pychemstation 0.5.11__py3-none-any.whl → 0.5.13__py3-none-any.whl

pychemstation/control/controllers/__init__.py

@@ -1,4 +1,9 @@
-from .method import MethodController
-from .sequence import SequenceController
-from .table_controller import TableController
+"""
+.. include:: README.md
+"""
+
 from .comm import CommunicationController
+from .devices.pump import PumpController
+from .devices.column import ColumnController
+from .tables.method import MethodController
+from .tables.sequence import SequenceController

pychemstation/control/controllers/devices/column.py

@@ -0,0 +1,12 @@
+from ....control.controllers import CommunicationController
+from .device import DeviceController
+from ....utils.table_types import Table
+
+
+class ColumnController(DeviceController):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, table)
+
+    def get_row(self, row: int):
+        pass

pychemstation/control/controllers/devices/device.py

@@ -0,0 +1,23 @@
+import abc
+from typing import Union
+
+from ....control.controllers import CommunicationController
+from ....control.controllers.tables.table import TableController
+from ....utils.chromatogram import AgilentChannelChromatogramData
+from ....utils.table_types import Table
+
+
+class DeviceController(TableController, abc.ABC):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, None, None, table)
+
+    @abc.abstractmethod
+    def get_row(self, row: int):
+        pass
+
+    def retrieve_recent_data_files(self):
+        raise NotImplementedError
+
+    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
+        raise NotImplementedError

pychemstation/control/controllers/devices/injector.py

@@ -0,0 +1,11 @@
+from ....control.controllers import CommunicationController
+from .device import DeviceController
+from ....utils.table_types import Table
+
+
+class InjectorController(DeviceController):
+    def get_row(self, row: int):
+        pass
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, table)

pychemstation/control/controllers/devices/pump.py

@@ -0,0 +1,43 @@
+from ....control.controllers import CommunicationController
+from .device import DeviceController
+from ....utils.pump_types import Pump
+from ....utils.table_types import Table
+
+
+class PumpController(DeviceController):
+
+    def __init__(self, controller: CommunicationController, table: Table):
+        super().__init__(controller, table)
+        self.A1 = Pump(in_use=True, solvent="A1")
+        self.B1 = Pump(in_use=True, solvent="B1")
+        self.A2 = Pump(in_use=False, solvent="A2")
+        self.B2 = Pump(in_use=False, solvent="B2")
+
+    def validate_pumps(self):
+        invalid_A_pump_usage = self.A1.in_use and self.A2.in_use
+        invalid_B_pump_usage = self.B1.in_use and self.B2.in_use
+        if invalid_A_pump_usage or invalid_B_pump_usage:
+            raise AttributeError
+
+    def switch_pump(self, num: int, pump: str):
+        if pump == "A":
+            if num == 1:
+                self.A1.in_use = True
+                self.A2.in_use = False
+            elif num == 2:
+                self.A1.in_use = False
+                self.A2.in_use = True
+        elif pump == "B":
+            if num == 1:
+                self.B1.in_use = True
+                self.B2.in_use = False
+            elif num == 2:
+                self.B1.in_use = False
+                self.B2.in_use = True
+        self.purge()
+
+    def purge(self):
+        pass
+
+    def get_row(self, row: int):
+        pass

pychemstation/control/controllers/table_controller.py

@@ -207,7 +207,7 @@ class TableController(abc.ABC):
         """
         timeout = 10 * 60
         if method:
-            timeout = ((method.first_row.maximum_run_time + 5) * 60)
+            timeout = ((method.stop_time + method.post_time + 3) * 60)
         if sequence:
             timeout *= len(sequence.rows)
 

