pychemstation 0.10.0__py3-none-any.whl → 0.10.2__py3-none-any.whl

pychemstation/control/controllers/sequence.py

@@ -1,190 +0,0 @@
-import os
-import time
-from typing import Optional
-
-from ...control.controllers.comm import CommunicationController
-from ...control.controllers.table_controller import TableController
-from ...utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentChannelChromatogramData
-from ...utils.macro import Command
-from ...utils.sequence_types import SequenceTable, SequenceEntry, SequenceDataFiles, InjectionSource, SampleType
-from ...utils.table_types import RegisterFlag, Table
-from ...utils.tray_types import TenVialColumn
-
-
-class SequenceController(TableController):
-    """
-    Class containing sequence related logic
-    """
-
-    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table, method_dir: str):
-        self.method_dir = method_dir
-        super().__init__(controller, src, data_dir, table)
-
-    def load(self) -> SequenceTable:
-        rows = self.get_num_rows()
-        self.send(Command.GET_SEQUENCE_CMD)
-        seq_name = self.receive()
-
-        if rows.is_ok() and seq_name.is_ok():
-            self.table_state = SequenceTable(
-                name=seq_name.ok_value.string_response.partition(".S")[0],
-                rows=[self.get_row(r + 1) for r in range(int(rows.ok_value.num_response))])
-            return self.table_state
-        raise RuntimeError(rows.err_value)
-
-    def get_row(self, row: int) -> SequenceEntry:
-        sample_name = self.get_text(row, RegisterFlag.NAME)
-        vial_location = int(self.get_num(row, RegisterFlag.VIAL_LOCATION))
-        method = self.get_text(row, RegisterFlag.METHOD)
-        num_inj = int(self.get_num(row, RegisterFlag.NUM_INJ))
-        inj_vol = int(self.get_text(row, RegisterFlag.INJ_VOL))
-        inj_source = InjectionSource(self.get_text(row, RegisterFlag.INJ_SOR))
-        sample_type = SampleType(self.get_num(row, RegisterFlag.SAMPLE_TYPE))
-        return SequenceEntry(sample_name=sample_name,
-                             vial_location=vial_location,
-                             method=None if len(method) == 0 else method,
-                             num_inj=num_inj,
-                             inj_vol=inj_vol,
-                             inj_source=inj_source,
-                             sample_type=sample_type)
-
-    def check(self) -> str:
-        time.sleep(2)
-        self.send(Command.GET_SEQUENCE_CMD)
-        time.sleep(2)
-        res = self.receive()
-        if res.is_ok():
-            return res.ok_value.string_response
-        return "ERROR"
-
-    def switch(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
-        """
-        self.send(f'_SeqFile$ = "{seq_name}.S"')
-        self.send(f'_SeqPath$ = "{self.src}"')
-        self.send(Command.SWITCH_SEQUENCE_CMD)
-        time.sleep(2)
-        self.send(Command.GET_SEQUENCE_CMD)
-        time.sleep(2)
-        parsed_response = self.receive().value.string_response
-
-        assert parsed_response == f"{seq_name}.S", "Switching sequence failed."
-        self.table_state = None
-
-    def edit(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:
-        """
-        self.table_state = sequence_table
-        rows = self.get_num_rows()
-        if rows.is_ok():
-            existing_row_num = rows.value.num_response
-            wanted_row_num = len(sequence_table.rows)
-            while existing_row_num != wanted_row_num:
-                if wanted_row_num > existing_row_num:
-                    self.add_row()
-                elif wanted_row_num < existing_row_num:
-                    self.delete_row(int(existing_row_num))
-                self.send(Command.SAVE_SEQUENCE_CMD)
-                existing_row_num = self.get_num_rows().ok_value.num_response
-            self.send(Command.SWITCH_SEQUENCE_CMD)
-
-            for i, row in enumerate(sequence_table.rows):
-                self.edit_row(row=row, row_num=i + 1)
-                self.sleep(1)
-            self.send(Command.SAVE_SEQUENCE_CMD)
-            self.send(Command.SWITCH_SEQUENCE_CMD)
-
-    def edit_row(self, row: SequenceEntry, row_num: int):
-        """
-        Edits a row in the sequence table. If a row does NOT exist, a new one will be created.
