pychemstation 0.4.7.dev2__py3-none-any.whl → 0.5.0__py3-none-any.whl

pychemstation/control/hplc.py

@@ -1,575 +1,137 @@
 """
-Module to provide API for the remote control of the Agilent HPLC systems.
+Module to provide API for higher-level HPLC actions.
 
-HPLCController sends commands to Chemstation software via a command file.
-Answers are received via reply file. On the Chemstation side, a custom
-Macro monitors the command file, executes commands and writes to the reply file.
-Each command is given a number (cmd_no) to keep track of which commands have
-been processed.
-
-Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
+Authors: Lucy Hao
 """
 
-import logging
-import os
-import time
-from typing import Union
-
-import polling
-from xsdata.formats.dataclass.parsers import XmlParser
+from typing import Union, Optional
 
-from .chromatogram import AgilentHPLCChromatogram, TIME_FORMAT
-from ..generated import PumpMethod, DadMethod
-from ..utils.constants import MAX_CMD_NO, SEQUENCE_TABLE, METHOD_TIMETABLE
-from ..utils.hplc_param_types import HPLCAvailStatus, Command, HPLCErrorStatus, Table, TableOperation, SequenceTable, \
-    SequenceEntry, RegisterFlag, MethodTimetable, Param, PType, str_to_status, HPLCRunningStatus, Entry, \
-    HPLCMethodParams
+from ..control import CommunicationController
+from ..control.table import MethodController, SequenceController
+from ..utils.chromatogram import AgilentHPLCChromatogram
+from ..utils.macro import Command, HPLCRunningStatus, HPLCAvailStatus, HPLCErrorStatus
+from ..utils.method_types import MethodTimetable
+from ..utils.sequence_types import SequenceTable, SequenceEntry
 
