pychemstation 0.10.6__tar.gz → 0.10.7__tar.gz

{pychemstation-0.10.6 → pychemstation-0.10.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pychemstation
-Version: 0.10.6
+Version: 0.10.7
 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
@@ -18,7 +18,7 @@ Requires-Dist: matplotlib>=3.7.5
 Requires-Dist: pandas>=2.0.3
 Requires-Dist: pdoc>=14.7.0
 Requires-Dist: polling>=0.3.2
-Requires-Dist: pre-commit>=4.2.0
+Requires-Dist: pre-commit>=3.5.0
 Requires-Dist: pytest>=7.3.5
 Requires-Dist: rainbow-api>=1.0.10
 Requires-Dist: result>=0.17.0
@@ -90,7 +90,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.6 → pychemstation-0.10.7}/README.md

@@ -59,7 +59,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.6 → pychemstation-0.10.7}/out.txt

@@ -375,3 +375,137 @@ LoadMethod "D:\Chemstation\1\Methods\", "GENERAL-POROSHELL-OPT.M"
 response$ = _MethFile$
 Rows = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
 response_num = TabHdrVal(RCPMP1Method[1], "Timetable", "NumberOfRows")
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+PrepRun
+SaveMethod _MethPath$, _MethFile$, "{commit_msg}"
+SaveSequence _SeqPath$, _SeqFile$
+response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
+response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
+response$ = _MethFile$
+RunSequence
+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$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+Local Rows
+SaveMethod _MethPath$, _MethFile$, "method saved by pychemstation"
+SaveSequence _SeqPath$, _SeqFile$
+LIDoOperation "TURN_ON"
+PrepRun
+_SeqFile$ = "hplc_testing.S"
+_SeqPath$ = "C:\1\Sequence\"
+LoadSequence _SeqPath$, _SeqFile$
+response$ = _SeqFile$
+Rows = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+response_num = TabHdrVal(_sequence[1], "SeqTable1", "NumberOfRows")
+Sleep 0.1
+Print Rows
+response$ = _SeqFile$
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "SampleName")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "Vial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "Method")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "InjVial")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjVolume")
+response$ = TabText$("_sequence[1]", "SeqTable1", 1, "InjectionSource")
+response_num = TabVal("_sequence[1]", "SeqTable1", 1, "SampleType")
+PrepRun
+SaveMethod _MethPath$, _MethFile$, "{commit_msg}"
+SaveSequence _SeqPath$, _SeqFile$
+response_num = ObjHdrVal("RCPMP1Method[1]", "PostTime_Time")
+response_num = ObjHdrVal("RCPMP1Method[1]", "StopTime_Time")
+response$ = _MethFile$
+RunSequence
+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$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$
+response$ = AcqStatus$

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/README.md

@@ -10,7 +10,7 @@ DATA_DIR_2 = "C:\\Users\\Public\\Documents\\ChemStation\\2\\Data"
 DATA_DIR_3 = "C:\\Users\\Public\\Documents\\ChemStation\\3\\Data"
 
 # Initialize HPLC Controller
-hplc_controller = HPLCController(data_dirs=[DATA_DIR_2, DATA_DIR_3],
+hplc_controller = HPLCController(extra_data_dirs=[DATA_DIR_2, DATA_DIR_3],
                                  comm_dir=DEFAULT_COMMAND_PATH,
                                  method_dir=DEFAULT_METHOD_DIR,
                                  sequence_dir=SEQUENCE_DIR)

{pychemstation-0.10.6/pychemstation/utils/mocking → pychemstation-0.10.7/pychemstation/control/controllers/abc_tables}/abc_comm.py

@@ -18,12 +18,7 @@ from typing import Union
 
 from result import Err, Ok, Result
 
-from ...utils.macro import (
-    HPLCAvailStatus,
-    Command,
-    Status,
-    Response,
-)
+from ....utils.macro import Status, HPLCAvailStatus, Command, Response
 
 
 class ABCCommunicationController(abc.ABC):

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/controllers/abc_tables/device.py

