pychemstation 0.8.3__tar.gz → 0.10.1__tar.gz

{pychemstation-0.8.3 → pychemstation-0.10.1}/.gitlab-ci.yml

@@ -13,6 +13,4 @@ pages:
     - mv doc/ ./public/
   artifacts:
     paths:
-    - public
-  rules:
-    - if: $CI_COMMIT_REF_NAME == $CI_DEFAULT_BRANCH
+    - public

{pychemstation-0.8.3/pychemstation.egg-info → pychemstation-0.10.1}/PKG-INFO

@@ -1,21 +1,32 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.7.0.dev2
-Summary: Library to interact with Chemstation software, primarily used in Hein lab
-Home-page: https://gitlab.com/heingroup/device-api/pychemstation
-Author: Lucy Hao
-Author-email: lhao03@student.ubc.ca
-Classifier: Programming Language :: Python :: 3
+Version: 0.10.1
+Summary: Library to interact with Chemstation software, primarily used in Hein lagit branch -mb
+Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
+Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation
+Author-email: lucyhao <hao.lucyy@gmail.com>
+License-File: LICENSE
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Requires-Dist: aghplctools>=4.8.8
+Requires-Dist: coverage>=7.6.1
+Requires-Dist: matplotlib>=3.7.5
+Requires-Dist: pandas>=2.0.3
+Requires-Dist: pdoc>=14.7.0
+Requires-Dist: polling>=0.3.2
+Requires-Dist: pytest>=7.3.5
+Requires-Dist: rainbow-api>=1.0.10
+Requires-Dist: result>=0.17.0
+Requires-Dist: scipy>=1.10.1
+Requires-Dist: seabreeze>=2.9.2
+Requires-Dist: setuptools>=75.3.2
+Requires-Dist: twine>=6.1.0
+Requires-Dist: xsdata>=24.9
 Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: polling
-Requires-Dist: seabreeze
-Requires-Dist: xsdata
-Requires-Dist: result
-Requires-Dist: rainbow-api
-Requires-Dist: aghplctools==4.8.6
 
 # Agilent HPLC Macro Control
 
@@ -23,8 +34,12 @@ Requires-Dist: aghplctools==4.8.6
 
 [![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
 
+> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **>=3.10**, use
+> version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
+> is not guaranteed!
+
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
-Check out the [docs](https://hein-analytical-control-5e6e85.gitlab.io/) for usage instructions. This project is under
+Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
 active development, and breaking changes may occur at any moment.
 
 ## Getting started
@@ -67,13 +82,14 @@ from pychemstation.control import HPLCController
 import pandas as pd
 
 # these paths will be unique to your Chemstation setup
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
 DEFAULT_METHOD = "GENERAL-POROSHELL"
+DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
 DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
-SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence"
+DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data\\"
+DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data\\"
+SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\2\\Sequence\\"
 
-hplc_controller = HPLCController(data_dir=DATA_DIR,
+hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  sequence_dir=SEQUENCE_DIR,
                                  method_dir=DEFAULT_METHOD_DIR)
@@ -105,6 +121,8 @@ Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
-- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI)
-  used in [**Operator-free HPLC automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
-  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.
+- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
+  automated method development guided by Bayesian optimization
+  **](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  created by members in the Bourne Group. Copyright © Bourne Group, used under
+  the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.8.3 → pychemstation-0.10.1}/README.md

@@ -4,8 +4,12 @@
 
 [![PyPI Latest Release](https://img.shields.io/pypi/v/pychemstation.svg)](https://pypi.org/project/pychemstation/)
 
+> **_NOTE:_** If you are running Python **3.8**, use versions 0.**8**.x. If you are running Python **>=3.10**, use
+> version 0.**10**.x. You are welcome to use newer pychemstation versions with older Python versions, but functionality
+> is not guaranteed!
+
 Unofficial Python package to control Agilent Chemstation; we are not affiliated with Agilent.
-Check out the [docs](https://hein-analytical-control-5e6e85.gitlab.io/) for usage instructions. This project is under
+Check out the [docs](https://pychemstation-e5a086.gitlab.io/pychemstation.html) for usage instructions. This project is under
 active development, and breaking changes may occur at any moment.
 