 
 class HPLCController:
-    """
-    Class to control Agilent HPLC systems via Chemstation Macros.
-    """
-
-    def __init__(
-            self,
-            comm_dir: str,
-            data_dir: str,
-            method_dir: str,
-            sequence_dir: str,
-            cmd_file: str = "cmd",
-            reply_file: str = "reply",
-    ):
+    def __init__(self,
+                 comm_dir: str,
+                 data_dir: str,
+                 method_dir: str,
+                 sequence_dir: str):
         """Initialize HPLC controller. The `hplc_talk.mac` macro file must be loaded in the Chemstation software.
         `comm_dir` must match the file path in the macro file.
-        
+
         :param comm_dir: Name of directory for communication, where ChemStation will read and write from. Can be any existing directory.
-        :param data_dir: Name of directory that ChemStation saves run data. Must be accessible by ChemStation.
-        :param cmd_file: Name of command file
-        :param reply_file: Name of reply file
         :raises FileNotFoundError: If either `data_dir`, `method_dir` or `comm_dir` is not a valid directory.
         """
-        if os.path.isdir(comm_dir):
-            self.cmd_file = os.path.join(comm_dir, cmd_file)
-            self.reply_file = os.path.join(comm_dir, reply_file)
-            self.cmd_no = 0
-        else:
-            raise FileNotFoundError(f"comm_dir: {comm_dir} not found.")
-        self._most_recent_hplc_status = None
-
-        if os.path.isdir(data_dir):
-            self.data_dir = data_dir
-        else:
-            raise FileNotFoundError(f"data_dir: {data_dir} not found.")
-
-        if os.path.isdir(method_dir):
-            self.method_dir = method_dir
-        else:
-            raise FileNotFoundError(f"method_dir: {method_dir} not found.")
-
-        if os.path.isdir(sequence_dir):
-            self.sequence_dir = sequence_dir
-        else:
-            raise FileNotFoundError(f"method_dir: {method_dir} not found.")
-
-        self.spectra = {
-            "A": AgilentHPLCChromatogram(self.data_dir),
-            "B": AgilentHPLCChromatogram(self.data_dir),
-            "C": AgilentHPLCChromatogram(self.data_dir),
-            "D": AgilentHPLCChromatogram(self.data_dir),
-        }
-
-        self.data_files: list[str] = []
-        self.internal_variables: list[dict[str, str]] = []
-
-        # Create files for Chemstation to communicate with Python
-        open(self.cmd_file, "a").close()
-        open(self.reply_file, "a").close()
-
-        self.logger = logging.getLogger("hplc_logger")
-        self.logger.addHandler(logging.NullHandler())
-
-        self.reset_cmd_counter()
-
-        self.logger.info("HPLC Controller initialized.")
-
-    def _set_status(self):
-        """Updates current status of HPLC machine"""
-        self._most_recent_hplc_status = self.status()[0]
-
-    def _check_data_status(self) -> bool:
-        """Checks if HPLC machine is in an available state, meaning a state that data is not being written.
-
-        :return: whether the HPLC machine is in a safe state to retrieve data back."""
-        old_status = self._most_recent_hplc_status
-        self._set_status()
-        file_exists = os.path.exists(self.data_files[-1]) if len(self.data_files) > 0 else False
-        done_writing_data = isinstance(self._most_recent_hplc_status,
-                                       HPLCAvailStatus) and old_status != self._most_recent_hplc_status and file_exists
-        return done_writing_data
-
-    def check_hplc_ready_with_data(self) -> bool:
-        """Checks if ChemStation has finished writing data and can be read back.
-
-        :param method: if you are running a method and want to read back data, the timeout period will be adjusted to be longer than the method's runtime
-
-        :return: Return True if data can be read back, else False.
-        """
-        self._set_status()
-
-        timeout = 10 * 60
-        hplc_run_done = polling.poll(
-            lambda: self._check_data_status(),
-            timeout=timeout,
-            step=30
-        )
-
-        return hplc_run_done
-
-    def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
-        """Low-level execution primitive. Sends a command string to HPLC.
-
-        :param cmd: string to be sent to HPLC
-        :param cmd_no: Command number
-        :param num_attempts: Number of attempts to send the command before raising exception.
-        :raises IOError: Could not write to command file.
-        """
-        err = None
-        for _ in range(num_attempts):
-            time.sleep(1)
-            try:
-                with open(self.cmd_file, "w", encoding="utf8") as cmd_file:
-                    cmd_file.write(f"{cmd_no} {cmd}")
-            except IOError as e:
-                err = e
-                self.logger.warning("Failed to send command; trying again.")
-                continue
-            else:
-                self.logger.info("Sent command #%d: %s.", cmd_no, cmd)
-                return
-        else:
-            raise IOError(f"Failed to send command #{cmd_no}: {cmd}.") from err
-
-    def _receive(self, cmd_no: int, num_attempts=100) -> str:
-        """Low-level execution primitive. Recives a response from HPLC.
-
-        :param cmd_no: Command number
-        :param num_attempts: Number of retries to open reply file
-        :raises IOError: Could not read reply file.
-        :return: ChemStation response 
-        """
-        err = None
-        for _ in range(num_attempts):
-            time.sleep(1)
-
-            try:
-                with open(self.reply_file, "r", encoding="utf_16") as reply_file:
-                    response = reply_file.read()
-            except OSError as e:
-                err = e
-                self.logger.warning("Failed to read from reply file; trying again.")
-                continue
-
-            try:
-                first_line = response.splitlines()[0]
-                response_no = int(first_line.split()[0])
-            except IndexError as e:
-                err = e
-                self.logger.warning("Malformed response %s; trying again.", response)
-                continue
-
-            # check that response corresponds to sent command
-            if response_no == cmd_no:
-                self.logger.info("Reply: \n%s", response)
-                return response
-            else:
-                self.logger.warning(
-                    "Response #: %d != command #: %d; trying again.",
-                    response_no,
-                    cmd_no,
-                )
-                continue
-        else:
-            raise IOError(f"Failed to receive reply to command #{cmd_no}.") from err
-
-    def sleepy_send(self, cmd: Union[Command, str]):
-        self.send("Sleep 0.1")
-        self.send(cmd)
-        self.send("Sleep 0.1")
+        self.comm = CommunicationController(comm_dir=comm_dir)
+        self.method_controller = MethodController(controller=self.comm, src=method_dir, data_dir=data_dir)
+        self.sequence_controller = SequenceController(controller=self.comm, src=sequence_dir, data_dir=data_dir)
 
     def send(self, cmd: Union[Command, str]):
-        """Sends a command to Chemstation.
-
-        :param cmd: Command to be sent to HPLC
-        """
-        if self.cmd_no == MAX_CMD_NO:
-            self.reset_cmd_counter()
-
-        cmd_to_send: str = cmd.value if isinstance(cmd, Command) else cmd
-        self.cmd_no += 1
-        self._send(cmd_to_send, self.cmd_no)
+        self.comm.send(cmd)
 
     def receive(self) -> str:
-        """Returns messages received in reply file.
-
-        :return: ChemStation response 
-        """
-        return self._receive(self.cmd_no)
-
-    def reset_cmd_counter(self):
-        """Resets the command counter."""
-        self._send(Command.RESET_COUNTER_CMD.value, cmd_no=MAX_CMD_NO + 1)
-        self._receive(cmd_no=MAX_CMD_NO + 1)
-        self.cmd_no = 0
-
-        self.logger.debug("Reset command counter")
+        return self.comm.receive()
 
