOGGER_NAME)
                log.error(str(ex))

                if redirect:
                    common.set_error_message(str(ex))
                    raise cherrypy.HTTPRedirect(ex.redirect_url)
                else:
                    raise cherrypy.HTTPError(ex.status, str(ex))

            except cherrypy.HTTPRedirect as ex:
                if redirect:
                    raise
                else:
                    log = get_logger(_LOGGER_NAME)
                    log.warn('Redirect converted to error: ' + str(ex))
                    # should we do this? Are browsers following redirects in ajax?
                    raise cherrypy.HTTPError(500, str(ex))

            except Exception:
                log = get_logger(_LOGGER_NAME)
                log.exception('An unexpected exception appeared')

                if redirect:
                    # set a default error message if one has not been set already
                    if not common.has_error_message():
                        common.set_error_message("An unexpected exception appeared. Please check the log files.")
                    raise cherrypy.HTTPRedirect("/tvb?error=True")
                else:
                    raise

def upgrade(migrate_engine):
    """
    Upgrade operations go here.
    Don't create your own engine; bind migrate_engine to your metadata.
    """
    meta.bind = migrate_engine

    table = meta.tables['DATA_TYPES_GROUPS']
    create_column(COL_RANGES_1, table)
    create_column(COL_RANGES_2, table)

    try:
        ## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
        previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")

        for group in previous_groups:

            operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
            #group.only_numeric_ranges = operation_group.has_only_numeric_ranges

            if operation_group.range3 is not None:
                group.no_of_ranges = 3
            elif operation_group.range2 is not None:
                group.no_of_ranges = 2
            elif operation_group.range1 is not None:
                group.no_of_ranges = 1
            else:
                group.no_of_ranges = 0

            dao.store_entity(group)

    except Exception as excep:
        ## we can live with a column only having default value. We will not stop the startup.
        logger = get_logger(__name__)
        logger.exception(excep)
        
    session = SA_SESSIONMAKER()
    session.execute(text("""UPDATE "OPERATIONS"
                               SET status = 
                                CASE
                                    WHEN status = 'FINISHED' THEN '4-FINISHED'
                                    WHEN status = 'STARTED' THEN '3-STARTED'
                                    WHEN status = 'CANCELED' THEN '2-CANCELED'
                                    ELSE '1-ERROR'
                                END
                             WHERE status IN ('FINISHED', 'CANCELED', 'STARTED', 'ERROR');"""))
    session.commit()
    session.close()

    try:
        session = SA_SESSIONMAKER()
        for sim_state in session.query(SimulationState).filter(SimulationState.fk_datatype_group is not None).all():
            session.delete(sim_state)
        session.commit()
        session.close()
    except Exception as excep:
        ## It might happen that SimulationState table is not yet created, e.g. if user has version 1.0.2
        logger = get_logger(__name__)
        logger.exception(excep)

    def prepare_adapter(adapter_class):
        """
        Having a subclass of ABCAdapter, prepare an instance for launching an operation with it.
        """
        try:
            if not issubclass(adapter_class, ABCAdapter):
                raise IntrospectionException("Invalid data type: It should extend adapters.ABCAdapter!")
            algo_group = dao.find_group(adapter_class.__module__, adapter_class.__name__)

            adapter_instance = adapter_class()
            adapter_instance.algorithm_group = algo_group
            return adapter_instance
        except Exception, excep:
            get_logger("ABCAdapter").exception(excep)
            raise IntrospectionException(str(excep))

    def __init__(self):
        self.logger = get_logger(self.__class__.__module__)

        self.user_service = UserService()
        self.flow_service = FlowService()

        analyze_category = self.flow_service.get_launchable_non_viewers()
        self.analyze_category_link = '/flow/step/' + str(analyze_category.id)
        self.analyze_adapters = None

        self.connectivity_tab_link = '/flow/step_connectivity'
        view_category = self.flow_service.get_visualisers_category()
        conn_id = self.flow_service.get_algorithm_by_module_and_class(CONNECTIVITY_MODULE, CONNECTIVITY_CLASS)[1].id
        connectivity_link = self.get_url_adapter(view_category.id, conn_id)

