pychemstation 0.8.2__py3-none-any.whl → 0.10.0__py3-none-any.whl

tests/test_stable.py

@@ -0,0 +1,276 @@
+import unittest
+
+from pychemstation.utils.macro import *
+from pychemstation.utils.tray_types import *
+from tests.constants import *
+
+
+class TestStable(unittest.TestCase):
+
+    def setUp(self):
+        self.hplc_controller = set_up_utils(242)
+
+    def test_status_check_standby(self):
+        self.hplc_controller.standby()
+        self.assertTrue(self.hplc_controller.status() in [HPLCAvailStatus.STANDBY, HPLCRunningStatus.NOTREADY])
+
+    def test_status_check_preprun(self):
+        self.hplc_controller.preprun()
+        self.assertTrue(self.hplc_controller.status() in [HPLCAvailStatus.PRERUN, HPLCAvailStatus.STANDBY,
+                                                          HPLCRunningStatus.NOTREADY])
+
+    def test_send_command(self):
+        try:
+            self.hplc_controller.send(Command.GET_METHOD_CMD)
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_send_str(self):
+        try:
+            self.hplc_controller.send("Local TestNum")
+            self.hplc_controller.send("TestNum = 0")
+            self.hplc_controller.send("Print TestNum")
+            self.hplc_controller.send("response_num = TestNum")
+            self.hplc_controller.send("Print response_num")
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_get_num(self):
+        try:
+            self.hplc_controller.send("response_num = 10")
+            res = self.hplc_controller.receive().num_response
+            self.assertEqual(res, 10)
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_get_response(self):
+        try:
+            self.hplc_controller.switch_method(method_name=DEFAULT_METHOD)
+            self.hplc_controller.send(Command.GET_METHOD_CMD)
+            res = self.hplc_controller.receive()
+            self.assertTrue(DEFAULT_METHOD in res.string_response)
+        except Exception as e:
+            self.fail(f"Should not throw error: {e}")
+
+    def test_edit_method(self):
+        self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
+        new_method = MethodDetails(name=DEFAULT_METHOD + ".M",
+                                   timetable=[TimeTableEntry(start_time=1.0,
+                                                             organic_modifer=20.0,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=2.0,
+                                                             organic_modifer=30.0,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=2.5,
+                                                             organic_modifer=60.0,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=3.0,
+                                                             organic_modifer=80.0,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=3.5,
+                                                             organic_modifer=100.0,
+                                                             flow=0.65)],
+                                   stop_time=4.0,
+                                   post_time=1.0,
+                                   params=HPLCMethodParams(organic_modifier=5.0, flow=0.65))
+        try:
+            self.hplc_controller.edit_method(new_method)
+            self.assertEqual(new_method, self.hplc_controller.load_method())
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+    def test_load_method(self):
+        self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
+        new_method = gen_rand_method()
+        try:
+            self.hplc_controller.edit_method(new_method)
+            loaded_method = self.hplc_controller.load_method()
+            self.assertEqual(new_method.params.organic_modifier,
+                             loaded_method.params.organic_modifier)
+            self.assertEqual(new_method.timetable[0].organic_modifer,
+                             loaded_method.timetable[0].organic_modifer)
+            self.assertEqual(round(new_method.params.flow, 2),
+                             round(loaded_method.params.flow, 2))
+        except Exception as e:
+            self.fail(f"Should have not failed: {e}")
+
+    def test_switch(self):
+        try:
+            self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        except Exception as e:
+            self.fail(f"Should have not expected: {e}")
+
+    def test_read(self):
+        try:
+            self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+            table = self.hplc_controller.load_sequence()
+            self.assertTrue(table)
+        except Exception as e:
+            self.fail(f"Should have not expected: {e}")
+
+    def test_edit_entire_table(self):
+        self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        seq_folder = self.hplc_controller.sequence_controller.src
+        meth_path = os.path.join(seq_folder, DEFAULT_METHOD)
+        try:
+            seq_table = SequenceTable(
+                name=DEFAULT_SEQUENCE,
+                rows=[
+                    SequenceEntry(
+                        vial_location=TenVialColumn.ONE,
+                        method=meth_path,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel1",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=FiftyFourVialPlate(plate=Plate.ONE, letter=Letter.A, num=Num.ONE),