-    def sleep(self, seconds: int):
-        """Tells the HPLC to wait for a specified number of seconds.
+    def status(self) -> list[HPLCRunningStatus | HPLCAvailStatus | HPLCErrorStatus]:
+        return self.comm.get_status()
 
-        :param seconds: number of seconds to wait
+    def switch_method(self, method_name: str):
         """
-        self.send(Command.SLEEP_CMD.value.format(seconds=seconds))
-        self.logger.debug("Sleep command sent.")
-
-    def standby(self):
-        """Switches all modules in standby mode. All lamps and pumps are switched off."""
-        self.send(Command.STANDBY_CMD)
-        self.logger.debug("Standby command sent.")
-
-    def preprun(self):
-        """ Prepares all modules for run. All lamps and pumps are switched on."""
-        self.send(Command.PREPRUN_CMD)
-        self.logger.debug("PrepRun command sent.")
-
-    def status(self) -> list[Union[HPLCRunningStatus, HPLCAvailStatus, HPLCErrorStatus]]:
-        """Get device status(es).
+        Allows the user to switch between pre-programmed methods. No need to append '.M'
+        to the end of the method name. For example. for the method named 'General-Poroshell.M',
+        only 'General-Poroshell' is needed.
 
-        :return: list of ChemStation's current status
+        :param method_name: any available method in Chemstation method directory
+        :raise IndexError: Response did not have expected format. Try again.
+        :raise AssertionError: The desired method is not selected. Try again.
         """
-        self.send(Command.GET_STATUS_CMD)
-        time.sleep(1)
-
-        try:
-            parsed_response = self.receive().splitlines()[1].split()[1:]
-        except IOError:
-            return [HPLCErrorStatus.NORESPONSE]
-        except IndexError:
-            return [HPLCErrorStatus.MALFORMED]
-        recieved_status = [str_to_status(res) for res in parsed_response]
-        self._most_recent_hplc_status = recieved_status[0]
-        return recieved_status
+        self.method_controller.switch(method_name)
 
-    def stop_macro(self):
-        """Stops Macro execution. Connection will be lost."""
-        self.send(Command.STOP_MACRO_CMD)
-
-    def add_table_row(self, table: Table):
-        """Adds a row to the provided table for currently loaded method or sequence.
-         Import either the SEQUENCE_TABLE or METHOD_TIMETABLE from hein_analytical_control.constants.
-        You can also provide your own table.
-
-        :param table: the table to add a new row to
+    def switch_sequence(self, sequence_name: str):
         """
-        self.sleepy_send(TableOperation.NEW_ROW.value.format(register=table.register, table_name=table.name))
+         Allows the user to switch between pre-programmed sequences. The sequence name does not need the '.S' extension.
+         For example. for the method named 'mySeq.S', only 'mySeq' is needed.
 
-    def delete_table(self, table: Table):
-        """Deletes the table for the current loaded method or sequence.
-         Import either the SEQUENCE_TABLE or METHOD_TIMETABLE from hein_analytical_control.constants.
-        You can also provide your own table.
-
-        :param table: the table to delete
+        :param seq_name: The name of the sequence file
         """
-        self.send(TableOperation.DELETE_TABLE.value.format(register=table.register, table_name=table.name))
+        self.sequence_controller.switch(sequence_name)
 
-    def new_table(self, table: Table):
-        """Creates the table for the currently loaded method or sequence.
-         Import either the SEQUENCE_TABLE or METHOD_TIMETABLE from hein_analytical_control.constants.
-        You can also provide your own table.
+    def run_method(self, experiment_name: str):
+        """
+        This is the preferred method to trigger a run.
+        Starts the currently selected method, storing data
+        under the <data_dir>/<experiment_name>.D folder.
+        The <experiment_name> will be appended with a timestamp in the '%Y-%m-%d-%H-%M' format.
+        Device must be ready.
 