@@ -13,3 +13,8 @@ class DeviceController(ABCTableController, ABC):
     ):
         super().__init__(controller=controller, table=table)
         self.offline = offline
+
+    def __new__(cls, *args, **kwargs):
+        if cls is ABCTableController:
+            raise TypeError(f"only children of '{cls.__name__}' may be instantiated")
+        return object.__new__(cls)

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/controllers/abc_tables/run.py

@@ -11,13 +11,17 @@ import math
 import os
 import time
 import warnings
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Dict, List, Optional, Tuple, Union, Set
 
 import polling
 import rainbow as rb
-from result import Err, Result, Ok
+from result import Err, Ok, Result
+
+from pychemstation.analysis.chromatogram import (
+    AgilentChannelChromatogramData,
+    AgilentHPLCChromatogram,
+)
 
-from .table import ABCTableController
 from ....analysis.process_report import (
     AgilentReport,
     CSVProcessor,
@@ -25,14 +29,11 @@ from ....analysis.process_report import (
     TXTProcessor,
 )
 from ....control.controllers.comm import CommunicationController
-from pychemstation.analysis.chromatogram import (
-    AgilentChannelChromatogramData,
-    AgilentHPLCChromatogram,
-)
-from ....utils.macro import HPLCRunningStatus
+from ....utils.macro import Command, HPLCRunningStatus
 from ....utils.method_types import MethodDetails
 from ....utils.sequence_types import SequenceTable
-from ....utils.table_types import Table, T
+from ....utils.table_types import T, Table
+from .table import ABCTableController
 
 TableType = Union[MethodDetails, SequenceTable]
 
@@ -47,12 +48,10 @@ class RunController(ABCTableController, abc.ABC):
         offline: bool = False,
     ):
         super().__init__(controller=controller, table=table)
-        warnings.warn(
-            "This abstract class is not meant to be initialized. Use MethodController or SequenceController."
-        )
         self.table_state: Optional[TableType] = None
         self.curr_run_starting_time: Optional[float] = None
         self.timeout: Optional[float] = None
+        self.current_run_child_files: Set[str] = set()
 
         if not offline:
             if src and not os.path.isdir(src):
@@ -79,8 +78,15 @@ class RunController(ABCTableController, abc.ABC):
         self.uv: Dict[int, AgilentHPLCChromatogram] = {}
         self.data_files: List = []
 
+    def __new__(cls, *args, **kwargs):
+        if cls is RunController:
+            raise TypeError(f"only children of '{cls.__name__}' may be instantiated")
+        return object.__new__(cls)
+
     @abc.abstractmethod
-    def fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[T, str]:
+    def fuzzy_match_most_recent_folder(
+        self, most_recent_folder: T, child_files: Set[str]
+    ) -> Result[T, str]:
         pass
 
     @abc.abstractmethod
@@ -120,6 +126,12 @@ class RunController(ABCTableController, abc.ABC):
 
     def check_hplc_run_finished(self) -> Tuple[float, bool]:
         if self.controller:
+            try:
+                _, current_run_file = self.get_current_run_data_dir_file()
+                sample_file, extension, _ = current_run_file.partition(".D")
+                self.current_run_child_files.add(sample_file)
+            except Exception:
+                pass
             done_running = self.controller.check_if_not_running()
             if self.curr_run_starting_time and self.timeout:
                 time_passed = time.time() - self.curr_run_starting_time
@@ -141,6 +153,7 @@ class RunController(ABCTableController, abc.ABC):
 
         :return: Data file object containing most recent run file information.
         """
+        self.current_run_child_files = set()
         if self.timeout is not None:
             finished_run = False
             minutes = math.ceil(self.timeout / 60)
@@ -170,7 +183,9 @@ class RunController(ABCTableController, abc.ABC):
         else:
             raise ValueError("Timeout value is None, no comparison can be made.")
 
