def _fake_restart_services(self, should_reset):
     """
     This function will replace the SettingsController._restart_service method,
     to avoid problems in tests due to restart.
     """
     self.was_reset = should_reset
     TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)

    def test_read_stored_settings(self):
        """
        Test to see that keys from the configuration dict is updated with
        the value from the configuration file after store.
        """
        initial_configurations = self.settings_service.configurable_keys
        to_store_data = {key: value['value'] for key, value in initial_configurations.iteritems()}
        for key, value in self.TEST_SETTINGS.iteritems():
            to_store_data[key] = value

        is_changed, shoud_reset = self.settings_service.save_settings(**to_store_data)
        assert shoud_reset and is_changed

        # enforce keys to get repopulated:
        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)
        self.settings_service = SettingsService()

        updated_configurations = self.settings_service.configurable_keys
        for key, value in updated_configurations.iteritems():
            if key in self.TEST_SETTINGS:
                assert self.TEST_SETTINGS[key] == value['value']
            elif key == SettingsService.KEY_ADMIN_PWD:
                assert TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD == value['value']
                assert TvbProfile.current.web.admin.ADMINISTRATOR_BLANK_PWD == initial_configurations[key]['value']
            else:
                assert initial_configurations[key]['value'] == value['value']

def setup_test_env():

    from tvb.basic.profile import TvbProfile
    if len(sys.argv) > 1:
        profile = sys.argv[1]
    else:
        profile = TvbProfile.TEST_SQLITE_PROFILE
    TvbProfile.set_profile(profile)

    def teardown_method(self):
        """
        Restore configuration file
        """
        if os.path.exists(TEST_CONFIG_FILE):
            os.remove(TEST_CONFIG_FILE)

        TvbProfile.current.__class__.TVB_CONFIG_FILE = self.old_config_file
        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)

    def cleanup(self):
        """
        Have a different name than transactional_teardown_method so we can use it safely in transactions and it will
        not be called after running actual test.
        Using transactional_teardown_method here won't WORK!! See TransactionalTest
        """
        if os.path.exists(TvbProfile.current.TVB_CONFIG_FILE):
            os.remove(TvbProfile.current.TVB_CONFIG_FILE)

        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)

    def setup_method(self):
        """
        Prepare the usage of a different config file for this class only.
        """
        if os.path.exists(TEST_CONFIG_FILE):
            os.remove(TEST_CONFIG_FILE)

        self.old_config_file = TvbProfile.current.TVB_CONFIG_FILE
        TvbProfile.current.__class__.TVB_CONFIG_FILE = TEST_CONFIG_FILE
        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)
        self.settings_service = SettingsService()

 def settings(self, save_settings=False, **data):
     """Main settings page submit and get"""
     template_specification = dict(mainContent="../settings/system_settings", title="System Settings")
     if save_settings:
         try:
             form = SettingsForm()
             data = form.to_python(data)
             isrestart, isreset = self.settingsservice.save_settings(**data)
             if isrestart:
                 thread = threading.Thread(target=self._restart_services, kwargs={'should_reset': isreset})
                 thread.start()
                 common.add2session(common.KEY_IS_RESTART, True)
                 common.set_important_message('Please wait until TVB is restarted properly!')
                 raise cherrypy.HTTPRedirect('/tvb')
             # Here we will leave the same settings page to be displayed.
             # It will continue reloading when CherryPy restarts.
         except formencode.Invalid as excep:
             template_specification[common.KEY_ERRORS] = excep.unpack_errors()
         except InvalidSettingsException as excep:
             self.logger.error('Invalid settings!  Exception %s was raised' % (str(excep)))
             common.set_error_message(excep.message)
     template_specification.update({'keys_order': self.settingsservice.KEYS_DISPLAY_ORDER,
                                    'config_data': self.settingsservice.configurable_keys,
                                    common.KEY_FIRST_RUN: TvbProfile.is_first_run()})
     return self.fill_default_attributes(template_specification)