-        :param table: the table to create
+        :param experiment_name: Name of the experiment
         """
-        self.send(TableOperation.CREATE_TABLE.value.format(register=table.register, table_name=table.name))
+        self.method_controller.run(experiment_name)
 
-    def edit_sequence_table(self, sequence_table: SequenceTable):
-        """Updates the currently loaded sequence table with the provided table. This method will delete the existing sequence table and remake it.
-        If you would only like to edit a single row of a sequence table, use `edit_sequence_table_row` instead.
-        :param sequence_table:
+    def run_sequence(self, sequence_table: SequenceTable):
         """
-        self.send("Local Rows")
-        self.sleep(1)
-        self.delete_table(SEQUENCE_TABLE)
-        self.sleep(1)
-        self.new_table(SEQUENCE_TABLE)
-        self.sleep(1)
-        self._get_table_rows(SEQUENCE_TABLE)
-        for i, row in enumerate(sequence_table.rows):
-            self.add_table_row(SEQUENCE_TABLE)
-            self.sleep(1)
-            self.send(Command.SAVE_SEQUENCE_CMD)
-            self.sleep(1)
-        self._get_table_rows(SEQUENCE_TABLE)
-        self.send(Command.SWITCH_SEQUENCE_CMD)
-        for i, row in enumerate(sequence_table.rows):
-            self.edit_sequence_table_row(row=row, row_num=i + 1)
-            self.sleep(1)
-            self.send(Command.SAVE_SEQUENCE_CMD)
-            self.sleep(1)
+        Starts the currently loaded sequence, storing data
+        under the <data_dir>/<sequence table name> folder.
+        Device must be ready.
 
-    def edit_sequence_table_row(self, row: SequenceEntry, row_num: int):
-        """Edits a row in the sequence table. Assumes the row already exists. If not, call `add_sequence_table_row`.
-        :param row: sequence row entry with updated information
-        :param row_num: the row to edit, based on 1-based indexing
+        :param sequence_table:
         """
-        if row.name:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.NAME,
-                                                                       val=row.name))
-        if row.vial_location:
-            self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=SEQUENCE_TABLE.register,
-                                                                      table_name=SEQUENCE_TABLE.name,
-                                                                      row=row_num,
-                                                                      col_name=RegisterFlag.VIAL_LOCATION,
-                                                                      val=row.vial_location))
-        if row.method:
-            self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(register=SEQUENCE_TABLE.register,
-                                                                       table_name=SEQUENCE_TABLE.name,
-                                                                       row=row_num,
-                                                                       col_name=RegisterFlag.NAME,
-                                                                       val=row.method))
-        if row.inj_vol:
-            self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=SEQUENCE_TABLE.register,
-                                                                      table_name=SEQUENCE_TABLE.name,
-                                                                      row=row_num,
-                                                                      col_name=RegisterFlag.NAME,
-                                                                      val=row.inj_vol))
+        self.sequence_controller.run(sequence_table)
 
     def edit_method(self, updated_method: MethodTimetable):
         """Updated the currently loaded method in ChemStation with provided values.
 
         :param updated_method: the method with updated values, to be sent to Chemstation to modify the currently loaded method.
         """
-        initial_organic_modifier: Param = updated_method.first_row.organic_modifier
-        max_time: Param = updated_method.first_row.maximum_run_time
-        temp: Param = updated_method.first_row.temperature
-        injvol: Param = updated_method.first_row.inj_vol
-        equalib_time: Param = updated_method.first_row.equ_time
-        flow: Param = updated_method.first_row.flow
-
-        # Method settings required for all runs
-        self.send(TableOperation.DELETE_TABLE.value.format(register=METHOD_TIMETABLE.register,
-                                                           table_name=METHOD_TIMETABLE.name, ))
-        self._update_method_param(initial_organic_modifier)
-        self._update_method_param(flow)
-        self._update_method_param(Param(val="Set",
-                                        chemstation_key=RegisterFlag.STOPTIME_MODE,
-                                        ptype=PType.STR))
-        self._update_method_param(max_time)
-        self._update_method_param(Param(val="Off",
-                                        chemstation_key=RegisterFlag.POSTIME_MODE,
-                                        ptype=PType.STR))
-
-        # TODO: set the oven temperature
-        # self._hplc_controller.update_method_param("str", "Set", "TemperatureControl_Mode")
-        # self._hplc_controller.update_method_param("num", temp, temp.chemstation_key[0])
-        # self._hplc_controller.update_method_param("num", temp, temp.chemstation_key[1])
-        # self._hplc_controller.update_method_param("str", "Set", "TemperatureControl2_Mode")
-        # self._hplc_controller.send("DownloadRCMethod PMP1")
+        self.method_controller.edit(updated_method)
 
