def find_data(file, instrument='', allow_multiple=False):
    """
        Finds a file path for the specified data set, which can either be:
            - a run number
            - an absolute path
            - a file name
        @param file: file name or part of a file name
        @param instrument: if supplied, FindNeXus will be tried as a last resort
    """
    # First, assume a file name
    file = str(file).strip()

    # If we allow multiple files, users may use ; as a separator,
    # which is incompatible with the FileFinder
    n_files = 1
    if allow_multiple:
        file=file.replace(';',',')
        toks = file.split(',')
        n_files = len(toks)

    instrument = str(instrument)
    file_path = FileFinder.getFullPath(file)
    if os.path.isfile(file_path):
        return file_path

    # Second, assume a run number and pass the instrument name as a hint
    try:
        # FileFinder doesn't like dashes...
        instrument=instrument.replace('-','')
        f = FileFinder.findRuns(instrument+file)
        if os.path.isfile(f[0]):
            if allow_multiple:
                # Mantid returns its own list object type, so make a real list out if it
                if len(f)==n_files:
                    return [i for i in f]
            else:
                return f[0]
    except:
        # FileFinder couldn't make sense of the the supplied information
        pass

    # Third, assume a run number, without instrument name to take care of list of full paths
    try:
        f = FileFinder.findRuns(file)
        if os.path.isfile(f[0]):
            if allow_multiple:
                # Mantid returns its own list object type, so make a real list out if it
                if len(f)==n_files:
                    return [i for i in f]
            else:
                return f[0]
    except:
        # FileFinder couldn't make sense of the the supplied information
        pass

    # If we didn't find anything, raise an exception
    Logger('find_data').error("\n\nCould not find a file for %s: check your reduction parameters\n\n" % str(file))
    raise RuntimeError("Could not find a file for %s" % str(file))

 def test_that_find_runs_accepts_a_list_of_string_and_a_bool(self):
     try:
         runs = FileFinder.findRuns("CNCS7860", useExtsOnly=True)
         FileFinder.findRuns("CNCS7860", [".nxs", ".txt"], useExtsOnly=True)
     except Exception as e:
         if type(e).__name__ == "ArgumentError":
             self.assertFalse(True, "Expected findRuns to accept a list of strings and a bool as input."
                                    " {} error was raised with message {}".format(type(e).__name__, str(e)))
     else:
         # Confirm that it works as above
         self.assertTrue(len(runs) == 1)
         self.assertTrue(os.path.exists(runs[0]))

    def __verifyRequiredFile(self, filename):
        '''Return True if the specified file name is findable by Mantid.'''
        from mantid.api import FileFinder

        # simple way is just getFullPath which never uses archive search
        if os.path.exists(FileFinder.getFullPath(filename)):
            return True

        # try full findRuns which will use archive search if it is turned on
        try:
            candidates = FileFinder.findRuns(filename)
            for item in candidates:
                if os.path.exists(item):
                    return True
        except RuntimeError, e:
            return False

    def setUp(self):
        self._qapp = mock_widget.mockQapp()
        # Store an empty widget to parent all the views, and ensure they are deleted correctly
        self.obj = QtGui.QWidget()
        ConfigService['default.instrument'] = 'MUSR'

        setup_context_for_tests(self)
        self.context.instrument = 'MUSR'
        self.load_file_view = BrowseFileWidgetView(self.obj)
        self.load_run_view = LoadRunWidgetView(self.obj)
        self.load_file_model = BrowseFileWidgetModel(self.loaded_data, self.context)
        self.load_run_model = LoadRunWidgetModel(self.loaded_data, self.context)

        self.view = LoadWidgetView(parent=self.obj, load_file_view=self.load_file_view,
                                   load_run_view=self.load_run_view)
        self.presenter = LoadWidgetPresenter(self.view, LoadWidgetModel(self.loaded_data, self.context))
        self.presenter.set_load_file_widget(BrowseFileWidgetPresenter(self.load_file_view, self.load_file_model))
        self.presenter.set_load_run_widget(LoadRunWidgetPresenter(self.load_run_view, self.load_run_model))

        self.presenter.load_file_widget._view.warning_popup = mock.MagicMock()
        self.presenter.load_run_widget._view.warning_popup = mock.MagicMock()

        self.view.multiple_loading_check.setCheckState(1)
        self.presenter.handle_multiple_files_option_changed()

        self.runs = [15196, 15197]
        self.workspaces = [self.create_fake_workspace(1) for _ in self.runs]
        self.filenames = FileFinder.findRuns('MUSR00015196.nxs, MUSR00015197.nxs')

    def _run(self):
        '''Defines the workflow for the test'''
        self.tolerance = 1e-3
        self.samples = [sample[:-4] for sample in self.samples]