def init_test_env():
    """
    This method prepares all necessary data for tests execution
    """
    # Set a default test profile, for when running tests from dev-env.
    if TvbProfile.CURRENT_PROFILE_NAME is None:
        TvbProfile.set_profile(TvbProfile.TEST_SQLITE_PROFILE)
        print "Not expected to happen except from PyCharm: setting profile", TvbProfile.CURRENT_PROFILE_NAME
        db_file = TvbProfile.current.db.DB_URL.replace("sqlite:///", "")
        if os.path.exists(db_file):
            os.remove(db_file)

    from tvb.core.entities.model_manager import reset_database
    from tvb.core.services.initializer import initialize

    reset_database()
    initialize(["tvb.config", "tvb.tests.framework"], skip_import=True)

def initialize(introspected_modules, load_xml_events=True):
    """
    Initialize when Application is starting.
    Check for new algorithms or new DataTypes.
    """
    SettingsService().check_db_url(TvbProfile.current.db.DB_URL)
    
    ## Initialize DB
    is_db_empty = initialize_startup()
    
    ## Create Projects storage root in case it does not exist.
    initialize_storage()
    
    ## Populate DB algorithms, by introspection
    event_folders = []
    start_introspection_time = datetime.datetime.now()
    for module in introspected_modules:
        introspector = Introspector(module)
        # Introspection is always done, even if DB was not empty.
        introspector.introspect(True)
        event_path = introspector.get_events_path()
        if event_path:
            event_folders.append(event_path)

    # Now remove or mark as removed any unverified Algo-Group, Algo-Category or Portlet
    to_invalidate, to_remove = dao.get_non_validated_entities(start_introspection_time)
    for entity in to_invalidate:
        entity.removed = True
    dao.store_entities(to_invalidate)
    for entity in to_remove:
        dao.remove_entity(entity.__class__, entity.id)
   
    ## Populate events
    if load_xml_events:
        read_events(event_folders)

    if not TvbProfile.is_first_run():
        ## Create default users.
        if is_db_empty:
            dao.store_entity(model.User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True, None))
            UserService().create_user(username=TvbProfile.current.web.admin.ADMINISTRATOR_NAME,
                                      password=TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD,
                                      email=TvbProfile.current.web.admin.ADMINISTRATOR_EMAIL,
                                      role=model.ROLE_ADMINISTRATOR)
        
        ## In case actions related to latest code-changes are needed, make sure they are executed.
        CodeUpdateManager().run_all_updates()

        ## In case the H5 version changed, run updates on all DataTypes
        if TvbProfile.current.version.DATA_CHECKED_TO_VERSION < TvbProfile.current.version.DATA_VERSION:
            thread = threading.Thread(target=FilesUpdateManager().run_all_updates)
            thread.start()

        ## Clean tvb-first-time-run temporary folder, as we are no longer at the first run:
        shutil.rmtree(TvbProfile.current.FIRST_RUN_STORAGE, True)

def setup():

    if sys.platform != 'darwin':
        unsupport_module('h5py')

    import logging
    logging.basicConfig(level=logging.DEBUG, stream=sys.stdout)

    from tvb.basic.profile import TvbProfile
    TvbProfile.set_profile(TvbProfile.MATLAB_PROFILE)

    # MATLAB states the module doesn't exist if not importable and provides no traceback
    # to diagnose the import error, so we'll need to workaround this in the future. For now,
    # just try to import the simlab and report if it worked or not.
    try:
        import tvb.simulator.lab
        print('TVB modules available.')
    except Exception as exc:
        #print 'failed to import all TVB modules, not all functionality may be .'
        pass

    def test_update_settings(self):
        """
        Test update of settings: correct flags should be returned, and check storage folder renamed
        """
        # 1. save on empty config-file:
        to_store_data = {key: value['value'] for key, value in self.settings_service.configurable_keys.iteritems()}
        for key, value in self.TEST_SETTINGS.iteritems():
            to_store_data[key] = value

        is_changed, shoud_reset = self.settings_service.save_settings(**to_store_data)
        assert shoud_reset and is_changed

