Improved reporting, price tracking

alembic.ini

@@ -56,6 +56,7 @@ version_path_separator = os  # Use os.pathsep. Default configuration used for ne
 # output_encoding = utf-8
 
 sqlalchemy.url = sqlite:///L:\Robotics Laboratory Support\Submissions\submissions.db
+; sqlalchemy.url = sqlite:///C:\Users\lwark\Documents\Archives\DB_backups\submissions-20230130.db
 
 
 [post_write_hooks]

alembic/versions/178203610c3b_updating_costs.py

@@ -0,0 +1,40 @@
+"""updating costs
+
+Revision ID: 178203610c3b
+Revises: afbdd9e46207
+Create Date: 2023-02-02 09:31:05.748477
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '178203610c3b'
+down_revision = 'afbdd9e46207'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_kits', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('mutable_cost', sa.FLOAT(precision=2), nullable=True))
+        batch_op.add_column(sa.Column('constant_cost', sa.FLOAT(precision=2), nullable=True))
+
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('run_cost', sa.FLOAT(precision=2), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.drop_column('run_cost')
+
+    with op.batch_alter_table('_kits', schema=None) as batch_op:
+        batch_op.drop_column('constant_cost')
+        batch_op.drop_column('mutable_cost')
+
+    # ### end Alembic commands ###

alembic/versions/afbdd9e46207_add_extraction_info_to_submissions.py

@@ -0,0 +1,40 @@
+"""add extraction info to submissions
+
+Revision ID: afbdd9e46207
+Revises: 8753ed70f148
+Create Date: 2023-01-30 13:05:42.858306
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'afbdd9e46207'
+down_revision = '8753ed70f148'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_contacts', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('organization_id', sa.INTEGER(), nullable=True))
+        batch_op.create_foreign_key('fk_contact_org_id', '_organizations', ['organization_id'], ['id'], ondelete='SET NULL')
+
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('extraction_info', sa.JSON(), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_submissions', schema=None) as batch_op:
+        batch_op.drop_column('extraction_info')
+
+    with op.batch_alter_table('_contacts', schema=None) as batch_op:
+        batch_op.drop_constraint('fk_contact_org_id', type_='foreignkey')
+        batch_op.drop_column('organization_id')
+
+    # ### end Alembic commands ###

src/submissions/backend/db/__init__.py

@@ -5,7 +5,7 @@ import sqlite3
 # from sqlalchemy.exc import IntegrityError, OperationalError
 # from sqlite3 import IntegrityError, OperationalError
 import logging
-from datetime import date, datetime
+from datetime import date, datetime, timedelta
 from sqlalchemy import and_
 import uuid
 import base64
@@ -132,6 +132,12 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         except AttributeError:
             logger.debug(f"Could not set attribute: {item} to {info_dict[item]}")
             continue
+        # calculate cost of the run: immutable cost + mutable times number of columns
+        try:
+            instance.run_cost = instance.extraction_kit.immutable_cost + (instance.extraction_kit.mutable_cost * ((instance.sample_count / 8)/12))
+        except TypeError:
+            logger.debug(f"Looks like that kit doesn't have cost breakdown yet, using full plate cost.")
+            instance.run_cost = instance.extraction_kit.cost_per_run
     logger.debug(f"Constructed instance: {instance.to_string()}")
     logger.debug(msg)
     return instance, {'message':msg}
@@ -395,12 +401,13 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
         exp (dict): Experiment dictionary created from yaml file
     """
     try:
-        super_users = ctx['super_users']
+        power_users = ctx['power_users']
     except KeyError:
         logger.debug("This user does not have permission to add kits.")
         return {'code':1,'message':"This user does not have permission to add kits."}
-    if getuser not in super_users:
-        logger.debug("This user does not have permission to add kits.")
+    logger.debug(f"Adding kit for user: {getuser()}")
+    if getuser() not in power_users:
+        logger.debug(f"{getuser()} does not have permission to add kits.")
         return {'code':1, 'message':"This user does not have permission to add kits."}
     for type in exp:
         if type == "password":
@@ -410,7 +417,7 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
             for r in exp[type]['kits'][kt]['reagenttypes']:
                 look_up = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==r).first()
                 if look_up == None:
-                    rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=datetime.timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
+                    rt = models.ReagentType(name=r.replace(" ", "_").lower(), eol_ext=timedelta(30*exp[type]['kits'][kt]['reagenttypes'][r]['eol_ext']), kits=[kit])
                 else:
                     rt = look_up
                     rt.kits.append(kit)