+                        method=meth_path,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=FiftyFourVialPlate(plate=Plate.ONE, letter=Letter.A, num=Num.TWO),
+                        method=meth_path,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=FiftyFourVialPlate(plate=Plate.ONE, letter=Letter.A, num=Num.THREE),
+                        method=meth_path,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    )
+                ]
+            )
+            self.hplc_controller.edit_sequence(seq_table)
+            self.assertEqual(seq_table,
+                             self.hplc_controller.load_sequence())
+        except Exception:
+            self.fail("Should have not occured")
+
+    def test_edit_entire_table_less_rows(self):
+        self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        try:
+            seq_table = SequenceTable(
+                name=DEFAULT_SEQUENCE,
+                rows=[
+                    SequenceEntry(
+                        vial_location=TenVialColumn.TEN,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=TenVialColumn.THREE,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    )
+                ]
+            )
+            self.hplc_controller.edit_sequence(seq_table)
+        except Exception:
+            self.fail("Should have not occured")
+
+    def test_load(self):
+        try:
+            seq = self.hplc_controller.load_sequence()
+            self.assertTrue(len(seq.rows) > 0)
+        except Exception as e:
+            self.fail(f"Should have not expected: {e}")
+
+    def test_tray_nums(self):
+        vial_locations = [
+            FiftyFourVialPlate.from_str('P1-A7'),
+            FiftyFourVialPlate.from_str('P1-B4'),
+            FiftyFourVialPlate.from_str('P1-C2'),
+            FiftyFourVialPlate.from_str('P1-D8'),
+            FiftyFourVialPlate.from_str('P1-E3'),
+            FiftyFourVialPlate.from_str('P1-F5'),
+            # plate 2
+            FiftyFourVialPlate.from_str('P2-A7'),
+            FiftyFourVialPlate.from_str('P2-B2'),
+            FiftyFourVialPlate.from_str('P2-C1'),
+            FiftyFourVialPlate.from_str('P2-D8'),
+            FiftyFourVialPlate.from_str('P2-E3'),
+            FiftyFourVialPlate.from_str('P2-F6'),
+        ]
+        seq_table = SequenceTable(
+            name=DEFAULT_SEQUENCE,
+            rows=[
+                SequenceEntry(
+                    vial_location=v,
+                    method=DEFAULT_METHOD,
+                    num_inj=3,
+                    inj_vol=4,
+                    sample_name="Sampel2",
+                    sample_type=SampleType.SAMPLE,
+                    inj_source=InjectionSource.HIP_ALS
+                ) for v in vial_locations
+            ]
+        )
+        self.hplc_controller.edit_sequence(seq_table)
+        loaded_table = self.hplc_controller.load_sequence()
+        for i in range(len(vial_locations)):
+            self.assertTrue(vial_locations[i].value()
+                            == seq_table.rows[i].vial_location.value()
+                            == loaded_table.rows[i].vial_location.value())
+
+    def test_tray_nums_only(self):
+        vial_locations = [
+            # plate 2
+            FiftyFourVialPlate.from_str('P2-A7'),
+            FiftyFourVialPlate.from_str('P2-B2'),
+            FiftyFourVialPlate.from_str('P2-C1'),
+            FiftyFourVialPlate.from_str('P2-D8'),
+            FiftyFourVialPlate.from_str('P2-E3'),
+            FiftyFourVialPlate.from_str('P2-F6'),
+            # plate 1
+            FiftyFourVialPlate.from_str('P1-A7'),
+            FiftyFourVialPlate.from_str('P1-B4'),
+            FiftyFourVialPlate.from_str('P1-C2'),
+            FiftyFourVialPlate.from_str('P1-D8'),
+            FiftyFourVialPlate.from_str('P1-E3'),
+            FiftyFourVialPlate.from_str('P1-F5'),
+        ]
+
+        for i in range(len(vial_locations)):
+            self.assertEqual(vial_locations[i], FiftyFourVialPlate.from_int(vial_locations[i].value()))
+
+    def test_get_last_run_sequence(self):
+        path = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data\\hplc_testing 2025-03-24 16-28-16"
+        folder_name = "hplc_testing 2025-03-24 16-28"
+        self.hplc_controller.sequence_controller.data_files.append(SequenceDataFiles(dir=folder_name,
+                                                                                     sequence_name=DEFAULT_SEQUENCE))
+        try:
+            most_recent_folder = self.hplc_controller.sequence_controller.retrieve_recent_data_files()
+            check_folder = self.hplc_controller.sequence_controller.fuzzy_match_most_recent_folder(
+                most_recent_folder=most_recent_folder)
+            self.assertEqual(check_folder.ok_value, path)
+            self.hplc_controller.sequence_controller.data_files[-1].dir = check_folder.ok_value
+            chrom = self.hplc_controller.get_last_run_sequence_data()
+            self.assertTrue(chrom)
+        except Exception:
+            self.fail()
+
+
+if __name__ == '__main__':
+    unittest.main()