        # 2. Reload and save with the same values (is_changed expected to be False)
        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)
        self.settings_service = SettingsService()
        to_store_data = {key: value['value'] for key, value in self.settings_service.configurable_keys.iteritems()}

        is_changed, shoud_reset = self.settings_service.save_settings(**to_store_data)
        assert not is_changed
        assert not shoud_reset

        # 3. Reload and check that changing TVB_STORAGE is done correctly
        TvbProfile._build_profile_class(TvbProfile.CURRENT_PROFILE_NAME)
        self.settings_service = SettingsService()
        to_store_data = {key: value['value'] for key, value in self.settings_service.configurable_keys.iteritems()}
        to_store_data[SettingsService.KEY_STORAGE] = os.path.join(TvbProfile.current.TVB_STORAGE, 'RENAMED')

        # Write a test-file and check that it is moved
        file_writer = open(os.path.join(TvbProfile.current.TVB_STORAGE, "test_rename-xxx43"), 'w')
        file_writer.write('test-content')
        file_writer.close()

        is_changed, shoud_reset = self.settings_service.save_settings(**to_store_data)
        assert is_changed
        assert not shoud_reset
        # Check that the file was correctly moved:
        data = open(os.path.join(TvbProfile.current.TVB_STORAGE, 'RENAMED', "test_rename-xxx43"), 'r').read()
        assert data == 'test-content'

        shutil.rmtree(os.path.join(TvbProfile.current.TVB_STORAGE, 'RENAMED'))
        os.remove(os.path.join(TvbProfile.current.TVB_STORAGE, "test_rename-xxx43"))

    def test_first_run_save(self):
        """
        Check that before setting something, all flags are pointing towards empty.
        After storing some configurations, check that flags are changed.
        """
        initial_configurations = self.settings_service.configurable_keys
        first_run = TvbProfile.is_first_run()
        assert first_run, "Invalid First_Run flag!!"
        assert not os.path.exists(TEST_CONFIG_FILE)
        assert len(TvbProfile.current.manager.stored_settings) == 0

        to_store_data = {key: value['value'] for key, value in initial_configurations.iteritems()}
        for key, value in self.TEST_SETTINGS.iteritems():
            to_store_data[key] = value
        _, shoud_reset = self.settings_service.save_settings(**to_store_data)

        assert shoud_reset
        first_run = TvbProfile.is_first_run()
        assert not first_run, "Invalid First_Run flag!!"
        assert os.path.exists(TEST_CONFIG_FILE)
        assert not len(TvbProfile.current.manager.stored_settings) == 0

    def __init__(self):
        self.logger = get_logger(__name__)
        first_run = TvbProfile.is_first_run()
        storage = TvbProfile.current.TVB_STORAGE if not first_run else TvbProfile.current.DEFAULT_STORAGE
        self.configurable_keys = {
            self.KEY_STORAGE: {'label': 'Root folder for all projects', 'value': storage,
                               'readonly': not first_run, 'type': 'text'},
            self.KEY_MAX_DISK_SPACE_USR: {'label': 'Max hard disk space per user (MBytes)',
                                          'value': TvbProfile.current.MAX_DISK_SPACE / 2 ** 10, 'type': 'text'},
            self.KEY_MATLAB_EXECUTABLE: {'label': 'Optional Matlab or Octave path', 'type': 'text',
                                         'value': TvbProfile.current.MATLAB_EXECUTABLE or get_matlab_executable() or '',
                                         'description': 'Some analyzers will not be available when '
                                                        'matlab/octave are not found'},
            self.KEY_SELECTED_DB: {'label': 'Select one DB engine', 'value': TvbProfile.current.db.SELECTED_DB,
                                   'type': 'select', 'readonly': not first_run,
                                   'options': TvbProfile.current.db.ACEEPTED_DBS},
            self.KEY_DB_URL: {'label': "DB connection URL",
                              'value': TvbProfile.current.db.ACEEPTED_DBS[TvbProfile.current.db.SELECTED_DB],
                              'type': 'text', 'readonly': TvbProfile.current.db.SELECTED_DB == 'sqlite'},