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

@@ -18,6 +18,8 @@ class KitType(Base):
     submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
     used_for = Column(JSON) #: list of names of sample types this kit can process
     cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit
+    mutable_cost = Column(FLOAT(2)) #: dollar amount that can change with number of columns (reagents, tips, etc)
+    constant_cost = Column(FLOAT(2)) #: dollar amount that will remain constant (plates, man hours, etc)
     reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
     reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
     

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

@@ -1,5 +1,5 @@
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
 from sqlalchemy.orm import relationship
 from datetime import datetime as dt
 
@@ -26,6 +26,8 @@ class BasicSubmission(Base):
     # Move this into custom types?
     reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions) #: relationship to reagents
     reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id")) #: id of used reagents
+    extraction_info = Column(JSON) #: unstructured output from the extraction table logger.
+    run_cost = Column(FLOAT(2))
 
     __mapper_args__ = {
         "polymorphic_identity": "basic_submission",
@@ -73,6 +75,7 @@ class BasicSubmission(Base):
             "Sample Count": self.sample_count,
             "Extraction Kit": ext_kit,
             "Technician": self.technician,
+            "Cost": self.run_cost,
         }
         return output
 
@@ -99,10 +102,11 @@ class BasicSubmission(Base):
         except AttributeError:
             ext_kit = None
         # get extraction kit cost from nested kittype object
-        try:
-            cost = self.extraction_kit.cost_per_run
-        except AttributeError:
-            cost = None
+        # depreciated as it will change kit cost overtime
+        # try:
+        #     cost = self.extraction_kit.cost_per_run
+        # except AttributeError:
+        #     cost = None
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
@@ -112,7 +116,7 @@ class BasicSubmission(Base):
             "Submitting Lab": sub_lab,
             "Sample Count": self.sample_count,
             "Extraction Kit": ext_kit,
-            "Cost": cost
+            "Cost": self.run_cost
         }
         return output
 