-        self.send("DownloadRCMethod PMP1")
-
-        self._update_method_timetable(updated_method.subsequent_rows)
-
-    def _get_table_rows(self, table: Table) -> str:
-        self.send(TableOperation.GET_OBJ_HDR_VAL.value.format(internal_val="Row",
-                                                              register=table.register,
-                                                              table_name=table.name,
-                                                              col_name=RegisterFlag.NUM_ROWS, ))
-        res = self.receive()
-        self.send("Sleep 1")
-        self.send('Print Rows')
-        return res
-
-    def _update_method_timetable(self, timetable_rows: list[Entry]):
-        """Updates the timetable, which is seen when right-clicking the pump GUI in Chemstation to get to the timetable.
-        :param updated_method:
+    def edit_sequence(self, updated_sequence: SequenceTable):
         """
-        self.send("Local Rows")
-
-        self.delete_table(METHOD_TIMETABLE)
-        res = self._get_table_rows(METHOD_TIMETABLE)
+        Updates the currently loaded sequence table with the provided table. This method will delete the existing sequence table and remake it.
+        If you would only like to edit a single row of a sequence table, use `edit_sequence_row` instead.
 
-        while "ERROR" not in res:
-            self.delete_table(METHOD_TIMETABLE)
-            res = self._get_table_rows(METHOD_TIMETABLE)
-        self.new_table(METHOD_TIMETABLE)
-        self._get_table_rows(METHOD_TIMETABLE)
-
-        for i, row in enumerate(timetable_rows):
-            self.send("Sleep 1")
-            self.send(TableOperation.NEW_ROW.value.format(register=METHOD_TIMETABLE.register,
-                                                          table_name=METHOD_TIMETABLE.name))
-            self.send("Sleep 1")
-
-            if i == 0:
-                self.sleepy_send(TableOperation.NEW_COL_TEXT.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    col_name="Function",
-                    val=RegisterFlag.SOLVENT_COMPOSITION.value))
-                self.sleepy_send(TableOperation.NEW_COL_VAL.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    col_name="Time",
-                    val=row.start_time))
-                self.sleepy_send(TableOperation.NEW_COL_VAL.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    col_name=RegisterFlag.SOLVENT_B_COMPOSITION.value,
-                    val=row.organic_modifer))
-            else:
-                self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    row="Rows",
-                    col_name="Function",
-                    val=RegisterFlag.SOLVENT_COMPOSITION.value))
-                self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    row="Rows",
-                    col_name="Time",
-                    val=row.start_time))
-                self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(
-                    register=METHOD_TIMETABLE.register,
-                    table_name=METHOD_TIMETABLE.name,
-                    row="Rows",
-                    col_name=RegisterFlag.SOLVENT_B_COMPOSITION.value,
-                    val=row.organic_modifer))
-
-            self.send("Sleep 1")
-            self.send("DownloadRCMethod PMP1")
-            self.send("Sleep 1")
-
-    def _update_method_param(self, method_param: Param):
-        """Change a method parameter, changes what is visibly seen in Chemstation GUI. (changes the first row in the timetable)
-
-        :param method_param: a parameter to update for currently loaded method.
+        :param sequence_table:
         """
-        register = METHOD_TIMETABLE.register
-        setting_command = TableOperation.UPDATE_OBJ_HDR_VAL if method_param.ptype == PType.NUM else TableOperation.UPDATE_OBJ_HDR_TEXT
-        if isinstance(method_param.chemstation_key, list):
-            for register_flag in method_param.chemstation_key:
-                self.send(setting_command.value.format(register=register,
-                                                       register_flag=register_flag,
-                                                       val=method_param.val))
-        else:
-            self.send(setting_command.value.format(register=register,
-                                                   register_flag=method_param.chemstation_key,
-                                                   val=method_param.val))
-        time.sleep(2)
+        self.sequence_controller.edit(updated_sequence)
 
-    def desired_method_already_loaded(self, method_name: str) -> bool:
-        """Checks if a given method is already loaded into Chemstation. Method name does not need the ".M" extension.
-
-        :param method_name: a Chemstation method
-        :return: True if method is already loaded
+    def edit_sequence_row(self, row: SequenceEntry, num: int):
         """
-        self.send(Command.GET_METHOD_CMD)
-        parsed_response = self.receive().splitlines()[1].split()[1:][0]
-        return method_name in parsed_response
-
-    def switch_method(self, method_name: str):
-        """Allows the user to switch between pre-programmed methods. No need to append '.M'
-        to the end of the method name. For example. for the method named 'General-Poroshell.M',
-        only 'General-Poroshell' is needed.
+        Edits a row in the sequence table. Assumes the row already exists.
 