        self.connectivity_submenu = [dict(title="Large Scale Connectivity", subsection="connectivity",
                                          description="View Connectivity Regions. Perform Connectivity lesions",
                                          link=connectivity_link),
                                     dict(title="Local Connectivity", subsection="local",
                                          link='/spatial/localconnectivity/step_1/1',
                                          description="Create or view existent Local Connectivity entities.")]
        self.burst_submenu = [dict(link='/burst', subsection='burst',
                                   title='Simulation Cockpit', description='Manage simulations'),
                              dict(link='/burst/dynamic', subsection='dynamic',
                                   title='Phase plane', description='Configure model dynamics')]

    def __init__(self):
        self.logger = get_logger(self.__class__.__module__)

        self.user_service = UserService()
        self.flow_service = FlowService()

        self.analyze_category_link = '/flow/step_analyzers'
        self.analyze_adapters = None

        self.connectivity_tab_link = '/flow/step_connectivity'
        view_category = self.flow_service.get_visualisers_category()
        conn_id = self.flow_service.get_algorithm_by_module_and_class(CONNECTIVITY_MODULE, CONNECTIVITY_CLASS).id
        connectivity_link = self.get_url_adapter(view_category.id, conn_id)

        self.connectivity_submenu = [dict(title="Large Scale Connectivity", link=connectivity_link,
                                          subsection=WebStructure.SUB_SECTION_CONNECTIVITY,
                                          description="View Connectivity Regions. Perform Connectivity lesions"),
                                     dict(title="Local Connectivity", link='/spatial/localconnectivity/step_1/1',
                                          subsection=WebStructure.SUB_SECTION_LOCAL_CONNECTIVITY,
                                          description="Create or view existent Local Connectivity entities.")]

        allen_algo = self.flow_service.get_algorithm_by_module_and_class(ALLEN_CREATOR_MODULE, ALLEN_CREATOR_CLASS)
        if allen_algo:
            # Only add the Allen Creator if AllenSDK is installed
            allen_link = self.get_url_adapter(allen_algo.fk_category, allen_algo.id)
            self.connectivity_submenu.append(dict(title="Allen Connectome Downloader", link=allen_link,
                                                  subsection=WebStructure.SUB_SECTION_ALLEN,
                                                  description="Download a mouse connectivity from Allen dataset"))

        self.burst_submenu = [dict(link='/burst', subsection=WebStructure.SUB_SECTION_BURST,
                                   title='Simulation Cockpit', description='Manage simulations'),
                              dict(link='/burst/dynamic', subsection='dynamic',
                                   title='Phase plane', description='Configure model dynamics')]

 def __init__(self, conf):
     """
     :param conf: burst configuration entity
     """
     self.logger = get_logger(__name__)
     self.flow_service = FlowService()
     self.conf = conf

def upgrade(migrate_engine):
    """
    Upgrade operations go here.
    Don't create your own engine; bind migrate_engine to your metadata.
    """
    try:
        meta.bind = migrate_engine
        table1 = meta.tables['MAPPED_SURFACE_DATA']

        create_column(COL_1, table1)
        create_column(COL_2, table1)
        create_column(COL_3, table1)

        try:
            session = SA_SESSIONMAKER()
            session.execute(text("UPDATE \"DATA_TYPES\" SET invalid=1 WHERE exists "
                                 "(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE  _number_of_split_slices > 1 "
                                 "and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
            session.commit()
            session.close()
        except ProgrammingError:
            # PostgreSQL
            session = SA_SESSIONMAKER()
            session.execute(text("UPDATE \"DATA_TYPES\" SET invalid=TRUE WHERE exists "
                                 "(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE  _number_of_split_slices > 1 "
                                 "and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
            session.commit()
            session.close()

    except Exception:
        logger = get_logger(__name__)
        logger.exception("Cold not create new column required by the update")
        raise