src/submissions/backend/excel/parser.py

@@ -89,6 +89,30 @@ class SheetParser(object):
         """
         pulls info specific to bacterial culture sample type
         """
+
+        def _parse_reagents(df:pd.DataFrame) -> None:
+            for ii, row in df.iterrows():
+                logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
+                try:
+                    check = not np.isnan(row[1])
+                except TypeError:
+                    check = True
+                if not isinstance(row[2], float) and check:
+                    # must be prefixed with 'lot_' to be recognized by gui
+                    try:
+                        reagent_type = row[1].replace(' ', '_').lower().strip()
+                    except AttributeError:
+                        pass
+                    if reagent_type == "//":
+                        reagent_type = row[0].replace(' ', '_').lower().strip()
+                    try:
+                        output_var = row[2].upper()
+                    except AttributeError:
+                        logger.debug(f"Couldn't upperize {row[2]}, must be a number")
+                        output_var = row[2]
+                    logger.debug(f"Output variable is {output_var}")
+                    self.sub[f"lot_{reagent_type}"] = output_var
+
         submission_info = self._parse_generic("Sample List")
         # iloc is [row][column] and the first row is set as header row so -2
         tech = str(submission_info.iloc[11][1])
@@ -100,16 +124,20 @@ class SheetParser(object):
         self.sub['technician'] = tech
         # reagents
         # must be prefixed with 'lot_' to be recognized by gui
-        self.sub['lot_wash_1'] = submission_info.iloc[1][6] #if pd.isnull(submission_info.iloc[1][6]) else string_formatter(submission_info.iloc[1][6])
-        self.sub['lot_wash_2'] = submission_info.iloc[2][6] #if pd.isnull(submission_info.iloc[2][6]) else string_formatter(submission_info.iloc[2][6])
-        self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] #if pd.isnull(submission_info.iloc[3][6]) else string_formatter(submission_info.iloc[3][6])
-        self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] #if pd.isnull(submission_info.iloc[4][6]) else string_formatter(submission_info.iloc[4][6])
-        self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] #if np.nan(submission_info.iloc[5][6]) else string_formatter(submission_info.iloc[5][6])
-        self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] #if pd.isnull(submission_info.iloc[6][6]) else string_formatter(submission_info.iloc[6][6])
-        self.sub['lot_isopropanol'] = submission_info.iloc[9][6] #if pd.isnull(submission_info.iloc[9][6]) else string_formatter(submission_info.iloc[9][6])
-        self.sub['lot_ethanol'] = submission_info.iloc[10][6] #if pd.isnull(submission_info.iloc[10][6]) else string_formatter(submission_info.iloc[10][6])
-        self.sub['lot_positive_control'] = submission_info.iloc[103][1] #if pd.isnull(submission_info.iloc[103][1]) else string_formatter(submission_info.iloc[103][1])
-        self.sub['lot_plate'] = submission_info.iloc[12][6] #if pd.isnull(submission_info.iloc[12][6]) else string_formatter(submission_info.iloc[12][6])
+        # Todo: find a more adaptable way to read reagents.
+
+        reagent_range = submission_info.iloc[1:13, 4:8]
+        _parse_reagents(reagent_range)
+        # self.sub['lot_wash_1'] = submission_info.iloc[1][6] #if pd.isnull(submission_info.iloc[1][6]) else string_formatter(submission_info.iloc[1][6])
+        # self.sub['lot_wash_2'] = submission_info.iloc[2][6] #if pd.isnull(submission_info.iloc[2][6]) else string_formatter(submission_info.iloc[2][6])
+        # self.sub['lot_binding_buffer'] = submission_info.iloc[3][6] #if pd.isnull(submission_info.iloc[3][6]) else string_formatter(submission_info.iloc[3][6])
+        # self.sub['lot_magnetic_beads'] = submission_info.iloc[4][6] #if pd.isnull(submission_info.iloc[4][6]) else string_formatter(submission_info.iloc[4][6])
+        # self.sub['lot_lysis_buffer'] = submission_info.iloc[5][6] #if np.nan(submission_info.iloc[5][6]) else string_formatter(submission_info.iloc[5][6])
+        # self.sub['lot_elution_buffer'] = submission_info.iloc[6][6] #if pd.isnull(submission_info.iloc[6][6]) else string_formatter(submission_info.iloc[6][6])
+        # self.sub['lot_isopropanol'] = submission_info.iloc[9][6] #if pd.isnull(submission_info.iloc[9][6]) else string_formatter(submission_info.iloc[9][6])
+        # self.sub['lot_ethanol'] = submission_info.iloc[10][6] #if pd.isnull(submission_info.iloc[10][6]) else string_formatter(submission_info.iloc[10][6])
+        # self.sub['lot_positive_control'] = submission_info.iloc[103][1] #if pd.isnull(submission_info.iloc[103][1]) else string_formatter(submission_info.iloc[103][1])
+        # self.sub['lot_plate'] = submission_info.iloc[12][6] #if pd.isnull(submission_info.iloc[12][6]) else string_formatter(submission_info.iloc[12][6])
         # get individual sample info
         sample_parser = SampleParser(submission_info.iloc[15:111])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
@@ -117,38 +145,71 @@ class SheetParser(object):
         self.sub['samples'] = sample_parse()
 