-        :param method_name: any available method in Chemstation method directory
-        :raise IndexError: Response did not have expected format. Try again.
-        :raise AssertionError: The desired method is not selected. Try again.
+        :param row: sequence row entry with updated information
+        :param row_num: the row to edit, based on -1-based indexing
         """
-        self.send(
-            Command.SWITCH_METHOD_CMD.value.format(method_dir=self.method_dir, method_name=method_name)
-        )
-
-        time.sleep(2)
-        self.send(Command.GET_METHOD_CMD)
-        time.sleep(2)
-        # check that method switched
-        for _ in range(10):
-            try:
-                parsed_response = self.receive().splitlines()[1].split()[1:][0]
-                break
-            except IndexError:
-                self.logger.debug("Malformed response. Trying again.")
-                continue
-
-        assert parsed_response == f"{method_name}.M", "Switching Methods failed."
+        self.sequence_controller.edit_row(row, num)
 
-    def load_method_details(self, method_name: str) -> MethodTimetable:
-        """Retrieve method details of an existing method. Don't need to append ".M" to the end. This assumes the
-        organic modifier is in Channel B and that Channel A contains the aq layer. Additionally, assumes
-         only two solvents are being used.
-
-        :param method_name: name of method to load details of
-        :raises FileNotFoundError: Method does not exist
-        :return: method details
+    def get_last_run_method_data(self) -> Optional[dict[str, AgilentHPLCChromatogram]]:
         """
-        method_folder = f"{method_name}.M"
-        method_path = os.path.join(self.method_dir, method_folder, "AgilentPumpDriver1.RapidControl.MethodXML.xml")
-        dad_path = os.path.join(self.method_dir, method_folder, "Agilent1200erDadDriver1.RapidControl.MethodXML.xml")
-
-        if os.path.exists(os.path.join(self.method_dir, f"{method_name}.M")):
-            parser = XmlParser()
-            method = parser.parse(method_path, PumpMethod)
-            dad = parser.parse(dad_path, DadMethod)
+        Returns the last run method data.
+        """
+        data_valid, data = self.method_controller.get_data()
+        if data_valid:
+            return data
+        return None
 
-            organic_modifier = None
-            aq_modifier = None
+    def get_last_run_sequence_data(self) -> Optional[list[dict[str, AgilentHPLCChromatogram]]]:
+        """
+        Returns data for all rows in the last run sequence data.
+        """
+        data_valid, data = self.sequence_controller.get_data()
+        if data_valid:
+            return data
+        return None
 
-            if len(method.solvent_composition.solvent_element) == 2:
-                for solvent in method.solvent_composition.solvent_element:
-                    if solvent.channel == "Channel_A":
-                        aq_modifier = solvent
-                    elif solvent.channel == "Channel_B":
-                        organic_modifier = solvent
+    def standby(self):
+        """Switches all modules in standby mode. All lamps and pumps are switched off."""
+        self.send(Command.STANDBY_CMD)
 
-            return MethodTimetable(
-                first_row=HPLCMethodParams(
-                    organic_modifier=Param(val=organic_modifier.percentage,
-                                           chemstation_key=RegisterFlag.SOLVENT_B_COMPOSITION,
-                                           ptype=PType.NUM),
-                    flow=Param(val=method.flow,
-                               chemstation_key=RegisterFlag.FLOW,
-                               ptype=PType.NUM),
-                    maximum_run_time=Param(val=method.stop_time,
-                                           chemstation_key=RegisterFlag.MAX_TIME,
-                                           ptype=PType.NUM),
-                    temperature=Param(val=None,
-                                      chemstation_key=[RegisterFlag.COLUMN_OVEN_TEMP1,
-                                                       RegisterFlag.COLUMN_OVEN_TEMP2],
-                                      ptype=PType.NUM),
-                    inj_vol=Param(val=None,
-                                  chemstation_key=None,
-                                  ptype=PType.NUM),
-                    equ_time=Param(val=None,
-                                   chemstation_key=None,
-                                   ptype=PType.NUM)),
-                subsequent_rows=[
-                    Entry(
-                        start_time=tte.time,
-                        organic_modifer=tte.percent_b,
-                        flow=method.flow
-                    ) for tte in method.timetable.timetable_entry
-                ],
-                dad_wavelengthes=dad.signals.signal,
-                organic_modifier=organic_modifier,
-                modifier_a=aq_modifier
-            )
-        else:
-            raise FileNotFoundError
+    def preprun(self):
+        """ Prepares all modules for run. All lamps and pumps are switched on."""
+        self.send(Command.PREPRUN_CMD)
 
