Checking kit integrity on import.

alembic.ini

@@ -55,8 +55,8 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # are written from script.py.mako
 # output_encoding = utf-8
 
-; sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
+sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
-sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230213.db
+; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230213.db
 
 
 [post_write_hooks]

alembic/versions/3d80e4a17a26_added_versions_to_ref_kraken.py

@@ -0,0 +1,59 @@
+"""added versions to ref/kraken
+
+Revision ID: 3d80e4a17a26
+Revises: 785bb1140878
+Create Date: 2023-03-02 13:09:30.750398
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = '3d80e4a17a26'
+down_revision = '785bb1140878'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    # op.drop_table('_alembic_tmp__submissions')
+    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('refseq_version', sa.String(length=16), nullable=True))
+        batch_op.add_column(sa.Column('kraken2_version', sa.String(length=16), nullable=True))
+        batch_op.add_column(sa.Column('kraken2_db_version', sa.String(length=32), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    
+    with op.batch_alter_table('_control_samples', schema=None) as batch_op:
+        batch_op.drop_column('kraken2_db_version')
+        batch_op.drop_column('kraken2_version')
+        batch_op.drop_column('refseq_version')
+
+    # op.create_table('_alembic_tmp__submissions',
+    # sa.Column('id', sa.INTEGER(), nullable=False),
+    # sa.Column('rsl_plate_num', sa.VARCHAR(length=32), nullable=False),
+    # sa.Column('submitter_plate_num', sa.VARCHAR(length=127), nullable=True),
+    # sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
+    # sa.Column('submitting_lab_id', sa.INTEGER(), nullable=True),
+    # sa.Column('sample_count', sa.INTEGER(), nullable=True),
+    # sa.Column('extraction_kit_id', sa.INTEGER(), nullable=True),
+    # sa.Column('submission_type', sa.VARCHAR(length=32), nullable=True),
+    # sa.Column('technician', sa.VARCHAR(length=64), nullable=True),
+    # sa.Column('reagents_id', sa.VARCHAR(), nullable=True),
+    # sa.Column('extraction_info', sqlite.JSON(), nullable=True),
+    # sa.Column('run_cost', sa.FLOAT(), nullable=True),
+    # sa.Column('uploaded_by', sa.VARCHAR(length=32), nullable=True),
+    # sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kits.id'], ondelete='SET NULL'),
+    # sa.ForeignKeyConstraint(['reagents_id'], ['_reagents.id'], ondelete='SET NULL'),
+    # sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organizations.id'], ondelete='SET NULL'),
+    # sa.PrimaryKeyConstraint('id'),
+    # sa.UniqueConstraint('rsl_plate_num'),
+    # sa.UniqueConstraint('submitter_plate_num')
+    # )
+    # ### end Alembic commands ###

src/submissions/__init__.py

@@ -1,6 +1,6 @@
 # __init__.py
 
 # Version of the realpython-reader package
-__version__ = "202302.3b"
+__version__ = "202303.1b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"

src/submissions/backend/db/__init__.py

@@ -576,17 +576,23 @@ def get_all_controls_by_type(ctx:dict, con_type:str, start_date:date|None=None,
         list: Control instances.
     """
     
-    # logger.debug(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
-    except AttributeError:
-        output = 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]
+        output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).filter(models.Control.submitted_date.between(start_date.strftime("%Y-%m-%d"), end_date.strftime("%Y-%m-%d"))).all()
-    # logger.debug(f"Type {con_type}: {query.first()}")
+    else:
+        output = ctx['database_session'].query(models.Control).join(models.ControlType).filter_by(name=con_type).all()
+    logger.debug(f"Returned controls between dates: {output}")
     return output
+    # query = ctx['database_session'].query(models.ControlType).filter_by(name=con_type)
+    # try:
+    #     output = query.first().instances
+    # except AttributeError:
+    #     output = 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]
+    # # logger.debug(f"Type {con_type}: {query.first()}")
+    # return output
 
 
 def get_control_subtypes(ctx:dict, type:str, mode:str) -> list[str]:

src/submissions/backend/db/models/controls.py

@@ -39,9 +39,18 @@ class Control(Base):
     # UniqueConstraint('name', name='uq_control_name')
     submission_id = Column(INTEGER, ForeignKey("_submissions.id")) #: parent submission id
     submission = relationship("BacterialCulture", back_populates="controls", foreign_keys=[submission_id]) #: parent submission
+    refseq_version = Column(String(16))
+    kraken2_version = Column(String(16))
+    kraken2_db_version = Column(String(32))
 