         
+
+
+
     def _parse_wastewater(self) -> None:
         """
         pulls info specific to wastewater sample type
         """        
+
+        def _parse_reagents(df:pd.DataFrame) -> None:
+            logger.debug(df)
+            for ii, row in df.iterrows():
+                try:
+                    check = not np.isnan(row[5])
+                except TypeError:
+                    check = True
+                if not isinstance(row[5], float) and check:
+                    # must be prefixed with 'lot_' to be recognized by gui
+                    output_key = re.sub(r"\d{1,3}%", "", row[0].replace(' ', '_').lower())
+                    try:
+                        output_var = row[5].upper()
+                    except AttributeError:
+                        logger.debug(f"Couldn't upperize {row[2]}, must be a number")
+                        output_var = row[5]
+                    self.sub[f"lot_{output_key}"] = output_var
+
         # submission_info = self.xl.parse("WW Submissions (ENTER HERE)")
         submission_info = self._parse_generic("WW Submissions (ENTER HERE)")
         enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
+        enr_reagent_range = enrichment_info.iloc[0:4, 9:20]
         extraction_info = self.xl.parse("Extraction Worksheet", dtype=object)
+        ext_reagent_range = extraction_info.iloc[0:5, 9:20]
         qprc_info = self.xl.parse("qPCR Worksheet", dtype=object)
+        pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
         self.sub['technician'] = f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}"
+        _parse_reagents(enr_reagent_range)
+        _parse_reagents(ext_reagent_range)
+        _parse_reagents(pcr_reagent_range)
         # reagents
-        logger.debug(qprc_info)
-        self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] #if pd.isnull(enrichment_info.iloc[0][14]) else string_formatter(enrichment_info.iloc[0][14])
-        self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] #if pd.isnull(enrichment_info.iloc[1][14]) else string_formatter(enrichment_info.iloc[1][14]) 
-        self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] #if pd.isnull(enrichment_info.iloc[2][14]) else string_formatter(enrichment_info.iloc[2][14])
-        self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] #if pd.isnull(enrichment_info.iloc[3][14]) else string_formatter(enrichment_info.iloc[3][14])
-        self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] #if pd.isnull(extraction_info.iloc[0][14]) else string_formatter(extraction_info.iloc[0][14])
-        self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] #if pd.isnull(extraction_info.iloc[1][14]) else string_formatter(extraction_info.iloc[1][14])
-        self.sub['lot_wash'] = extraction_info.iloc[2][14] #if pd.isnull(extraction_info.iloc[2][14]) else string_formatter(extraction_info.iloc[2][14])
-        self.sub['lot_ethanol'] = extraction_info.iloc[3][14] #if pd.isnull(extraction_info.iloc[3][14]) else string_formatter(extraction_info.iloc[3][14])
-        self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] #if pd.isnull(extraction_info.iloc[4][14]) else string_formatter(extraction_info.iloc[4][14])
-        self.sub['lot_master_mix'] = qprc_info.iloc[0][14] #if pd.isnull(qprc_info.iloc[0][14]) else string_formatter(qprc_info.iloc[0][14])
-        self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] #if pd.isnull(qprc_info.iloc[1][14]) else string_formatter(qprc_info.iloc[1][14])
-        self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
-        self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
-        self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
+        # logger.debug(qprc_info)
+        # self.sub['lot_lysis_buffer'] = enrichment_info.iloc[0][14] #if pd.isnull(enrichment_info.iloc[0][14]) else string_formatter(enrichment_info.iloc[0][14])
+        # self.sub['lot_proteinase_K'] = enrichment_info.iloc[1][14] #if pd.isnull(enrichment_info.iloc[1][14]) else string_formatter(enrichment_info.iloc[1][14]) 
+        # self.sub['lot_magnetic_virus_particles'] = enrichment_info.iloc[2][14] #if pd.isnull(enrichment_info.iloc[2][14]) else string_formatter(enrichment_info.iloc[2][14])
+        # self.sub['lot_enrichment_reagent_1'] = enrichment_info.iloc[3][14] #if pd.isnull(enrichment_info.iloc[3][14]) else string_formatter(enrichment_info.iloc[3][14])
+        # self.sub['lot_binding_buffer'] = extraction_info.iloc[0][14] #if pd.isnull(extraction_info.iloc[0][14]) else string_formatter(extraction_info.iloc[0][14])
+        # self.sub['lot_magnetic_beads'] = extraction_info.iloc[1][14] #if pd.isnull(extraction_info.iloc[1][14]) else string_formatter(extraction_info.iloc[1][14])
+        # self.sub['lot_wash'] = extraction_info.iloc[2][14] #if pd.isnull(extraction_info.iloc[2][14]) else string_formatter(extraction_info.iloc[2][14])
+        # self.sub['lot_ethanol'] = extraction_info.iloc[3][14] #if pd.isnull(extraction_info.iloc[3][14]) else string_formatter(extraction_info.iloc[3][14])
+        # self.sub['lot_elution_buffer'] = extraction_info.iloc[4][14] #if pd.isnull(extraction_info.iloc[4][14]) else string_formatter(extraction_info.iloc[4][14])
+        # self.sub['lot_master_mix'] = qprc_info.iloc[0][14] #if pd.isnull(qprc_info.iloc[0][14]) else string_formatter(qprc_info.iloc[0][14])
+        # self.sub['lot_pre_mix_1'] = qprc_info.iloc[1][14] #if pd.isnull(qprc_info.iloc[1][14]) else string_formatter(qprc_info.iloc[1][14])
+        # self.sub['lot_pre_mix_2'] = qprc_info.iloc[2][14] #if pd.isnull(qprc_info.iloc[2][14]) else string_formatter(qprc_info.iloc[2][14])
+        # self.sub['lot_positive_control'] = qprc_info.iloc[3][14] #if pd.isnull(qprc_info.iloc[3][14]) else string_formatter(qprc_info.iloc[3][14])
+        # self.sub['lot_ddh2o'] = qprc_info.iloc[4][14] #if pd.isnull(qprc_info.iloc[4][14]) else string_formatter(qprc_info.iloc[4][14])
         # gt individual sample info
         sample_parser = SampleParser(submission_info.iloc[16:40])
         sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type'].lower()}_samples")
         self.sub['samples'] = sample_parse()
 
         
+
+
+
+    
+
+
 class SampleParser(object):
     """
     object to pull data for samples in excel sheet and construct individual sample objects

src/submissions/backend/excel/reports.py

@@ -1,9 +1,21 @@
-import pandas as pd
-from pandas import DataFrame
-import numpy as np
+
+from pandas import DataFrame, concat
 from backend.db import models
 import json
 import logging
+from jinja2 import Environment, FileSystemLoader
+from datetime import date
+import sys
+from pathlib import Path
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+if getattr(sys, 'frozen', False):
+    loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
+else:
+    loader_path = Path(__file__).parents[2].joinpath('templates').absolute().__str__()
+loader = FileSystemLoader(loader_path)
+env = Environment(loader=loader)
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -22,12 +34,50 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
     df = df.sort_values("Submitting Lab")
     # aggregate cost and sample count columns
     df2 = df.groupby(["Submitting Lab", "Extraction Kit"]).agg({'Cost': ['sum', 'count'], 'Sample Count':['sum']})
-    logger.debug(df2.columns)
     # apply formating to cost column
-    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('${:,.2f}'.format)
+    # df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')] = df2.iloc[:, (df2.columns.get_level_values(1)=='sum') & (df2.columns.get_level_values(0)=='Cost')].applymap('${:,.2f}'.format)
     return df2
 