 ## Getting started
@@ -87,6 +91,8 @@ Lucy Hao, Maria Politi
 
 - Adapted from [**AnalyticalLabware**](https://github.com/croningp/analyticallabware), created by members in the Cronin
   Group. Copyright © Cronin Group, used under the [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) license.
-- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI)
-  used in [**Operator-free HPLC automated method development guided by Bayesian optimization**](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
-  created by members in the Bourne Group.  Copyright © Bourne Group, used under the [MIT](https://opensource.org/license/mit) license.
+- Adapted from the [MACROS](https://github.com/Bourne-Group/HPLCMethodOptimisationGUI) used in [**Operator-free HPLC
+  automated method development guided by Bayesian optimization
+  **](https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00062e),
+  created by members in the Bourne Group. Copyright © Bourne Group, used under
+  the [MIT](https://opensource.org/license/mit) license.

{pychemstation-0.8.3 → pychemstation-0.10.1}/build/lib/pychemstation/analysis/__init__.py

@@ -1 +1,5 @@
 from .base_spectrum import AbstractSpectrum
+
+__all__ = [
+    'AbstractSpectrum',
+]

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/analysis/base_spectrum.py

@@ -6,12 +6,12 @@ from abc import ABC, abstractmethod
 import matplotlib.pyplot as plt
 import numpy as np
 from scipy import (
-    sparse,
-    signal,
     integrate,
+    signal,
+    sparse,
 )
 
-from .utils import interpolate_to_index, find_nearest_value_index
+from ..utils.num_utils import find_nearest_value_index, interpolate_to_index
 
 
 class AbstractSpectrum(ABC):
@@ -197,10 +197,10 @@ class AbstractSpectrum(ABC):
             return (self.x.copy()[full_mask], self.y.copy()[full_mask])
 
     def show_spectrum(
-        self,
-        filename=None,
-        title=None,
-        label=None,
+            self,
+            filename=None,
+            title=None,
+            label=None,
     ):
         """Plots the spectral data using matplotlib.pyplot module.
 
@@ -385,12 +385,12 @@ class AbstractSpectrum(ABC):
 
         if rule == "trapz":
             return integrate.trapz(
-                self.y[left_idx : right_idx + 1], self.x[left_idx : right_idx + 1]
+                self.y[left_idx: right_idx + 1], self.x[left_idx: right_idx + 1]
             )
 
         elif rule == "simps":
             return integrate.simps(
-                self.y[left_idx : right_idx + 1], self.x[left_idx : right_idx + 1]
+                self.y[left_idx: right_idx + 1], self.x[left_idx: right_idx + 1]
             )
 
         else:

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/analysis/process_report.py

@@ -4,15 +4,21 @@ import re
 from abc import abstractmethod
 from dataclasses import dataclass
 from enum import Enum
-from typing import List, AnyStr, Dict, Optional, Pattern
+from typing import AnyStr, Dict, List, Optional, Pattern
 
 import pandas as pd
-from aghplctools.ingestion.text import _no_peaks_re, _area_report_re, _header_block_re, _signal_info_re, \
-    _signal_table_re, chunk_string
-from result import Result, Err, Ok
+from aghplctools.ingestion.text import (
+    _area_report_re,
+    _header_block_re,
+    _no_peaks_re,
+    _signal_info_re,
+    _signal_table_re,
+    chunk_string,
+)
+from result import Err, Ok, Result
 
 from pychemstation.utils.chromatogram import AgilentHPLCChromatogram
-from pychemstation.utils.tray_types import Tray, FiftyFourVialPlate
+from pychemstation.utils.tray_types import FiftyFourVialPlate, Tray
 
 
 @dataclass
@@ -70,7 +76,7 @@ class CSVProcessor(ReportProcessor):
         :returns: subset of complete report details, specifically the sample location, solvents in pumps,
          and list of peaks at each wavelength channel.
         """
-        labels = os.path.join(self.path, f'REPORT00.CSV')
+        labels = os.path.join(self.path, 'REPORT00.CSV')
         if os.path.exists(labels):
             df_labels: Dict[int, Dict[int: AnyStr]] = pd.read_csv(labels, encoding="utf-16", header=None).to_dict()
             vial_location = []
@@ -200,7 +206,7 @@ class TXTProcessor(ReportProcessor):
         should be able to use the `parse_area_report` method of aghplctools v4.8.8
         """
         if re.search(_no_peaks_re, report_text):  # There are no peaks in Report.txt
-            raise ValueError(f'No peaks found in Report.txt')
+            raise ValueError('No peaks found in Report.txt')
         blocks = _header_block_re.split(report_text)
         signals = {}  # output dictionary
         for ind, block in enumerate(blocks):

