pychemstation 0.10.9__tar.gz → 0.10.11__tar.gz

{pychemstation-0.10.9 → pychemstation-0.10.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.9
+Version: 0.10.11
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
 Project-URL: Documentation, https://pychemstation-e5a086.gitlab.io/pychemstation.html
 Project-URL: Repository, https://gitlab.com/heingroup/device-api/pychemstation

{pychemstation-0.10.9 → pychemstation-0.10.11}/pychemstation/control/controllers/data_aq/method.py

@@ -114,23 +114,20 @@ class MethodController(RunController):
         return entries
 
     def load(self) -> MethodDetails:
-        rows = self.get_num_rows()
-        if rows.is_ok():
-            method_name = self.get_method_name()
-            timetable_rows = self.get_timetable(int(rows.ok_value.num_response))
-            params = self.get_method_params()
-            stop_time = self.get_stop_time()
-            post_time = self.get_post_time()
-            self.table_state = MethodDetails(
-                name=method_name,
-                timetable=timetable_rows,
-                stop_time=stop_time,
-                post_time=post_time,
-                params=params,
-            )
-            return self.table_state
-        else:
-            raise RuntimeError(rows.err_value)
+        rows = self.get_row_count_safely()
+        method_name = self.get_method_name()
+        timetable_rows = self.get_timetable(rows)
+        params = self.get_method_params()
+        stop_time = self.get_stop_time()
+        post_time = self.get_post_time()
+        self.table_state = MethodDetails(
+            name=method_name,
+            timetable=timetable_rows,
+            stop_time=stop_time,
+            post_time=post_time,
+            params=params,
+        )
+        return self.table_state
 
     def get_method_name(self):
         self.send(Command.GET_METHOD_CMD)
@@ -443,62 +440,6 @@ class MethodController(RunController):
         self.download()
         return time_added, flow_added, om_added, function_added
 
-        # if first_row:
-        #     time_added = False
-        #     flow_row_method: Callable = (
-        #         self.add_new_col_text
-        #         if row.flow and not row.organic_modifer
-        #         else self._edit_row_text
-        #     )
-        #     if row.organic_modifer:
-        #         self.add_row()
-        #         self.add_new_col_text(
-        #             col_name=RegisterFlag.FUNCTION,
-        #             val=RegisterFlag.SOLVENT_COMPOSITION.value,
-        #         )
-        #         if not time_added:
-        #             time_added = True
-        #             self.add_new_col_num(col_name=RegisterFlag.TIME, val=row.start_time)
-        #         self.add_new_col_num(
-        #             col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION,
-        #             val=row.organic_modifer,
-        #         )
-        #     if row.flow:
-        #         self.add_row()
-        #         self.get_num_rows()
-        #         flow_row_method(
-        #             col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value
-        #         )
-        #         if not time_added:
-        #             time_added = True
-        #             self.add_new_col_num(col_name=RegisterFlag.TIME, val=row.start_time)
-        #         self.add_new_col_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
-        #         self._edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
-        #     self.download()
-        # else:
-        #     if row.organic_modifer:
-        #         self.add_row()
-        #         self.get_num_rows()
-        #         self._edit_row_text(
-        #             col_name=RegisterFlag.FUNCTION,
-        #             val=RegisterFlag.SOLVENT_COMPOSITION.value,
-        #         )
-        #         self._edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
-        #         self._edit_row_num(
-        #             col_name=RegisterFlag.TIMETABLE_SOLVENT_B_COMPOSITION,
-        #             val=row.organic_modifer,
-        #         )
-        #         self.download()
-        #     if row.flow:
-        #         self.add_row()
-        #         self.get_num_rows()
-        #         self._edit_row_text(
-        #             col_name=RegisterFlag.FUNCTION, val=RegisterFlag.FLOW.value
-        #         )
-        #         self._edit_row_num(col_name=RegisterFlag.TIMETABLE_FLOW, val=row.flow)
-        #         self._edit_row_num(col_name=RegisterFlag.TIME, val=row.start_time)
-        #         self.download()
-
     def edit_method_timetable(self, timetable_rows: List[TimeTableEntry]):
         self.get_num_rows()
         self.delete_table()
@@ -508,8 +449,8 @@ class MethodController(RunController):
             res = self.get_num_rows()
 
         self.new_table()
-        num_rows = self.get_num_rows()
-        if num_rows.ok_value.num_response != 0:
+        num_rows = self.get_row_count_safely()
+        if num_rows != 0:
             raise ValueError("Should be zero rows!")
 