pychemstation/control/controllers/tables/method.py

@@ -0,0 +1,351 @@
+import os
+import time
+
+from xsdata.formats.dataclass.parsers import XmlParser
+
+from .table import TableController
+from ....control.controllers import CommunicationController
+from ....generated import PumpMethod, DadMethod, SolventElement
+from ....utils.chromatogram import TIME_FORMAT, AgilentChannelChromatogramData
+from ....utils.macro import *
+from ....utils.method_types import *
+from ....utils.table_types import *
+
+
+class MethodController(TableController):
+    """
+    Class containing method related logic
+    """
+
+    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table, offline: bool):
+        super().__init__(controller, src, data_dir, table, offline=offline)
+
+    def check(self) -> str:
+        time.sleep(2)
+        self.send(Command.GET_METHOD_CMD)
+        time.sleep(2)
+        res = self.receive()
+        if res.is_ok():
+            return res.ok_value.string_response
+        return "ERROR"
+
+    def get_method_params(self) -> HPLCMethodParams:
+        return HPLCMethodParams(organic_modifier=self.controller.get_num_val(
+            cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                register=self.table.register,
+                register_flag=RegisterFlag.SOLVENT_B_COMPOSITION
+            )
+        ),
+            flow=self.controller.get_num_val(
+                cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                    register=self.table.register,
+                    register_flag=RegisterFlag.FLOW
+                )
+            ),
+        )
+
+    def get_row(self, row: int) -> TimeTableEntry:
+        flow = None
+        om = None
+
+        try:
+            flow = self.get_num(row, RegisterFlag.TIMETABLE_FLOW)
+        except RuntimeError:
+            pass
+        try:
+            om = self.get_num(row, RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION)
+        except RuntimeError:
+            pass
+
+        return TimeTableEntry(start_time=self.get_num(row, RegisterFlag.TIME),
+                              organic_modifer=om,
+                              flow=flow)
+
+    def get_timetable(self, rows: int):
+        uncoalesced_timetable_rows = [self.get_row(r + 1) for r in range(rows)]
+        timetable_rows = {}
+        for row in uncoalesced_timetable_rows:
+            time_key = str(row.start_time)
+            if time_key not in timetable_rows.keys():
+                timetable_rows[time_key] = TimeTableEntry(start_time=row.start_time,
+                                                          flow=row.flow,
+                                                          organic_modifer=row.organic_modifer)
+            else:
+                if row.flow:
+                    timetable_rows[time_key].flow = row.flow
+                if row.organic_modifer:
+                    timetable_rows[time_key].organic_modifer = row.organic_modifer
+        entries = list(timetable_rows.values())
+        entries.sort(key=lambda e: e.start_time)
+        return entries
+
+    def load(self) -> MethodDetails:
+        rows = self.get_num_rows()
+        if rows.is_ok():
+            self.send(Command.GET_METHOD_CMD)
+            res = self.receive()
+            method_name = res.ok_value.string_response
+            timetable_rows = self.get_timetable(int(rows.ok_value.num_response))
+            params = self.get_method_params()
+            stop_time = self.controller.get_num_val(
+                cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                    register=self.table.register,
+                    register_flag=RegisterFlag.MAX_TIME))
+            post_time = self.controller.get_num_val(
+                cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
+                    register=self.table.register,
+                    register_flag=RegisterFlag.POST_TIME))
+            self.table_state = MethodDetails(name=method_name,
+                                             timetable=timetable_rows,
+                                             stop_time=stop_time,
+                                             post_time=post_time,
+                                             params=params)
+            return self.table_state
+        else:
+            raise RuntimeError(rows.err_value)
+
+    def current_method(self, method_name: str):
+        """
+        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
+        """
+        self.send(Command.GET_METHOD_CMD)
+        parsed_response = self.receive()
+        return method_name in parsed_response
+
+    def switch(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.
+
+        :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.SWITCH_METHOD_CMD.value.format(method_dir=self.src,
+                                                         method_name=method_name))
+
+        time.sleep(2)
+        self.send(Command.GET_METHOD_CMD)
+        time.sleep(2)
+        res = self.receive()
+        if res.is_ok():
+            parsed_response = res.ok_value.string_response
+            assert parsed_response == f"{method_name}.M", "Switching Methods failed."
+        self.table_state = None
+
+    def load_from_disk(self, method_name: str) -> MethodDetails:
+        """
+        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
+        """
+        method_folder = f"{method_name}.M"
+        method_path = os.path.join(self.src, method_folder, "AgilentPumpDriver1.RapidControl.MethodXML.xml")
+        dad_path = os.path.join(self.src, method_folder, "Agilent1200erDadDriver1.RapidControl.MethodXML.xml")
+
+        if os.path.exists(os.path.join(self.src, f"{method_name}.M")):
+            parser = XmlParser()
+            method = parser.parse(method_path, PumpMethod)
+            dad = parser.parse(dad_path, DadMethod)
+
+            organic_modifier: Optional[SolventElement] = None
+            aq_modifier: Optional[SolventElement] = 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
+
+            self.table_state = MethodDetails(name=method_name,
+                                             params=HPLCMethodParams(organic_modifier=organic_modifier.percentage,
+                                                                     flow=method.flow),
+                                             stop_time=method.stop_time.stop_time_value,
+                                             post_time=method.post_time.post_time_value,
+                                             timetable=[TimeTableEntry(start_time=tte.time,
+                                                                       organic_modifer=tte.percent_b,
+                                                                       flow=method.flow
+                                                                       ) for tte in method.timetable.timetable_entry],