        # Load files into Mantid
        for sample in self.samples:
            LoadNexus(sample, OutputWorkspace=sample)
        LoadNexus(FileFinder.getFullPath(self.resolution), OutputWorkspace=self.resolution)

        _, iqt_ws = TransformToIqt(SampleWorkspace=self.samples[0],
                                   ResolutionWorkspace=self.resolution,
                                   EnergyMin=self.e_min,
                                   EnergyMax=self.e_max,
                                   BinReductionFactor=self.num_bins,
                                   DryRun=False,
                                   NumberOfIterations=200)

        # Test IqtFit Sequential
        iqtfitSeq_ws, params, fit_group = IqtFitSequential(InputWorkspace=iqt_ws, Function=self.func,
                                                           StartX=self.startx, EndX=self.endx,
                                                           SpecMin=0, SpecMax=self.spec_max)

        self.result_names = [iqt_ws.name(),
                             iqtfitSeq_ws[0].name()]

        # Remove workspaces from Mantid
        for sample in self.samples:
            DeleteWorkspace(sample)
        DeleteWorkspace(params)
        DeleteWorkspace(fit_group)
        DeleteWorkspace(self.resolution)

    def getDataFileNames(self, runsetupdict, advsetupdict):
        """ Obtain the data file names (run names + SUFFIX)

        Return: list of files
        """

        runnumbers_str = str(runsetupdict["RunNumber"])
        if runnumbers_str.count(':') > 0:
            runnumbers_str = runnumbers_str.replace(':', '-')
        runnumbers_str = FileFinder.findRuns('{}{}'.format(self.instrument_name, runnumbers_str))
        runnumbers_str = [os.path.split(filename)[-1] for filename in runnumbers_str]

        # create an integer version
        runnumbers = []
        for filename in runnumbers_str:
            for extension in ['_event.nxs', '.nxs.h5']:
                filename = filename.replace(extension, '')
            runnumber = filename.split('_')[-1]
            runnumbers.append(int(runnumber))

        # put together the output
        datafilenames = []
        for (filename, runnumber) in zip(runnumbers_str, runnumbers):
            datafilenames.append((runnumber, filename))

        return datafilenames

def find_sans_file(file_name):
    """
    Finds a SANS file.
    The file can be specified as:
    1. file.ext or  path1 path2 file.ext
    2. run number
    :param file_name: a file name or a run number.
    :return: the full path.
    """
    error_message = "Trying to find the SANS file {0}, but cannot find it. Make sure that "\
                    "the relevant paths are added and the correct instrument is selected."
    try:
        full_path = find_full_file_path(file_name)
        if not full_path and not file_name.endswith('.nxs'):
            full_path = find_full_file_path(file_name + '.nxs')
        if not full_path:
            # TODO: If we only provide a run number for example 98843 for LOQ measurments, but have LARMOR specified as the
            #       Mantid instrument, then the FileFinder will search itself to death. This is a general Mantid issue.
            #       One way to handle this graceful would be a timeout option.
            file_name_as_bytes = str.encode(file_name)
            assert(type(file_name_as_bytes) == bytes)
            runs = FileFinder.findRuns(file_name_as_bytes)
            if runs:
                full_path = runs[0]
    except RuntimeError:
        raise RuntimeError(error_message.format(file_name))

    if not full_path:
        raise RuntimeError(error_message.format(file_name))
    return full_path

    def _create_peaks_workspace(self):
        """Create a dummy peaks workspace"""
        path = FileFinder.getFullPath("IDFs_for_UNIT_TESTING/MINITOPAZ_Definition.xml")
        inst = LoadEmptyInstrument(Filename=path)
        ws = CreatePeaksWorkspace(inst, 0)
        DeleteWorkspace(inst)
        SetUB(ws, 1, 1, 1, 90, 90, 90)