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/control/__init__.py

@@ -2,3 +2,7 @@
 .. include:: README.md
 """
 from .hplc import HPLCController
+
+__all__ = [
+    'HPLCController',
+]

{pychemstation-0.8.3 → pychemstation-0.10.1}/build/lib/pychemstation/control/controllers/__init__.py

@@ -3,7 +3,11 @@
 """
 
 from .comm import CommunicationController
-from .devices.pump import PumpController
-from .devices.column import ColumnController
 from .tables.method import MethodController
 from .tables.sequence import SequenceController
+
+__all__ = [
+    'CommunicationController',
+    'MethodController',
+    'SequenceController'
+]

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/control/controllers/comm.py

@@ -11,11 +11,18 @@ Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
 """
 import os
 import time
-from typing import Optional
+from typing import Optional, Union
 
-from result import Result, Ok, Err
+from result import Err, Ok, Result
 
-from ...utils.macro import *
+from ...utils.macro import (
+    str_to_status,
+    HPLCAvailStatus,
+    HPLCErrorStatus,
+    Command,
+    Status,
+    Response,
+)
 
 
 class CommunicationController:
@@ -193,14 +200,14 @@ class CommunicationController:
         str_response_prefix = "String Responses:"
         possible_response = self._receive(self.cmd_no)
         if possible_response.is_ok():
-            lines = possible_response.value.splitlines()
+            lines = possible_response.ok_value.splitlines()
             for line in lines:
                 if str_response_prefix in line and num_response_prefix in line:
                     string_responses_dirty, _, numerical_responses = line.partition(num_response_prefix)
                     _, _, string_responses = string_responses_dirty.partition(str_response_prefix)
                     return Ok(Response(string_response=string_responses.strip(),
                                        num_response=float(numerical_responses.strip())))
-            return Err(f"Could not retrieve HPLC response")
+            return Err("Could not retrieve HPLC response")
         else:
             return Err(f"Could not establish response to HPLC: {possible_response}")
 

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/control/controllers/devices/device.py

@@ -1,13 +1,13 @@
 import abc
-from typing import Union, List
+from typing import List, Union, Dict, Optional
 
 from result import Result
 
-from ....analysis.process_report import ReportType, AgilentReport
+from ....analysis.process_report import AgilentReport, ReportType
 from ....control.controllers import CommunicationController
 from ....control.controllers.tables.table import TableController
-from ....utils.chromatogram import AgilentChannelChromatogramData
-from ....utils.table_types import Table, T
+from ....utils.chromatogram import AgilentChannelChromatogramData, AgilentHPLCChromatogram
+from ....utils.table_types import T, Table
 
 
 class DeviceController(TableController, abc.ABC):
@@ -26,11 +26,14 @@ class DeviceController(TableController, abc.ABC):
     def retrieve_recent_data_files(self):
         raise NotImplementedError
 
-    def get_data(self) -> Union[List[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
-        raise NotImplementedError
-
     def fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[T, str]:
         raise NotImplementedError
 
     def get_report(self, report_type: ReportType = ReportType.TXT) -> List[AgilentReport]:
         raise NotImplementedError
+
+    def get_data_uv(self) -> Union[List[Dict[str, AgilentHPLCChromatogram]], Dict[str, AgilentHPLCChromatogram]]:
+        raise NotImplementedError
+
+    def get_data(self, custom_path: Optional[str] = None) -> Union[List[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
+        raise NotImplementedError

pychemstation-0.10.1/build/lib/pychemstation/control/controllers/devices/injector.py

@@ -0,0 +1,51 @@
+from __future__ import annotations
+
+from .device import DeviceController
+from ....control.controllers import CommunicationController
+from ....utils.injector_types import (
+    Draw,
+    Inject,
+    InjectorTable,
+    Mode,
+    Remote,
+    RemoteCommand,
+    SourceType,
+    Wait,
+)
+from ....utils.table_types import RegisterFlag, Table
+from ....utils.tray_types import Tray
+
+
+class InjectorController(DeviceController):
+
+    def __init__(self, controller: CommunicationController, table: Table, offline: bool):
+        super().__init__(controller, table, offline)
+
+    def get_row(self, row: int) -> None | Remote | Draw | Wait | Inject:
+        def return_tray_loc() -> Tray:
+            pass
+
+        function = self.get_text(row, RegisterFlag.FUNCTION)
+        if function == "Wait":
+            return Wait(duration=self.get_num(row, RegisterFlag.TIME))
+        elif function == "Inject":
+            return Inject()
+        elif function == "Draw":
+            # TODO: better error handling
+            is_source = SourceType(self.get_text(row, RegisterFlag.DRAW_SOURCE))
+            is_volume = Mode(self.get_text(row, RegisterFlag.DRAW_VOLUME))
+            vol = self.get_num(row, RegisterFlag.DRAW_VOLUME_VALUE) if is_volume == Mode.SET else None
+            if is_source is SourceType.SPECIFIC_LOCATION:
+                return Draw(amount=vol, source=return_tray_loc())
+            elif is_source is SourceType.LOCATION:
+                return Draw(amount=vol, location=self.get_text(row, RegisterFlag.DRAW_LOCATION))
+        elif function == "Remote":
+            return Remote(command=RemoteCommand(self.get_text(row, RegisterFlag.REMOTE)),
+                          duration=self.get_num(row, RegisterFlag.REMOTE_DUR))
+
+    def load(self) -> InjectorTable | None:
+        rows = self.get_num_rows()
+        if rows.is_ok():
+            return InjectorTable(functions=[self.get_row(i) for i in range(int(rows.ok_value.num_response))])
+
+   

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/control/controllers/tables/method.py

@@ -1,6 +1,7 @@
 import os
 import time
-from typing import List
+import warnings
+from typing import Dict, List, Optional, Union
 
 from result import Err, Ok, Result
 from xsdata.formats.dataclass.parsers import XmlParser
@@ -13,9 +14,15 @@ from ....utils.chromatogram import (
     AgilentChannelChromatogramData,
     AgilentHPLCChromatogram,
 )
-from ....utils.macro import *
-from ....utils.method_types import *
-from ....utils.table_types import *
+from ....utils.macro import Command
+from ....utils.method_types import (
+    HPLCMethodParams,
+    MethodDetails,
+    Param,
+    PType,
+    TimeTableEntry,
+)
+from ....utils.table_types import RegisterFlag, T, Table, TableOperation
 from ..devices.injector import InjectorController
 from .table import TableController
 
@@ -129,6 +136,10 @@ class MethodController(TableController):
                 register=self.table_locator.register,
                 register_flag=RegisterFlag.MAX_TIME))
 
+    def get_total_runtime(self) -> Union[int, float]:
+        """Returns total method runtime in minutes."""
+        return self.get_post_time() + self.get_stop_time()
+
     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.
@@ -173,6 +184,7 @@ class MethodController(TableController):
         :raises FileNotFoundError: Method does not exist
         :return: method details
         """
+        warnings.warn("This method is not actively maintained.")
         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")
@@ -347,29 +359,39 @@ class MethodController(TableController):
             raise RuntimeError("Method failed to start.")
 
         self.data_files.append(os.path.join(self.data_dirs[0], folder_name))
+        self.timeout = (self.get_total_runtime()) * 60
 
         if stall_while_running:
-            self.timeout = (self.get_stop_time() + self.get_post_time()) * 60
             run_completed = self.check_hplc_done_running()
             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] = self.fuzzy_match_most_recent_folder(folder_name).ok_value
+            folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
+            while folder.is_err():
+                folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
+            if folder.is_ok():
+                self.data_files[-1] = folder.ok_value
+            else:
+                warning = f"Data folder {self.data_files[-1]} may not exist, returning and will check again after run is done."
+                warnings.warn(warning)
+
 
     def fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[T, str]:
         if os.path.exists(most_recent_folder):
             return Ok(most_recent_folder)
         return Err("Folder not found!")
 