-
-        :param row: sequence row entry with updated information
-        :param row_num: the row to edit, based on 1-based indexing
-        """
-        num_rows = self.get_num_rows()
-        if num_rows.is_ok():
-            while num_rows.ok_value.num_response < row_num:
-                self.add_row()
-                self.send(Command.SAVE_SEQUENCE_CMD)
-                num_rows = self.get_num_rows()
-
-        if row.vial_location:
-            loc = row.vial_location
-            if isinstance(row.vial_location, TenVialColumn):
-                loc = row.vial_location.value
-            self.edit_row_num(row=row_num, col_name=RegisterFlag.VIAL_LOCATION, val=loc)
-
-        if row.method:
-            possible_path = os.path.join(self.method_dir, row.method) + ".M\\"
-            method = row.method
-            if os.path.exists(possible_path):
-                method = os.path.join(self.method_dir, row.method)
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.METHOD, val=method)
-
-        if row.num_inj:
-            self.edit_row_num(row=row_num, col_name=RegisterFlag.NUM_INJ, val=row.num_inj)
-
-        if row.inj_vol:
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.INJ_VOL, val=row.inj_vol)
-
-        if row.inj_source:
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.INJ_SOR, val=row.inj_source.value)
-
-        if row.sample_name:
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.NAME, val=row.sample_name)
-            self.edit_row_text(row=row_num, col_name=RegisterFlag.DATA_FILE, val=row.sample_name)
-
-        if row.sample_type:
-            self.edit_row_num(row=row_num, col_name=RegisterFlag.SAMPLE_TYPE, val=row.sample_type.value)
-
-        self.send(Command.SAVE_SEQUENCE_CMD)
-
-    def run(self, stall_while_running: bool = True):
-        """
-        Starts the currently loaded sequence, storing data
-        under the <data_dir>/<sequence table name> folder.
-        Device must be ready.
-        """
-        if not self.table_state:
-            self.table_state = self.load()
-
-        timestamp = time.strftime(SEQUENCE_TIME_FORMAT)
-        self.send(Command.RUN_SEQUENCE_CMD.value)
-
-        if self.check_hplc_is_running():
-            folder_name = f"{self.table_state.name} {timestamp}"
-            self.data_files.append(SequenceDataFiles(dir=folder_name,
-                                                     sequence_name=self.table_state.name))
-
-            if stall_while_running:
-                run_completed = self.check_hplc_done_running(sequence=self.table_state)
-                if run_completed.is_ok():
-                    self.data_files[-1].dir = run_completed.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:
-        sequence_data_files: SequenceDataFiles = self.data_files[-1]
-        return sequence_data_files.dir
-
-    def get_data(self, custom_path: Optional[str] = None) -> list[AgilentChannelChromatogramData]:
-        parent_dir = self.data_files[-1].dir if not custom_path else custom_path
-        subdirs = [x[0] for x in os.walk(self.data_dir)]
-        potential_folders = sorted(list(filter(lambda d: parent_dir in d, subdirs)))
-        self.data_files[-1].child_dirs = [f for f in potential_folders if
-                                          parent_dir in f and ".M" not in f and ".D" in f]
-
-        spectra: list[AgilentChannelChromatogramData] = []
-        for row in self.data_files[-1].child_dirs:
-            self.get_spectrum(row)
-            spectra.append(AgilentChannelChromatogramData(**self.spectra))
-        return spectra

pychemstation/control/controllers/table_controller.py

@@ -1,266 +0,0 @@
-"""
-Abstract module containing shared logic for Method and Sequence tables.
-
-Authors: Lucy Hao
-"""
-
-import abc
-import os
-from typing import Union, Optional
-
-import polling
-from result import Result, Ok, Err
-
-from ...control.controllers.comm import CommunicationController
-from ...utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
-from ...utils.macro import Command, HPLCRunningStatus, Response
-from ...utils.method_types import MethodDetails
-from ...utils.sequence_types import SequenceDataFiles, SequenceTable
-from ...utils.table_types import Table, TableOperation, RegisterFlag
-
-TableType = Union[MethodDetails, SequenceTable]
-
-
-class TableController(abc.ABC):
-
-    def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
-        self.controller = controller
-        self.table = table
-        self.table_state: Optional[TableType] = None
-
-        if os.path.isdir(src):
-            self.src: str = src
-        else:
-            raise FileNotFoundError(f"dir: {src} not found.")