    def __init__(self, obj_file):
        """
        Create a surface from an obj file
        """
        self.logger = get_logger(__name__)

        try:
            obj = ObjParser()
            obj.read(obj_file)

            self.triangles = []
            self.vertices = obj.vertices
            self.normals = [(0.0, 0.0, 0.0)] * len(self.vertices)
            self.have_normals = len(obj.normals)

            for face in obj.faces:
                triangles = self._triangulate(face)
                for v_idx, t_idx, n_idx in triangles:
                    self.triangles.append(v_idx)
                    if n_idx != -1:
                        # last normal index wins
                        # alternative: self.normals[v_idx] += obj.normals[n_idx]
                        # The correct behaviour is to duplicate the vertex
                        # self.vertices.append(self.vertices[v_idx])
                        # self.tex_coords.append(self.tex_coords[v_idx])
                        self.normals[v_idx] = obj.normals[n_idx]
            # checks
            if not self.vertices or not self.triangles:
                raise ParseException("No geometry data in file.")
            self._to_numpy()
        except ValueError as ex:
            self.logger.exception(" Error in obj")
            raise ParseException(str(ex))

    def __init__(self, tvb_root_folder, dist_folder, library_path):
        """
        Creates a new instance.
        :param tvb_root_folder: root tvb folder.  
        :param dist_folder: folder where distribution is built.  
        :param library_path: folder where TVB code is put into final distribution.  
        """
        self.logger = get_logger(self.__class__.__name__)
        self._dist_folder = dist_folder
        self._tvb_root_folder = tvb_root_folder
        self._manuals_folder = os.path.join(tvb_root_folder, self.DOCS_SRC, self.MANUALS)
        self._styles_folder = os.path.join(self._manuals_folder, self.STYLES)

        # Folders where to store results
        self._dist_docs_folder = os.path.join(self._dist_folder, self.DOCS)
        self._dist_api_folder = os.path.join(self._dist_folder, self.API)
        self._dist_online_help_folder = os.path.join(library_path, self.ONLINE_HELP)
        self._dist_styles_folder = os.path.join(self._dist_online_help_folder, self.STYLES)

        # Check if folders exist. If not create them 
        if not os.path.exists(self._dist_docs_folder):
            os.makedirs(self._dist_docs_folder)
        if os.path.exists(self._dist_online_help_folder):
            shutil.rmtree(self._dist_online_help_folder)
        if not os.path.exists(self._dist_api_folder):
            os.makedirs(self._dist_api_folder)
        os.makedirs(self._dist_online_help_folder)

    def launch(self, data_file, apply_corrections=False, mappings_file=None, connectivity=None):
        """
        Execute import operations:
        """
        self.data_file = data_file

        try:
            self.parser = NIFTIParser(data_file)

            volume = self._create_volume()

            if connectivity:
                rm = self._create_region_map(volume, connectivity, apply_corrections, mappings_file)
                return [volume, rm]

            if self.parser.has_time_dimension:
                time_series = self._create_time_series(volume)
                return [volume, time_series]

            # no connectivity and no time
            mri = self._create_mri(volume)
            return [volume, mri]

        except ParseException as excep:
            logger = get_logger(__name__)
            logger.exception(excep)
            raise LaunchException(excep)

    def __init__(self, data_file):

        self.logger = get_logger(__name__)

        if data_file is None:
            raise ParseException("Please select NIFTI file which contains data to import")

        if not os.path.exists(data_file):
            raise ParseException("Provided file %s does not exists" % data_file)

        try:
            self.nifti_image = nib.load(data_file)
        except nib.spatialimages.ImageFileError as e:
            self.logger.exception(e)
            msg = "File: %s does not have a valid NIFTI-1 format." % data_file
            raise ParseException(msg)

        nifti_image_hdr = self.nifti_image.get_header()

        # Check if there is a time dimensions (4th dimension).
        nifti_data_shape = nifti_image_hdr.get_data_shape()
        self.has_time_dimension = len(nifti_data_shape) > 3
        self.time_dim_size = nifti_data_shape[3] if self.has_time_dimension else 1

