pychemstation 0.5.3.dev1__py3-none-any.whl → 0.5.4__py3-none-any.whl

pychemstation/control/comm.py

@@ -86,17 +86,18 @@ class CommunicationController:
 
     def set_status(self):
         """Updates current status of HPLC machine"""
-        self._most_recent_hplc_status = self.get_status()[0]
+        self._most_recent_hplc_status = self.get_status()
 
-    def check_if_running(self, data_path: str) -> bool:
+    def check_if_running(self) -> bool:
         """Checks if HPLC machine is in an available state, meaning a state that data is not being written.
 
         :return: whether the HPLC machine is in a safe state to retrieve data back."""
         self.set_status()
-        file_exists = os.path.exists(data_path)
         hplc_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
-        done_writing_data = hplc_avail and file_exists
-        return done_writing_data
+        time.sleep(30)
+        self.set_status()
+        hplc_actually_avail = isinstance(self._most_recent_hplc_status, HPLCAvailStatus)
+        return hplc_avail and hplc_actually_avail
 
     def _send(self, cmd: str, cmd_no: int, num_attempts=5) -> None:
         """Low-level execution primitive. Sends a command string to HPLC.
@@ -170,6 +171,9 @@ class CommunicationController:
         cmd_to_send: str = cmd.value if isinstance(cmd, Command) else cmd
         self.cmd_no += 1
         self._send(cmd_to_send, self.cmd_no)
+        f = open("out.txt", "a")
+        f.write(cmd_to_send + "\n")
+        f.close()
 
     def receive(self) -> Result[Response, str]:
         """Returns messages received in reply file.

pychemstation/control/hplc.py

@@ -91,15 +91,15 @@ class HPLCController:
         """
         self.method_controller.run(experiment_name)
 
-    def run_sequence(self, sequence_table: SequenceTable):
+    def run_sequence(self):
         """
         Starts the currently loaded sequence, storing data
         under the <data_dir>/<sequence table name> folder.
         Device must be ready.
 
-        :param sequence_table:
+        :param sequence_name:
         """
-        self.sequence_controller.run(sequence_table)
+        self.sequence_controller.run()
 
     def edit_method(self, updated_method: MethodTimetable, save: bool = False):
         """Updated the currently loaded method in ChemStation with provided values.
@@ -114,7 +114,7 @@ class HPLCController:
         Updates the currently loaded sequence table with the provided table. This method will delete the existing sequence table and remake it.
         If you would only like to edit a single row of a sequence table, use `edit_sequence_row` instead.
 
-        :param sequence_table:
+        :param updated_sequence:
         """
         self.sequence_controller.edit(updated_sequence)
 

pychemstation/control/table/sequence.py

@@ -30,7 +30,7 @@ class SequenceController(TableController):
 
         if rows.is_ok() and seq_name.is_ok():
             return SequenceTable(
-                name=seq_name.ok_value.num_response,
+                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))])
         raise RuntimeError(rows.err_value)
 
@@ -73,34 +73,25 @@ class SequenceController(TableController):
 
         :param sequence_table:
         """
-        self.send("Local Rows")
-        self.sleep(1)
-        self.delete_table()
-        self.sleep(1)
-        self.new_table()
-        self.sleep(1)
-        self.get_num_rows()
-
-        if True:
-            for _ in sequence_table.rows:
-                self.add_row()
-                self.sleep(1)
+
+        rows = self.get_num_rows()
+        if rows.is_ok():
+            existing_row_num = rows.value.num_response
+            wanted_row_num = len(sequence_table.rows)
+            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_SEQUENCE_CMD)
-            self.get_num_rows()
-            self.send(Command.SAVE_SEQUENCE_CMD)
+                existing_row_num = self.get_num_rows().ok_value.num_response
+            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.send(Command.SAVE_SEQUENCE_CMD)
-        else:
-            for i, row in enumerate(sequence_table.rows):
-                self.add_row()
-                self.sleep(0.1)
-                self.edit_row(row=row, row_num=i + 1)
-                self.sleep(0.1)
-                rows = self.get_num_rows()
-                self.send(Command.SAVE_SEQUENCE_CMD)
-                self.send(Command.SWITCH_SEQUENCE_CMD)
+            self.send(Command.SWITCH_SEQUENCE_CMD)
 
     def edit_row(self, row: SequenceEntry, row_num: int):
         """
@@ -120,13 +111,16 @@ class SequenceController(TableController):
         table_name = self.table.name
 
         if row.vial_location:
+            loc = row.vial_location
+            if isinstance(row.vial_location, InjectionSource):
+                loc = row.vial_location.value
             self.sleepy_send(TableOperation.EDIT_ROW_VAL.value.format(register=table_register,
                                                                       table_name=table_name,
                                                                       row=row_num,
                                                                       col_name=RegisterFlag.VIAL_LOCATION,
-                                                                      val=row.vial_location.value))
+                                                                      val=loc))
         if row.method:
-            possible_path = os.path.join(self.method_dir, row.method)
+            possible_path = os.path.join(self.method_dir, row.method) + ".M\\"
             method = row.method
             if os.path.exists(possible_path):
                 method = os.path.join(self.method_dir, row.method)
@@ -177,23 +171,22 @@ class SequenceController(TableController):
 
         self.send(Command.SAVE_SEQUENCE_CMD)
 
-    def run(self, sequence_table: SequenceTable):
+    def run(self):
         """
         Starts the currently loaded sequence, storing data
         under the <data_dir>/<sequence table name> folder.
         Device must be ready.
-
-        :param sequence_table:
         """
         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"{sequence_table.name} {timestamp}"
+            folder_name = f"{seq_table.name} {timestamp}"
             self.data_files.append(SequenceDataFiles(dir=folder_name,
-                                                     sequence_name=sequence_table.name, ))
+                                                     sequence_name=seq_table.name))
 
-        run_completed = self.check_hplc_done_running()
+        run_completed = self.check_hplc_done_running(sequence=seq_table)
 
         if run_completed.is_ok():
             self.data_files[-1].dir = run_completed.value
@@ -202,16 +195,16 @@ class SequenceController(TableController):
 
     def retrieve_recent_data_files(self):
         sequence_data_files: SequenceDataFiles = self.data_files[-1]
-        return os.path.join(sequence_data_files.dir, sequence_data_files.child_dirs[-1])
+        return sequence_data_files.dir
 
     def get_data(self) -> list[dict[str, AgilentHPLCChromatogram]]:
-        sequence_data_files: SequenceDataFiles = self.data_files[-1]
+        parent_dir = self.data_files[-1].dir
         subdirs = [x[0] for x in os.walk(self.data_dir)]
-        potential_folders = sorted(list(filter(lambda d: sequence_data_files.dir in d, subdirs)))
-        self.data_files[-1].child_dirs = potential_folders
+        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 parent_dir in f and ".M" not in f and ".D" in f]
+
         spectra: list[dict[str, AgilentHPLCChromatogram]] = []
-        for row in sequence_data_files.child_dirs:
-            data_path = os.path.join(sequence_data_files.dir, row)
-            self.get_spectrum(data_path)
+        for row in self.data_files[-1].child_dirs:
+            self.get_spectrum(row)
             spectra.append(deepcopy(self.spectra))
         return spectra

pychemstation/control/table/table_controller.py

@@ -6,6 +6,7 @@ Authors: Lucy Hao
 
 import abc
 import os
+import time
 from typing import Union, Optional
 
 import polling
@@ -15,7 +16,7 @@ from ...control import CommunicationController
 from ...utils.chromatogram import AgilentHPLCChromatogram
 from ...utils.macro import Command, HPLCRunningStatus, Response
 from ...utils.method_types import MethodTimetable
-from ...utils.sequence_types import SequenceDataFiles
+from ...utils.sequence_types import SequenceDataFiles, SequenceTable
 from ...utils.table_types import Table, TableOperation, RegisterFlag
 
 
@@ -82,6 +83,11 @@ class TableController(abc.ABC):
     def get_row(self, row: int):
         pass
 
+    def delete_row(self, row: int):
+        self.sleepy_send(TableOperation.DELETE_ROW.value.format(register=self.table.register,
+                                                                table_name=self.table.name,
+                                                                row=row))
+
     def add_row(self):
         """
         Adds a row to the provided table for currently loaded method or sequence.
@@ -124,7 +130,7 @@ class TableController(abc.ABC):
         res = self.controller.receive()
 
         if res.is_ok():
-            self.send("Sleep 1")
+            self.send("Sleep 0.1")
             self.send('Print Rows')
             return res
         else:
@@ -137,24 +143,42 @@ class TableController(abc.ABC):
             max_tries=10)
         return started_running
 
-    def check_hplc_done_running(self, method: Optional[MethodTimetable] = None) -> Result[str, str]:
+    def check_hplc_done_running(self,
+                                method: Optional[MethodTimetable] = None,
+                                sequence: Optional[SequenceTable] = None) -> Result[str, str]:
         """
         Checks if ChemStation has finished running and can read data back
 
         :param method: if you are running a method and want to read back data, the timeout period will be adjusted to be longer than the method's runtime
         :return: Return True if data can be read back, else False.
         """
-        timeout = 10 * 60 if method is None else (method.first_row.maximum_run_time + 2) * 60
+        timeout = 10 * 60
+        if method:
+            timeout = ((method.first_row.maximum_run_time + 2) * 60)
+        if sequence:
+            timeout *= len(sequence.rows)
+
         most_recent_folder = self.retrieve_recent_data_files()
         finished_run = polling.poll(
-            lambda: self.controller.check_if_running(most_recent_folder),
+            lambda: self.controller.check_if_running(),
             timeout=timeout,
-            step=30
+            step=60
         )
+
         if finished_run:
-            subdirs = [x[0] for x in os.walk(self.data_dir)]
-            potential_folders = sorted(list(filter(lambda d: most_recent_folder in d, subdirs)))
-            return Ok(potential_folders[0])
+            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)
         else:
             return Err("Run did not complete as expected")
 

pychemstation/utils/table_types.py

@@ -9,6 +9,7 @@ class TableOperation(Enum):
     DELETE_TABLE = 'DelTab {register}, "{table_name}"'
     CREATE_TABLE = 'NewTab {register}, "{table_name}"'
     NEW_ROW = 'InsTabRow {register}, "{table_name}"'
+    DELETE_ROW = 'DelTabRow {register}, "{table_name}", {row}'
     EDIT_ROW_VAL = 'SetTabVal "{register}", "{table_name}", {row}, "{col_name}", {val}'
     EDIT_ROW_TEXT = 'SetTabText "{register}", "{table_name}", {row}, "{col_name}", "{val}"'
     GET_ROW_VAL = 'TabVal("{register}", "{table_name}", {row}, "{col_name}")'

{pychemstation-0.5.3.dev1.dist-info → pychemstation-0.5.4.dist-info}/METADATA

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: pychemstation
-Version: 0.5.3.dev1
+Version: 0.5.4
 Summary: Library to interact with Chemstation software, primarily used in Hein lab
-Home-page: https://gitlab.com/heingroup/pychemstation
+Home-page: https://gitlab.com/heingroup/device-api/pychemstation
 Author: Lucy Hao
 Author-email: lhao03@student.ubc.ca
 Classifier: Programming Language :: Python :: 3
@@ -12,6 +12,7 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: polling
 Requires-Dist: seabreeze
+Requires-Dist: xsdata
 
 # Agilent HPLC Macro Control
 

{pychemstation-0.5.3.dev1.dist-info → pychemstation-0.5.4.dist-info}/RECORD

@@ -4,12 +4,12 @@ pychemstation/analysis/base_spectrum.py,sha256=FBvwzLtF9mdqW7f8ETY9G4cpfJ-SzbiSk
 pychemstation/analysis/spec_utils.py,sha256=8NZMV0dtfxZLARjWzM5ks0tgEYQv_SKUiZzba2IoKgw,10505
 pychemstation/analysis/utils.py,sha256=ISupAOb_yqA4_DZRK9v18UL-XjUQccAicIJKb1VMnGg,2055
 pychemstation/control/__init__.py,sha256=aH9cPf-ljrVeVhN0K3cyEcAavmPXCjhhOnpLNf8qLqE,106
-pychemstation/control/comm.py,sha256=19RaKugJ7TbBfW-OM8fHxf90cfXCiDnNnZWPAOiWpGQ,7266
-pychemstation/control/hplc.py,sha256=r1N8kf5o1kAoY1taALvLJoIxNEbuOYsjwZ8eljrMZRM,6763
+pychemstation/control/comm.py,sha256=u44g1hTluQ0yUG93Un-QAshScoDpgYRrZfFTgweP5tY,7386
+pychemstation/control/hplc.py,sha256=huEUl90Ylvzvy2TXWUjhyDU4PazrK7Z51M8spquHvVg,6719
 pychemstation/control/table/__init__.py,sha256=RgMN4uIWHdNUHpGRBWdzmzAbk7XEKl6Y-qtqWCxzSZU,124
 pychemstation/control/table/method.py,sha256=THVoGomSXff_CTU3eAYme0BYwkPzab5UgZKsiZ29QSk,12196
-pychemstation/control/table/sequence.py,sha256=iTpk1oiGByut7MSFDHKpTlKUCYzXENOB6EMSKaWJWVY,10651
-pychemstation/control/table/table_controller.py,sha256=eq9P213Jslr1gJnjZEuvyQ4TpgrxdIXFXHwtQbJkrg0,7131
+pychemstation/control/table/sequence.py,sha256=Eri52AnbE3BGthfrRSvYKYciquUzvHKo0lYUTySYYE8,10542
+pychemstation/control/table/table_controller.py,sha256=F5lv1DlPkEDcFmtwVT-E9Kq075jnWIN-iZIM3_mTt5E,8115
 pychemstation/generated/__init__.py,sha256=GAoZFAYbPVEJDkcOw3e1rgOqd7TCW0HyKNPM8OMehMg,1005
 pychemstation/generated/dad_method.py,sha256=0W8Z5WDtF5jpIcudMqb7XrkTnR2EGg_QOCsHRFQ0rmM,8402
 pychemstation/generated/pump_method.py,sha256=sUhE2Oo00nzVcoONtq3EMWsN4wLSryXbG8f3EeViWKg,12174
@@ -19,16 +19,16 @@ pychemstation/utils/macro.py,sha256=BAIcE_dppNffwrSqGq8gh0ccE9YAJfQFQZHXJgA1WtA,
 pychemstation/utils/method_types.py,sha256=YngbyHg96JSFnvhm5Zd7wJvLTQPPQsLbvbyz3HlGLYY,862
 pychemstation/utils/parsing.py,sha256=bnFIsZZwFy9NKzVUf517yN-ogzQbm0hp_aho3KUD6Is,9317
 pychemstation/utils/sequence_types.py,sha256=3VqiUHsfFEdynAxfR-z8JIWBCo7PdnGwTvsk7sm7Ij8,1055
-pychemstation/utils/table_types.py,sha256=HAxAsqmyWsCqGwhg4LadGlX6ubacsd8tjXXz-6DL2nI,2287
+pychemstation/utils/table_types.py,sha256=cN51Ry2pammDdk85cabVH3qkchjKKIzZfAH87Poty80,2350
 pychemstation/utils/tray_types.py,sha256=UUDED-IAf-8FmPVZezuWSiIQE_HgiZQMV2sTqu4oZw8,177
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/constants.py,sha256=CqahQtWK0NSGIpoCOY_uoN4BwR6TFtaX9wPAkPkG9BE,2074
-tests/test_comb.py,sha256=IrCqsGEBdrAqoGBQuKiJiaGRW9Ym9UNlVjPA9gc2UrA,5431
+tests/constants.py,sha256=lLwT_QaVriivL5llkul6RxXxPriwUp1E-Y3G9fejvbo,2092
+tests/test_comb.py,sha256=faF4764oJEZ2vhG9-zLmQxjATseipRKXrStehuDCXOI,5638
 tests/test_comm.py,sha256=1ZZd0UrIBOKe91wzA-XI-gSRgXmId9mLWYSMeche82Y,2973
 tests/test_method.py,sha256=uCPpZVYKPz1CNWwhmBo_8TH0ku2V0ZpDZJj3f8iINB4,2440
-tests/test_sequence.py,sha256=w_WQj97hlaZtcW1Zibzlrq0p179c-4-otM-ik_1EXME,2937
-pychemstation-0.5.3.dev1.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
-pychemstation-0.5.3.dev1.dist-info/METADATA,sha256=YIbggvShXX-YxNtMFlMXfJIIB0LanjwtYBLz7O5Ttdw,3964
-pychemstation-0.5.3.dev1.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-pychemstation-0.5.3.dev1.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
-pychemstation-0.5.3.dev1.dist-info/RECORD,,
+tests/test_sequence.py,sha256=yIQGhUTehtHz6D1ai5W6AlP0zes2icF0VdQ0IGJ2CbQ,4901
+pychemstation-0.5.4.dist-info/LICENSE,sha256=9bdF75gIf1MecZ7oymqWgJREVz7McXPG-mjqrTmzzD8,18658
+pychemstation-0.5.4.dist-info/METADATA,sha256=TN5NWM9_QmES6TmIm_pXGvQxlNTQsHJDiP1wd1dRktA,3992
+pychemstation-0.5.4.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+pychemstation-0.5.4.dist-info/top_level.txt,sha256=zXfKu_4nYWwPHo3OsuhshMNC3SPkcoTGCyODjURaghY,20
+pychemstation-0.5.4.dist-info/RECORD,,

tests/constants.py

@@ -4,7 +4,7 @@ from pychemstation.utils.method_types import *
 from pychemstation.utils.sequence_types import *
 
 DEFAULT_METHOD = "GENERAL-POROSHELL-OPT"
-DEFAULT_SEQUENCE = "hplc_testing"
+DEFAULT_SEQUENCE = "LLETest"
 
 # CONSTANTS: paths only work in Hein group HPLC machine in room 242
 DEFAULT_COMMAND_PATH = "C:\\Users\\User\\Desktop\\Lucy\\"
@@ -20,8 +20,8 @@ HEIN_LAB_CONSTANTS = [DEFAULT_COMMAND_PATH,
 # these CONSTANTS work in rm 254
 DEFAULT_COMMAND_PATH_254 = "D:\\\git_repositories\\\hplc_comm\\"
 DEFAULT_METHOD_DIR_254 = "D:\\Chemstation\\1\\Methods\\"
-DATA_DIR_254 = "D:\\Chemstation\\1\\Data"
-SEQUENCE_DIR_254 = "C:\\1\\Sequence"
+DATA_DIR_254 = "D:\\Chemstation\\1\\Data\\2024-12\\"
+SEQUENCE_DIR_254 = "C:\\1\\Sequence\\"
 
 HEIN_LAB_CONSTANTS_254 = [DEFAULT_COMMAND_PATH_254,
                           DEFAULT_METHOD_DIR_254,
@@ -42,7 +42,7 @@ def gen_rand_method():
     return MethodTimetable(
         first_row=HPLCMethodParams(
             organic_modifier=org_modifier,
-            flow=random.random(),
+            flow=round(random.random(), 2),
             maximum_run_time=max_run_time),
         subsequent_rows=[
             TimeTableEntry(

tests/test_comb.py

@@ -5,9 +5,7 @@ import unittest
 from pychemstation.control import HPLCController
 from tests.constants import *
 
-run_too = False
-
-
+run_too = True
 
 
 class TestCombinations(unittest.TestCase):
@@ -24,11 +22,23 @@ class TestCombinations(unittest.TestCase):
                                               sequence_dir=path_constants[3])
 
     def test_run_method_after_update(self):
-        self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
-
         try:
-            rand_method = gen_rand_method()
-            self.hplc_controller.edit_method(rand_method)
+            self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
+            rand_method = MethodTimetable(
+                first_row=HPLCMethodParams(
+                    organic_modifier=5,
+                    flow=0.65,
+                    maximum_run_time=2),
+                subsequent_rows=[
+                    TimeTableEntry(
+                        start_time=0.10,
+                        organic_modifer=5,
+                        flow=0.34),
+                    TimeTableEntry(
+                        start_time=1,
+                        organic_modifer=98,
+                        flow=0.55)])
+            self.hplc_controller.edit_method(rand_method, save=True)
             if run_too:
                 self.hplc_controller.run_method(experiment_name="changed_method")
         except Exception as e:
@@ -38,13 +48,24 @@ class TestCombinations(unittest.TestCase):
         try:
             self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
             seq_table = self.hplc_controller.load_sequence()
-            seq_table.rows[0].vial_location = TenColumn.FIVE
-            seq_table.rows[1].vial_location = TenColumn.ONE
-            seq_table.rows[0].inj_source = InjectionSource.HIP_ALS
-            seq_table.rows[1].inj_source = InjectionSource.MANUAL
+            seq_table.rows.append(SequenceEntry(
+                vial_location=TenColumn.ONE,
+                method=DEFAULT_METHOD,
+                num_inj=3,
+                inj_vol=4,
+                sample_name="Sampel1",
+                sample_type=SampleType.SAMPLE,
+            ))
+            seq_table.rows[0] = SequenceEntry(
+                vial_location=TenColumn.ONE,
+                method=DEFAULT_METHOD,
+                num_inj=3,
+                inj_vol=4,
+                sample_name="Sampel2",
+                sample_type=SampleType.SAMPLE)
             self.hplc_controller.edit_sequence(seq_table)
             if run_too:
-                self.hplc_controller.run_sequence(seq_table)
+                self.hplc_controller.run_sequence()
                 chrom = self.hplc_controller.get_last_run_sequence_data()
                 self.assertTrue(len(chrom) == 2)
         except Exception as e:
@@ -56,7 +77,7 @@ class TestCombinations(unittest.TestCase):
             seq_table = self.hplc_controller.load_sequence()
             self.hplc_controller.edit_sequence_row(seq_entry, 1)
             if run_too:
-                self.hplc_controller.run_sequence(seq_table)
+                self.hplc_controller.run_sequence()
                 chrom = self.hplc_controller.get_last_run_sequence_data()
                 self.assertTrue(len(chrom) == 2)
         except Exception:
@@ -65,65 +86,58 @@ class TestCombinations(unittest.TestCase):
     def test_update_method_update_seq_table_run(self):
         try:
             self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
-            rand_method = gen_rand_method()
+            rand_method = MethodTimetable(
+                first_row=HPLCMethodParams(
+                    organic_modifier=5,
+                    flow=0.65,
+                    maximum_run_time=2),
+                subsequent_rows=[
+                    TimeTableEntry(
+                        start_time=0.50,
+                        organic_modifer=99,
+                        flow=0.34)])
             self.hplc_controller.edit_method(rand_method, save=True)
 