-
-        if os.path.isdir(data_dir):
-            self.data_dir: str = data_dir
-        else:
-            raise FileNotFoundError(f"dir: {data_dir} not found.")
-
-        self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
-            "A": AgilentHPLCChromatogram(self.data_dir),
-            "B": AgilentHPLCChromatogram(self.data_dir),
-            "C": AgilentHPLCChromatogram(self.data_dir),
-            "D": AgilentHPLCChromatogram(self.data_dir),
-            "E": AgilentHPLCChromatogram(self.data_dir),
-            "F": AgilentHPLCChromatogram(self.data_dir),
-            "G": AgilentHPLCChromatogram(self.data_dir),
-            "H": AgilentHPLCChromatogram(self.data_dir),
-        }
-
-        self.data_files: Union[list[SequenceDataFiles], list[str]] = []
-
-        # Initialize row counter for table operations
-        self.send('Local Rows')
-
-    def receive(self) -> Result[Response, str]:
-        for _ in range(10):
-            try:
-                return self.controller.receive()
-            except IndexError:
-                continue
-        return Err("Could not parse response")
-
-    def send(self, cmd: Union[Command, str]):
-        if not self.controller:
-            raise RuntimeError(
-                "Communication controller must be initialized before sending command. It is currently in offline mode.")
-        self.controller.send(cmd)
-
-    def sleepy_send(self, cmd: Union[Command, str]):
-        self.controller.sleepy_send(cmd)
-
-    def sleep(self, seconds: int):
-        """
-        Tells the HPLC to wait for a specified number of seconds.
-
-        :param seconds: number of seconds to wait
-        """
-        self.send(Command.SLEEP_CMD.value.format(seconds=seconds))
-
-    def get_num(self, row: int, col_name: RegisterFlag) -> float:
-        return self.controller.get_num_val(TableOperation.GET_ROW_VAL.value.format(register=self.table.register,
-                                                                                   table_name=self.table.name,
-                                                                                   row=row,
-                                                                                   col_name=col_name.value))
-
-    def get_text(self, row: int, col_name: RegisterFlag) -> str:
-        return self.controller.get_text_val(TableOperation.GET_ROW_TEXT.value.format(register=self.table.register,
-                                                                                     table_name=self.table.name,
-                                                                                     row=row,
-                                                                                     col_name=col_name.value))
-
-    def add_new_col_num(self,
-                        col_name: RegisterFlag,
-                        val: Union[int, float]):
-        self.sleepy_send(TableOperation.NEW_COL_VAL.value.format(
-            register=self.table.register,
-            table_name=self.table.name,
-            col_name=col_name,
-            val=val))
-
-    def add_new_col_text(self,
-                         col_name: RegisterFlag,
-                         val: str):
-        self.sleepy_send(TableOperation.NEW_COL_TEXT.value.format(
-            register=self.table.register,
-            table_name=self.table.name,
-            col_name=col_name,
-            val=val))
-
-    def edit_row_num(self,
-                     col_name: RegisterFlag,
-                     val: Union[int, float],
-                     row: Optional[int] = None):
-        self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(
-            register=self.table.register,
-            table_name=self.table.name,
-            row=row if row is not None else 'Rows',
-            col_name=col_name,
-            val=val))
-
-    def edit_row_text(self,
-                      col_name: RegisterFlag,
-                      val: str,
-                      row: Optional[int] = None):
-        self.sleepy_send(TableOperation.EDIT_ROW_TEXT.value.format(
-            register=self.table.register,
-            table_name=self.table.name,
-            row=row if row is not None else 'Rows',
-            col_name=col_name,
-            val=val))
-
-    @abc.abstractmethod
-    def get_row(self, row: int):
-        pass
-
-    def delete_row(self, row: int):
-        self.sleepy_send(TableOperation.DELETE_ROW.value.format(register=self.table.register,
-                                                                table_name=self.table.name,
-                                                                row=row))
-
-    def add_row(self):
-        """
-        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
-        """
-        self.sleepy_send(TableOperation.NEW_ROW.value.format(register=self.table.register,
-                                                             table_name=self.table.name))
-
-    def delete_table(self):
-        """
-        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
-        """
-        self.sleepy_send(TableOperation.DELETE_TABLE.value.format(register=self.table.register,
-                                                                  table_name=self.table.name))
-
-    def new_table(self):
-        """
-        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.