        # Add a bunch of random peaks that happen to fall on the
        # detetor bank defined in the IDF
        center_q = np.array([-5.1302,2.5651,3.71809])
        qs = []
        for i in np.arange(0, 1, 0.1):
            for j in np.arange(-0.5, 0, 0.1):
                q = center_q.copy()
                q[1] += j
                q[2] += i
                qs.append(q)

        # Add the peaks to the PeaksWorkspace with dummy values for intensity,
        # Sigma, and HKL
        for q in qs:
            peak = ws.createPeak(q)
            peak.setIntensity(100)
            peak.setSigmaIntensity(10)
            peak.setHKL(1, 1, 1)
            ws.addPeak(peak)

        return ws

 def _get_workspace(self, file_name):
     full_file_name = FileFinder.findRuns(file_name)[0]
     load_name = "Load"
     load_options = {"Filename": full_file_name,
                     "OutputWorkspace": EMPTY_NAME}
     load_alg = create_unmanaged_algorithm(load_name, **load_options)
     load_alg.execute()
     return load_alg.getProperty("OutputWorkspace").value

 def cleanup(self):
     Files = ["TOPAZ_3132.hkl",
     "TOPAZ_3132FFT.hkl"]
     for file in Files:
         absfile = FileFinder.getFullPath(file)
         if os.path.exists(absfile):
             os.remove(absfile)
     return True

def do_cleanup():
    Files = ["BioSANS_test_data_reduction.log",
             "BioSANS_test_data_Iq.xml",
             "BioSANS_test_data_Iq.txt",
             "BioSANS_test_data_Iqxy.dat"]
    for filename in Files:
        absfile = FileFinder.getFullPath(filename)
        if os.path.exists(absfile):
            os.remove(absfile)
    return True

def do_cleanup():
    Files = ["PG3_9829.gsa",
    "PG3_9829.py",
    "PG3_9830.gsa",
    "PG3_9830.py"]
    for file in Files:
        absfile = FileFinder.getFullPath(file)
        if os.path.exists(absfile):
            os.remove(absfile)
    return True

    def test_browse_clicked_suceeds_if_table_in_ADS(self):
        filename = FileFinder.findRuns('MUSR00015196.nxs')[0]
        self.view.show_file_browser_and_return_selection = mock.MagicMock(return_value=[filename])
        self.model.check_dead_time_file_selection = mock.MagicMock(return_value=True)

        self.view.dead_time_browse_button.clicked.emit(True)

        self.assertEqual(self.view.dead_time_selector.currentIndex(), 2)
        self.view.warning_popup.assert_not_called()
        self.assertEqual(self.view.dead_time_file_selector.currentText(), 'MUSR00015196_deadTimes')
        self.gui_variable_observer.update.assert_called_once_with(self.gui_context.gui_variables_notifier, None)

    def runTest(self):
        UseCompatibilityMode()
        SANS2D()
        Set1D()
        Detector("rear-detector")
        MaskFile('MASKSANS2Doptions.091A')
        Gravity(True)

        csv_file = FileFinder.getFullPath('SANS2D_periodTests.csv')

        BatchReduce(csv_file, 'nxs', plotresults=False, saveAlgs={'SaveCanSAS1D': 'xml', 'SaveNexus': 'nxs'})
        os.remove(os.path.join(config['defaultsave.directory'], '5512p7_SANS2DBatch.xml'))

    def runTest(self):
        UseCompatibilityMode()
        SANS2D()
        Set1D()
        Detector("rear-detector")
        MaskFile('MASKSANS2Doptions.091A')
        Gravity(True)

        csv_file = FileFinder.getFullPath('SANS2D_multiPeriodTests.csv')