            self.KEY_PORT: {'label': 'Port to run Cherrypy on',
                            'value': TvbProfile.current.web.SERVER_PORT, 'dtype': 'primitive', 'type': 'text'},
            self.KEY_PORT_MPLH5: {'label': 'Port to run Matplotlib on', 'type': 'text', 'dtype': 'primitive',
                                  'value': TvbProfile.current.web.MPLH5_SERVER_PORT},
            self.KEY_URL_WEB: {'label': 'URL for accessing web',
                               'value': TvbProfile.current.web.BASE_URL, 'type': 'text', 'dtype': 'primitive'},
            self.KEY_URL_MPLH5: {'label': 'URL for accessing MPLH5 visualizers', 'type': 'text',
                                 'value': TvbProfile.current.web.MPLH5_SERVER_URL, 'dtype': 'primitive'},

            self.KEY_MAX_NR_THREADS: {'label': 'Maximum no. of threads for local installations', 'type': 'text',
                                      'value': TvbProfile.current.MAX_THREADS_NUMBER, 'dtype': 'primitive'},
            self.KEY_MAX_RANGE: {'label': 'Maximum no. of operations in one PSE',
                                 'description': "Parameters Space Exploration (PSE) maximum number of operations",
                                 'value': TvbProfile.current.MAX_RANGE_NUMBER, 'type': 'text', 'dtype': 'primitive'},
            self.KEY_MAX_NR_SURFACE_VERTEX: {'label': 'Maximum no. of vertices in a surface',
                                             'type': 'text', 'dtype': 'primitive',
                                             'value': TvbProfile.current.MAX_SURFACE_VERTICES_NUMBER},
            self.KEY_CLUSTER: {'label': 'Deploy on cluster', 'value': TvbProfile.current.cluster.IS_DEPLOY,
                               'description': 'Check this only if on the web-server machine OARSUB command is enabled.',
                               'dtype': 'primitive', 'type': 'boolean'},
            self.KEY_ADMIN_NAME: {'label': 'Administrator User Name',
                                  'value': TvbProfile.current.web.admin.ADMINISTRATOR_NAME,
                                  'type': 'text', 'readonly': not first_run,
                                  'description': ('Password and Email can be edited after first run, '
                                                  'from the profile page directly.')},
            self.KEY_ADMIN_PWD: {'label': 'Password',
                                 'value': TvbProfile.current.web.admin.ADMINISTRATOR_BLANK_PWD if first_run
                                 else TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD,
                                 'type': 'password', 'readonly': not first_run},
            self.KEY_ADMIN_EMAIL: {'label': 'Administrator Email',
                                   'value': TvbProfile.current.web.admin.ADMINISTRATOR_EMAIL,
                                   'readonly': not first_run, 'type': 'text'}}

def init_test_env():
    """
    This method prepares all necessary data for tests execution
    """
    # Set a default test profile, for when running tests from dev-env.
    if TvbProfile.CURRENT_PROFILE_NAME is None:
        profile = TvbProfile.TEST_SQLITE_PROFILE
        if len(sys.argv) > 1:
            for i in range(1,len(sys.argv)-1):
                if "--profile=" in sys.argv[i]:
                    profile = sys.argv[i].split("=")[1]
        TvbProfile.set_profile(profile)
        print("Not expected to happen except from PyCharm: setting profile", TvbProfile.CURRENT_PROFILE_NAME)
        db_file = TvbProfile.current.db.DB_URL.replace('sqlite:///', '')
        if os.path.exists(db_file):
            os.remove(db_file)

    from tvb.core.entities.model_manager import reset_database
    from tvb.core.services.initializer import initialize

    reset_database()
    initialize(["tvb.config", "tvb.tests.framework"], skip_import=True)

    def run_all_updates(self):
        """
        Upgrade the code to current version. 
        Go through all update scripts with lower SVN version than the current running version.
        """
        if TvbProfile.is_first_run():
            ## We've just started with a clean TVB. No need to upgrade anything.
            return

        super(CodeUpdateManager, self).run_all_updates()

        if self.checked_version < self.current_version:
            TvbProfile.current.manager.add_entries_to_config_file(
                {stored.KEY_LAST_CHECKED_CODE_VERSION: TvbProfile.current.version.SVN_VERSION})

#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
This is intended to be a Benchmarking  and Validator script.

