pychemstation 0.5.5__py3-none-any.whl → 0.5.6.dev1__py3-none-any.whl

pychemstation/control/controllers/method.py

@@ -51,9 +51,10 @@ class MethodController(TableController):
         rows = self.get_num_rows()
         if rows.is_ok():
             timetable_rows = [self.get_row(r + 1) for r in range(int(rows.ok_value.num_response))]
-            return MethodTimetable(
+            self.table_state = MethodTimetable(
                 first_row=self.get_method_params(),
                 subsequent_rows=timetable_rows)
+            return self.table_state
         else:
             raise RuntimeError(rows.err_value)
 
@@ -88,6 +89,7 @@ class MethodController(TableController):
         if res.is_ok():
             parsed_response = res.ok_value.string_response
             assert parsed_response == f"{method_name}.M", "Switching Methods failed."
+        self.table_state = None
 
     def load_from_disk(self, method_name: str) -> MethodTimetable:
         """
@@ -118,7 +120,7 @@ class MethodController(TableController):
                     elif solvent.channel == "Channel_B":
                         organic_modifier = solvent
 
-            return MethodTimetable(
+            self.table_state = MethodTimetable(
                 first_row=HPLCMethodParams(
                     organic_modifier=organic_modifier.percentage,
                     flow=method.flow,
@@ -135,6 +137,7 @@ class MethodController(TableController):
                 organic_modifier=organic_modifier,
                 modifier_a=aq_modifier
             )
+            return self.table_state
         else:
             raise FileNotFoundError
 
@@ -242,7 +245,7 @@ class MethodController(TableController):
         """
         self.send(Command.STOP_METHOD_CMD)
 
-    def run(self, experiment_name: str):
+    def run(self, experiment_name: str, stall_while_running: bool = True):
         """
         This is the preferred method to trigger a run.
         Starts the currently selected method, storing data
@@ -261,14 +264,21 @@ class MethodController(TableController):
             folder_name = f"{experiment_name}_{timestamp}.D"
             self.data_files.append(os.path.join(self.data_dir, folder_name))
 
-        run_completed = self.check_hplc_done_running()
-
-        if not run_completed.is_ok():
-            raise RuntimeError("Run did not complete as expected")
+            if stall_while_running:
+                run_completed = self.check_hplc_done_running(method=self.table_state)
+                if run_completed.is_ok():
+                    self.data_files[-1] = run_completed.value
+                else:
+                    raise RuntimeError("Run error has occurred.")
+            else:
+                self.data_files[-1].dir = self.fuzzy_match_most_recent_folder(folder_name).ok_value
 
     def retrieve_recent_data_files(self) -> str:
         return self.data_files[-1]
 
-    def get_data(self) -> AgilentChannelChromatogramData:
-        self.get_spectrum(self.data_files[-1])
+    def get_data(self, custom_path: Optional[str] = None) -> AgilentChannelChromatogramData:
+        if not custom_path:
+            self.get_spectrum(self.data_files[-1])
+        else:
+            self.get_spectrum(custom_path)
         return AgilentChannelChromatogramData(**self.spectra)

pychemstation/control/controllers/sequence.py

@@ -1,3 +1,6 @@
+from typing import  Optional
+
+
 import os
 import time
 
@@ -24,9 +27,10 @@ class SequenceController(TableController):
         seq_name = self.receive()
 
         if rows.is_ok() and seq_name.is_ok():
-            return SequenceTable(
+            self.table_state = SequenceTable(
                 name=seq_name.ok_value.string_response.partition(".S")[0],
                 rows=[self.get_row(r + 1) for r in range(int(rows.ok_value.num_response))])
+            return self.table_state
         raise RuntimeError(rows.err_value)
 
     def get_row(self, row: int) -> SequenceEntry:
@@ -60,6 +64,7 @@ class SequenceController(TableController):
         parsed_response = self.receive().value.string_response
 
         assert parsed_response == f"{seq_name}.S", "Switching sequence failed."
+        self.table_state = None
 
     def edit(self, sequence_table: SequenceTable):
         """
@@ -166,7 +171,7 @@ class SequenceController(TableController):
 
         self.send(Command.SAVE_SEQUENCE_CMD)
 