 
+def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
+    
+    """
+    generates html from the report dataframe
+
+    Args:
+        df (DataFrame): input dataframe generated from 'make_report_xlsx' above
+        start_date (date): starting date of the report period
+        end_date (date): ending date of the report period
+
+    Returns:
+        str: html string
+    """    
+    old_lab = ""
+    output = []
+    for ii, row in enumerate(df.iterrows()):
+        row = [item for item in row]
+        lab = row[0][0]
+        logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
+        kit = dict(name=row[0][1], cost=row[1][('Cost', 'sum')], plate_count=int(row[1][('Cost', 'count')]), sample_count=int(row[1][('Sample Count', 'sum')]))
+        if lab == old_lab:
+            output[ii-1]['kits'].append(kit)
+            output[ii-1]['total_cost'] += kit['cost']
+            output[ii-1]['total_samples'] += kit['sample_count']
+            output[ii-1]['total_plates'] += kit['plate_count']
+        else:
+            adder = dict(lab=lab, kits=[kit], total_cost=kit['cost'], total_samples=kit['sample_count'], total_plates=kit['plate_count'])
+            output.append(adder)
+        old_lab = lab
+    logger.debug(output)
+    dicto = {'start_date':start_date, 'end_date':end_date, 'labs':output}#, "table":table}
+    temp = env.get_template('summary_report.html')
+    html = temp.render(input=dicto)
+    return html
+
+
+            
+
+
 # def split_controls_dictionary(ctx:dict, input_dict) -> list[dict]:
 #     # this will be the date in string form
 #     dict_name = list(input_dict.keys())[0]
@@ -126,3 +176,4 @@ def convert_data_list_to_df(ctx:dict, input:list[dict], subtype:str|None=None) -
                 del df[column]
     # logger.debug(df)
     return df
+

src/submissions/configure/__init__.py

@@ -226,6 +226,8 @@ def copy_settings(settings_path:Path, settings:dict) -> dict:
     # if the current user is not a superuser remove the superusers entry
     if not getpass.getuser() in settings['super_users']:
         del settings['super_users']
+    if not getpass.getuser() in settings['power_users']:
+        del settings['power_users']
     with open(settings_path, 'w') as f:
         yaml.dump(settings, f)
     return settings

src/submissions/frontend/__init__.py

@@ -14,6 +14,8 @@ from PyQt6.QtWebEngineWidgets import QWebEngineView
 
 from pathlib import Path
 import plotly
+import pandas as pd
+from xhtml2pdf import pisa
 # import plotly.express as px
 import yaml
 
@@ -25,7 +27,7 @@ from backend.db import (construct_submission_info, lookup_reagent,
     get_all_Control_Types_names, create_kit_from_yaml, get_all_available_modes, get_all_controls_by_type,
     get_control_subtypes
 )
-from backend.excel.reports import make_report_xlsx
+from backend.excel.reports import make_report_xlsx, make_report_html
 import numpy
 from frontend.custom_widgets import AddReagentQuestion, AddReagentForm, SubmissionsSheet, ReportDatePicker, KitAdder, ControlsDatePicker, OverwriteSubQuestion
 import logging
@@ -362,16 +364,21 @@ class App(QMainWindow):
             subs = lookup_submissions_by_date_range(ctx=self.ctx, start_date=info['start_date'], end_date=info['end_date'])
             # convert each object to dict
             records = [item.report_dict() for item in subs]
-            # make dataframe from record dictionaries
             df = make_report_xlsx(records=records)
-            # setup filedialog to handle save location of report
-            home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.xlsx").resolve().__str__()
-            fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
-            # save file
-            try:
-                df.to_excel(fname, engine="openpyxl")
-            except PermissionError:
-                pass
+            html = make_report_html(df=df, start_date=info['start_date'], end_date=info['end_date'])
+            # make dataframe from record dictionaries
+            # df = make_report_xlsx(records=records)
+            # # setup filedialog to handle save location of report
+            home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submissions_Report_{info['start_date']}-{info['end_date']}.pdf").resolve().__str__()
+            # fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".xlsx")[0])
+            fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
+            # logger.debug(f"report output name: {fname}")
+            # df.to_excel(fname, engine='openpyxl')
+            with open(fname, "w+b") as f:
+                pisa.CreatePDF(html, dest=f)
+            df.to_excel(fname.with_suffix(".xlsx"), engine='openpyxl')       
+
+            
             
 
     def add_kit(self):

