hitpicking complete, pre-addition of WW-Arctic parsers and models.

CHANGELOG.md

@@ -1,3 +1,13 @@
+## 202305.05
+
+- Hitpicking now creates source plate map image.
+- Hitpick plate map is now included in exported plate results.
+
+## 202305.04
+
+- Added in hitpicking for plates with PCR results
+- Fixed error when expiry date stored as int in excel sheet.
+
 ## 202305.03
 
 - Added a detailed tab to the cost report.

README.md

@@ -62,3 +62,8 @@ This is meant to import .xslx files created from the Design & Analysis Software
 ## Linking PCR Logs:
 1. Click "Monthly" -> "Link PCR Logs".
 2. Chose the .csv file taken from the PCR table runlogs folder.
+
+## Hitpicking:
+1. Select all submissions you wish to hitpick using "Ctrl + click". All must have PCR results.
+2. Right click on the last sample and select "Hitpick" from the contex menu.
+3. Select location to save csv file.

TODO.md

@@ -1,3 +1,4 @@
+- [ ] Create a method for creation of hitpicking .csvs because of reasons that may or may not exist.
 - [x] Create a method for commenting submissions.
 - [x] Create barcode generator, because of reasons that may or may not exist.
 - [x] Move bulk of functions from frontend.__init__ to frontend.functions as __init__ is getting bloated.

alembic/versions/64fec6271a50_added_elution_well_to_ww_sample.py

@@ -0,0 +1,31 @@
+"""added elution well to ww_sample
+
+Revision ID: 64fec6271a50
+Revises: a31943b2284c
+Create Date: 2023-05-24 14:43:25.477637
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import sqlite
+
+# revision identifiers, used by Alembic.
+revision = '64fec6271a50'
+down_revision = 'a31943b2284c'
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
+        batch_op.add_column(sa.Column('elution_well', sa.String(length=8), nullable=True))
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table('_ww_samples', schema=None) as batch_op:
+        batch_op.drop_column('elution_well')
+    # ### end Alembic commands ###

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202305.3b"
+__version__ = "202305.4b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 
@@ -24,7 +24,7 @@ class bcolors:
 # Hello Landon, this is your past self here. I'm trying not to screw you over like I usually do, so I will
 # set out the workflow I've imagined for creating new submission types.
 # First of all, you will need to write new parsing methods in backend.excel.parser to pull information out of the submission form
-# for the submission itself as well as for any samples you can pull out of that same sheet.
+# for the submission itself as well as for any samples you can pull out of that same workbook.
 # Second, you will have to update the model in backend.db.models.submissions and provide a new polymorph to the BasicSubmission object.
 # The BSO should hold the majority of the general info.
 # You can also update any of the parsers to pull out any custom info you need, like enforcing RSL plate numbers, scraping PCR results, etc.