-        check_folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
+        check_folder = self.fuzzy_match_most_recent_folder(
+            self.data_files[-1], self.current_run_child_files
+        )
         if check_folder.is_ok() and finished_run:
             return check_folder
         elif check_folder.is_ok():
@@ -226,3 +241,16 @@ class RunController(ABCTableController, abc.ABC):
     def _reset_time(self):
         self.curr_run_starting_time = None
         self.timeout = None
+
+    def get_current_run_data_dir_file(self) -> Tuple[str, str]:
+        self.send(Command.GET_CURRENT_RUN_DATA_DIR)
+        full_path_name = self.receive()
+        self.send(Command.GET_CURRENT_RUN_DATA_FILE)
+        current_sample_file = self.receive()
+        if full_path_name.is_ok() and current_sample_file.is_ok():
+            return (
+                full_path_name.ok_value.string_response,
+                current_sample_file.ok_value.string_response,
+            )
+        else:
+            raise ValueError("Couldn't read data dir and file.")

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/controllers/abc_tables/table.py

@@ -7,7 +7,6 @@ Authors: Lucy Hao
 from __future__ import annotations
 
 import abc
-import warnings
 from typing import Optional, Union
 
 from result import Err, Result
@@ -27,13 +26,15 @@ class ABCTableController(abc.ABC):
         controller: Optional[CommunicationController],
         table: Table,
     ):
-        warnings.warn(
-            "This abstract class is not meant to be initialized. Use MethodController or SequenceController."
-        )
         self.controller = controller
         self.table_locator = table
         self.table_state: Optional[TableType] = None
 
+    def __new__(cls, *args, **kwargs):
+        if cls is ABCTableController:
+            raise TypeError(f"only children of '{cls.__name__}' may be instantiated")
+        return object.__new__(cls, *args, **kwargs)
+
     def receive(self) -> Result[Response, str]:
         if self.controller:
             for _ in range(10):
@@ -93,6 +94,8 @@ class ABCTableController(abc.ABC):
             raise ValueError("Controller is offline")
 
     def add_new_col_num(self, col_name: RegisterFlag, val: Union[int, float]):
+        if not (isinstance(val, int) or isinstance(val, float)):
+            raise ValueError(f"{val} must be an int or float.")
         self.sleepy_send(
             TableOperation.NEW_COL_VAL.value.format(
                 register=self.table_locator.register,
@@ -103,6 +106,8 @@ class ABCTableController(abc.ABC):
         )
 
     def add_new_col_text(self, col_name: RegisterFlag, val: str):
+        if not isinstance(val, str):
+            raise ValueError(f"{val} must be a str.")
         self.sleepy_send(
             TableOperation.NEW_COL_TEXT.value.format(
                 register=self.table_locator.register,
@@ -115,10 +120,12 @@ class ABCTableController(abc.ABC):
     def _edit_row_num(
         self, col_name: RegisterFlag, val: Union[int, float], row: Optional[int] = None
     ):
+        if not (isinstance(val, int) or isinstance(val, float)):
+            raise ValueError(f"{val} must be an int or float.")
         if row:
             num_rows = self.get_num_rows()
             if num_rows.is_ok():
-                if num_rows.value.num_response < row:
+                if num_rows.ok_value.num_response < row:
                     raise ValueError("Not enough rows to edit!")
 
         self.sleepy_send(
@@ -134,10 +141,12 @@ class ABCTableController(abc.ABC):
     def _edit_row_text(
         self, col_name: RegisterFlag, val: str, row: Optional[int] = None
     ):
+        if not isinstance(val, str):
+            raise ValueError(f"{val} must be a str.")
         if row:
             num_rows = self.get_num_rows()
             if num_rows.is_ok():
-                if num_rows.value.num_response < row:
+                if num_rows.ok_value.num_response < row:
                     raise ValueError("Not enough rows to edit!")
 
         self.sleepy_send(

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/controllers/comm.py

@@ -11,17 +11,17 @@ Authors: Alexander Hammer, Hessam Mehr, Lucy Hao
 """
 
 import time
-from typing import Optional, Union
+from typing import Optional, Union, Tuple, List
 
 from result import Err, Ok, Result
 
 from ...utils.macro import (
-    str_to_status,
-    HPLCErrorStatus,
     Command,
+    HPLCErrorStatus,
     Status,
+    str_to_status,
 )
-from ...utils.mocking.abc_comm import ABCCommunicationController
+from .abc_tables.abc_comm import ABCCommunicationController
 