+                                             dad_wavelengthes=dad.signals.signal)
+            return self.table_state
+        else:
+            raise FileNotFoundError
+
+    def edit(self, updated_method: MethodDetails, save: bool):
+        """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.
+        :param save: if false only modifies the method, otherwise saves to disk
+        """
+        self.table_state = updated_method
+        initial_organic_modifier: Param = Param(val=updated_method.params.organic_modifier,
+                                                chemstation_key=RegisterFlag.SOLVENT_B_COMPOSITION,
+                                                ptype=PType.NUM)
+        max_time: Param = Param(val=updated_method.stop_time,
+                                chemstation_key=RegisterFlag.MAX_TIME,
+                                ptype=PType.NUM)
+        post_time: Param = Param(val=updated_method.post_time,
+                                 chemstation_key=RegisterFlag.POST_TIME,
+                                 ptype=PType.NUM)
+        flow: Param = Param(val=updated_method.params.flow,
+                            chemstation_key=RegisterFlag.FLOW,
+                            ptype=PType.NUM)
+
+        # Method settings required for all runs
+        self.update_method_params(flow, initial_organic_modifier, max_time, post_time)
+        self._update_method_timetable(updated_method.timetable)
+
+        if save:
+            self.send(Command.SAVE_METHOD_CMD.value.format(
+                commit_msg=f"saved method at {str(time.time())}"
+            ))
+
+    def update_method_params(self, flow, initial_organic_modifier, max_time, post_time):
+        self.delete_table()
+        self._update_param(initial_organic_modifier)
+        self._update_param(flow)
+        if self.table_state.stop_time:
+            self._update_param(Param(val="Set", chemstation_key=RegisterFlag.STOPTIME_MODE, ptype=PType.STR))
+            self._update_param(max_time)
+        else:
+            self._update_param(Param(val="Off", chemstation_key=RegisterFlag.STOPTIME_MODE, ptype=PType.STR))
+        if self.table_state.post_time:
+            self._update_param(Param(val="Set", chemstation_key=RegisterFlag.POSTIME_MODE, ptype=PType.STR))
+            self._update_param(post_time)
+        else:
+            self._update_param(Param(val="Off", chemstation_key=RegisterFlag.POSTIME_MODE, ptype=PType.STR))
+        self.download()
+
+    def _update_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.
+        """
+        register = self.table.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)
+
+    def download(self):
+        self.send('Sleep 1')
+        self.sleepy_send("DownloadRCMethod PMP1")
+        self.send('Sleep 1')
+
+    def edit_row(self, row: TimeTableEntry, first_row: bool = False):
+        if first_row:
+            if row.organic_modifer:
+                self.add_row()
+                self.add_new_col_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.SOLVENT_COMPOSITION.value)
+                self.add_new_col_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION, val=row.organic_modifer)
+            if row.flow:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
+                self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+            self.download()
+        else:
+            if row.organic_modifer:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.SOLVENT_COMPOSITION.value)
+                self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION, val=row.organic_modifer)
+                self.download()
+            if row.flow:
+                self.add_row()
+                self.get_num_rows()
+                self.edit_row_text(col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value)
+                self.edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
+                self.edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
+                self.download()
+
+    def _update_method_timetable(self, timetable_rows: list[TimeTableEntry]):
+        self.get_num_rows()
+
+        self.delete_table()
+        res = self.get_num_rows()
+        while not res.is_err():
+            self.delete_table()
+            res = self.get_num_rows()
+
+        self.new_table()
+        self.get_num_rows()
+
+        for i, row in enumerate(timetable_rows):
+            self.edit_row(row=row, first_row=i == 0)
+
+    def stop(self):
+        """
+        Stops the method run. A dialog window will pop up and manual intervention may be required.\
+        """
+        self.send(Command.STOP_METHOD_CMD)
+
+    def run(self, experiment_name: str, stall_while_running: bool = True):
+        """
+        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
+        """
+        if not self.table_state:
+            self.table_state = self.load()
+
+        folder_name = ""
+        hplc_is_running = False
+        tries = 0
+        while tries < 10 and not hplc_is_running:
+            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"
+            hplc_is_running = self.check_hplc_is_running()
+            tries += 1
+
+        if not hplc_is_running:
+            raise RuntimeError("Method failed to start.")
+
+        self.data_files.append(os.path.join(self.data_dir, folder_name))
+
+        if stall_while_running:
+            run_completed = self.check_hplc_done_running(method=self.table_state)
+            if run_completed.is_ok():
+                self.data_files[-1] = run_completed.ok_value
+            else:
+                raise RuntimeError("Run error has occurred.")
+        else:
+            self.data_files[-1].dir = self.fuzzy_match_most_recent_folder(folder_name).ok_value
+
+    def retrieve_recent_data_files(self) -> str:
+        return self.data_files[-1]
+
+    def get_data(self, custom_path: Optional[str] = None,
+                 read_uv: bool = False) -> AgilentChannelChromatogramData:
+        if not custom_path:
+            self.get_spectrum(self.data_files[-1], read_uv)
+        else:
+            self.get_spectrum(custom_path, read_uv)
+        return AgilentChannelChromatogramData(**self.spectra) if not read_uv else self.uv

pychemstation/control/controllers/tables/ms.py

@@ -0,0 +1,21 @@
+from typing import Union
+
+from ....control.controllers import CommunicationController
+from ....control.controllers.tables.table import TableController
+from ....utils.chromatogram import AgilentChannelChromatogramData
+from ....utils.table_types import Table
+
+
+class MassSpecController(TableController):
+
+    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
+        super().__init__(controller, src, data_dir, table)
+
+    def get_row(self, row: int):
+        pass
+
+    def retrieve_recent_data_files(self):
+        pass
+
+    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
+        pass