.. moduleauthor:: bogdan.neacsa
"""

if __name__ == '__main__':
    from tvb.basic.profile import TvbProfile
    TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE)

import sys
from time import sleep
from tvb.config import SIMULATOR_MODULE, SIMULATOR_CLASS
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.services.flow_service import FlowService
from tvb.core.services.operation_service import OperationService
from tvb.core.entities.storage import dao
from tvb.core.entities.model import STATUS_STARTED, STATUS_FINISHED, STATUS_ERROR, PARAM_RANGE_PREFIX

KEY_PROJECT = 'project'



class ModelValidator(object):

    def setUp(self):

        self.init(with_data=False)
        self.settings_c = SettingsController()
        self.assertTrue(TvbProfile.is_first_run())

4 is the operation id stored in the DataBase in the table "OPERATIONS"
It gets the algorithm, and the adapter with its parameters from database.
And finally launches the computation.
The results of the computation will be stored by the adapter itself.

.. moduleauthor:: Bogdan Neacsa <[email protected]>
.. moduleauthor:: Lia Domide <[email protected]>
.. moduleauthor:: Yann Gordon <[email protected]>

"""

## Make sure selected profile is propagated when launching an operation.
import sys
from tvb.basic.profile import TvbProfile as tvb_profile

tvb_profile.set_profile(sys.argv)

### Overwrite PostgreSQL number of connections when executed in the context of a node
from tvb.basic.config.settings import TVBSettings

TVBSettings.MAX_DB_CONNECTIONS = TVBSettings.MAX_DB_ASYNC_CONNECTIONS
TVBSettings.OPERATION_EXECUTION_PROCESS = True

import matplotlib
from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.entities.storage import dao
from tvb.core.utils import parse_json_parameters
from tvb.core.traits import db_events
from tvb.core.services.operation_service import OperationService
from tvb.core.services.workflow_service import WorkflowService

import sys
import ctypes
mex = ctypes.CDLL('libmex')

class mexOut(object):
    def write(self, s):
        mex.mexPrintf(s)
    def flush(self):
        mex.mexEvalString('drawnow;')

mex_out = mexOut()
if False:
    sys.stdout = sys.stderr = mexOut()
    print 'Python stdout/err -> mexPrintf enabled.'

import logging
logging.basicConfig(level=logging.DEBUG, stream=mex_out)
LOG = logging.getLogger('helpers')
LOG.info('ready')
from tvb.basic.profile import TvbProfile
TvbProfile.set_profile(TvbProfile.MATLAB_PROFILE)

                if isrestart:
                    thread = threading.Thread(target=self._restart_services, kwargs={'should_reset': isreset})
                    thread.start()
                    common.add2session(common.KEY_IS_RESTART, True)
                    common.set_important_message('Please wait until TVB is restarted properly!')
                    raise cherrypy.HTTPRedirect('/tvb')
                # Here we will leave the same settings page to be displayed.
                # It will continue reloading when CherryPy restarts.
            except formencode.Invalid, excep:
                template_specification[common.KEY_ERRORS] = excep.unpack_errors()
            except InvalidSettingsException, excep:
                self.logger.error('Invalid settings!  Exception %s was raised' % (str(excep)))
                common.set_error_message(excep.message)
        template_specification.update({'keys_order': self.settingsservice.KEYS_DISPLAY_ORDER,
                                       'config_data': self.settingsservice.configurable_keys,
                                       common.KEY_FIRST_RUN: TvbProfile.is_first_run()})
        return self.fill_default_attributes(template_specification)


    def _restart_services(self, should_reset):
        """
        Restart CherryPy and Backend.
        """
        mplh5 = TvbProfile.current.web.MPLH5_Server_Thread
        if mplh5 is not None:
            mplh5.shutdown()
            mplh5.server_close()
        else:
            self.logger.warning('For some reason the mplh5 never started.')
        cherrypy.engine.exit()