pychemstation/control/README.md

@@ -1,124 +0,0 @@
-#  Examples of usecases
-
-## Initialization
-```python
-from pychemstation.control import HPLCController
-
-DEFAULT_METHOD_DIR = "C:\\ChemStation\\1\\Methods\\"
-DATA_DIR = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
-SEQUENCE_DIR = "C:\\USERS\\PUBLIC\\DOCUMENTS\\CHEMSTATION\\3\\Sequence"
-DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
-
-hplc_controller = HPLCController(data_dir=DATA_DIR,
-                                 comm_dir=DEFAULT_COMMAND_PATH,
-                                 method_dir=DEFAULT_METHOD_DIR,
-                                 sequence_dir=SEQUENCE_DIR)
-```
-
-## Switching a method
-```python
-hplc_controller.switch_method("General-Poroshell")
-```
-
-## Editing a method
-
-```python
-from pychemstation.utils.method_types import *
-
-new_method = MethodDetails(
-    name="My_Method",
-    params=HPLCMethodParams(
-        organic_modifier=7,
-        flow=0.44),
-    timetable=[
-        TimeTableEntry(
-            start_time=0.10,
-            organic_modifer=7,
-            flow=0.34
-        ),
-        TimeTableEntry(
-            start_time=1,
-            organic_modifer=99,
-            flow=0.55
-        )
-    ],
-    stop_time=5,
-    post_time=2
-)
-
-hplc_controller.edit_method(new_method)
-```
-
-## Running a method and get data from last run method
-```python
-hplc_controller.run_method(experiment_name="test_experiment")
-chrom = hplc_controller.get_last_run_method_data()
-channel_a_time = chrom.A.x
-```
-
-## Switching a sequence
-```python
-hplc_controller.switch_sequence(sequence_name="hplc_testing")
-```
-## Editing a Sequence Row
-```python
-from pychemstation.utils.sequence_types import *
-from pychemstation.utils.tray_types import *
-
-hplc_controller.edit_sequence_row(SequenceEntry(
-    vial_location=FiftyFourVialPlate(plate=Plate.TWO, letter=Letter.A, num=Num.SEVEN).value(),
-    method="General-Poroshell",
-    num_inj=3,
-    inj_vol=4,
-    sample_name="Blank",
-    sample_type=SampleType.BLANK,
-    inj_source=InjectionSource.HIP_ALS
-), 1)
-```
-
-## Editing entire Sequence Table
-```python
-from pychemstation.utils.tray_types import *
-from pychemstation.utils.sequence_types import *
-
-seq_table = SequenceTable(
-    name=DEFAULT_SEQUENCE,
-    rows=[
-        SequenceEntry(
-            vial_location=FiftyFourVialPlate(plate=Plate.TWO, letter=Letter.A, num=Num.SEVEN).value(),
-            method="General-Poroshell",
-            num_inj=3,
-            inj_vol=4,
-            sample_name="Control",
-            sample_type=SampleType.CONTROL,
-            inj_source=InjectionSource.MANUAL
-        ),
-        SequenceEntry(
-            vial_location=TenVialColumn.ONE.value,
-            method="General-Poroshell",
-            num_inj=1,
-            inj_vol=1,
-            sample_name="Sample",
-            sample_type=SampleType.SAMPLE,
-            inj_source=InjectionSource.AS_METHOD
-        ),
-        SequenceEntry(
-            vial_location=10,
-            method="General-Poroshell",
-            num_inj=3,
-            inj_vol=4,
-            sample_name="Blank",
-            sample_type=SampleType.BLANK,
-            inj_source=InjectionSource.HIP_ALS
-        ),
-    ]
-)
-hplc_controller.edit_sequence(seq_table)
-```
-
-## Running a sequence and get data from last run sequence
-```python
-hplc_controller.run_sequence(seq_table)
-chroms = hplc_controller.get_last_run_sequence_data()
-channel_A_time = chroms[0].A.x
-```

