pychemstation 0.5.14__tar.gz → 0.5.15__tar.gz

{pychemstation-0.5.14 → pychemstation-0.5.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.14
+Version: 0.5.15
 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-0.5.14 → pychemstation-0.5.15}/pychemstation/control/controllers/devices/injector.py

@@ -1,6 +1,7 @@
 from ....control.controllers import CommunicationController
 from .device import DeviceController
 from ....utils.injector_types import *
+from ....utils.macro import Command
 from ....utils.table_types import Table, RegisterFlag
 
 
@@ -19,10 +20,14 @@ class InjectorController(DeviceController):
         elif function == "Inject":
             return Inject()
         elif function == "Draw":
+            # TODO: better error handling
             is_source = SourceType(self.get_text(row, RegisterFlag.DRAW_SOURCE))
             is_volume = Mode(self.get_text(row, RegisterFlag.DRAW_VOLUME))
-            return Draw(amount=self.get_num(row, RegisterFlag.DRAW_VOLUME_VALUE) if is_volume == Mode.SET else None,
-                        source=return_tray_loc() if is_source == SourceType.SPECIFIC_LOCATION else None)
+            vol = self.get_num(row, RegisterFlag.DRAW_VOLUME_VALUE) if is_volume == Mode.SET else None
+            if is_source is SourceType.SPECIFIC_LOCATION:
+                return Draw(amount=vol, source=return_tray_loc())
+            elif is_source is SourceType.LOCATION:
+                return Draw(amount=vol, location=self.get_text(row, RegisterFlag.DRAW_LOCATION))
         elif function == "Remote":
             return Remote(command=RemoteCommand(self.get_text(row, RegisterFlag.REMOTE)),
                           duration=self.get_num(row, RegisterFlag.REMOTE_DUR))
@@ -30,17 +35,21 @@ class InjectorController(DeviceController):
     def load(self) -> InjectorTable:
         rows = self.get_num_rows()
         if rows.is_ok():
-            return InjectorTable(functions=[self.get_row(i + 1) for i in range(rows.ok_value.num_response)])
+            return InjectorTable(functions=[self.get_row(i + 1) for i in range(int(rows.ok_value.num_response))])
 
     def edit(self, injector_table: InjectorTable):
-        self.delete_table()
-        res = self.get_num_rows()
-        while not res.is_err():
-            self.delete_table()
-            res = self.get_num_rows()
-
-        self.new_table()
-        self.get_num_rows()
+        rows = self.get_num_rows()
+        if rows.is_ok():
+            existing_row_num = rows.value.num_response
+            wanted_row_num = len(injector_table.functions)
+            while existing_row_num != wanted_row_num:
+                if wanted_row_num > existing_row_num:
+                    self.add_row()
+                elif wanted_row_num < existing_row_num:
+                    self.delete_row(int(existing_row_num))
+                self.send(Command.SAVE_METHOD_CMD)
+                existing_row_num = self.get_num_rows().ok_value.num_response
+            self.send(Command.SWITCH_METHOD_CMD)
 
         columns_added = set()
 
@@ -72,7 +81,10 @@ class InjectorController(DeviceController):
             else:
                 add_table_val(col_name=RegisterFlag.DRAW_VOLUME, val=Mode.DEFAULT.value)
 
-            if draw.source:
+            if draw.location:
+                add_table_val(col_name=RegisterFlag.DRAW_SOURCE, val=SourceType.LOCATION.value)
+                add_table_val(col_name=RegisterFlag.DRAW_LOCATION, val=draw.location)
+            elif draw.source:
                 add_table_val(col_name=RegisterFlag.DRAW_SOURCE, val=SourceType.SPECIFIC_LOCATION.value)
                 add_table_val(col_name=RegisterFlag.DRAW_LOCATION_UNIT, val=1)
                 add_table_val(col_name=RegisterFlag.DRAW_LOCATION_TRAY, val=1)
@@ -101,6 +113,10 @@ class InjectorController(DeviceController):
             elif isinstance(function, Remote):
                 add_remote(function)
             self.download()
+        self.send(Command.SAVE_METHOD_CMD)
+        self.send(Command.SWITCH_METHOD_CMD)
 
     def download(self):
-        pass
+        self.send('Sleep 1')
+        self.sleepy_send("DownloadLWls 1")
+        self.send('Sleep 1')

