logging and scrollable form

2023-01-24 15:22:15 -06:00
parent 7a53cfd9a1
commit f53d420d56
9 changed files with 129 additions and 121 deletions
--- a/src/submissions/main.py
+++ b/src/submissions/main.py
@@ -6,12 +6,11 @@ if getattr(sys, 'frozen', False):
 else :
    pass
 from configure import get_config, create_database_session, setup_logger
+logger = setup_logger(verbosity=3)
 ctx = get_config(None)
 from PyQt6.QtWidgets import QApplication
 from frontend import App

-logger = setup_logger(verbose=True)
-
 ctx["database_session"] = create_database_session(Path(ctx['database']))

 if __name__ == '__main__':
--- a/src/submissions/backend/db/init.py
+++ b/src/submissions/backend/db/init.py
@@ -11,7 +11,7 @@ from sqlalchemy import JSON
 import json
 from dateutil.relativedelta import relativedelta

-logger = logging.getLogger(__name__)
+logger = logging.getLogger(f"submissions.{__name__}")

 def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
    pass
@@ -35,7 +35,7 @@ def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:


 def store_reagent(ctx:dict, reagent:models.Reagent) -> None:
-    print(reagent.__dict__)
+    logger.debug(reagent.__dict__)
    ctx['database_session'].add(reagent)
    ctx['database_session'].commit()

@@ -46,18 +46,18 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
    info_dict['submission_type'] = info_dict['submission_type'].replace(" ", "_").lower()
    instance = model()
    for item in info_dict:
-        print(f"Setting {item} to {info_dict[item]}")
+        logger.debug(f"Setting {item} to {info_dict[item]}")
        match item:
            case "extraction_kit":
                q_str = info_dict[item]
-                print(f"Looking up kit {q_str}")
+                logger.debug(f"Looking up kit {q_str}")
                field_value = lookup_kittype_by_name(ctx=ctx, name=q_str)
-                print(f"Got {field_value} for kit {q_str}")
+                logger.debug(f"Got {field_value} for kit {q_str}")
            case "submitting_lab":
                q_str = info_dict[item].replace(" ", "_").lower()
-                print(f"looking up organization: {q_str}")
+                logger.debug(f"looking up organization: {q_str}")
                field_value = lookup_org_by_name(ctx=ctx, name=q_str)
-                print(f"Got {field_value} for organization {q_str}")
+                logger.debug(f"Got {field_value} for organization {q_str}")
            case "submitter_plate_num":
                # Because of unique constraint, the submitter plate number cannot be None, so...
                if info_dict[item] == None:
@@ -72,16 +72,16 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
        try:
            setattr(instance, item, field_value)
        except AttributeError:
-            print(f"Could not set attribute: {item} to {info_dict[item]}")
+            logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
            continue
-    # print(instance.__dict__)
+    # logger.debug(instance.__dict__)
    return instance
    # looked_up = []
    # for reagent in reagents:
    #     my_reagent = lookup_reagent(reagent)
-    #     print(my_reagent)
+    #     logger.debug(my_reagent)
    #     looked_up.append(my_reagent)
-    # print(looked_up)
+    # logger.debug(looked_up)
    # instance.reagents = looked_up
    # ctx['database_session'].add(instance)
    # ctx['database_session'].commit()
@@ -89,7 +89,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
 def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
    reagent = models.Reagent()
    for item in info_dict:
-        print(f"Reagent info item: {item}")
+        logger.debug(f"Reagent info item: {item}")
        match item:
            case "lot":
                reagent.lot = info_dict[item].upper()
@@ -100,7 +100,7 @@ def construct_reagent(ctx:dict, info_dict:dict) -> models.Reagent:
    try:
        reagent.expiry = reagent.expiry + reagent.type.eol_ext
    except TypeError as e:
-        print(f"WE got a type error: {e}.")
+        logger.debug(f"WE got a type error: {e}.")
    except AttributeError:
        pass
    return reagent
@@ -116,9 +116,9 @@ def get_all_reagenttype_names(ctx:dict) -> list[str]:
    return lookedup

 def lookup_reagenttype_by_name(ctx:dict, rt_name:str) -> models.ReagentType:
-    print(f"Looking up ReagentType by name: {rt_name}")
+    logger.debug(f"Looking up ReagentType by name: {rt_name}")
    lookedup = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
-    print(f"Found ReagentType: {lookedup}")
+    logger.debug(f"Found ReagentType: {lookedup}")
    return lookedup


@@ -127,7 +127,7 @@ def lookup_kittype_by_use(ctx:dict, used_by:str) -> list[models.KitType]:
    return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by))

 def lookup_kittype_by_name(ctx:dict, name:str) -> models.KitType:
-    print(f"Querying kittype: {name}")
+    logger.debug(f"Querying kittype: {name}")
    return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()


@@ -154,11 +154,11 @@ def lookup_all_orgs(ctx:dict) -> list[models.Organization]:
    return ctx['database_session'].query(models.Organization).all()

 def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
-    print(f"Querying organization: {name}")
+    logger.debug(f"Querying organization: {name}")
    return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()

 def submissions_to_df(ctx:dict, type:str|None=None):
-    print(f"Type: {type}")
+    logger.debug(f"Type: {type}")
    subs = [item.to_dict() for item in lookup_all_submissions_by_type(ctx=ctx, type=type)]
    df = pd.DataFrame.from_records(subs)
    return df
@@ -205,7 +205,7 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
    except (UnicodeDecodeError, AttributeError):
        exp['password'] = exp['password'].encode()
    if base64.b64encode(exp['password']) != b'cnNsX3N1Ym1pNTVpb25z':
-        print(f"Not the correct password.")
+        logger.debug(f"Not the correct password.")
        return
    for type in exp:
        if type == "password":
@@ -220,8 +220,8 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
                    rt = look_up
                    rt.kits.append(kit)
                ctx['database_session'].add(rt)
-                print(rt.__dict__)
-            print(kit.__dict__)
+                logger.debug(rt.__dict__)
+            logger.debug(kit.__dict__)
        ctx['database_session'].add(kit)
    ctx['database_session'].commit()

@@ -252,7 +252,7 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
        list: Control instances.
    """
    
-    # print(f"Using dates: {start_date} to {end_date}")
+    # logger.debug(f"Using dates: {start_date} to {end_date}")
    query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
    try:
        output = query.first().instances
@@ -261,7 +261,7 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
    # Hacky solution to my not being able to get the sql query to work.
    if start_date != None and end_date != None:
        output = [item for item in output if item.submitted_date.date() > start_date and item.submitted_date.date() < end_date]
-    # print(f"Type {con_type}: {query.first()}")
+    # logger.debug(f"Type {con_type}: {query.first()}")
    return output


@@ -271,7 +271,7 @@ def get_control_subtypes(ctx:dict, type:str, mode:str):
    except TypeError:
        return []
    jsoner = json.loads(getattr(outs, mode))
-    print(f"JSON out: {jsoner}")
+    logger.debug(f"JSON out: {jsoner}")
    try:
        genera = list(jsoner.keys())[0]
    except IndexError:
--- a/src/submissions/backend/db/models/submissions.py
+++ b/src/submissions/backend/db/models/submissions.py
@@ -1,13 +1,12 @@
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint, Table
-from sqlalchemy.orm import relationship, relationships
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
+from sqlalchemy.orm import relationship
 from datetime import datetime as dt

 reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))

 class BasicSubmission(Base):

-    # TODO: Figure out if I want seperate tables for different sample types.
    __tablename__ = "_submissions"

    id = Column(INTEGER, primary_key=True) #: primary key   
@@ -32,7 +31,6 @@ class BasicSubmission(Base):
    }

    def to_dict(self):
-        print(self.submitting_lab)
        try:
            sub_lab = self.submitting_lab.name
        except AttributeError:
--- a/src/submissions/backend/excel/parser.py
+++ b/src/submissions/backend/excel/parser.py
@@ -13,11 +13,14 @@ logger = logging.getLogger(f"submissions.{__name__}")
 class SheetParser(object):

    def __init__(self, filepath:Path|None = None, **kwargs):
+        logger.debug(f"Parsing {filepath.__str__()}")
        for kwarg in kwargs:
            setattr(self, f"_{kwarg}", kwargs[kwarg])
        if filepath == None:
+            logger.debug(f"No filepath.")
            self.xl = None
        else:
+            
            try:
                self.xl = pd.ExcelFile(filepath.__str__())
            except ValueError:
@@ -76,6 +79,7 @@ class SheetParser(object):
        self.sub['lot_plate'] = submission_info.iloc[12][6]
        sample_parser = SampleParser(submission_info.iloc[15:111])
        sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
+        logger.debug(f"Parser result: {self.sub}")
        self.sub['samples'] = sample_parse()


@@ -121,9 +125,10 @@ class SampleParser(object):
            new.sample_id = sample['Unnamed: 1']
            new.organism = sample['Unnamed: 2']
            new.concentration = sample['Unnamed: 3']
-            # print(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
+            # logger.debug(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
+            logger.debug(f"Got sample_id: {new.sample_id}")
            try:
-                not_a_nan = not np.isnan(new.sample_id) and new.sample_id.lower() != 'blank'
+                not_a_nan = not np.isnan(new.sample_id) and str(new.sample_id).lower() != 'blank'
            except TypeError:
                not_a_nan = True
            if not_a_nan:
--- a/src/submissions/backend/excel/reports.py
+++ b/src/submissions/backend/excel/reports.py
@@ -3,6 +3,9 @@ from pandas import DataFrame
 import numpy as np
 from backend.db import models
 import json
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")

 def make_report_xlsx(records:list[dict]) -> DataFrame:
    df = DataFrame.from_records(records)
@@ -10,7 +13,7 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
    # table = df.pivot_table(values="Cost", index=["Submitting Lab", "Extraction Kit"], columns=["Cost", "Sample Count"], aggfunc={'Cost':np.sum,'Sample Count':np.sum})
    df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Cost': ['sum', 'count'], 'Sample Count':['sum']})
    # df2['Cost'] = df2['Cost'].map('${:,.2f}'.format)
-    print(df2.columns)
+    logger.debug(df2.columns)
    # df2['Cost']['sum'] = df2['Cost']['sum'].apply('${:,.2f}'.format)
    df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
    return df2
@@ -27,7 +30,7 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
 #     for ii in range(data_size):
 #         new_dict = {}
 #         for genus in sub_dict:
-#             print(genus)
+#             logger.debug(genus)
 #             sub_name = list(sub_dict[genus].keys())[ii]
 #             new_dict[genus] = sub_dict[genus][sub_name]
 #         output.append({"date":dict_name, "name": sub_name, "data": new_dict})
@@ -55,10 +58,10 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
 #         #     col_dict = entry[col_name]
 #         #     series = pd.Series(data=col_dict.values(), index=col_dict.keys(), name=col_name)
 #         #     # df[col_name] = series.values
-#         #     # print(df.index)
+#         #     # logger.debug(df.index)
 #         #     series_list.append(series)
 #         # df = DataFrame(series_list).T.fillna(0)
-#         # print(df)
+#         # logger.debug(df)
 #         dfs['name'] = df
 #     return dfs

@@ -74,14 +77,14 @@ def convert_control_by_mode(ctx:dict, control:models.Control, mode:str):
        for key in data[genus]:
            _dict[key] = data[genus][key]
        output.append(_dict)
-    # print(output)
+    # logger.debug(output)
    return output


 def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -> DataFrame:
    df = DataFrame.from_records(input)
    safe = ['name', 'submitted_date', 'genus', 'target']
-    print(df)
+    logger.debug(df)
    for column in df.columns:
        if "percent" in column:
            count_col = [item for item in df.columns if "count" in item][0]
@@ -90,5 +93,5 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
        if column not in safe:
            if subtype != None and column != subtype:
                del df[column]
-    # print(df)
+    # logger.debug(df)
    return df
--- a/src/submissions/configure/init.py
+++ b/src/submissions/configure/init.py
@@ -1,5 +1,5 @@
 import yaml
-import sys, os, stat, platform
+import sys, os, stat, platform, shutil
 import logging
 from logging import handlers
 from pathlib import Path
@@ -8,17 +8,17 @@ from sqlalchemy.orm import Session
 from sqlalchemy import create_engine


-logger = logging.getLogger(__name__)
+logger = logging.getLogger(f"submissions.{__name__}")

 package_dir = Path(__file__).parents[2].resolve()
 logger.debug(f"Package dir: {package_dir}")

-if platform.system == "Windows":
-    os_config_dir = "AppData"
-    logger.debug(f"Got platform Windows, config_dir: {os_config_dir}")
+if platform.system() == "Windows":
+    os_config_dir = "AppData/local"
+    print(f"Got platform Windows, config_dir: {os_config_dir}")
 else:
    os_config_dir = ".config"
-    logger.debug(f"Got platform other, config_dir: {os_config_dir}")
+    print(f"Got platform other, config_dir: {os_config_dir}")


 main_aux_dir = Path.home().joinpath(f"{os_config_dir}/submissions")
@@ -27,6 +27,8 @@ CONFIGDIR = main_aux_dir.joinpath("config")
 LOGDIR = main_aux_dir.joinpath("logs")


+
+
 class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):

    def doRollover(self):
@@ -79,6 +81,16 @@ def get_config(settings_path: str|None) -> dict:
    ## register the tag handler
    yaml.add_constructor('!join', join)
    # if user hasn't defined config path in cli args
+    logger.debug(f"Making directory: {CONFIGDIR.__str__()}")
+    try:
+        CONFIGDIR.mkdir(parents=True)
+    except FileExistsError:
+        pass
+    logger.debug(f"Making directory: {LOGDIR.__str__()}")
+    try:
+        LOGDIR.mkdir(parents=True)
+    except FileExistsError:
+        pass
    if settings_path == None:
        # Check user .config/ozma directory
        # if Path.exists(Path.joinpath(CONFIGDIR, "config.yml")):
@@ -94,6 +106,7 @@ def get_config(settings_path: str|None) -> dict:
                settings_path = Path(sys._MEIPASS).joinpath("files", "config.yml")
            else:
                settings_path = package_dir.joinpath('config.yml')
+            shutil.copyfile(settings_path.__str__(), CONFIGDIR.joinpath("config.yml").__str__())
    else:
        if Path(settings_path).is_dir():
            settings_path = settings_path.joinpath("config.yml")
@@ -103,6 +116,7 @@ def get_config(settings_path: str|None) -> dict:
            logger.error("No config.yml file found. Using empty dictionary.")
            return {}
    logger.debug(f"Using {settings_path} for config file.")
+    
    with open(settings_path, "r") as stream:
        try:
            settings = yaml.load(stream, Loader=yaml.Loader)
@@ -141,7 +155,7 @@ def create_database_session(database_path: Path|None) -> Session:
    return session


-def setup_logger(verbose:bool=False):
+def setup_logger(verbosity:int=3):
    """Set logger levels using settings.

    Args:
@@ -161,34 +175,38 @@ def setup_logger(verbose:bool=False):
    fh.setLevel(logging.DEBUG)
    fh.name = "File"
    # create console handler with a higher log level
-    ch = logging.StreamHandler()
-    if verbose:
-        ch.setLevel(logging.DEBUG)
-    else:
-        ch.setLevel(logging.WARNING)
+    ch = logging.StreamHandler(stream=sys.stdout)
+    match verbosity:
+        case 3:
+            ch.setLevel(logging.DEBUG)
+        case 2:
+            ch.setLevel(logging.INFO)
+        case 1:
+            ch.setLevel(logging.WARNING)
    ch.name = "Stream"
    # create formatter and add it to the handlers
    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
    fh.setFormatter(formatter)
    ch.setFormatter(formatter)
-    ch.setLevel(logging.ERROR)
+    # ch.setLevel(logging.ERROR)
    # add the handlers to the logger
    logger.addHandler(fh)
    logger.addHandler(ch)
-    stderr_logger = logging.getLogger('STDERR')
+    # stderr_logger = logging.getLogger('STDERR')
+    
    return logger
    # sl = StreamToLogger(stderr_logger, logging.ERROR)
    # sys.stderr = sl

-def set_logger_verbosity(verbosity):
-    """Does what it says.
-    """
-    handler = [item for item in logger.parent.handlers if item.name == "Stream"][0]
-    match verbosity:
-        case 3:
-            handler.setLevel(logging.DEBUG)
-        case 2:
-            handler.setLevel(logging.INFO)
-        case 1:
-            handler.setLevel(logging.WARNING)
+# def set_logger_verbosity(verbosity):
+#     """Does what it says.
+#     """
+#     handler = [item for item in logger.parent.handlers if item.name == "Stream"][0]
+#     match verbosity:
+#         case 3:
+#             handler.setLevel(logging.DEBUG)
+#         case 2:
+#             handler.setLevel(logging.INFO)
+#         case 1:
+#             handler.setLevel(logging.WARNING)

--- a/src/submissions/frontend/init.py
+++ b/src/submissions/frontend/init.py
@@ -4,7 +4,7 @@ from PyQt6.QtWidgets import (
    QTabWidget, QWidget, QVBoxLayout,
    QPushButton, QMenuBar, QFileDialog,
    QLineEdit, QMessageBox, QComboBox, QDateEdit, QHBoxLayout,
-    QSpinBox
+    QSpinBox, QScrollArea
 )
 from PyQt6.QtGui import QAction, QIcon
 from PyQt6.QtCore import QDateTime, QDate, QSignalBlocker
@@ -108,8 +108,9 @@ class App(QMainWindow):
            prsr = SheetParser(fname, **self.ctx)
        except PermissionError:
            return
-        print(f"prsr.sub = {prsr.sub}")
+        logger.debug(f"prsr.sub = {prsr.sub}")
        # replace formlayout with tab1.layout
+        # self.form = self.table_widget.formlayout
        for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
            item.setParent(None)
        variable_parser = re.compile(r"""
@@ -128,11 +129,11 @@ class App(QMainWindow):
                mo = variable_parser.fullmatch(item).lastgroup
            except AttributeError:
                mo = "other"
-            print(f"Mo: {mo}")
+            logger.debug(f"Mo: {mo}")
            match mo:
                case 'submitting_lab':
                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-                    print(f"{item}: {prsr.sub[item]}")
+                    logger.debug(f"{item}: {prsr.sub[item]}")
                    add_widget = QComboBox()
                    labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
                    try:
@@ -167,15 +168,15 @@ class App(QMainWindow):
                    add_widget.setEditable(True)
                    # Ensure that all reagenttypes have a name that matches the items in the excel parser
                    query_var = item.replace("lot_", "")
-                    print(f"Query for: {query_var}")
+                    logger.debug(f"Query for: {query_var}")
                    if isinstance(prsr.sub[item], numpy.float64):
-                        print(f"{prsr.sub[item]} is a numpy float!")
+                        logger.debug(f"{prsr.sub[item]} is a numpy float!")
                        try:
                            prsr.sub[item] = int(prsr.sub[item])
                        except ValueError:
                            pass
                    relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name_and_kit_name(ctx=self.ctx, type_name=query_var, kit_name=prsr.sub['extraction_kit'])]
-                    print(f"Relevant reagents: {relevant_reagents}")
+                    logger.debug(f"Relevant reagents: {relevant_reagents}")
                    if prsr.sub[item] not in relevant_reagents and prsr.sub[item] != 'nan':
                        try:
                            check = not numpy.isnan(prsr.sub[item])
@@ -187,7 +188,7 @@ class App(QMainWindow):
                    add_widget.addItems(relevant_reagents)
                # TODO: make samples not appear in frame.
                case 'samples':
-                    print(f"{item}: {prsr.sub[item]}")
+                    logger.debug(f"{item}: {prsr.sub[item]}")
                    self.samples = prsr.sub[item]
                case _:
                    self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
@@ -216,28 +217,7 @@ class App(QMainWindow):
        html += '</body></html>'
        self.table_widget.webengineview.setHtml(html)
        self.table_widget.webengineview.update()
-        # type = self.table_widget.control_typer.currentText()
-        # mode = self.table_widget.mode_typer.currentText()
-        # controls = get_all_controls_by_type(ctx=self.ctx, type=type)
-        # data = []
-        # for control in controls:
-        #     dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=mode)
-        #     data.append(dicts)
-        # data = [item for sublist in data for item in sublist]
-        # # print(data)
-        # df = convert_data_list_to_df(ctx=self.ctx, input=data)
-        # fig = create_charts(ctx=self.ctx, df=df)
-        
-        # print(fig)
-        # html = '<html><body>'
-        # html += plotly.offline.plot(fig, output_type='div', auto_open=True, image = 'png', image_filename='plot_image')
-        # html += '</body></html>'
-        # html = plotly.io.to_html(fig)
-        # # print(html)
-        # # with open("C:\\Users\\lwark\\Desktop\\test.html", "w") as f:
-        # #     f.write(html)
-        # self.table_widget.webengineview.setHtml(html)
-        # self.table_widget.webengineview.update()
+


    def submit_new_sample(self):
@@ -297,8 +277,8 @@ class App(QMainWindow):
                case QLineEdit():
                    # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
                    if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox):
-                        print(f"Previous: {prev_item}")
-                        print(f"Item: {item}")
+                        logger.debug(f"Previous: {prev_item}")
+                        logger.debug(f"Item: {item}")
                        values.append(item.text())
                case QComboBox():
                    values.append(item.currentText())
@@ -346,7 +326,7 @@ class App(QMainWindow):
        except TypeError:
            pass
        if self.table_widget.datepicker.start_date.date() > self.table_widget.datepicker.end_date.date():
-            print("that is not allowed!")
+            logger.warning("Start date after end date is not allowed!")
            # self.table_widget.datepicker.start_date.setDate(e_date)
            threemonthsago = self.table_widget.datepicker.end_date.date().addDays(-90)
            with QSignalBlocker(self.table_widget.datepicker.start_date) as blocker:
@@ -372,12 +352,12 @@ class App(QMainWindow):
        
        
    def chart_maker(self):
-        print(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
+        logger.debug(f"Control getter context: \n\tControl type: {self.con_type}\n\tMode: {self.mode}\n\tStart Date: {self.start_date}\n\tEnd Date: {self.end_date}")
        if self.table_widget.sub_typer.currentText() == "":
            self.subtype = None
        else:
            self.subtype = self.table_widget.sub_typer.currentText()
-        print(f"Subtype: {self.subtype}")
+        logger.debug(f"Subtype: {self.subtype}")
        controls = get_all_controls_by_type(ctx=self.ctx, con_type=self.con_type, start_date=self.start_date, end_date=self.end_date)
        if controls == None:
            return
@@ -386,14 +366,14 @@ class App(QMainWindow):
            dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
            data.append(dicts)
        data = [item for sublist in data for item in sublist]
-        # print(data)
+        # logger.debug(data)
        df = convert_data_list_to_df(ctx=self.ctx, input=data, subtype=self.subtype)
        if self.subtype == None:
            title = self.mode
        else:
            title = f"{self.mode} - {self.subtype}"
        fig = create_charts(ctx=self.ctx, df=df, ytitle=title)
-        print(f"Updating figure...")
+        logger.debug(f"Updating figure...")
        html = '<html><body>'
        if fig != None:
            html += plotly.offline.plot(fig, output_type='div', include_plotlyjs='cdn')#, image = 'png', auto_open=True, image_filename='plot_image')
@@ -404,7 +384,7 @@ class App(QMainWindow):
        #     f.write(html)
        self.table_widget.webengineview.setHtml(html)
        self.table_widget.webengineview.update()
-        print("Figure updated... I hope.")
+        logger.debug("Figure updated... I hope.")


    # def datechange(self):
@@ -412,7 +392,7 @@ class App(QMainWindow):
    #     s_date = self.table_widget.datepicker.start_date.date()
    #     e_date = self.table_widget.datepicker.end_date.date()
    #     if s_date > e_date:
-    #         print("that is not allowed!")
+    #         logger.debug("that is not allowed!")
    #         # self.table_widget.datepicker.start_date.setDate(e_date)
    #         threemonthsago = e_date.addDays(-90)
    #         self.table_widget.datepicker.start_date.setDate(threemonthsago)
@@ -448,6 +428,12 @@ class AddSubForm(QWidget):
        self.formlayout = QVBoxLayout(self)
        self.formwidget.setLayout(self.formlayout)
        self.formwidget.setFixedWidth(300)
+        
+        self.interior = QScrollArea()
+        self.interior.setWidgetResizable(True)
+        self.interior.setFixedWidth(325)
+        self.interior.setParent(self.tab1)
+        self.interior.setWidget(self.formwidget)

        self.sheetwidget = QWidget(self)
        self.sheetlayout = QVBoxLayout(self)
@@ -455,22 +441,16 @@ class AddSubForm(QWidget):
        self.sub_wid = SubmissionsSheet(parent.ctx)
        self.sheetlayout.addWidget(self.sub_wid)

-
        self.tab1.layout = QHBoxLayout(self)
        self.tab1.setLayout(self.tab1.layout)
        # self.tab1.layout.addLayout(self.formlayout)
+        
+        # self.tab1.layout.addWidget(self.formwidget)
        self.tab1.layout.addWidget(self.formwidget)
        self.tab1.layout.addWidget(self.sheetwidget)
        # self.tab1.layout.addLayout(self.sheetlayout)
-        # self.tab1.setWidgetResizable(True)
-        # self.tab1.setVerticalScrollBar(QScrollBar())
-        # self.tab1.layout.addWidget(self.scroller)
-        # self.tab1.setWidget(self.scroller)
-        # self.tab1.setMinimumHeight(300)
        self.datepicker = ControlsDatePicker()
        self.webengineview = QWebEngineView()
-        # data = '''<html>Hello World</html>'''
-        # self.webengineview.setHtml(data)
        self.tab2.layout = QVBoxLayout(self)
        self.control_typer = QComboBox()
        con_types = get_all_Control_Types_names(ctx=parent.ctx)
@@ -493,3 +473,5 @@ class AddSubForm(QWidget):
        self.tab3.setLayout(self.tab3.layout)
        self.layout.addWidget(self.tabs)
        self.setLayout(self.layout)
+        print(self.tab1.layout.parentWidget().findChildren(QScrollArea))
+        
--- a/src/submissions/frontend/custom_widgets/init.py
+++ b/src/submissions/frontend/custom_widgets/init.py
@@ -14,6 +14,9 @@ from jinja2 import Environment, FileSystemLoader

 import sys
 from pathlib import Path
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")

 if getattr(sys, 'frozen', False):
    loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
@@ -62,7 +65,7 @@ class AddReagentForm(QDialog):
        exp_input.setDate(QDate.currentDate())
        type_input = QComboBox()
        type_input.addItems([item.replace("_", " ").title() for item in get_all_reagenttype_names(ctx=ctx)])
-        print(f"Trying to find index of {reagent_type}")
+        logger.debug(f"Trying to find index of {reagent_type}")
        try:
            reagent_type = reagent_type.replace("_", " ").title()
        except AttributeError:
@@ -132,7 +135,7 @@ class SubmissionsSheet(QTableView):

    def show_details(self, item):
        index=(self.selectionModel().currentIndex())
-        # print(index)
+        # logger.debug(index)
        value=index.sibling(index.row(),0).data()
        dlg = SubmissionDetails(ctx=self.ctx, id=value)
        # dlg.show()
@@ -245,7 +248,7 @@ class KitAdder(QWidget):
    def submit(self):
        labels, values, reagents = self.extract_form_info(self)
        info = {item[0]:item[1] for item in zip(labels, values)}
-        print(info)
+        logger.debug(info)
        # info['reagenttypes'] = reagents
        # del info['name']
        # del info['extension_of_life_(months)']
@@ -257,7 +260,7 @@ class KitAdder(QWidget):
        yml_type[used]['kits'][info['kit_name']] = {}
        yml_type[used]['kits'][info['kit_name']]['cost'] = info['cost_per_run']
        yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
-        print(yml_type)
+        logger.debug(yml_type)
        create_kit_from_yaml(ctx=self.ctx, exp=yml_type)

    def extract_form_info(self, object):
@@ -265,7 +268,7 @@ class KitAdder(QWidget):
        values = []
        reagents = {}
        for item in object.findChildren(QWidget):
-            print(item.parentWidget())
+            logger.debug(item.parentWidget())
            # if not isinstance(item.parentWidget(), ReagentTypeForm):
            match item:
                case QLabel():
@@ -273,8 +276,8 @@ class KitAdder(QWidget):
                case QLineEdit():
                    # ad hoc check to prevent double reporting of qdatedit under lineedit for some reason
                    if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
-                        print(f"Previous: {prev_item}")
-                        print(f"Item: {item}, {item.text()}")
+                        logger.debug(f"Previous: {prev_item}")
+                        logger.debug(f"Item: {item}, {item.text()}")
                        values.append(item.text())
                case QComboBox():
                    values.append(item.currentText())
@@ -286,7 +289,7 @@ class KitAdder(QWidget):
                    
                    re_labels, re_values, _ = self.extract_form_info(item) 
                    reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
-                    print(reagent)
+                    logger.debug(reagent)
                    # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
                    reagents[reagent['name']] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
            prev_item = item
--- a/src/submissions/frontend/visualizations/charts.py
+++ b/src/submissions/frontend/visualizations/charts.py
@@ -5,7 +5,7 @@ from plotly.graph_objects import Figure
 import logging
 from backend.excel import get_unique_values_in_df_column

-logger = logging.getLogger("controls.tools.vis_functions")
+logger = logging.getLogger(f"submissions.{__name__}")


 def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
@@ -160,7 +160,7 @@ def construct_chart(ctx:dict, df:pd.DataFrame, modes:list, ytitle:str|None=None)
            color_discrete_sequence=None
        else:
            color = "target"
-            print(get_unique_values_in_df_column(df, 'target'))
+            # print(get_unique_values_in_df_column(df, 'target'))
            match get_unique_values_in_df_column(df, 'target'):
                case ['Target']:
                    color_discrete_sequence=["blue"]