             self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
-            seq_table = self.hplc_controller.load_sequence()
-            seq_table.rows[0].vial_location = TenColumn.ONE
-            seq_table.rows[0].inj_source = InjectionSource.HIP_ALS
-            seq_table.rows[1].vial_location = TenColumn.TWO
-            seq_table.rows[1].inj_source = InjectionSource.HIP_ALS
-            self.hplc_controller.edit_sequence(seq_table)
-
-            if run_too:
-                self.hplc_controller.run_sequence(seq_table)
-                chrom = self.hplc_controller.get_last_run_sequence_data()
-                self.assertTrue(len(chrom) == 2)
-        except Exception:
-            self.fail("Failed")
-
-    def test_update_table_then_row(self):
-        try:
-            self.hplc_controller.method_controller.switch(DEFAULT_METHOD)
-            self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
-            rand_method = gen_rand_method()
-            self.hplc_controller.edit_method(rand_method, save=True)
-
-            seq_table = self.hplc_controller.load_sequence()
-            seq_table.rows[0].vial_location = TenColumn.ONE
-            seq_table.rows[0].inj_source = InjectionSource.HIP_ALS
-            seq_table.rows[0].method = DEFAULT_METHOD
-            seq_table.rows[1].vial_location = TenColumn.TWO
-            seq_table.rows[1].inj_source = InjectionSource.HIP_ALS
-            seq_table.rows[1].method = DEFAULT_METHOD
+            seq_table = SequenceTable(
+                name=DEFAULT_SEQUENCE,
+                rows=[
+                    SequenceEntry(
+                        vial_location=8320,
+                        sample_name="WM-01-001_Cr-Org",
+                        method=DEFAULT_METHOD,
+                        inj_source=InjectionSource.HIP_ALS,
+                        inj_vol=2,
+                        num_inj=1,
+                        sample_type=SampleType.SAMPLE
+                    ),
+                    SequenceEntry(
+                        vial_location=8448,
+                        sample_name="WM-01-001_Cr-Aq",
+                        method=DEFAULT_METHOD,
+                        inj_source=InjectionSource.HIP_ALS,
+                        inj_vol=2,
+                        num_inj=1,
+                        sample_type=SampleType.SAMPLE
+                    ),
+                ]
+            )
 
             self.hplc_controller.edit_sequence(seq_table)
-            self.hplc_controller.edit_sequence_row(
-                SequenceEntry(
-                    vial_location=TenColumn.ONE,
-                    method=DEFAULT_METHOD,
-                    num_inj=3,
-                    inj_vol=4,
-                    sample_name="Blank",
-                    sample_type=SampleType.BLANK,
-                )
-            )
             if run_too:
-                self.hplc_controller.run_sequence(seq_table)
+                self.hplc_controller.preprun()
+                self.hplc_controller.run_sequence()
                 chrom = self.hplc_controller.get_last_run_sequence_data()
                 self.assertTrue(len(chrom) == 2)
         except Exception:
             self.fail("Failed")
 
-    def test_run_after_new_row_edit(self):
+    def test_run_sequence(self):
         try:
             self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
-            seq_table = self.hplc_controller.load_sequence()
-            self.hplc_controller.edit_sequence_row(seq_entry, 3)
-            if run_too:
-                self.hplc_controller.run_sequence(seq_table)
-                chrom = self.hplc_controller.get_last_run_sequence_data()
-                self.assertTrue(len(chrom) == 2)
+            self.hplc_controller.preprun()
+            self.hplc_controller.run_sequence()
+            chrom = self.hplc_controller.get_last_run_sequence_data()
+            self.assertTrue(len(chrom) == 2)
         except Exception:
             self.fail("Failed")

tests/test_sequence.py

@@ -63,6 +63,54 @@ class TestSequence(unittest.TestCase):
                         sample_name="Sampel2",
                         sample_type=SampleType.SAMPLE,
                         inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=TenColumn.TEN,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=TenColumn.THREE,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    )
+                ]
+            )
+            self.hplc_controller.edit_sequence(seq_table)
+        except Exception:
+            self.fail("Should have not occured")
+
+    def test_edit_entire_table_less_rows(self):
+        self.hplc_controller.switch_sequence(sequence_name=DEFAULT_SEQUENCE)
+        try:
+            seq_table = SequenceTable(
+                name=DEFAULT_SEQUENCE,
+                rows=[
+                    SequenceEntry(
+                        vial_location=TenColumn.TEN,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
+                    ),
+                    SequenceEntry(
+                        vial_location=TenColumn.THREE,
+                        method=DEFAULT_METHOD,
+                        num_inj=3,
+                        inj_vol=4,
+                        sample_name="Sampel2",
+                        sample_type=SampleType.SAMPLE,
+                        inj_source=InjectionSource.HIP_ALS
                     )
                 ]
             )