{pychemstation-0.5.14 → pychemstation-0.5.15}/pychemstation/control/controllers/tables/table.py

@@ -6,6 +6,7 @@ Authors: Lucy Hao
 
 import abc
 import os
+import warnings
 from dataclasses import dataclass
 from typing import Union, Optional
 
@@ -33,8 +34,8 @@ class ChromData:
 class TableController(abc.ABC):
 
     def __init__(self, controller: CommunicationController,
-                 src: str,
-                 data_dir: str,
+                 src: Optional[str],
+                 data_dir: Optional[str],
                  table: Table,
                  offline: bool = False):
         self.controller = controller
@@ -45,26 +46,27 @@ class TableController(abc.ABC):
             # Initialize row counter for table operations
             self.send('Local Rows')
 
-            if os.path.isdir(src):
+            if src and os.path.isdir(src):
                 self.src: str = src
             else:
-                raise FileNotFoundError(f"dir: {src} not found.")
+                warnings.warn(f"dir: {src} not found.")
 
-            if os.path.isdir(data_dir):
+            if data_dir and os.path.isdir(data_dir):
                 self.data_dir: str = data_dir
             else:
-                raise FileNotFoundError(f"dir: {data_dir} not found.")
-
-            self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
-                "A": AgilentHPLCChromatogram(self.data_dir),
-                "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),
-            }
+                warnings.warn(f"dir: {data_dir} not found.")
+
+            if hasattr(self, "data_dir"):
+                self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
+                    "A": AgilentHPLCChromatogram(self.data_dir),
+                    "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),
+                }
         else:
             self.spectra: dict[str, Optional[AgilentHPLCChromatogram]] = {
                 "A": AgilentHPLCChromatogram(),

{pychemstation-0.5.14 → pychemstation-0.5.15}/pychemstation/utils/injector_types.py

@@ -8,6 +8,7 @@ from pychemstation.utils.tray_types import Tray
 class SourceType(Enum):
     DEFAULT = "ActualPosition"
     SPECIFIC_LOCATION = "ActualPositionPlusLocation"
+    LOCATION = "Location"
 
 
 class Mode(Enum):
@@ -18,6 +19,7 @@ class Mode(Enum):
 @dataclass
 class Draw:
     amount: Optional[float] = None
+    location: Optional[str] = None
     source: Optional[Tray] = None
 
 

{pychemstation-0.5.14 → pychemstation-0.5.15}/pychemstation/utils/macro.py

@@ -37,7 +37,7 @@ class Command(Enum):
     # Method and Sequence Related
     GET_METHOD_CMD = "response$ = _MethFile$"
     GET_ROWS_CMD = 'response_num = TabHdrVal({register}, "{table_name}", "{col_name}")'
-    SWITCH_METHOD_CMD = 'LoadMethod "{method_dir}", "{method_name}.M"'
+    SWITCH_METHOD_CMD = 'LoadMethod _MethPath$, _MethFile$'
     START_METHOD_CMD = "StartMethod"
     RUN_METHOD_CMD = 'RunMethod "{data_dir}",, "{experiment_name}_{timestamp}"'
     STOP_METHOD_CMD = "StopMethod"

{pychemstation-0.5.14 → pychemstation-0.5.15}/pychemstation/utils/table_types.py

@@ -71,7 +71,9 @@ class RegisterFlag(Enum):
     DRAW_VOLUME = "DrawVolume_Mode"
     DRAW_SPEED = "DrawSpeed_Mode"
     DRAW_OFFSET = "DrawOffset_Mode"
+    # SetObjHdrVal RCWLS1Pretreatment[1], "DrawVolume_Value", 1
     DRAW_VOLUME_VALUE = "DrawVolume_Value"
+    DRAW_LOCATION = "DrawLocation"
     DRAW_LOCATION_TRAY = "DrawLocationPlus_Tray"
     DRAW_LOCATION_UNIT = "DrawLocationPlus_Unit"
     DRAW_LOCATION_ROW = "DrawLocationPlus_Row"