-    def run(self):
+    def run(self, stall_while_running: bool = True):
         """
         Starts the currently loaded sequence, storing data
         under the <data_dir>/<sequence table name> folder.
@@ -181,19 +186,21 @@ class SequenceController(TableController):
             self.data_files.append(SequenceDataFiles(dir=folder_name,
                                                      sequence_name=seq_table.name))
 
-        run_completed = self.check_hplc_done_running(sequence=seq_table)
-
-        if run_completed.is_ok():
-            self.data_files[-1].dir = run_completed.value
-        else:
-            raise RuntimeError("Run error has occured.")
+            if stall_while_running:
+                run_completed = self.check_hplc_done_running(sequence=seq_table)
+                if run_completed.is_ok():
+                    self.data_files[-1].dir = run_completed.value
+                else:
+                    raise RuntimeError("Run error has occurred.")
+            else:
+                self.data_files[-1].dir = self.fuzzy_match_most_recent_folder(folder_name).ok_value
 
     def retrieve_recent_data_files(self):
         sequence_data_files: SequenceDataFiles = self.data_files[-1]
         return sequence_data_files.dir
 
-    def get_data(self) -> list[AgilentChannelChromatogramData]:
-        parent_dir = self.data_files[-1].dir
+    def get_data(self, custom_path:Optional[str] = None ) -> list[AgilentChannelChromatogramData]:
+        parent_dir = self.data_files[-1].dir if not custom_path else custom_path
         subdirs = [x[0] for x in os.walk(self.data_dir)]
         potential_folders = sorted(list(filter(lambda d: parent_dir in d, subdirs)))
         self.data_files[-1].child_dirs = [f for f in potential_folders if
@@ -202,10 +209,5 @@ class SequenceController(TableController):
         spectra: list[AgilentChannelChromatogramData] = []
         for row in self.data_files[-1].child_dirs:
             self.get_spectrum(row)
-            spectra.append(
-                AgilentChannelChromatogramData(
-                    A=self.spectra["A"],
-                    B=self.spectra["B"],
-                    C=self.spectra["C"],
-                    D=self.spectra["D"]))
+            spectra.append(AgilentChannelChromatogramData(**self.spectra))
         return spectra

pychemstation/control/controllers/table_controller.py

@@ -6,7 +6,6 @@ Authors: Lucy Hao
 
 import abc
 import os
-import time
 from typing import Union, Optional
 
 import polling
@@ -25,6 +24,7 @@ class TableController(abc.ABC):
     def __init__(self, controller: CommunicationController, src: str, data_dir: str, table: Table):
         self.controller = controller
         self.table = table
+        self.table_state : Optional[TableController] = None
 
         if os.path.isdir(src):
             self.src: str = src
@@ -120,7 +120,7 @@ class TableController(abc.ABC):
         self.send(TableOperation.CREATE_TABLE.value.format(register=self.table.register,
                                                            table_name=self.table.name))
 
-    def get_num_rows(self) -> Result[int, str]:
+    def get_num_rows(self) -> Result[Response, str]:
         self.send(TableOperation.GET_NUM_ROWS.value.format(register=self.table.register,
                                                            table_name=self.table.name,
                                                            col_name=RegisterFlag.NUM_ROWS))
@@ -139,8 +139,8 @@ class TableController(abc.ABC):
     def check_hplc_is_running(self) -> bool:
         started_running = polling.poll(
             lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-            step=30,
-            max_tries=10)
+            step=5,
+            max_tries=100)
         return started_running
 
     def check_hplc_done_running(self,
@@ -154,7 +154,7 @@ class TableController(abc.ABC):
         """
         timeout = 10 * 60
         if method:
-            timeout = ((method.first_row.maximum_run_time + 2) * 60)
+            timeout = ((method.first_row.maximum_run_time + 5) * 60)
         if sequence:
             timeout *= len(sequence.rows)
 