 
-    def to_sub_dict(self):
+    def to_sub_dict(self) -> dict:
+        """
+        Converts object into convenient dictionary for use in submission summary
+
+        Returns:
+            dict: output dictionary containing: Name, Type, Targets, Top Kraken results
+        """        
         kraken = json.loads(self.kraken)
         kraken_cnt_total = sum([kraken[item]['kraken_count'] for item in kraken])
         new_kraken = []
@@ -61,3 +70,46 @@ class Control(Base):
         }
         return output
 
+    def convert_by_mode(self, mode:str) -> list[dict]:
+        """
+        split control object into analysis types
+
+        Args:
+            control (models.Control): control to be parsed into list
+            mode (str): analysis type
+
+        Returns:
+            list[dict]: list of records
+        """    
+        output = []
+        data = json.loads(getattr(self, mode))
+        # if len(data) == 0:
+        #     data = self.create_dummy_data(mode)
+        logger.debug(f"Length of data: {len(data)}")
+        for genus in data:
+            _dict = {}
+            _dict['name'] = self.name
+            _dict['submitted_date'] = self.submitted_date
+            _dict['genus'] = genus
+            _dict['target'] = 'Target' if genus.strip("*") in self.controltype.targets else "Off-target"
+            
+            for key in data[genus]:
+                _dict[key] = data[genus][key]
+                if _dict[key] == {}:
+                    print(self.name, mode)
+            output.append(_dict)
+        # logger.debug(output)
+        return output
+    
+    def create_dummy_data(self, mode):
+        match mode:
+            case "contains":
+                data = {"Nothing": {"contains_hashes":"0/400", "contains_ratio":0.0}}
+            case "matches":
+                data = {"Nothing": {"matches_hashes":"0/400", "matches_ratio":0.0}}
+            case "kraken":
+                data = {"Nothing": {"kraken_percent":0.0, "kraken_count":0}}
+            case _:
+                data = {}
+        return data
+

src/submissions/backend/db/models/submissions.py

@@ -4,6 +4,7 @@ from sqlalchemy.orm import relationship
 from datetime import datetime as dt
 import logging
 import json
+from json.decoder import JSONDecodeError
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -74,6 +75,9 @@ class BasicSubmission(Base):
             ext_info = json.loads(self.extraction_info)
         except TypeError:
             ext_info = None
+        except JSONDecodeError as e:
+            ext_info = None
+            logger.debug(f"Json error in {self.rsl_plate_num}: {e}")
         try:
             reagents = [item.to_sub_dict() for item in self.reagents]
         except:

src/submissions/backend/excel/reports.py

@@ -1,10 +1,11 @@
 
 from pandas import DataFrame, concat
-from backend.db import models
+from operator import itemgetter
+# from backend.db import models
 import json
 import logging
 from jinja2 import Environment, FileSystemLoader
-from datetime import date
+from datetime import date, timedelta
 import sys
 from pathlib import Path
 
@@ -139,31 +140,32 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
 #         dfs['name'] = df
 #     return dfs
 
-def convert_control_by_mode(ctx:dict, control:models.Control, mode:str) -> list[dict]:
+# def convert_control_by_mode(ctx:dict, control:models.Control, mode:str) -> list[dict]:
-    """
+#     """
-    split control object into analysis types
+#     split control object into analysis types... can I move this into the class itself?
+#     turns out I can
 
-    Args:
+#     Args:
-        ctx (dict): settings passed from gui
+#         ctx (dict): settings passed from gui
-        control (models.Control): control to be parsed into list
+#         control (models.Control): control to be parsed into list
-        mode (str): analysis type
+#         mode (str): analysis type
 