pychemstation/control/controllers/README.md

@@ -1 +0,0 @@
-# Chemstation Devices and Tables

pychemstation/out.txt

@@ -1,145 +0,0 @@
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Sleep 0.1
-Print Rows
-response$ = _MethFile$
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "FlowFlow")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "SolventCompositionPumpChannel2_Percentage")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PumpChannel2_CompositionPercentage")
-response_num = ObjHdrVal("RCPMP1Method[1]", "Flow")
-response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-22-32-44"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-22-36-41"
-response$ = AcqStatus$
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-22-37-41"
-response$ = AcqStatus$
-response$ = AcqStatus$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-46-39"
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-46-52"
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-47-43"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Sleep 0.1
-Print Rows
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-48-45"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Sleep 0.1
-Print Rows
-response$ = _MethFile$
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "FlowFlow")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "SolventCompositionPumpChannel2_Percentage")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PumpChannel2_CompositionPercentage")
-response_num = ObjHdrVal("RCPMP1Method[1]", "Flow")
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-50-02"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Sleep 0.1
-Print Rows
-response$ = _MethFile$
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "FlowFlow")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "SolventCompositionPumpChannel2_Percentage")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PumpChannel2_CompositionPercentage")
-response_num = ObjHdrVal("RCPMP1Method[1]", "Flow")
-response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-27-23-59-41"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-Local Rows
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-28-00-01-48"
-Local Rows
-Local Rows
-Local Rows
-LoadMethod "C:\\Users\\Public\\Documents\\ChemStation\\1\\Methods\\", "testing.M"
-response$ = _MethFile$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-28-00-02-04"
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-28-00-02-22"
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Local Rows
-Local Rows
-Local Rows
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-28-00-13-10"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
-Sleep 0.1
-Print Rows
-response$ = _MethFile$
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "FlowFlow")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "SolventCompositionPumpChannel2_Percentage")
-response_num = TabVal("RCPMP1Method[1]", "Timetable", 1, "Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PumpChannel2_CompositionPercentage")
-response_num = ObjHdrVal("RCPMP1Method[1]", "Flow")
-response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
-response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
-response$ = AcqStatus$
-RunMethod "C:\Users\Public\Documents\ChemStation\1\data\",, "run_test_2025-03-28-00-14-53"
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$
-response$ = AcqStatus$