 
 class CommunicationController(ABCCommunicationController):
@@ -76,7 +76,7 @@ class CommunicationController(ABCCommunicationController):
             if res.is_err():
                 return HPLCErrorStatus.NORESPONSE
             if res.is_ok():
-                parsed_response = self.receive().value.string_response
+                parsed_response = self.receive().ok_value.string_response
                 self._most_recent_hplc_status = str_to_status(parsed_response)
                 return self._most_recent_hplc_status
             else:
@@ -148,3 +148,24 @@ class CommunicationController(ABCCommunicationController):
             return Err(
                 f"Failed to receive reply to command #{cmd_no} due to {err} caused by {err_msg}."
             )
+
+    def get_chemstation_dirs(self) -> Tuple[str, str, List[str]]:
+        method_dir, sequence_dir, data_dirs = None, None, None
+        self.send(Command.GET_METHOD_DIR)
+        res = self.receive()
+        if res.is_ok():
+            method_dir = res.ok_value.string_response
+        self.send(Command.GET_SEQUENCE_DIR)
+        res = self.receive()
+        if res.is_ok():
+            sequence_dir = res.ok_value.string_response
+        self.send(Command.GET_DATA_DIRS)
+        res = self.receive()
+        if res.is_ok():
+            data_dirs = res.ok().string_response.split("|")
+        if method_dir and sequence_dir and data_dirs:
+            return method_dir, sequence_dir, data_dirs
+        else:
+            raise ValueError(
+                "Please provide the method, sequence and data directories, could not be found."
+            )

{pychemstation-0.10.6 → pychemstation-0.10.7}/pychemstation/control/controllers/data_aq/method.py

@@ -3,7 +3,7 @@ from __future__ import annotations
 import os
 import time
 import warnings
-from typing import List, Optional, Union, Dict
+from typing import List, Optional, Union, Dict, Set
 
 from result import Err, Ok, Result
 
@@ -413,8 +413,6 @@ class MethodController(RunController):
         :param stall_while_running: whether to stall or immediately return
         :param add_timestamp: if should add timestamp to experiment name
         """
-
-        folder_name = ""
         hplc_is_running = False
         tries = 0
         while tries < 10 and not hplc_is_running:
@@ -427,18 +425,15 @@ class MethodController(RunController):
                     else experiment_name,
                 )
             )
-            folder_name = (
-                f"{experiment_name}_{timestamp}.D"
-                if add_timestamp
-                else f"{experiment_name}.D"
-            )
+
             hplc_is_running = self.check_hplc_is_running()
             tries += 1
 
+        data_dir, data_file = self.get_current_run_data_dir_file()
         if not hplc_is_running:
             raise RuntimeError("Method failed to start.")
 
-        self.data_files.append(os.path.join(self.data_dirs[0], folder_name))
+        self.data_files.append(os.path.join(os.path.normpath(data_dir), data_file))
         self.timeout = (self.get_total_runtime()) * 60
 
         if stall_while_running:
@@ -446,18 +441,20 @@ class MethodController(RunController):
             if run_completed.is_ok():
                 self.data_files[-1] = run_completed.ok_value
             else:
-                raise RuntimeError("Run error has occurred.")
+                raise RuntimeError(f"Run error has occurred:{run_completed.err_value}.")
         else:
-            folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
+            folder = self.fuzzy_match_most_recent_folder(self.data_files[-1], None)
             while folder.is_err():
-                folder = self.fuzzy_match_most_recent_folder(self.data_files[-1])
+                folder = self.fuzzy_match_most_recent_folder(self.data_files[-1], None)
             if folder.is_ok():
                 self.data_files[-1] = folder.ok_value
             else:
                 warning = f"Data folder {self.data_files[-1]} may not exist, returning and will check again after run is done."
                 warnings.warn(warning)
 
-    def fuzzy_match_most_recent_folder(self, most_recent_folder: T) -> Result[str, str]:
+    def fuzzy_match_most_recent_folder(
+        self, most_recent_folder: T, child_dirs: Optional[Set[str]]
+    ) -> Result[str, str]:
         if isinstance(most_recent_folder, str) or isinstance(most_recent_folder, bytes):
             if os.path.exists(most_recent_folder):
                 return Ok(most_recent_folder)