src/submissions/frontend/custom_widgets/__init__.py

@@ -302,11 +302,16 @@ class KitAdder(QWidget):
         used_for.setEditable(True)
         self.grid.addWidget(used_for,3,1)
         # set cost per run
-        self.grid.addWidget(QLabel("Cost per run:"),4,0)
+        self.grid.addWidget(QLabel("Constant cost per full plate (plates, work hours, etc.):"),4,0)
         cost = QSpinBox()
         cost.setMinimum(0)
         cost.setMaximum(9999)
         self.grid.addWidget(cost,4,1)
+        self.grid.addWidget(QLabel("Mutable cost per full plate (tips, reagents, etc.):"),5,0)
+        cost = QSpinBox()
+        cost.setMinimum(0)
+        cost.setMaximum(9999)
+        self.grid.addWidget(cost,5,1)
         # button to add additional reagent types
         self.add_RT_btn = QPushButton("Add Reagent Type")
         self.grid.addWidget(self.add_RT_btn)
@@ -338,7 +343,8 @@ class KitAdder(QWidget):
         yml_type[used] = {}
         yml_type[used]['kits'] = {}
         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']]['constant_cost'] = info["Constant cost per full plate (plates, work hours, etc.)"]
+        yml_type[used]['kits'][info['kit_name']]['mutable_cost'] = info["Mutable cost per full plate (tips, reagents, etc.)"]
         yml_type[used]['kits'][info['kit_name']]['reagenttypes'] = reagents
         logger.debug(yml_type)
         # send to kit constructor
@@ -381,20 +387,19 @@ class KitAdder(QWidget):
                     if not isinstance(prev_item, QDateEdit) and not isinstance(prev_item, QComboBox) and not isinstance(prev_item, QSpinBox) and not isinstance(prev_item, QScrollBar):
                         logger.debug(f"Previous: {prev_item}")
                         logger.debug(f"Item: {item}, {item.text()}")
-                        values.append(item.text())
+                        values.append(item.text().strip())
                 case QComboBox():
-                    values.append(item.currentText())
+                    values.append(item.currentText().strip())
                 case QDateEdit():
                     values.append(item.date().toPyDate())
                 case QSpinBox():
                     values.append(item.value())
                 case ReagentTypeForm():
-                    
                     re_labels, re_values, _ = self.extract_form_info(item) 
                     reagent = {item[0]:item[1] for item in zip(re_labels, re_values)}
                     logger.debug(reagent)
                     # reagent = {reagent['name:']:{'eol':reagent['extension_of_life_(months):']}}
-                    reagents[reagent['name']] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
+                    reagents[reagent["name_(*exactly*_as_it_appears_in_the_excel_submission_form)"].strip()] = {'eol_ext':int(reagent['extension_of_life_(months)'])}
             prev_item = item
         return labels, values, reagents
 
@@ -408,7 +413,7 @@ class ReagentTypeForm(QWidget):
         super().__init__()
         grid = QGridLayout()
         self.setLayout(grid)
-        grid.addWidget(QLabel("Name:"),0,0)
+        grid.addWidget(QLabel("Name (*Exactly* as it appears in the excel submission form):"),0,0)
         reagent_getter = QComboBox()
         # lookup all reagent type names from db
         reagent_getter.addItems(get_all_reagenttype_names(ctx=parent_ctx))

src/submissions/templates/summary_report.html

@@ -0,0 +1,22 @@
+<!doctype html>
+<html>
+    <head>
+        <title>Submissions Report for {{ input['start_date'] }} - {{ input['end_date'] }}</title>
+    </head>
+    <body>
+        <h2>Submissions Report {{ input['start_date'] }} - {{ input['end_date'] }}</h2>
+        <br>
+        {{ input['table'] }}
+        <br>
+        {% for lab in input['labs'] %}
+        <h3><u>{{ lab['lab'] }}:</u></h3>
+            {% for kit in lab['kits'] %}
+            <p><b>{{ kit['name'] }}</b></p>
+                <p>     Plates: {{ kit['plate_count'] }}, Samples: {{ kit['sample_count'] }}, Cost: {{ "${:,.2f}".format(kit['cost']) }}</p>
+            {% endfor %}
+            <p><b>Lab total:</b></p>
+                <p>     Plates: {{ lab['total_plates'] }}, Samples: {{ lab['total_samples'] }}, Cost: {{ "${:,.2f}".format(lab['total_cost']) }}</p>
+        <br>
+        {% endfor %}
+    </body>
+</html>