        # Extract sample unit measure
        self.units = nifti_image_hdr.get_xyzt_units()

        # Usually zooms defines values for x, y, z, time and other dimensions
        self.zooms = nifti_image_hdr.get_zooms()

def do_operation_launch(operation_id):
    """
    Event attached to the local queue for executing an operation, when we will have resources available.
    """
    LOGGER = get_logger('tvb.core.operation_async_launcher')

    try:
        LOGGER.debug("Loading operation with id=%s" % operation_id)
        curent_operation = dao.get_operation_by_id(operation_id)
        stored_adapter = curent_operation.algorithm
        LOGGER.debug("Importing Algorithm: " + str(stored_adapter.classname) +
                     " for Operation:" + str(curent_operation.id))
        PARAMS = parse_json_parameters(curent_operation.parameters)
        adapter_instance = ABCAdapter.build_adapter(stored_adapter)

        ## Un-comment bellow for profiling an operation:
        ## import cherrypy.lib.profiler as profiler
        ## p = profiler.Profiler("/Users/lia.domide/TVB/profiler/")
        ## p.run(OperationService().initiate_prelaunch, curent_operation, adapter_instance, {}, **PARAMS)

        OperationService().initiate_prelaunch(curent_operation, adapter_instance, {}, **PARAMS)
        LOGGER.debug("Successfully finished operation " + str(operation_id))

    except Exception as excep:
        LOGGER.error("Could not execute operation " + str(sys.argv[1]))
        LOGGER.exception(excep)
        parent_burst = dao.get_burst_for_operation_id(operation_id)
        if parent_burst is not None:
            WorkflowService().mark_burst_finished(parent_burst, error_message=str(excep))

def get_matlab_executable():
    """
    Check If MATLAB is installed on current system.
    Return True or False.
    Return True, when MATLAB executable is found in Path.
    """
    matlab_exe_path = None
    if sys.platform.startswith('win'):
        split_char = ";"
        octave_exec = OCTAVE + ".exe"
        matlab_exec = MATLAB + ".exe"
    else:
        split_char = ":"
        octave_exec = OCTAVE
        matlab_exec = MATLAB
    logger = get_logger(__name__)
    logger.debug("Searching Matlab in path: " + str(os.environ["PATH"]))
    for path in os.environ["PATH"].split(split_char):
        if os.path.isfile(os.path.join(path, matlab_exec)):
            matlab_exe_path = os.path.join(path, matlab_exec)
            logger.debug("MATLAB was found:" + path)
            return matlab_exe_path
    for path in os.environ["PATH"].split(split_char):
        if os.path.isfile(os.path.join(path, octave_exec)):
            logger.debug("OCTAVE was found:" + path)
            matlab_exe_path = os.path.join(path, octave_exec)
            return matlab_exe_path
    return matlab_exe_path

def upgrade(migrate_engine):
    """
    Upgrade operations go here.
    Don't create your own engine; bind migrate_engine to your metadata.
    """
    meta.bind = migrate_engine

    table = meta.tables['DATA_TYPES_GROUPS']
    create_column(COL_RANGES_1, table)
    create_column(COL_RANGES_2, table)

    try:
        ## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
        previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")

        for group in previous_groups:

            operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
            #group.only_numeric_ranges = operation_group.has_only_numeric_ranges

            if operation_group.range3 is not None:
                group.no_of_ranges = 3
            elif operation_group.range2 is not None:
                group.no_of_ranges = 2
            elif operation_group.range1 is not None:
                group.no_of_ranges = 1
            else:
                group.no_of_ranges = 0

            dao.store_entity(group)

    except Exception, excep:
        ## we can live with a column only having default value. We will not stop the startup.
        logger = get_logger(__name__)
        logger.exception(excep)

def get_logger(name):
    try:
        from tvb.basic.logger.builder import get_logger
        return get_logger(__name__)
    except ImportError:
        import logging
        return logging.getLogger(name)