pychemstation 0.6.1__py3-none-any.whl → 0.6.3__py3-none-any.whl

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/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/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/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/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.dist-info → pychemstation-0.6.3.dist-info}/METADATA

@@ -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.dist-info → pychemstation-0.6.3.dist-info}/RECORD

@@ -1,7 +1,7 @@
 pychemstation/__init__.py,sha256=SpTl-Tg1B1HTyjNOE-8ue-N2wGnXN_2zl7RFUSxlkiM,33
 pychemstation/analysis/__init__.py,sha256=EWoU47iyn9xGS-b44zK9eq50bSjOV4AC5dvt420YMI4,44
 pychemstation/analysis/base_spectrum.py,sha256=XPf9eJ72uz0CnxCY5uFOyu1MbVX-OTTXeN1tLzIMok4,16536
-pychemstation/analysis/process_report.py,sha256=d290KgPY-cMlQg4yHaspLFxgso_yu9qNxXG6SF2qpuo,9054
+pychemstation/analysis/process_report.py,sha256=l7LiCBctXUAcINGwBetAlSAziSKhxG7v7wuM9aWFrUU,10409
 pychemstation/analysis/spec_utils.py,sha256=UOo9hJR3evJfmaohEEsyb7aq6X996ofuUfu-GKjiDi8,10201
 pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
 pychemstation/control/__init__.py,sha256=4xTy8X-mkn_PPZKr7w9rnj1wZhtmTesbQptPhpYmKXs,64
@@ -19,10 +19,10 @@ pychemstation/control/controllers/devices/device.py,sha256=QUFpUwmGxMzmG1CiRhNau
 pychemstation/control/controllers/devices/injector.py,sha256=Kxf4NjxPUt2xjOmJ9Pea1b9YzWyGcpW8VdOlx9Jo-Nw,5540
 pychemstation/control/controllers/devices/pump.py,sha256=DJQh4lNXEraeC1CWrsKmsITOjuYlRI3tih_XRB3F1hg,1404
 pychemstation/control/controllers/tables/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/control/controllers/tables/method.py,sha256=3GdAQ6Cwf20QL3v7eMkwNieWbJdtr9GN12USbSVl_iE,16426
+pychemstation/control/controllers/tables/method.py,sha256=Bzo0BHatMOFf_TmMBVuQbtLvZRTARaW5q1e2-WKJVHY,16435
 pychemstation/control/controllers/tables/ms.py,sha256=JFD-tOhu8uRyKdl-E3-neRssii8MNqVRIlsrnFhNY_M,682
 pychemstation/control/controllers/tables/sequence.py,sha256=vqwJeV38YWdFnaDXvZVOGYl-UCV9lmMbh8Fj5kQ3mqY,8815
-pychemstation/control/controllers/tables/table.py,sha256=J-uNIFHVznPJqOKPmmqrJBXt70KlxmZlSdtEVM2pEKM,12576
+pychemstation/control/controllers/tables/table.py,sha256=GjZ15aJhsCQ9Ps9imOh3Q5NgK97kzangrJcOGa8bjKA,12610
 pychemstation/control/table/__init__.py,sha256=RgMN4uIWHdNUHpGRBWdzmzAbk7XEKl6Y-qtqWCxzSZU,124
 pychemstation/control/table/method.py,sha256=THVoGomSXff_CTU3eAYme0BYwkPzab5UgZKsiZ29QSk,12196
 pychemstation/control/table/sequence.py,sha256=Eri52AnbE3BGthfrRSvYKYciquUzvHKo0lYUTySYYE8,10542
@@ -33,23 +33,23 @@ pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8
 pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pychemstation/utils/chromatogram.py,sha256=-q3_hL9GTyi4C95os7IwAiOrkTM4EXIiigm-nW9pFmM,3221
 pychemstation/utils/injector_types.py,sha256=SD452SwEHNx4Xs2p-mhg6X0pd99XewQ1Zbu-r9kPOJs,817
-pychemstation/utils/macro.py,sha256=o1dypIKhEMbDea34VFh4gKu-kWIjXZAFyqK4FYjCKjo,2836
+pychemstation/utils/macro.py,sha256=PZ916baFfqCkPaSqpdjm2N5mhfg4V4H8KQl7N5l3rUw,2916
 pychemstation/utils/method_types.py,sha256=3qxKeREl_97GnQ74qcA3kxibnvWI4ueb-6XZlxcV2Hg,1632
 pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
 pychemstation/utils/pump_types.py,sha256=HWQHxscGn19NTrfYBwQRCO2VcYfwyko7YfBO5uDhEm4,93
 pychemstation/utils/sequence_types.py,sha256=4cNpmRdPLN5oGN7ozHgT21E65aBO8vV3ZcRXMOQ3EA8,1084
 pychemstation/utils/table_types.py,sha256=0kg7gZXFk7O5l0K1BEBaF4OFFdja3-hFUG9UbN5PBcs,3173
-pychemstation/utils/tray_types.py,sha256=MaHN36rhcEI5mAY95VU8hfP9HhAlngQvMYq-2oyC0hc,764
+pychemstation/utils/tray_types.py,sha256=NZVMi2bYfUApMPEigFacKzEQL3-6J2e7kD8pq-lbFqE,849
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/constants.py,sha256=55DOLpylLt12mb_gSgzEo-EYynwTmI2uH7PcrTM6Iq0,2455
 tests/test_comb.py,sha256=TS-CbtiPbntL4u6E1gSZ6xquNp6cQxIFdJqUr2ak7PA,5515
 tests/test_comm.py,sha256=iwl-Ey-xoytXmlNrjG84pDm82Ry_QUX6wY4gmVh4NDc,2516
-tests/test_inj.py,sha256=Blpk-z9PQuqo4xQ7AUi0CS2czMiYm-pqZe75OFTXru4,1092
+tests/test_inj.py,sha256=UakPA1Sd1GAbFvFepEredWcWPoW7PMLKotfqVZ1i4hE,1434
 tests/test_method.py,sha256=KB7yAtVb4gZftnYzh-VfPb9LGVZOHUIW6OljEYRtbhA,4570
-tests/test_proc_rep.py,sha256=WhUiFqDD1Aey_Nc6Hvbd2zo48K4MWjwDhfO9LiwEQ7M,703
+tests/test_proc_rep.py,sha256=sxRiTBybVm6lyAqmgrri-T2EfZgs27oSgbYXSsN9CwU,1380
 tests/test_sequence.py,sha256=vs5-dqkItRds_tPM2-N6MNJ37FB0nLRFaDzBV8d42i8,4880
-pychemstation-0.6.1.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.6.1.dist-info/METADATA,sha256=oGTCg13YoFF8G2T3aPXss0aKXNveIK9n_UMLpdYQVxM,4370
-pychemstation-0.6.1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.6.1.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
-pychemstation-0.6.1.dist-info/RECORD,,
+pychemstation-0.6.3.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.6.3.dist-info/METADATA,sha256=cfjChXxJ_G29LqdihU0BapRxhWhzkdSMH9sfBQFCKWk,4370
+pychemstation-0.6.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.6.3.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
+pychemstation-0.6.3.dist-info/RECORD,,

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__':

tests/test_proc_rep.py

@@ -7,18 +7,43 @@ from pychemstation.analysis.process_report import process_csv_report
 
 class TestReport(unittest.TestCase):
 
-    def test_process_reporttxt(self):
+    def test_build_peak_regex(self):
         try:
             # TODO
             print('yes')
         except Exception as e:
             self.fail(f"Should have not failed, {e}")
 
-    def test_report_csv(self):
+    def test_parse_area_report(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)
+            # 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}")