        BatchReduce(csv_file, 'nxs', saveAlgs={})
        self.reduced = '5512_SANS2DBatch'

    def __init__(self):
        ISISIndirectInelasticConvFit.__init__(self)
        self.sample = 'osi97935_graphite002_red.nxs'
        self.resolution = FileFinder.getFullPath('osi97935_graphite002_res.nxs')
        #ConvFit fit function
        self.func = 'name=LinearBackground,A0=0,A1=0;(composite=Convolution,FixResolution=true,NumDeriv=true;'\
                    'name=Resolution,Workspace=\"%s\";name=Lorentzian,Amplitude=2,PeakCentre=0,FWHM=0.05)' % self.resolution
        self.startx = -0.2
        self.endx = 0.2
        self.bg = 'Fit Linear'
        self.spectra_min = 0
        self.spectra_max = 41
        self.ties = False

        self.result_names = ['osi97935_graphite002_conv_1LFitL_s0_to_41_Result']

def do_cleanup():
    Files = ["PG3_9829.getn",
             "PG3_9829.gsa",
             "PG3_9829.py",
             'sum_PG3_9829.gsa',
             'sum_PG3_9829.py',
             "PG3_9830.gsa",
             "PG3_9830.py",
             "PG3_4844-1.dat",
             "PG3_4844.getn",
             "PG3_4844.gsa",
             "PG3_4844.py",
             "PG3_4866.gsa"]
    for filename in Files:
        absfile = FileFinder.getFullPath(filename)
        if os.path.exists(absfile):
            os.remove(absfile)
    return True

    def setUp(self):
        setup_context_for_tests(self)
        self.frequency_context = FrequencyContext(self.context)
        self.gui_variable_observer = Observer()
        self.gui_variable_observer.update = mock.MagicMock()
        self.gui_context.gui_variables_notifier.add_subscriber(self.gui_variable_observer)
        self.data_context.instrument = 'CHRONUS'
        self.gui_variable_observer = Observer()
        self.gui_variable_observer.update = mock.MagicMock()
        self.gui_context.gui_variables_notifier.add_subscriber(self.gui_variable_observer)

        filepath = FileFinder.findRuns('CHRONUS00003422.nxs')[0]

        load_result, run, filename = load_workspace_from_filename(filepath)

        self.loaded_data.add_data(workspace=load_result, run=[run], filename=filename, instrument='CHRONUS')
        self.data_context.current_runs = [[run]]
        self.context.update_current_data()

    def test_runinfo_correct(self):
        file_path = FileFinder.findRuns('MUSR00022725.nxs')[0]
        ws, run, filename = load_utils.load_workspace_from_filename(file_path)
        self.data_context._loaded_data.remove_data(run=run)
        self.data_context._loaded_data.add_data(run=[run], workspace=ws, filename=filename, instrument='MUSR')
        self.data_context.current_runs = [[22725]]
        self.context.update_current_data()
        test_pair = MuonPair('test_pair', 'top', 'bottom', alpha=0.75)
        self.group_context.add_pair(pair=test_pair)

        self.presenter.update_view_from_model()

        expected_string_list = ['Instrument:MUSR', 'Run:22725', 'Title:FeTeSeT=1F=100', 'Comment:FCfirstsample',
                                'Start:2009-03-24T04:18:58', 'End:2009-03-24T04:56:26', 'Counts(MEv):20.076704',
                                'GoodFrames:88540', 'CountsperGoodFrame:226.753',
                                'CountsperGoodFrameperdet:3.543', 'AverageTemperature(K):2.53386',
                                'SampleTemperature(K):1.0', 'SampleMagneticField(G):100.0']

        self.assertEqual(str(self.view.run_info_box.toPlainText()).replace(' ', '').splitlines(), expected_string_list)

    def runTest(self):
        UseCompatibilityMode()
        LOQ()
        Detector("main-detector-bank")
        csv_file = FileFinder.getFullPath('batch_input.csv')

        Set1D()
        MaskFile('MASK.094AA')
        Gravity(True)

        BatchReduce(csv_file, 'raw', plotresults=False, saveAlgs={'SaveCanSAS1D': 'xml', 'SaveNexus': 'nxs'})

        LoadNexus(Filename='54433sans.nxs', OutputWorkspace='result')
        Plus(LHSWorkspace='result', RHSWorkspace='99630sanotrans', OutputWorkspace= 'result')

        os.remove(os.path.join(config['defaultsave.directory'],'54433sans.nxs'))
        os.remove(os.path.join(config['defaultsave.directory'],'99630sanotrans.nxs'))
        os.remove(os.path.join(config['defaultsave.directory'],'54433sans.xml'))
        os.remove(os.path.join(config['defaultsave.directory'],'99630sanotrans.xml'))