-    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
+    def get_data(self, custom_path: Optional[str] = None) -> AgilentChannelChromatogramData:
+        custom_path = custom_path if custom_path else self.data_files[-1]
+        self.get_spectrum_at_channels(custom_path)
+        return AgilentChannelChromatogramData(**self.spectra)
+
+    def get_data_uv(self, custom_path: Optional[str] = None) -> Dict[str, AgilentHPLCChromatogram]:
+        custom_path = custom_path if custom_path else self.data_files[-1]
+        self.get_uv_spectrum(custom_path)
+        return self.uv
 
     def get_report(self, custom_path: Optional[str] = None,
                    report_type: ReportType = ReportType.TXT) -> List[AgilentReport]:

{pychemstation-0.8.3 → pychemstation-0.10.1/build/lib}/pychemstation/control/controllers/tables/sequence.py

@@ -1,19 +1,29 @@
 import os
 import time
-from typing import Optional, List, Dict
+from typing import Dict, List, Optional
 
-from result import Result, Ok, Err
+from result import Err, Ok, Result
 from typing_extensions import override
 
-from .table import TableController
-from .. import MethodController
-from ....analysis.process_report import ReportType, AgilentReport
+from ....analysis.process_report import AgilentReport, ReportType
 from ....control.controllers.comm import CommunicationController
-from ....utils.chromatogram import SEQUENCE_TIME_FORMAT, AgilentChannelChromatogramData, AgilentHPLCChromatogram
+from ....utils.chromatogram import (
+    SEQUENCE_TIME_FORMAT,
+    AgilentChannelChromatogramData,
+    AgilentHPLCChromatogram,
+)
 from ....utils.macro import Command
-from ....utils.sequence_types import SequenceTable, SequenceEntry, SequenceDataFiles, InjectionSource, SampleType
+from ....utils.sequence_types import (
+    InjectionSource,
+    SampleType,
+    SequenceDataFiles,
+    SequenceEntry,
+    SequenceTable,
+)
 from ....utils.table_types import RegisterFlag, Table
-from ....utils.tray_types import TenVialColumn, FiftyFourVialPlate
+from ....utils.tray_types import FiftyFourVialPlate, TenVialColumn
+from .. import MethodController
+from .table import TableController
 
 
 class SequenceController(TableController):
@@ -82,7 +92,7 @@ class SequenceController(TableController):
         time.sleep(2)
         self.send(Command.GET_SEQUENCE_CMD)
         time.sleep(2)
-        parsed_response = self.receive().value.string_response
+        parsed_response = self.receive().ok_value.string_response
 
         assert parsed_response == f"{seq_name}.S", "Switching sequence failed."
         self.table_state = None
@@ -97,7 +107,7 @@ class SequenceController(TableController):
         self.table_state = sequence_table
         rows = self.get_num_rows()
         if rows.is_ok():
-            existing_row_num = rows.value.num_response
+            existing_row_num = rows.ok_value.num_response
             wanted_row_num = len(sequence_table.rows)
             while existing_row_num != wanted_row_num:
                 if wanted_row_num > existing_row_num:
@@ -127,7 +137,6 @@ class SequenceController(TableController):
                 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(loc, TenVialColumn):
@@ -135,7 +144,6 @@ class SequenceController(TableController):
             elif isinstance(loc, FiftyFourVialPlate):
                 loc = row.vial_location.value()
             self._edit_row_num(row=row_num, col_name=RegisterFlag.VIAL_LOCATION, val=loc)
-
         if row.method:
             method_dir = self.method_controller.src
             possible_path = os.path.join(method_dir, row.method) + ".M\\"
@@ -143,23 +151,18 @@ class SequenceController(TableController):
             if os.path.exists(possible_path):
                 method = os.path.join(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)
             if row.data_file:
                 self._edit_row_text(row=row_num, col_name=RegisterFlag.DATA_FILE, val=row.data_file)
             else:
                 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)
 
