autonoms.agilent_methods package

Submodules

autonoms.agilent_methods.CCSCal module

autonoms.agilent_methods.rf_rpyc_server module

autonoms.agilent_methods.splitterExtract module

autonoms.agilent_methods.splitterExtract.get_args()

Helper function for initializing arguments on command line invocation :return: Parameter arguments :rtype: Namespace

autonoms.agilent_methods.splitterExtract.get_splits(splitterLog, RFDB, dFile)

Extract split start and end times from the splitter log produced by RapidFire UI splitter output

Parameters:

  • splitterLog (str) – Path to RapidFire UI splitter output log

  • RFDB (str) – Path to RFDatabase.xml output file from RapidFire sequence on which UI splitter was run

  • dFile (str) – .d file on which splitter was run

Returns:

List of strings of individual well split start and end times

Return type:

list

autonoms.agilent_methods.splitterExtract.main()

autonoms.agilent_methods.utils_6560 module

autonoms.agilent_methods.utils_6560.get_instrument_state(window)

Function for monitoring the 6560 instrument state in the main MH Data Acquisition Window

Parameters:

window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

Returns:

Instrument state

Return type:

str

autonoms.agilent_methods.utils_6560.initialize_app(search_str='Agilent MassHunter Workstation Data Acquisition', backend='uia')

Finds the (open) MassHunter Acquisition application and returns its handles

Parameters:

  • search_str (str, optional) – Identifying application text to search for, defaults to “Agilent MassHunter Workstation Data Acquisition”

  • backend (str, optional) – pywinauto backend to use, defaults to “uia”

Returns:

Respectively the pywinauto application and pywinauto window corresponding to MassHunter Workstation Data Acquisition

Return type:

tuple

autonoms.agilent_methods.utils_6560.open_ms_method(window, method_name)

Loads an MS acquisition method by name

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

  • method_name (str) – Acquisition method name

autonoms.agilent_methods.utils_6560.run_calibration_B(ms_method_name, output_d_filename_full, sample_name='CalB', runtime=30, manual_stop=True, overwrite=True, timeout_seconds=900)

Runs calibrant line B using the specified MS method acquisition parameters and saves the output

Parameters:

  • ms_method_name (str) – Path to .m file for the MS acquisition method

  • output_d_filename_full (str) – Path to output .d file

  • sample_name (str, optional) – Sample name in metadata entry, defaults to “CalB”

  • runtime (float, optional) – Acquisition time (in seconds), defaults to 30

  • manual_stop (bool, optional) – If true, leave to the user to close dialog boxes after run has stopped, defaults to True

  • overwrite (bool, optional) – If true, overwrite existing output file, defaults to True

  • timeout_seconds (float, optional) – Allowed wait time for instrument to reach ready and idle states, defaults to 900

autonoms.agilent_methods.utils_6560.set_calibration_output(window, sample_name, out_d_file_name)

Sets the output filename of a single-sample instrument run

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

  • sample_name (str) – Output metadata sample name

  • out_d_file_name (str) – Output .d file name

Returns:

Full path to the output .d file

Return type:

str

autonoms.agilent_methods.utils_6560.start_sample_run(window, overwrite=True)

Starts a single sample run

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

  • overwite (bool, optional) – Overwrite existing output file, defaults to True

autonoms.agilent_methods.utils_6560.stop_sample_run(window)

Stops a running single sample run

Parameters:

window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

autonoms.agilent_methods.utils_6560.wait_for_state(window, state, timeout_seconds)

Waits for 6560 to reach a given state by monitoring the main MH Data Acquisition window

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to MassHunter Workstation Data Acquisition

  • state (str) – Desired state (one of [“idle”, “not read”, “run”, “prerun”])

  • timeout_seconds (float) – Seconds to wait for instrument to reach state before erroring

autonoms.agilent_methods.utils_plates module

autonoms.agilent_methods.utils_rapidFire module

autonoms.agilent_methods.utils_rapidFire.check_vac_pressure(window, level_check=-50)

Ensures the RF pump vacuum pressure is below a certain threshold level (meaning that the pump is on and functioning)

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to the RapidFire UI

  • level_check (float, optional) – Pressure level (in kPa) above which error gets thrown (-60 kPa or below means pump is in good condition), defaults to -50

autonoms.agilent_methods.utils_rapidFire.copy_last_run_output(out_dir, rf_cfg_file, overwrite=True)

Copies the newest RF run data to a new directory

Parameters:

  • out_dir (str) – Path to output directory

  • rf_cfg_file (str) – Path to RF configuration file

  • overwrite (bool, optional) – Overwrite existing files, defaults to True

autonoms.agilent_methods.utils_rapidFire.find_latest_dir(base_path, sequence_name=None, start_year=2021, path_convert=None)

Gets the latest directory in the RapidFire data file tree

Parameters:

  • base_path – Path to base RapidFire data directory

  • start_year (int) – Starting year to look for in the RapidFire file tree, defaults to 2021

  • path_convert (dict) – If provided a dictionary of pathname swaps between the 6560 and RF computers on the shared drive

Sequence_name:

If provided, only check output directories containing data from RF sequence with given name, defaults to None

Returns:

Path to the latest-modified directory in the RF data file tree

Return type:

str

autonoms.agilent_methods.utils_rapidFire.get_rf_output_dir(rf_cfg_file)

Checks the RapidFire output directory for a given RF configuration file

Parameters:

rf_cfg_file (str) – Path to RF configuration file

Returns:

Path to the RF data output directory

Return type:

str

autonoms.agilent_methods.utils_rapidFire.initialize_app(search_str='RapidFire :')

Finds the (open) RapidFire UI application and returns its handles

Parameters:

search_str (str, optional) – Identifying application text to search for, defaults to “RapidFire :”

Returns:

Respectively the pywinauto application and pywinauto window corresponding to RapidFire UI

Return type:

tuple

autonoms.agilent_methods.utils_rapidFire.load_rf_batch(window, rfbat_file)

Loads a RF Batch (.rfbat)

Parameters:

  • window (pywinauto.application.Application) – pywinauto window corresponding to the RapidFire UI

  • rfbat_file (str) – Path to .rfbat file (on RapidFire drive)

autonoms.agilent_methods.utils_rapidFire.load_rf_method(window, rfcfg_file)

Loads a RF method (.rfcfg)

Parameters:

window (pywinauto.application.Application) – pywinauto window corresponding to the RapidFire UI

autonoms.agilent_methods.utils_rapidFire.open_log_view(window, app)

Opens the RapidFire System Log window

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

  • app (pywinauto.application.Application) – pywinauto application corresponding to RapidFire UI

Returns:

The pywinauto window object corresponding to the RF log window

Return type:

pywinauto.Application.WindowSpecification

autonoms.agilent_methods.utils_rapidFire.open_splitter_view(window, app)

Opens the file splitter dialogue in the RF UI

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

  • app (pywinauto.application.Application) – pywinauto application corresponding to RapidFire UI

Returns:

pywinauto window corresponding to the file splitter dialogue

Return type:

pywinauto.application.WindowSpecification

autonoms.agilent_methods.utils_rapidFire.press_start_button(window)

Presses the start (run) button

Parameters:

window (pywinauto.Application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

autonoms.agilent_methods.utils_rapidFire.remote_file_split(test=False, *args, **kwargs)

Runs file splitting through the file splitter dialogue

Parameters:

  • test (bool, optional) – Run in test mode, defaults to False

  • data_dir (str) – Path to RF directory containing run output files

  • timeout_seconds (float) – Seconds to wait before erroring

autonoms.agilent_methods.utils_rapidFire.remote_run_rfbat(test=False, *args, **kwargs)

Runs a sequence on the RF

Parameters:

  • test (bool, optional) – Run in test mode, defaults to False

  • rf_base_data_dir (str) – Path to RF base data dir

  • rfcfg_file (str) – Path to RF .rfcfg method file

  • rfbat_file (str) – Path to RF .rfbat batch file

  • timeout_seconds (float) – Seconds to wait before erroring

Returns:

Path to directory containing run output files

Return type:

str

autonoms.agilent_methods.utils_rapidFire.run_split(splitter_window, split_dir, multiple_injections=True)

Runs file splitting through the file splitter dialogue

Parameters:

  • splitter_window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to the file splitter dialogue

  • split_dir (str) – Path to directory containing RF sequence output to split. Output split files will be placed here as well

  • multiple_injections (bool, optional) – Run multiple splits at once in parallel, defaults to True

autonoms.agilent_methods.utils_rapidFire.set_run_mode(window, mode)

Sets the RF run mode (between plates and sequences)

Parameters:

window (pywinauto.Application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

Mode:

Desired run mode

autonoms.agilent_methods.utils_rapidFire.set_splitter_autoconvert(splitter_window, state)

Sets the file splitter dialogue state for the auto conversion option

Parameters:

  • splitter_window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to the file splitter dialogue

  • state (bool) – desired auto conversion setting

autonoms.agilent_methods.utils_rapidFire.start_run(window, app, plate_timeout=180)

Sets the RF run mode (between plates and sequences)

Parameters:

  • window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

  • app (pywinauto.application.Application) – pywinauto application corresponding to RapidFire UI

  • plate_timeout (float, optional) – Seconds to wait for plate run window to appear before erroring, defaults to 180

autonoms.agilent_methods.utils_rapidFire.stop_run(window)

Stops a run

Parameters:

window (pywinauto.application.WindowSpecification) – pywinauto window corresponding to RapidFire UI

Module contents