pychemstation 0.5.6.dev1__py3-none-any.whl → 0.5.7.dev1__py3-none-any.whl

pychemstation/control/controllers/comm.py

@@ -9,7 +9,7 @@ been processed.
 
 Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
 """
-
+import logging
 import os
 import time
 
@@ -97,6 +97,7 @@ class CommunicationController:
         time.sleep(30)
         self.set_status()
         hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
+        logging.info("Still running")
         return hplc_avail and hplc_actually_avail
 
     def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
@@ -183,7 +184,7 @@ class CommunicationController:
         num_response_prefix = "Numerical Responses:"
         str_response_prefix = "String Responses:"
         possible_response = self._receive(self.cmd_no)
-        if Ok(possible_response):
+        if possible_response.is_ok():
             lines = possible_response.value.splitlines()
             for line in lines:
                 if str_response_prefix in line and num_response_prefix in line:

pychemstation/control/controllers/method.py

@@ -21,6 +21,14 @@ class MethodController(TableController):
     def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
         super().__init__(controller, src, data_dir, table)
 
+    def check_loaded_method(self):
+        time.sleep(2)
+        self.send(Command.GET_METHOD_CMD)
+        time.sleep(2)
+        res = self.receive()
+        if res.is_ok():
+            return res.ok_value.string_response
+
     def get_method_params(self) -> HPLCMethodParams:
         return HPLCMethodParams(organic_modifier=self.controller.get_num_val(
             cmd=TableOperation.GET_OBJ_HDR_VAL.value.format(
@@ -50,8 +58,12 @@ class MethodController(TableController):
     def load(self) -> MethodTimetable:
         rows = self.get_num_rows()
         if rows.is_ok():
+            self.send(Command.GET_METHOD_CMD)
+            res = self.receive()
+            method_name = res.ok_value.string_response
             timetable_rows = [self.get_row(r + 1) for r in range(int(rows.ok_value.num_response))]
             self.table_state = MethodTimetable(
+                name=method_name,
                 first_row=self.get_method_params(),
                 subsequent_rows=timetable_rows)
             return self.table_state
@@ -124,8 +136,7 @@ class MethodController(TableController):
                 first_row=HPLCMethodParams(
                     organic_modifier=organic_modifier.percentage,
                     flow=method.flow,
-                    maximum_run_time=method.stop_time,
-                    temperature=-1),
+                    maximum_run_time=method.stop_time),
                 subsequent_rows=[
                     TimeTableEntry(
                         start_time=tte.time,
@@ -146,6 +157,7 @@ class MethodController(TableController):
 
         :param updated_method: the method with updated values, to be sent to Chemstation to modify the currently loaded method.
         """
+        self.table_state = updated_method
         initial_organic_modifier: Param = Param(val=updated_method.first_row.organic_modifier,
                                                 chemstation_key=RegisterFlag.SOLVENT_B_COMPOSITION,
                                                 ptype=PType.NUM)
@@ -255,6 +267,9 @@ class MethodController(TableController):
 
         :param experiment_name: Name of the experiment
         """
+        if not self.table_state:
+            self.table_state = self.load()
+
         timestamp = time.strftime(TIME_FORMAT)
         self.send(Command.RUN_METHOD_CMD.value.format(data_dir=self.data_dir,
                                                       experiment_name=experiment_name,

pychemstation/control/controllers/sequence.py

@@ -73,7 +73,7 @@ class SequenceController(TableController):
 
         :param sequence_table:
         """
-
+        self.table_state = sequence_table
         rows = self.get_num_rows()
         if rows.is_ok():
             existing_row_num = rows.value.num_response
@@ -177,17 +177,19 @@ class SequenceController(TableController):
         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)
-        seq_table = self.load()
         self.send(Command.RUN_SEQUENCE_CMD.value)
 
         if self.check_hplc_is_running():
-            folder_name = f"{seq_table.name} {timestamp}"
+            folder_name = f"{self.table_state.name} {timestamp}"
             self.data_files.append(SequenceDataFiles(dir=folder_name,
-                                                     sequence_name=seq_table.name))
+                                                     sequence_name=self.table_state.name))
 
             if stall_while_running:
-                run_completed = self.check_hplc_done_running(sequence=seq_table)
+                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:

pychemstation/control/controllers/table_controller.py

@@ -41,6 +41,10 @@ class TableController(abc.ABC):
             "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]] = []

pychemstation/control/hplc.py

@@ -138,6 +138,9 @@ class HPLCController:
         """
         return self.sequence_controller.get_data()
 