@@ -162,26 +162,36 @@ class TableController(abc.ABC):
         finished_run = polling.poll(
             lambda: self.controller.check_if_running(),
             timeout=timeout,
-            step=60
-        )
-
-        if finished_run:
-            if os.path.exists(most_recent_folder):
-                return Ok(most_recent_folder)
-            else:
-                subdirs = [x[0] for x in os.walk(self.data_dir)]
-                potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
-                parent_dirs = []
-                for folder in potential_folders:
-                    path = os.path.normpath(folder)
-                    split_folder = path.split(os.sep)
-                    if most_recent_folder in split_folder[-1]:
-                        parent_dirs.append(folder)
-                parent_dir = sorted(parent_dirs, reverse=True)[0]
-                return Ok(parent_dir)
+            step=18)
+
+        check_folder = self.fuzzy_match_most_recent_folder(most_recent_folder)
+        if check_folder.is_ok() and finished_run:
+            return check_folder
+        elif check_folder.is_ok():
+            finished_run = polling.poll(
+                lambda: self.controller.check_if_running(),
+                timeout=timeout,
+                step=12)
+            if finished_run:
+                return check_folder
         else:
             return Err("Run did not complete as expected")
 
+    def fuzzy_match_most_recent_folder(self, most_recent_folder) -> Result[str, str]:
+        if os.path.exists(most_recent_folder):
+            return Ok(most_recent_folder)
+
+        subdirs = [x[0] for x in os.walk(self.data_dir)]
+        potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
+        parent_dirs = []
+        for folder in potential_folders:
+            path = os.path.normpath(folder)
+            split_folder = path.split(os.sep)
+            if most_recent_folder in split_folder[-1]:
+                parent_dirs.append(folder)
+        parent_dir = sorted(parent_dirs, reverse=True)[0]
+        return Ok(parent_dir)
+
     @abc.abstractmethod
     def retrieve_recent_data_files(self):
         pass

pychemstation/control/table/table_controller.py

@@ -12,8 +12,8 @@ from typing import Union, Optional
 import polling
 from result import Result, Ok, Err
 
-from ...control import CommunicationController
-from ...utils.chromatogram import AgilentHPLCChromatogram
+from ...control.controllers.comm import CommunicationController
+from ...utils.chromatogram import AgilentHPLCChromatogram, AgilentChannelChromatogramData
 from ...utils.macro import Command, HPLCRunningStatus, Response
 from ...utils.method_types import MethodTimetable
 from ...utils.sequence_types import SequenceDataFiles, SequenceTable
@@ -139,8 +139,8 @@ class TableController(abc.ABC):
     def check_hplc_is_running(self) -> bool:
         started_running = polling.poll(
             lambda: isinstance(self.controller.get_status(), HPLCRunningStatus),
-            step=30,
-            max_tries=10)
+            step=5,
+            max_tries=100)
         return started_running
 
     def check_hplc_done_running(self,
@@ -162,32 +162,35 @@ class TableController(abc.ABC):
         finished_run = polling.poll(
             lambda: self.controller.check_if_running(),
             timeout=timeout,
-            step=60
+            step=12
         )
 
         if finished_run:
             if os.path.exists(most_recent_folder):
                 return Ok(most_recent_folder)
             else:
-                subdirs = [x[0] for x in os.walk(self.data_dir)]
-                potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
-                parent_dirs = []
-                for folder in potential_folders:
-                    path = os.path.normpath(folder)
-                    split_folder = path.split(os.sep)
-                    if most_recent_folder in split_folder[-1]:
-                        parent_dirs.append(folder)
-                parent_dir = sorted(parent_dirs, reverse=True)[0]
-                return Ok(parent_dir)
+                return self.fuzzy_match_most_recent_folder(most_recent_folder)
         else:
             return Err("Run did not complete as expected")
 
+    def fuzzy_match_most_recent_folder(self, most_recent_folder) -> Result[str, str]:
+        subdirs = [x[0] for x in os.walk(self.data_dir)]
+        potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
+        parent_dirs = []
+        for folder in potential_folders:
+            path = os.path.normpath(folder)
+            split_folder = path.split(os.sep)
+            if most_recent_folder in split_folder[-1]:
+                parent_dirs.append(folder)
+        parent_dir = sorted(parent_dirs, reverse=True)[0]
+        return Ok(parent_dir)
+
     @abc.abstractmethod
     def retrieve_recent_data_files(self):
         pass
 
     @abc.abstractmethod
-    def get_data(self) -> tuple[bool,]:
+    def get_data(self) -> Union[list[AgilentChannelChromatogramData], AgilentChannelChromatogramData]:
         pass
 
     def get_spectrum(self, data_file: str):

pychemstation/utils/chromatogram.py

@@ -16,7 +16,7 @@ ACQUISITION_PARAMETERS = "acq.txt"
 