-
-        :param table: the table to create
-        """
-        self.send(TableOperation.CREATE_TABLE.value.format(register=self.table.register,
-                                                           table_name=self.table.name))
-
-    def get_num_rows(self) -> Result[Response, str]:
-        self.send(TableOperation.GET_NUM_ROWS.value.format(register=self.table.register,
-                                                           table_name=self.table.name,
-                                                           col_name=RegisterFlag.NUM_ROWS))
-        self.send(Command.GET_ROWS_CMD.value.format(register=self.table.register,
-                                                    table_name=self.table.name,
-                                                    col_name=RegisterFlag.NUM_ROWS))
-        res = self.controller.receive()
-
-        if res.is_ok():
-            self.send("Sleep 0.1")
-            self.send('Print Rows')
-            return res
-        else:
-            return Err("No rows could be read.")
-
-    def check_hplc_is_running(self) -> bool:
-        started_running = polling.poll(
-            lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-            step=5,
-            max_tries=100)
-        return started_running
-
-    def check_hplc_done_running(self,
-                                method: Optional[MethodDetails] = None,
-                                sequence: Optional[SequenceTable] = None) -> Result[str, str]:
-        """
-        Checks if ChemStation has finished running and can read data 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
-        :param sequence: if you are running a sequence and want to read back data, the timeout period will be adjusted to be longer than the sequence's runtime
-        :return: Return True if data can be read back, else False.
-        """
-        timeout = 10 * 60
-        if method:
-            timeout = ((method.stop_time + method.post_time + 3) * 60)
-        if sequence:
-            timeout *= len(sequence.rows)
-
-        most_recent_folder = self.retrieve_recent_data_files()
-        finished_run = polling.poll(
-            lambda: self.controller.check_if_running(),
-            timeout=timeout,
-            step=50)
-
-        check_folder = self.fuzzy_match_most_recent_folder(most_recent_folder)
-        if check_folder.is_ok() and finished_run:
-            return check_folder
-        elif check_folder.is_ok():
-            finished_run = polling.poll(
-                lambda: self.controller.check_if_running(),
-                timeout=timeout,
-                step=50)
-            if finished_run:
-                return check_folder
-            return check_folder
-        else:
-            return Err("Run did not complete as expected")
-
-    def fuzzy_match_most_recent_folder(self, most_recent_folder) -> Result[str, str]:
-        if os.path.exists(most_recent_folder):
-            return Ok(most_recent_folder)
-
-        subdirs = [x[0] for x in os.walk(self.data_dir)]
-        potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
-        parent_dirs = []
-        for folder in potential_folders:
-            path = os.path.normpath(folder)
-            split_folder = path.split(os.sep)
-            if most_recent_folder in split_folder[-1]:
-                parent_dirs.append(folder)
-        parent_dir = sorted(parent_dirs, reverse=True)[0]
-        return Ok(parent_dir)
-
-    @abc.abstractmethod
-    def retrieve_recent_data_files(self):
-        pass
-
-    @abc.abstractmethod
-    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
-        pass
-
-    def get_spectrum(self, data_file: str):
-        """
-        Load chromatogram for any channel in spectra dictionary.
-        """
-        for channel, spec in self.spectra.items():
-            try:
-                spec.load_spectrum(data_path=data_file, channel=channel)
-            except FileNotFoundError:
-                self.spectra[channel] = None
-                print(f"No data at channel: {channel}")

pychemstation/control/table/__init__.py

@@ -1,3 +0,0 @@
-from .method import MethodController
-from .sequence import SequenceController
-from .table_controller import TableController