+    def check_loaded_method(self) -> str:
+        return self.method_controller.check_loaded_method()
+
     def load_method(self) -> MethodTimetable:
         """
         Returns the currently loaded method, including its timetable.

pychemstation/utils/chromatogram.py

@@ -109,3 +109,7 @@ class AgilentChannelChromatogramData:
     B: AgilentHPLCChromatogram
     C: AgilentHPLCChromatogram
     D: AgilentHPLCChromatogram
+    E: AgilentHPLCChromatogram
+    F: AgilentHPLCChromatogram
+    G: AgilentHPLCChromatogram
+    H: AgilentHPLCChromatogram

pychemstation/utils/method_types.py

@@ -6,6 +6,7 @@ from .table_types import RegisterFlag
 from ..generated import Signal, SolventElement
 
 
+
 class PType(Enum):
     STR = "str"
     NUM = "num"
@@ -34,6 +35,7 @@ class TimeTableEntry:
 
 @dataclass
 class MethodTimetable:
+    name: str
     first_row: HPLCMethodParams
     subsequent_rows: list[TimeTableEntry]
     dad_wavelengthes: Optional[list[Signal]] = None

pychemstation/utils/table_types.py

@@ -46,6 +46,9 @@ class RegisterFlag(Enum):
 
     # for Method Timetable
     SOLVENT_COMPOSITION = "SolventComposition"
+    PRESSURE = "Pressure"
+    EXTERNAL_CONTACT = "ExternalContact"
+
 
     # for Sequence
     VIAL_LOCATION = "Vial"

{pychemstation-0.5.6.dev1.dist-info → pychemstation-0.5.7.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.6.dev1
+Version: 0.5.7.dev1
 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-0.5.6.dev1.dist-info → pychemstation-0.5.7.dev1.dist-info}/RECORD

@@ -5,12 +5,12 @@ pychemstation/analysis/spec_utils.py,sha256=8NZMV0dtfxZLARjWzM5ks0tgEYQv_SKUiZzb
 pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
 pychemstation/control/__init__.py,sha256=4xTy8X-mkn_PPZKr7w9rnj1wZhtmTesbQptPhpYmKXs,64
 pychemstation/control/comm.py,sha256=u44g1hTluQ0yUG93Un-QAshScoDpgYRrZfFTgweP5tY,7386
-pychemstation/control/hplc.py,sha256=L1-cBQ7-thuITx1Mqq3lYXo832nEQtRJEX7nlLvRYrg,6732
+pychemstation/control/hplc.py,sha256=s600b9Oq_muO3uNilMpvSfP4XQIl5A07QzppmdOMPmc,6835
 pychemstation/control/controllers/__init__.py,sha256=di3ytLIK-35XC_THw4IjNaOtCUTe7GuEOFb-obmREw4,166
-pychemstation/control/controllers/comm.py,sha256=iltKMNfdp_8INA5Vss9asI2LxJam_Ro3YWBHBQFr4t0,7353
-pychemstation/control/controllers/method.py,sha256=GNGvGUF9LUCcHAe37SIdnQQ_RzwgnU2ba1oWLXnOp8w,12816
-pychemstation/control/controllers/sequence.py,sha256=f4ZhzkM2hY8xk8dUyiCpmZ5fwU4ev2-CNSbyFeFVe_w,10963
-pychemstation/control/controllers/table_controller.py,sha256=DnusCG5ySR8gA-oe3K_EJfAPlYhmW33epiCi4YVUKJg,8648
+pychemstation/control/controllers/comm.py,sha256=-fJqPcis30fbWS07Tiv68lRFk7ALKC8OitcEBQ_xDTE,7409
+pychemstation/control/controllers/method.py,sha256=dzP8mvgVOOpeAPMp4PLNYxqvaBrGkAe3lPfHWZaD2uk,13290
+pychemstation/control/controllers/sequence.py,sha256=Oi74EhVSgbDVQBxPvITvK5Eo52Ugtz_xCHFYCIq_4Oo,11070
+pychemstation/control/controllers/table_controller.py,sha256=U7oa_mwIKsySASMVWx-heD6C6tVkf5Yb26ksu9x5lQQ,8876
 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
@@ -19,21 +19,21 @@ pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8
 pychemstation/generated/dad_method.py,sha256=0W8Z5WDtF5jpIcudMqb7XrkTnR2EGg_QOCsHRFQ0rmM,8402
 pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8f3EeViWKg,12174
 pychemstation/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-pychemstation/utils/chromatogram.py,sha256=RiKWQG2FIlDzddhgABV-WIJg_BsCTL_wPfyYGikyxoM,3097
+pychemstation/utils/chromatogram.py,sha256=-q3_hL9GTyi4C95os7IwAiOrkTM4EXIiigm-nW9pFmM,3221
 pychemstation/utils/macro.py,sha256=BAIcE_dppNffwrSqGq8gh0ccE9YAJfQFQZHXJgA1WtA,2586
-pychemstation/utils/method_types.py,sha256=YngbyHg96JSFnvhm5Zd7wJvLTQPPQsLbvbyz3HlGLYY,862
+pychemstation/utils/method_types.py,sha256=Hyd_Kxf-ygKW7LlOtEhGG-uujwFPE1w-orqyxcDz17E,877
 pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
 pychemstation/utils/sequence_types.py,sha256=3VqiUHsfFEdynAxfR-z8JIWBCo7PdnGwTvsk7sm7Ij8,1055
-pychemstation/utils/table_types.py,sha256=cN51Ry2pammDdk85cabVH3qkchjKKIzZfAH87Poty80,2350
+pychemstation/utils/table_types.py,sha256=H67-7I96X8Zkm2HygHYttYwG_XuNDmV2AKZW10yZbiA,2418
 pychemstation/utils/tray_types.py,sha256=UUDED-IAf-8FmPVZezuWSiIQE_HgiZQMV2sTqu4oZw8,177
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/constants.py,sha256=lLwT_QaVriivL5llkul6RxXxPriwUp1E-Y3G9fejvbo,2092
-tests/test_comb.py,sha256=CF6nSxUMBJeUjA-IfgPcBGV5oIG4aH1-RA26oIATa-s,5640
+tests/test_comb.py,sha256=pfPpw2wKuF7_v39SOmT4tbbarqBa7NfcRTUVdLLsvWw,5769
 tests/test_comm.py,sha256=1ZZd0UrIBOKe91wzA-XI-gSRgXmId9mLWYSMeche82Y,2973
 tests/test_method.py,sha256=uCPpZVYKPz1CNWwhmBo_8TH0ku2V0ZpDZJj3f8iINB4,2440
 tests/test_sequence.py,sha256=yIQGhUTehtHz6D1ai5W6AlP0zes2icF0VdQ0IGJ2CbQ,4901
-pychemstation-0.5.6.dev1.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.5.6.dev1.dist-info/METADATA,sha256=7Pj5MObTqRmX3B19nhA70BzBRyHSA7bDku7O1-D89lE,4312
-pychemstation-0.5.6.dev1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.5.6.dev1.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
-pychemstation-0.5.6.dev1.dist-info/RECORD,,
+pychemstation-0.5.7.dev1.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.5.7.dev1.dist-info/METADATA,sha256=-JJQIwuYuatng6sohJy6y7-7WV8UBUOSJgMqkoi8OZ8,4312
+pychemstation-0.5.7.dev1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.5.7.dev1.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
+pychemstation-0.5.7.dev1.dist-info/RECORD,,

tests/test_comb.py

@@ -41,6 +41,8 @@ class TestCombinations(unittest.TestCase):
             self.hplc_controller.edit_method(rand_method, save=True)
             if run_too:
                 self.hplc_controller.run_method(experiment_name="changed_method")
+                chrom = self.hplc_controller.get_last_run_method_data()
+                self.assertEqual(len(chrom.__dict__), 8)
         except Exception as e:
             self.fail(f"Should have not failed: {e}")
 
@@ -138,6 +140,6 @@ class TestCombinations(unittest.TestCase):
             self.hplc_controller.preprun()
             self.hplc_controller.run_sequence()
             chrom = self.hplc_controller.get_last_run_sequence_data()
-            self.assertTrue(len(chrom) == 2)
+            self.assertTrue(len(chrom) == 1)
         except Exception:
             self.fail("Failed")