@@ -179,15 +182,15 @@ class SequenceController(TableController):
 
         total_runtime = 0
         for entry in self.table_state.rows:
-            curr_method_runtime = self.method_controller.get_post_time() + self.method_controller.get_stop_time()
-            loaded_method = self.method_controller.get_method_name()[:-2]
+            curr_method_runtime = self.method_controller.get_total_runtime()
+            loaded_method = self.method_controller.get_method_name().removesuffix(".M")
             method_path = entry.method.split(sep="\\")
             method_name = method_path[-1]
             if loaded_method != method_name:
-                method_dir = os.path.join(*method_path[:-1]) if len(method_path) > 1 else None
+                method_dir = "\\".join(method_path[:-1])+"\\" if len(method_path) > 1 else None
                 self.method_controller.switch(method_name=method_name,
                                               alt_method_dir=method_dir)
-                curr_method_runtime = self.method_controller.get_post_time() + self.method_controller.get_stop_time()
+                curr_method_runtime = self.method_controller.get_total_runtime()
             total_runtime += curr_method_runtime
 
         timestamp = time.strftime(SEQUENCE_TIME_FORMAT)
@@ -196,8 +199,8 @@ class SequenceController(TableController):
 
         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))
+            data_file = SequenceDataFiles(dir=folder_name, sequence_name=self.table_state.name)
+            self.data_files.append(data_file)
 
             if stall_while_running:
                 run_completed = self.check_hplc_done_running()
@@ -205,10 +208,8 @@ class SequenceController(TableController):
                     self.data_files[-1] = run_completed.ok_value
                 else:
                     raise RuntimeError("Run error has occurred.")
-            else:
-                self.data_files[-1] = SequenceDataFiles(dir=folder_name,
-                                                        child_dirs=[],
-                                                        sequence_name=self.table_state.name)
+        else:
+            raise RuntimeError("Sequence run did not start.")
 
     @override
     def fuzzy_match_most_recent_folder(self, most_recent_folder: SequenceDataFiles) -> Result[SequenceDataFiles, str]:
@@ -248,17 +249,25 @@ class SequenceController(TableController):
         except Exception:
             return Err("Failed to get sequence folder")
 
-    def get_data(self, custom_path: Optional[str] = None,
-                 read_uv: bool = False) -> List[AgilentChannelChromatogramData]:
-        if len(self.data_files[-1].child_dirs) == 0:
-            self.data_files[-1] = self.fuzzy_match_most_recent_folder(self.data_files[-1]).ok_value
-        spectra: list[AgilentChannelChromatogramData] = []
-        all_w_spectra: list[Dict[str, AgilentHPLCChromatogram]] = []
+    def get_data_uv(self,custom_path: Optional[str] = None) -> List[Dict[str, AgilentHPLCChromatogram]]:
+        custom_path = SequenceDataFiles(dir=custom_path, child_dirs=[], sequence_name="") if custom_path else self.data_files[-1]
+        if len(custom_path.child_dirs) == 0:
+            self.data_files[-1] = self.fuzzy_match_most_recent_folder(custom_path).ok_value
+        all_w_spectra: List[Dict[str, AgilentHPLCChromatogram]] = []
         for row in self.data_files[-1].child_dirs:
-            self.get_spectrum(row, read_uv)
-            spectra.append(AgilentChannelChromatogramData(**self.spectra))
+            self.get_uv_spectrum(row)
             all_w_spectra.append(self.uv)
-        return spectra if not read_uv else all_w_spectra
+        return all_w_spectra
+
+    def get_data(self, custom_path: Optional[str] = None) -> List[AgilentChannelChromatogramData]:
+        custom_path = SequenceDataFiles(dir=custom_path, child_dirs=[], sequence_name="") if custom_path else self.data_files[-1]
+        if len(custom_path.child_dirs) == 0:
+            self.data_files[-1] = self.fuzzy_match_most_recent_folder(custom_path).ok_value
+        spectra: List[AgilentChannelChromatogramData] = []
+        for row in self.data_files[-1].child_dirs:
+            self.get_spectrum_at_channels(row)
+            spectra.append(AgilentChannelChromatogramData(**self.spectra))
+        return spectra
 
     def get_report(self, custom_path: Optional[str] = None,
                    report_type: ReportType = ReportType.TXT) -> List[AgilentReport]:
@@ -268,7 +277,7 @@ class SequenceController(TableController):
                                                                                          child_dirs=[],
                                                                                          sequence_name="NA")).ok_value)
         parent_dir = self.data_files[-1]
-        spectra = self.get_data(custom_path=custom_path)
+        spectra = self.get_data()
         reports = []
         for i, child_dir in enumerate(parent_dir.child_dirs):
             metd_report = self.get_report_details(child_dir, report_type)