         time_added = False

{pychemstation-0.10.9 → pychemstation-0.10.11}/pychemstation/control/controllers/data_aq/sequence.py

@@ -55,19 +55,20 @@ class SequenceController(RunController):
         )
 
     def load(self) -> SequenceTable:
-        rows = self.get_num_rows()
+        rows = self.get_row_count_safely()
         self.send(Command.GET_SEQUENCE_CMD)
         seq_name = self.receive()
 
-        if rows.is_ok() and seq_name.is_ok():
+        if seq_name.is_ok():
             self.table_state: SequenceTable = 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))
-                ],
+                rows=[self.get_row(r + 1) for r in range(int(rows))],
             )
             return self.table_state
-        raise RuntimeError(rows.err_value)
+        else:
+            raise RuntimeError(
+                f"couldn't read rows or sequence name: {seq_name.err_value}"
+            )
 
     def try_int(self, val: Any) -> Optional[int]:
         try:
@@ -136,23 +137,21 @@ class SequenceController(RunController):
         :param sequence_table:
         """
         self.table_state = sequence_table
-        rows = self.get_num_rows()
-        if rows.is_ok():
-            existing_row_num = rows.ok_value.num_response
-            wanted_row_num = len(sequence_table.rows)
-            for i in range(int(existing_row_num)):
-                self.delete_row(int(existing_row_num - i))
-                self.send(Command.SAVE_SEQUENCE_CMD)
-            for i in range(int(wanted_row_num)):
-                self.add_row()
-                self.save()
-            self.send(Command.SWITCH_SEQUENCE_CMD)
-
-            for i, row in enumerate(sequence_table.rows):
-                self._edit_row(row=row, row_num=i + 1)
-                self.sleep(1)
+        rows = self.get_row_count_safely()
+        existing_row_num = rows
+        wanted_row_num = len(sequence_table.rows)
+        for i in range(int(existing_row_num)):
+            self.delete_row(int(existing_row_num - i))
+            self.send(Command.SAVE_SEQUENCE_CMD)
+        for i in range(int(wanted_row_num)):
+            self.add_row()
             self.save()
-            self.send(Command.SWITCH_SEQUENCE_CMD)
+        self.send(Command.SWITCH_SEQUENCE_CMD)
+        for i, row in enumerate(sequence_table.rows):
+            self._edit_row(row=row, row_num=i + 1)
+            self.sleep(1)
+        self.save()
+        self.send(Command.SWITCH_SEQUENCE_CMD)
 
     def _edit_row(self, row: SequenceEntry, row_num: int):
         """
@@ -161,12 +160,11 @@ class SequenceController(RunController):
         :param row: sequence row entry with updated information
         :param row_num: the row to edit, based on 1-based indexing
         """
-        num_rows = self.get_num_rows()
-        if num_rows.is_ok():
-            while num_rows.ok_value.num_response < row_num:
-                self.add_row()
-                self.save()
-                num_rows = self.get_num_rows()
+        num_rows = self.get_row_count_safely()
+        while num_rows < row_num:
+            self.add_row()
+            self.save()
+            num_rows = self.get_row_count_safely()
         if row.vial_location:
             self.edit_vial_location(row.vial_location, row_num, save=False)
         if row.method:
@@ -268,7 +266,7 @@ class SequenceController(RunController):
             elif isinstance(loc, VialBar) or isinstance(loc, FiftyFourVialPlate):
                 self.add_row()
                 previous_contents.vial_location = loc
-                num_rows = self.get_num_rows().ok_value.num_response
+                num_rows = self.get_row_count_safely()
                 self._edit_row(previous_contents, num_rows)
                 self.move_row(int(num_rows), row_num)
                 self.delete_row(row_num + 1)
@@ -339,6 +337,8 @@ class SequenceController(RunController):
             hplc_running = self.check_hplc_is_running()
             if hplc_running:
                 break
+            else:
+                self.send(Command.RUN_SEQUENCE_CMD.value)
 
         if hplc_running:
             full_path_name, current_sample_file = self.try_getting_run_info(folder_name)

{pychemstation-0.10.9 → pychemstation-0.10.11}/pychemstation/control/controllers/devices/injector.py

@@ -15,7 +15,6 @@ from ....utils.injector_types import (
     DrawDefaultVolume,
     DrawDefaultLocation,
 )
-from ....utils.macro import Response
 from ....utils.table_types import RegisterFlag, Table
 from ....utils.tray_types import Tray, FiftyFourVialPlate, VialBar, LocationPlus
 
@@ -93,14 +92,5 @@ class InjectorController(DeviceController):
         raise ValueError("No valid function found.")
 
     def load(self) -> InjectorTable | None:
-        rows = self.get_num_rows()
-        if rows.is_ok():
-            row_response = rows.value
-            if isinstance(row_response, Response):
-                return InjectorTable(
-                    functions=[
-                        self.get_row(i + 1)
-                        for i in range(int(row_response.num_response))
-                    ]
-                )
-        raise ValueError("Couldn't read injector table rows.")
+        rows = self.get_row_count_safely()
+        return InjectorTable(functions=[self.get_row(i + 1) for i in range(rows)])

{pychemstation-0.10.9 → pychemstation-0.10.11}/pychemstation/utils/abc_tables/table.py

@@ -126,11 +126,9 @@ class ABCTableController(abc.ABC):
     ):
         if not (isinstance(val, int) or isinstance(val, float)):
             raise ValueError(f"{val} must be an int or float.")
-        num_rows = self.get_num_rows()
-        if row:
-            if num_rows.is_ok():
-                if num_rows.ok_value.num_response < row:
-                    raise ValueError("Not enough rows to edit!")
+        num_rows = self.get_row_count_safely()
+        if row and num_rows < row:
+            raise ValueError("Not enough rows to edit!")
 
         self.sleepy_send(
             TableOperation.EDIT_ROW_VAL.value.format(
@@ -147,11 +145,9 @@ class ABCTableController(abc.ABC):
     ):
         if not isinstance(val, str):
             raise ValueError(f"{val} must be a str.")
-        num_rows = self.get_num_rows()
-        if row:
-            if num_rows.is_ok():
-                if num_rows.ok_value.num_response < row:
-                    raise ValueError("Not enough rows to edit!")
+        num_rows = self.get_row_count_safely()
+        if row and num_rows < row:
+            raise ValueError("Not enough rows to edit!")
 
         self.sleepy_send(
             TableOperation.EDIT_ROW_TEXT.value.format(
@@ -176,15 +172,27 @@ class ABCTableController(abc.ABC):
             )
         )
 
+    def get_row_count_safely(self) -> int:
+        row_count = self.get_num_rows()
+        tries = 10
+        i = 0
+        while row_count.is_err() and i < tries:
+            row_count = self.get_num_rows()
+            i += 1
+        if row_count.is_ok():
+            return int(row_count.ok_value.num_response)
+        else:
+            raise ValueError("couldn't read row count, table might not exist")
+
     def add_row(self):
         """Adds a row to the provided table for currently loaded method or sequence."""
-        previous_row_count = self.get_num_rows().ok_value.num_response
+        previous_row_count = self.get_row_count_safely()
         self.sleepy_send(
             TableOperation.NEW_ROW.value.format(
                 register=self.table_locator.register, table_name=self.table_locator.name
             )
         )
-        new_row_count = self.get_num_rows().ok_value.num_response
+        new_row_count = self.get_row_count_safely()
         if previous_row_count + 1 != new_row_count:
             raise ValueError("Row could not be added.")
 

{pychemstation-0.10.9 → pychemstation-0.10.11}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "pychemstation"
-version = "0.10.9"
+version = "0.10.11"
 description = "Library to interact with Chemstation software, primarily used in Hein lab"
 authors = [{ name = "lucyhao", email = "hao.lucyy@gmail.com" }]
 requires-python = ">=3.10"