{pychemstation-0.5.14 → pychemstation-0.5.15}/pychemstation.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.14
+Version: 0.5.15
 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-0.5.14 → pychemstation-0.5.15}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setuptools.setup(
     name="pychemstation",
-    version="0.5.14",
+    version="0.5.15",
     author="Lucy Hao",
     author_email="lhao03@student.ubc.ca",
     description="Library to interact with Chemstation software, primarily used in Hein lab",

{pychemstation-0.5.14 → pychemstation-0.5.15}/tests/test_inj.py

@@ -9,7 +9,7 @@ from tests.constants import *
 
 class TestInj(unittest.TestCase):
     def setUp(self):
-        path_constants = room(242)
+        path_constants = room(254)
         for path in path_constants:
             if not os.path.exists(path):
                 self.fail(
@@ -23,7 +23,8 @@ class TestInj(unittest.TestCase):
     def test_load_inj(self):
         self.hplc_controller.switch_method(DEFAULT_METHOD)
         try:
-            self.hplc_controller.load_injector_program()
+            inj_table = self.hplc_controller.load_injector_program()
+            self.assertTrue(len(inj_table.functions) == 2)
         except Exception as e:
             self.fail(f"Should have not failed, {e}")
 
@@ -32,23 +33,8 @@ class TestInj(unittest.TestCase):
         try:
             injector_program = InjectorTable(
                 functions=[
-                    Draw(
-                        amount=0.3,
-                        source=FiftyFourVialPlate(
-                            plate=Plate.ONE,
-                            letter=Letter.A,
-                            num=Num.EIGHT)),
-                    Remote(
-                        command=RemoteCommand.PREPARE,
-                        duration=10,
-                    ),
-                    Wait(
-                        duration=2
-                    ),
-                    Inject(
-
-                    )
-                ]
+                    Draw(amount=0.3, location="P1-A2"),
+                           Inject()]
             )
             self.hplc_controller.edit_injector_program(injector_program)
         except Exception as e:
@@ -58,19 +44,8 @@ class TestInj(unittest.TestCase):
         self.hplc_controller.switch_method(DEFAULT_METHOD)
         try:
             injector_program = InjectorTable(
-                functions=[
-                    Draw(
-                        amount=0.3,
-                        source=FiftyFourVialPlate(
-                            plate=Plate.ONE,
-                            letter=Letter.A,
-                            num=Num.EIGHT)),
-                    Inject(
-
-                    )
-                ]
+                functions=[Draw(location="P1-F2"), Inject()]
             )
-
             self.hplc_controller.edit_injector_program(injector_program)
         except Exception as e:
             self.fail(f"Should have not failed: {e}")

{pychemstation-0.5.14 → pychemstation-0.5.15}/tests/test_method.py

@@ -7,7 +7,7 @@ from tests.constants import *
 
 class TestMethod(unittest.TestCase):
     def setUp(self):
-        path_constants = room(242)
+        path_constants = room(254)
         for path in path_constants:
             if not os.path.exists(path):
                 self.fail(
@@ -28,7 +28,25 @@ class TestMethod(unittest.TestCase):
 
     def test_edit_method(self):
         self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
-        new_method = gen_rand_method()
+        new_method = MethodDetails(name=DEFAULT_METHOD,
+                                   timetable=[TimeTableEntry(start_time=1,
+                                                             organic_modifer=20,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=2,
+                                                             organic_modifer=30,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=2.5,
+                                                             organic_modifer=60,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=3,
+                                                             organic_modifer=80,
+                                                             flow=0.65),
+                                              TimeTableEntry(start_time=3.5,
+                                                             organic_modifer=100,
+                                                             flow=0.65)],
+                                   stop_time=4,
+                                   post_time=1,
+                                   params=HPLCMethodParams(organic_modifier=5, flow=0.65))
         try:
             self.hplc_controller.edit_method(new_method)
         except Exception as e: