pychemstation 0.6.1__tar.gz → 0.6.3__tar.gz

{pychemstation-0.6.1 → pychemstation-0.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.6.1
+Version: 0.6.3
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation/analysis/process_report.py

@@ -1,18 +1,15 @@
-"""
-pip install pandas
-pip install aghplctools==4.8.6
-"""
-
 import os
 import re
 from dataclasses import dataclass
-from typing import List, AnyStr
+from typing import List, AnyStr, Dict
 
 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 pychemstation.utils.tray_types import FiftyFourVialPlate, int_to_ffvp, Tray
+
 
 @dataclass
 class AgilentPeak:
@@ -25,6 +22,13 @@ class AgilentPeak:
     height_percent: float
 
 
+@dataclass
+class AgilentReport:
+    vial_location: Tray
+    signals: Dict[AnyStr, List[AgilentPeak]]
+    solvents: Dict[AnyStr, AnyStr]
+
+
 _column_re_dictionary = {  # regex matches for column and unit combinations
     'Peak': {  # peak index
         '#': '[ ]+(?P<Peak>[\d]+)',  # number
@@ -51,7 +55,7 @@ _column_re_dictionary = {  # regex matches for column and unit combinations
 }
 
 
-def build_peak_regex(signal_table: str):
+def build_peak_regex(signal_table: str) -> re.Pattern[AnyStr]:
     """
     Builds a peak regex from a signal table
 
@@ -211,9 +215,40 @@ def process_folder(folder_path, target_wavelengths=None, min_retention_time=0, m
     return results_df
 
 
-def process_csv_report(folder_path: str, num: int) -> Result[List[AgilentPeak], AnyStr]:
-    potential_report = os.path.join(folder_path, f'REPORT0{num}.CSV')
-    if os.path.exists(potential_report):
-        df = pd.read_csv(potential_report, encoding="utf-16", header=None)
-        return Ok(df.apply(lambda row: AgilentPeak(*row), axis=1))
+def process_csv_report(folder_path: str) -> Result[AgilentReport, AnyStr]:
+    labels = os.path.join(folder_path, f'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 = []
+        signals = {}
+        solvents = {}
+        for pos, val in df_labels[0].items():
+            if val == "Location":
+                vial_location = df_labels[1][pos]
+            elif "Solvent" in val:
+                if val not in solvents.keys():
+                    solvents[val] = df_labels[2][pos]
+            elif val == "Number of Signals":
+                num_signals = int(df_labels[1][pos])
+                for s in range(1, num_signals + 1):
+                    peaks = process_peaks(os.path.join(folder_path, f'REPORT0{s}.CSV'))
+                    if peaks.is_ok():
+                        wavelength = df_labels[1][pos + s].partition(",4 Ref=off")[0][-3:]
+                        signals[wavelength] = peaks.ok_value
+                break
+
+        return Ok(AgilentReport(
+            signals=signals,
+            vial_location=int_to_ffvp(vial_location),
+            solvents=solvents
+        ))
+
     return Err("No report found")
+
+
+def process_peaks(folder_path: str) -> Result[List[AgilentPeak], AnyStr]:
+    try:
+        df = pd.read_csv(folder_path, encoding="utf-16", header=None)
+        return Ok(df.apply(lambda row: AgilentPeak(*row), axis=1))
+    except Exception:
+        return Err("Trouble reading report")

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation/control/controllers/tables/method.py

@@ -132,7 +132,7 @@ class MethodController(TableController):
         :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,
+        self.send(Command.SWITCH_METHOD_CMD_SPECIFIC.value.format(method_dir=self.src,
                                                          method_name=method_name))
 
         time.sleep(2)

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation/control/controllers/tables/table.py

@@ -305,5 +305,5 @@ class TableController(abc.ABC):
             try:
                 spec.load_spectrum(data_path=data_path, channel=channel)
             except FileNotFoundError:
-                self.spectra[channel] = None
+                self.spectra[channel] = AgilentHPLCChromatogram(self.data_dir)
                 print(f"No data at channel: {channel}")

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation/utils/macro.py

@@ -38,6 +38,7 @@ class Command(Enum):
     GET_METHOD_CMD = "response$ = _MethFile$"
     GET_ROWS_CMD = 'response_num = TabHdrVal({register}, "{table_name}", "{col_name}")'
     SWITCH_METHOD_CMD = 'LoadMethod _MethPath$, _MethFile$'
+    SWITCH_METHOD_CMD_SPECIFIC = 'LoadMethod "{method_dir}", "{method_name}.M"'
     START_METHOD_CMD = "StartMethod"
     RUN_METHOD_CMD = 'RunMethod "{data_dir}",, "{experiment_name}_{timestamp}"'
     STOP_METHOD_CMD = "StopMethod"