 # format used in acquisition parameters
 TIME_FORMAT = "%Y-%m-%d %H-%M-%S"
-SEQUENCE_TIME_FORMAT = "%Y-%m-%d %H"
+SEQUENCE_TIME_FORMAT = "%Y-%m-%d %H-%M"
 
 
 class AgilentHPLCChromatogram(AbstractSpectrum):

{pychemstation-0.5.5.dist-info → pychemstation-0.5.6.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.5
+Version: 0.5.6.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-0.5.5.dist-info → pychemstation-0.5.6.dev1.dist-info}/RECORD

@@ -8,18 +8,18 @@ pychemstation/control/comm.py,sha256=u44g1hTluQ0yUG93Un-QAshScoDpgYRrZfFTgweP5tY
 pychemstation/control/hplc.py,sha256=L1-cBQ7-thuITx1Mqq3lYXo832nEQtRJEX7nlLvRYrg,6732
 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=SoKwteVfalgP1z7aKPNlaUJ01Gsr0MIoa7f-c2sjDrE,12259
-pychemstation/control/controllers/sequence.py,sha256=bHx15uSA0ZjAy6xpyxwhWUNP54WcEL0nJ24bzYCa4rc,10719
-pychemstation/control/controllers/table_controller.py,sha256=N47eiowmmy9gi18fChNh-cW6z8bbRSF30pLzhnWG9_k,8227
+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/table/__init__.py,sha256=RgMN4uIWHdNUHpGRBWdzmzAbk7XEKl6Y-qtqWCxzSZU,124
 pychemstation/control/table/method.py,sha256=THVoGomSXff_CTU3eAYme0BYwkPzab5UgZKsiZ29QSk,12196
 pychemstation/control/table/sequence.py,sha256=Eri52AnbE3BGthfrRSvYKYciquUzvHKo0lYUTySYYE8,10542
-pychemstation/control/table/table_controller.py,sha256=F5lv1DlPkEDcFmtwVT-E9Kq075jnWIN-iZIM3_mTt5E,8115
+pychemstation/control/table/table_controller.py,sha256=HVNYUXqtyFTAvb67fa3RO5RHgmBTFMsYRHKpiXdYcfs,8313
 pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8OMehMg,1005
 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=KzhEQbxKbwOu4OjKa4XJFq2y08JUwMRoaupHrDR8cLM,3094
+pychemstation/utils/chromatogram.py,sha256=RiKWQG2FIlDzddhgABV-WIJg_BsCTL_wPfyYGikyxoM,3097
 pychemstation/utils/macro.py,sha256=BAIcE_dppNffwrSqGq8gh0ccE9YAJfQFQZHXJgA1WtA,2586
 pychemstation/utils/method_types.py,sha256=YngbyHg96JSFnvhm5Zd7wJvLTQPPQsLbvbyz3HlGLYY,862
 pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
@@ -28,12 +28,12 @@ pychemstation/utils/table_types.py,sha256=cN51Ry2pammDdk85cabVH3qkchjKKIzZfAH87P
 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=faF4764oJEZ2vhG9-zLmQxjATseipRKXrStehuDCXOI,5638
+tests/test_comb.py,sha256=CF6nSxUMBJeUjA-IfgPcBGV5oIG4aH1-RA26oIATa-s,5640
 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-0.5.5.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.5.5.dist-info/METADATA,sha256=sAsryhHjIHyT6y10BQP2rEUh49dLJ_2wCchNgQ1M4JY,4307
-pychemstation-0.5.5.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.5.5.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
-pychemstation-0.5.5.dist-info/RECORD,,
+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,,

tests/test_comb.py

@@ -28,14 +28,14 @@ class TestCombinations(unittest.TestCase):
                 first_row=HPLCMethodParams(
                     organic_modifier=5,
                     flow=0.65,
-                    maximum_run_time=2),
+                    maximum_run_time=1),
                 subsequent_rows=[
                     TimeTableEntry(
                         start_time=0.10,
                         organic_modifer=5,
                         flow=0.34),
                     TimeTableEntry(
-                        start_time=1,
+                        start_time=0.5,
                         organic_modifer=98,
                         flow=0.55)])
             self.hplc_controller.edit_method(rand_method, save=True)