     def lamp_on(self):
         """Turns the UV lamp on."""
@@ -586,88 +148,3 @@ class HPLCController:
     def pump_off(self):
         """Turns the pump off."""
         self.send(Command.PUMP_OFF_CMD)
-
-    def switch_sequence(self, seq_name: str):
-        """Switch to the specified sequence. The sequence name does not need the '.S' extension.
-        :param seq_name: The name of the sequence file
-        :param sequence_dir: The directory where the sequence file resides
-        """
-        self.send(f'_SeqFile$ = "{seq_name}.S"')
-        self.send(f'_SeqPath$ = "{self.sequence_dir}"')
-        self.send(Command.SWITCH_SEQUENCE_CMD)
-
-        time.sleep(2)
-        self.send(Command.GET_SEQUENCE_CMD)
-        time.sleep(2)
-        # check that method switched
-        for _ in range(10):
-            try:
-                parsed_response = self.receive().splitlines()[1].split()[1:][0]
-                break
-            except IndexError:
-                self.logger.debug("Malformed response. Trying again.")
-                continue
-
-        assert parsed_response == f"{seq_name}.S", "Switching sequence failed."
-
-    def run_sequence(self, experiment_name: str):
-        """Starts the currently loaded sequence, storing data
-        under the <data_dir>/<experiment_name>.D folder.
-        The <experiment_name> will be appended with a timestamp in the '%Y-%m-%d-%H-%M' format.
-        Device must be ready.
-
-        :param experiment_name: Name of the experiment
-        """
-        timestamp = time.strftime(TIME_FORMAT)
-
-        self.send(
-            Command.RUN_SEQUENCE_CMD.value.format(
-                data_dir=self.data_dir, experiment_name=experiment_name, timestamp=timestamp
-            )
-        )
-
-        folder_name = f"{experiment_name}_{timestamp}.D"
-        self.data_files.append(os.path.join(self.data_dir, folder_name))
-        self.logger.info("Started HPLC run:  %s.", folder_name)
-
-    def start_method(self):
-        """Starts and executes currently loaded method to run according to Run Time Checklist. Device must be ready.
-         Does not store the folder where data is saved.
-         """
-        self.send(Command.START_METHOD_CMD)
-
-    def run_method(self, experiment_name: str):
-        """This is the preferred method to trigger a run.
-        Starts the currently selected method, storing data
-        under the <data_dir>/<experiment_name>.D folder.
-        The <experiment_name> will be appended with a timestamp in the '%Y-%m-%d-%H-%M' format.
-        Device must be ready.
-
-        :param experiment_name: Name of the experiment
-        """
-        timestamp = time.strftime(TIME_FORMAT)
-
-        self.send(
-            Command.RUN_METHOD_CMD.value.format(
-                data_dir=self.data_dir, experiment_name=experiment_name, timestamp=timestamp
-            )
-        )
-
-        folder_name = f"{experiment_name}_{timestamp}.D"
-        self.data_files.append(os.path.join(self.data_dir, folder_name))
-        self.logger.info("Started HPLC run:  %s.", folder_name)
-
-    def stop_method(self):
-        """Stops the run. A dialog window will pop up and manual intervention may be required."""
-        self.send(Command.STOP_METHOD_CMD)
-
-    def get_spectrum(self):
-        """ Load last chromatogram for any channel in spectra dictionary."""
-        last_file = self.data_files[-1] if len(self.data_files) > 0 else None
-
-        if last_file is None:
-            raise IndexError
-
-        for channel, spec in self.spectra.items():
-            spec.load_spectrum(data_path=last_file, channel=channel)
-            self.logger.info("%s chromatogram loaded.", channel)