-    Returns:
+#     Returns:
-        list[dict]: list of records
+#         list[dict]: list of records
-    """    
+#     """    
-    output = []
+#     output = []
-    data = json.loads(getattr(control, mode))
+#     data = json.loads(getattr(control, mode))
-    for genus in data:
+#     for genus in data:
-        _dict = {}
+#         _dict = {}
-        _dict['name'] = control.name
+#         _dict['name'] = control.name
-        _dict['submitted_date'] = control.submitted_date
+#         _dict['submitted_date'] = control.submitted_date
-        _dict['genus'] = genus
+#         _dict['genus'] = genus
-        _dict['target'] = 'Target' if genus.strip("*") in control.controltype.targets else "Off-target"
+#         _dict['target'] = 'Target' if genus.strip("*") in control.controltype.targets else "Off-target"
-        for key in data[genus]:
+#         for key in data[genus]:
-            _dict[key] = data[genus][key]
+#             _dict[key] = data[genus][key]
-        output.append(_dict)
+#         output.append(_dict)
-    # logger.debug(output)
+#     # logger.debug(output)
-    return output
+#     return output
 
 
 def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -> DataFrame:
@@ -178,17 +180,81 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
     Returns:
         DataFrame: _description_
     """    
+    # copy = input
+    # for item in copy:
+    #     item['submitted_date'] = item['submitted_date'].strftime("%Y-%m-%d")
+    # with open("controls.json", "w") as f:
+    #     f.write(json.dumps(copy))
+    # for item in input:
+    #     logger.debug(item.keys())
     df = DataFrame.from_records(input)
+    df.to_excel("test.xlsx", engine="openpyxl")
     safe = ['name', 'submitted_date', 'genus', 'target']
     # 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]
             # The actual percentage from kraken was off due to exclusion of NaN, recalculating.
-            df[column] = 100 * df[count_col] / df.groupby('submitted_date')[count_col].transform('sum')
+            # df[column] = 100 * df[count_col] / df.groupby('submitted_date')[count_col].transform('sum')
+            df[column] = 100 * df[count_col] / df.groupby('name')[count_col].transform('sum')
         if column not in safe:
             if subtype != None and column != subtype:
                 del df[column]
     # logger.debug(df)
+    # df.sort_values('submitted_date').to_excel("controls.xlsx", engine="openpyxl")
+    df = displace_date(df)
+    df.sort_values('submitted_date').to_excel("controls.xlsx", engine="openpyxl")
+    df = df_column_renamer(df=df)
+    return df
+
+
+def df_column_renamer(df:DataFrame) -> DataFrame:
+    """
+    Ad hoc function I created to clarify some fields
+
+    Args:
+        df (DataFrame): input dataframe
+
+    Returns:
+        DataFrame: dataframe with 'clarified' column names
+    """  
+    df = df[df.columns.drop(list(df.filter(regex='_hashes')))]  
+    return df.rename(columns = {
+        "contains_ratio":"contains_shared_hashes_ratio",
+        "matches_ratio":"matches_shared_hashes_ratio",
+        "kraken_count":"kraken2_read_count",
+        "kraken_percent":"kraken2_read_percent"
+    })
+
+
+def displace_date(df:DataFrame) -> DataFrame:
+    """
+    This function serves to split samples that were submitted on the same date by incrementing dates.
+
+    Args:
+        df (DataFrame): input dataframe composed of control records
+
+    Returns:
+        DataFrame: output dataframe with dates incremented.
+    """    
+    # dict_list = []
+    # for item in df['name'].unique():
+    #     dict_list.append(dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']))
+    logger.debug(f"Unique items: {df['name'].unique()}")
+    # logger.debug(df.to_string())
+    # the assumption is that closest names will have closest dates...
+    dict_list = [dict(name=item, date=df[df.name == item].iloc[0]['submitted_date']) for item in sorted(df['name'].unique())]
+    for ii, item in enumerate(dict_list):
+        # if ii > 0:
+        try:
+            check = item['date'] == dict_list[ii-1]['date']
+        except IndexError:
+            check = False
+        if check:
+            logger.debug(f"We found one! Increment date!\n{item['date'] - timedelta(days=1)}")
+            mask = df['name'] == item['name']
+            # logger.debug(f"We will increment dates in: {df.loc[mask, 'submitted_date']}")
+            df.loc[mask, 'submitted_date'] = df.loc[mask, 'submitted_date'].apply(lambda x: x + timedelta(days=1))
+            # logger.debug(f"Do these look incremented: {df.loc[mask, 'submitted_date']}")
     return df
                 

src/submissions/frontend/__init__.py

@@ -20,17 +20,18 @@ from xhtml2pdf import pisa
 import yaml
 import pprint
 from backend.excel.parser import SheetParser
-from backend.excel.reports import convert_control_by_mode, convert_data_list_to_df
+from backend.excel.reports import convert_data_list_to_df
 from backend.db import (construct_submission_info, lookup_reagent, 
-    construct_reagent, store_reagent, store_submission, lookup_kittype_by_use,
+    construct_reagent, store_submission, lookup_kittype_by_use,
     lookup_regent_by_type_name, lookup_all_orgs, lookup_submissions_by_date_range,
     get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
     get_control_subtypes, lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num,
     create_org_from_yaml
 )
+from backend.db import lookup_kittype_by_name
 
 from .functions import check_kit_integrity
-from tools import check_not_nan
+from tools import check_not_nan, create_reagent_list
 from backend.excel.reports import make_report_xlsx, make_report_html
 
 import numpy
@@ -108,8 +109,8 @@ class App(QMainWindow):
         self.importAction = QAction("&Import", self)
         self.addReagentAction = QAction("Add Reagent", self)
         self.generateReportAction = QAction("Make Report", self)
-        self.addKitAction = QAction("Add Kit", self)
+        self.addKitAction = QAction("Import Kit", self)
-        self.addOrgAction = QAction("Add Org", self)
+        self.addOrgAction = QAction("Import Org", self)
         self.joinControlsAction = QAction("Link Controls")
         self.joinExtractionAction = QAction("Link Ext Logs")
         self.helpAction = QAction("&About", self)
@@ -137,6 +138,40 @@ class App(QMainWindow):
         about = AlertPop(message=output, status="information")
         about.exec()
 
+    def insert_reagent_import(self, item:str, prsr:SheetParser|None=None) -> QComboBox:
+        add_widget = QComboBox()
+        add_widget.setEditable(True)
+        # Ensure that all reagenttypes have a name that matches the items in the excel parser
+        query_var = item.replace("lot_", "")
+        logger.debug(f"Query for: {query_var}")
+        if prsr != None:
+            if isinstance(prsr.sub[item], numpy.float64):
+                logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
+                try:
+                    prsr.sub[item] = int(prsr.sub[item]['lot'])
+                except ValueError:
+                    pass
+        # query for reagents using type name from sheet and kit from sheet
+        logger.debug(f"Attempting lookup of reagents by type: {query_var}")
+        # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
+        relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
+        output_reg = []
+        for reagent in relevant_reagents:
+            if isinstance(reagent, set):
+                for thing in reagent:
+                    output_reg.append(thing)
+            elif isinstance(reagent, str):
+                output_reg.append(reagent)
+        relevant_reagents = output_reg
+        # if reagent in sheet is not found insert it into items
+        if prsr != None:
+            logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
+            if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
+                if check_not_nan(prsr.sub[item]['lot']):
+                    relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
+        logger.debug(f"New relevant reagents: {relevant_reagents}")
+        add_widget.addItems(relevant_reagents)
+        return add_widget
 
     def importSubmission(self):
         """
@@ -155,6 +190,7 @@ class App(QMainWindow):
         try:
             prsr = SheetParser(fname, **self.ctx)
         except PermissionError:
+            logger.error(f"Couldn't get permission to access file: {fname}")
             return
         logger.debug(f"prsr.sub = {prsr.sub}")
         # destroy any widgets from previous imports
@@ -169,6 +205,7 @@ class App(QMainWindow):
             (?P<samples>)^samples$ |
             (?P<reagent>^lot_.*$)
         """, re.VERBOSE)
+        # reagents = []
         for item in prsr.sub:
             logger.debug(f"Item: {item}")
             # attempt to match variable name to regex group
@@ -207,6 +244,7 @@ class App(QMainWindow):
                         add_widget.addItems(uses)
                     else:
                         add_widget.addItems(['bacterial_culture'])
+                    self.ext_kit = prsr.sub[item]
                 case 'submitted_date':
                     # create label
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
@@ -219,40 +257,41 @@ class App(QMainWindow):
                     except:
                         add_widget.setDate(date.today())
                 case 'reagent':
+                    # TODO make this a function so I can add in missing reagents below when checking kit integrity.
                     # create label
                     self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-                    add_widget = QComboBox()
+                    # add_widget = QComboBox()
-                    add_widget.setEditable(True)
+                    # add_widget.setEditable(True)
-                    # Ensure that all reagenttypes have a name that matches the items in the excel parser
+                    # # Ensure that all reagenttypes have a name that matches the items in the excel parser
-                    query_var = item.replace("lot_", "")
+                    # query_var = item.replace("lot_", "")
-                    logger.debug(f"Query for: {query_var}")
+                    # logger.debug(f"Query for: {query_var}")
-                    if isinstance(prsr.sub[item], numpy.float64):
+                    # if isinstance(prsr.sub[item], numpy.float64):
-                        logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
+                    #     logger.debug(f"{prsr.sub[item]['lot']} is a numpy float!")
-                        try:
+                    #     try:
-                            prsr.sub[item] = int(prsr.sub[item]['lot'])
+                    #         prsr.sub[item] = int(prsr.sub[item]['lot'])
-                        except ValueError:
+                    #     except ValueError:
-                            pass
+                    #         pass
-                    # query for reagents using type name from sheet and kit from sheet
+                    # # query for reagents using type name from sheet and kit from sheet
-                    logger.debug(f"Attempting lookup of reagents by type: {query_var}")
+                    # logger.debug(f"Attempting lookup of reagents by type: {query_var}")
-                    # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
+                    # # below was lookup_reagent_by_type_name_and_kit_name, but I couldn't get it to work.
-                    relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
+                    # relevant_reagents = [item.__str__() for item in lookup_regent_by_type_name(ctx=self.ctx, type_name=query_var)]#, kit_name=prsr.sub['extraction_kit'])]
-                    output_reg = []
+                    # output_reg = []
-                    for reagent in relevant_reagents:
+                    # for reagent in relevant_reagents:
-                        if isinstance(reagent, set):
+                    #     if isinstance(reagent, set):
-                            for thing in reagent:
+                    #         for thing in reagent:
-                                output_reg.append(thing)
+                    #             output_reg.append(thing)
-                        elif isinstance(reagent, str):
+                    #     elif isinstance(reagent, str):
-                            output_reg.append(reagent)
+                    #         output_reg.append(reagent)
-                    relevant_reagents = output_reg
+                    # relevant_reagents = output_reg
-                    logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
+                    # logger.debug(f"Relevant reagents for {prsr.sub[item]}: {relevant_reagents}")
-                    # if reagent in sheet is not found insert it into items
+                    # # if reagent in sheet is not found insert it into items
-                    if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
+                    # if str(prsr.sub[item]['lot']) not in relevant_reagents and prsr.sub[item]['lot'] != 'nan':
-                        if check_not_nan(prsr.sub[item]['lot']):
+                    #     if check_not_nan(prsr.sub[item]['lot']):
-                            relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
+                    #         relevant_reagents.insert(0, str(prsr.sub[item]['lot']))
-                    logger.debug(f"New relevant reagents: {relevant_reagents}")
+                    # logger.debug(f"New relevant reagents: {relevant_reagents}")
-                    add_widget.addItems(relevant_reagents)
+                    # add_widget.addItems(relevant_reagents)
+                    add_widget = self.insert_reagent_import(item, prsr=prsr)
                     self.reagents[item] = prsr.sub[item]
-                # TODO: make samples not appear in frame.
                 case 'samples':
                     # hold samples in 'self' until form submitted
                     logger.debug(f"{item}: {prsr.sub[item]}")
@@ -263,6 +302,17 @@ class App(QMainWindow):
                     add_widget = QLineEdit()
                     add_widget.setText(str(prsr.sub[item]).replace("_", " "))
             self.table_widget.formlayout.addWidget(add_widget)
+        # compare self.reagents with expected reagents in kit
+        if hasattr(self, 'ext_kit'):
+            kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
+            kit_integrity = check_kit_integrity(kit, [item.replace("lot_", "") for item in self.reagents])
+            if kit_integrity != None:
+                msg = AlertPop(message=kit_integrity['message'], status="critical")
+                msg.exec()
+                for item in kit_integrity['missing']:
+                    self.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
+                    add_widget =self.insert_reagent_import(item)
+                    self.table_widget.formlayout.addWidget(add_widget)
         # create submission button
         submit_btn = QPushButton("Submit")
         self.table_widget.formlayout.addWidget(submit_btn)
@@ -580,11 +630,14 @@ class App(QMainWindow):
             # return
             fig = None
         else:
-            data = []
+            # data = []
-            for control in controls:
+            # for control in controls:
+            #     # change each control to list of dicts
+            #     # dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
+            #     dicts = control.convert_by_mode(mode=self.mode)
+            #     data.append(dicts)
             # change each control to list of dicts
-                dicts = convert_control_by_mode(ctx=self.ctx, control=control, mode=self.mode)
+            data = [control.convert_by_mode(mode=self.mode) for control in controls]
-                data.append(dicts)
             # flatten data to one dimensional list
             data = [item for sublist in data for item in sublist]
             # logger.debug(data)
@@ -677,6 +730,7 @@ class App(QMainWindow):
         with open(fname.__str__(), 'r') as f:
             runs = [col.strip().split(",") for col in f.readlines()]
         # check = []
+        count = 0
         for run in runs:
             obj = dict(
                     start_time=run[0].strip(), 
@@ -693,21 +747,42 @@ class App(QMainWindow):
             sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=obj['rsl_plate_num'])
             try:
                 logger.debug(f"Found submission: {sub.rsl_plate_num}")
+                count += 1
             except AttributeError:
                 continue
-            output = json.dumps(obj)
+            # output = json.dumps(obj)
+            if sub.extraction_info != None:
+                # try:
+                # logger.debug(f"Attempting update on ext info: {sub.extraction_info} for {sub.rsl_plate_num}")
+                existing = json.loads(sub.extraction_info)
+                # except:
+                    # existing = None
+            else:
+                existing = None
             try:
-                if output in sub.extraction_info:
+                if json.dumps(obj) in sub.extraction_info:
                     logger.debug(f"Looks like we already have that info.")
                     continue
             except TypeError:
                 pass
+            if existing != None:
                 try:
-                sub.extraction_info += output
+                    # sub.extraction_info += output
+                    logger.debug(f"Updating {type(existing)}: {existing} with {type(obj)}: {obj}")
+                    existing.append(obj)
+                    logger.debug(f"Setting: {existing}")
+                    sub.extraction_info = json.dumps(existing)
                 except TypeError:
-                sub.extraction_info = output
+                    logger.error(f"Error updating!")
+                    sub.extraction_info = json.dumps([obj])
+                logger.debug(f"Final ext info for {sub.rsl_plate_num}: {sub.extraction_info}")
+            else:
+                sub.extraction_info = json.dumps([obj])        
             self.ctx['database_session'].add(sub)
             self.ctx["database_session"].commit()
+        dlg = AlertPop(message=f"We added {count} logs to the database.", status='information')
+        dlg.exec()
+
 
 
 class AddSubForm(QWidget):

src/submissions/frontend/custom_widgets/__init__.py

@@ -260,6 +260,7 @@ class ControlsDatePicker(QWidget):
 
         self.start_date = QDateEdit(calendarPopup=True)
         # start date is three month prior to end date by default
+        # edit: 2 month, but the variable name is the same cause I'm lazy
         threemonthsago = QDate.currentDate().addDays(-60)
         self.start_date.setDate(threemonthsago)
         self.end_date = QDateEdit(calendarPopup=True)

src/submissions/frontend/functions.py

@@ -1,14 +1,20 @@
 # from ..models import *
 from backend.db.models import *
+# from backend.db import lookup_kittype_by_name
 import logging
 import numpy as np
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
-def check_kit_integrity(sub:BasicSubmission):
+def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
+    logger.debug(type(sub))
+    match sub:
+        case BasicSubmission():
             ext_kit_rtypes = [reagenttype.name for reagenttype in sub.extraction_kit.reagent_types]
-    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
             reagenttypes = [reagent.type.name for reagent in sub.reagents]
+        case KitType():
+            ext_kit_rtypes = [reagenttype.name for reagenttype in sub.reagent_types]
+    logger.debug(f"Kit reagents: {ext_kit_rtypes}")
     logger.debug(f"Submission reagents: {reagenttypes}")
     check = set(ext_kit_rtypes) == set(reagenttypes)
     logger.debug(f"Checking if reagents match kit contents: {check}")
@@ -17,7 +23,11 @@ def check_kit_integrity(sub:BasicSubmission):
     if check:
         result = None
     else:
-        result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[x.upper() for x in ext_kit_rtypes if x not in common]}\n\nAlternatively, you may have set the wrong extraction kit."}
+        missing = [x for x in ext_kit_rtypes if x not in common]
+        result = {'message' : f"Couldn't verify reagents match listed kit components.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.", 'missing': missing}
     return result
 
 
+
+    
+

src/submissions/frontend/visualizations/charts.py

@@ -25,6 +25,7 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
     genera = []
     if df.empty:
         return None
+
     for item in df['genus'].to_list():
         try:
             if item[-1] == "*":
@@ -41,7 +42,7 @@ def create_charts(ctx:dict, df:pd.DataFrame, ytitle:str|None=None) -> Figure:
     # sort by and exclude from
     sorts = ['submitted_date', "target", "genus"]
     exclude = ['name', 'genera']
-    modes = [item for item in df.columns if item not in sorts and item not in exclude and "_hashes" not in item]
+    modes = [item for item in df.columns if item not in sorts and item not in exclude]# and "_hashes" not in item]
     # Set descending for any columns that have "{mode}" in the header.
     ascending = [False if item == "target" else True for item in sorts]
     df = df.sort_values(by=sorts, ascending=ascending)

src/submissions/templates/submission_details.html

@@ -47,8 +47,9 @@
         {% endfor %}
         {% endif %}
         {% if sub['ext_info'] %}
+        {% for entry in sub['ext_info'] %}
         <h3><u>Extraction Status:</u></h3>
-        <p>{% for key, value in sub['ext_info'].items() %}
+        <p>{% for key, value in entry.items() %}
             {% if loop.index == 1%}
                 &nbsp;&nbsp;&nbsp;{{ key|replace('_', ' ')|title() }}: {{ value }}<br>
             {% else %}
@@ -59,6 +60,7 @@
                 {% endif %}
             {% endif %}
         {% endfor %}</p>
+        {% endfor %}
         {% endif %}
     </body>
 </html>

src/submissions/templates/submission_details.txt

@@ -19,8 +19,9 @@ Attached Controls:
         {% for genera in item['kraken'] %}
             {{ genera['name'] }}: {{ genera['kraken_count'] }} ({{ genera['kraken_percent'] }}){% endfor %}{% endif %}
 {% endfor %}{% endif %}
-{% if sub['ext_info'] %}
+{% if sub['ext_info'] %}{% for entry in sub['ext_info'] %}
 Extraction Status:
-{% for key, value in sub['ext_info'].items() %}
+{% for key, value in entry.items() %}
     {{ key|replace('_', ' ')|title() }}: {{ value }}{% endfor %}
+{% endfor %}
 {% endif %}

src/submissions/tools/__init__.py

@@ -23,3 +23,7 @@ def check_is_power_user(ctx:dict) -> bool:
         logger.debug(f"Check encounteded unknown error: {type(e).__name__} - {e}")
         check = False
     return check
+
+
+def create_reagent_list(in_dict:dict) -> list[str]:
+    return [item.strip("lot_") for item in in_dict.keys()]