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation/utils/tray_types.py

@@ -18,16 +18,16 @@ class Num(Enum):
 
 
 class Plate(Enum):
-    ONE = "1"
-    TWO = "2"
+    ONE = 0
+    TWO = 4000
 
 
 class Letter(Enum):
-    A = 8191
-    B = 8255
-    C = 8319
-    D = 8383
-    F = 8447
+    A = 4191
+    B = 4255
+    C = 4319
+    D = 4383
+    F = 4447
 
 
 @dataclass
@@ -37,7 +37,11 @@ class FiftyFourVialPlate:
     num: Num
 
     def value(self) -> int:
-        return self.letter.value + self.num.value
+        return self.plate.value + self.letter.value + self.num.value
+
+
+def int_to_ffvp(num: int) -> FiftyFourVialPlate:
+    return num
 
 
 class TenVialColumn(Enum):
@@ -53,4 +57,4 @@ class TenVialColumn(Enum):
     TEN = 10
 
 
-Tray = Union[FiftyFourVialPlate, TenVialColumn]
+Tray = Union[FiftyFourVialPlate, TenVialColumn]

{pychemstation-0.6.1 → pychemstation-0.6.3}/pychemstation.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.6.1
+Version: 0.6.3
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao

{pychemstation-0.6.1 → pychemstation-0.6.3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pychemstation",
-    version="0.6.1",
+    version="0.6.3",
     author="Lucy Hao",
     author_email="lhao03@student.ubc.ca",
     description="Library to interact with Chemstation software, primarily used in Hein lab",

{pychemstation-0.6.1 → pychemstation-0.6.3}/tests/test_inj.py

@@ -2,22 +2,27 @@ import os
 import unittest
 
 from pychemstation.control import HPLCController
+from pychemstation.utils.tray_types import FiftyFourVialPlate, Letter, Plate, Num
 from tests.constants import *
 
+offline = True
+
 
 class TestInj(unittest.TestCase):
     def setUp(self):
         path_constants = room(254)
         for path in path_constants:
-            if not os.path.exists(path):
+            if not offline and not os.path.exists(path):
                 self.fail(
                     f"{path} does not exist on your system. If you would like to run tests, please change this path.")
 
-        self.hplc_controller = HPLCController(comm_dir=path_constants[0],
+        self.hplc_controller = HPLCController(offline=offline,
+                                              comm_dir=path_constants[0],
                                               method_dir=path_constants[1],
                                               data_dir=path_constants[2],
                                               sequence_dir=path_constants[3])
-        # self.hplc_controller.switch_method(DEFAULT_METHOD)
+        if not offline:
+            self.hplc_controller.switch_method(DEFAULT_METHOD)
 
     def test_load_inj(self):
         try:
@@ -26,7 +31,8 @@ class TestInj(unittest.TestCase):
         except Exception as e:
             self.fail(f"Should have not failed, {e}")
 
-
+    def test_plate_number(self):
+        self.assertEqual(4096, FiftyFourVialPlate(plate=Plate.ONE, letter=Letter.A, num=Num.FOUR).value())
 
 
 if __name__ == '__main__':

pychemstation-0.6.3/tests/test_proc_rep.py

@@ -0,0 +1,52 @@
+import unittest
+
+from result import Result
+
+from pychemstation.analysis.process_report import process_csv_report
+
+
+class TestReport(unittest.TestCase):
+
+    def test_build_peak_regex(self):
+        try:
+            # TODO
+            print('yes')
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_parse_area_report(self):
+        try:
+            # TODO
+            print('yes')
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_process_export_report(self):
+        try:
+            import pandas as pd
+
+            file_path = "/Users/lucyhao/Codes/pychemstation/tests/0_2025-03-15 19-14-35.D/Report00.CSV"
+            df = pd.read_csv(file_path, encoding="utf-16")
+
+            # Print the first column
+            print(df)
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_process_folder(self):
+        try:
+            # TODO
+            print('yes')
+        except Exception as e:
+            self.fail(f"Should have not failed, {e}")
+
+    def test_report_csv(self):
+        try:
+            report: Result = process_csv_report(folder_path="0_2025-03-15 19-14-35.D")
+            print(report)
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+
+if __name__ == '__main__':
+    unittest.main()

pychemstation-0.6.1/tests/test_proc_rep.py

@@ -1,27 +0,0 @@
-import unittest
-
-from result import Result
-
-from pychemstation.analysis.process_report import process_csv_report
-
-
-class TestReport(unittest.TestCase):
-
-    def test_process_reporttxt(self):
-        try:
-            # TODO
-            print('yes')
-        except Exception as e:
-            self.fail(f"Should have not failed, {e}")
-
-    def test_report_csv(self):
-        try:
-            possible_peaks: Result = process_csv_report(folder_path="0_2025-03-15 19-14-35.D", num=1)
-            self.assertTrue(len(possible_peaks.ok_value) == 16)
-            print('yes')
-        except Exception as e:
-            self.fail(f"Should have not failed: {e}")
-
-
-if __name__ == '__main__':
-    unittest.main()