src/submissions/backend/db/functions.py

@@ -20,7 +20,6 @@ from getpass import getuser
 import numpy as np
 import yaml
 from pathlib import Path
-from math import ceil
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -136,7 +135,13 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
                 try:
                     field_value = lookup_kittype_by_name(ctx=ctx, name=q_str)
                 except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
-                    logger.error(f"Hit an integrity error: {e}")
+                    logger.error(f"Hit an integrity error looking up kit type: {e}")
+                    logger.error(f"Details: {e.__dict__}")
+                    if "submitter_plate_num" in e.__dict__['statement']:
+                        msg = "SQL integrity error. Submitter plate id is a duplicate or invalid."
+                    else:
+                        msg = "SQL integrity error of unknown origin."
+                    return instance, dict(code=2, message=msg)
                 logger.debug(f"Got {field_value} for kit {q_str}")
             case "submitting_lab":
                 q_str = info_dict[item].replace(" ", "_").lower()
@@ -179,7 +184,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         discounts = sum(discounts)
         instance.run_cost = instance.run_cost - discounts
     except Exception as e:
-        logger.error(f"An unknown exception occurred: {e}")
+        logger.error(f"An unknown exception occurred when calculating discounts: {e}")
     # We need to make sure there's a proper rsl plate number
     logger.debug(f"We've got a total cost of {instance.run_cost}")
     try:
@@ -748,9 +753,15 @@ def update_ww_sample(ctx:dict, sample_obj:dict):
     ww_samp = lookup_ww_sample_by_sub_sample_rsl(ctx=ctx, sample_rsl=sample_obj['sample'], plate_rsl=sample_obj['plate_rsl'])
     # ww_samp = lookup_ww_sample_by_sub_sample_well(ctx=ctx, sample_rsl=sample_obj['sample'], well_num=sample_obj['well_num'], plate_rsl=sample_obj['plate_rsl'])
     if ww_samp != None:
+        # del sample_obj['well_number']
         for key, value in sample_obj.items():
-            logger.debug(f"Setting {key} to {value}")
             # set attribute 'key' to 'value'
+            try:
+                check = getattr(ww_samp, key)
+            except AttributeError:
+                continue
+            if check == None:
+                logger.debug(f"Setting {key} to {value}")
                 setattr(ww_samp, key, value)
     else:
         logger.error(f"Unable to find sample {sample_obj['sample']}")
@@ -763,3 +774,28 @@ def lookup_discounts_by_org_and_kit(ctx:dict, kit_id:int, lab_id:int):
         models.KitType.id==kit_id, 
         models.Organization.id==lab_id
         )).all()
+
+
+def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list:
+    plate_dicto = []
+    for sample in submission.samples:
+        # have sample report back its info if it's positive, otherwise, None
+        samp = sample.to_hitpick()
+        if samp == None:
+            continue
+        else:
+            logger.debug(f"Item name: {samp['name']}")
+            # plate can handle 88 samples to leave column for controls
+            # if len(dicto) < 88:
+            this_sample = dict(
+                plate_number = plate_number,
+                sample_name = samp['name'],
+                column = samp['col'],
+                row = samp['row'],
+                plate_name = submission.rsl_plate_num
+            )
+            # append to plate samples
+            plate_dicto.append(this_sample)
+            # append to all samples
+    # image = make_plate_map(plate_dicto)
+    return plate_dicto

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

@@ -4,6 +4,9 @@ All models for individual samples.
 from . import Base
 from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, FLOAT, BOOLEAN, JSON
 from sqlalchemy.orm import relationship
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
 
 
 class WWSample(Base):
@@ -19,7 +22,7 @@ class WWSample(Base):
     rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
     rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
     collection_date = Column(TIMESTAMP) #: Date submission received
-    well_number = Column(String(8)) #: location on plate
+    well_number = Column(String(8)) #: location on 24 well plate
     # The following are fields from the sample tracking excel sheet Ruth put together.
     # I have no idea when they will be implemented or how.
     testing_type = Column(String(64)) 
@@ -33,6 +36,7 @@ class WWSample(Base):
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
     pcr_results = Column(JSON)
+    elution_well = Column(String(8)) #: location on 96 well plate
     
 
     def to_string(self) -> str:
@@ -51,6 +55,10 @@ class WWSample(Base):
         Returns:
             dict: well location and id NOTE: keys must sync with BCSample to_sub_dict below
         """
+        # well_col = self.well_number[1:]
+        # well_row = self.well_number[0]
+        # if well_col > 4:
+        #     well
         if self.ct_n1 != None and self.ct_n2 != None:
             name = f"{self.ww_sample_full_id}\n\t- ct N1: {'{:.2f}'.format(self.ct_n1)} ({self.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.ct_n2)} ({self.n2_status})"
         else:
@@ -60,6 +68,34 @@ class WWSample(Base):
             "name": name,
         }
     
+    def to_hitpick(self) -> dict|None:
+        """
+        Outputs a dictionary of locations if sample is positive
+
+        Returns:
+            dict: dictionary of sample id, row and column in elution plate
+        """        
+        # dictionary to translate row letters into numbers
+        row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
+        # if either n1 or n2 is positive, include this sample
+        try:
+            positive = any(["positive" in item for item in [self.n1_status, self.n2_status]])
+        except TypeError as e:
+            logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
+            return None
+        if positive:
+            try:
+                # The first character of the elution well is the row
+                well_row = row_dict[self.elution_well[0]]
+                # The remaining charagers are the columns
+                well_col = self.elution_well[1:]
+            except TypeError as e:
+                logger.error(f"This sample doesn't have elution plate info.")
+                return None
+            return dict(name=self.ww_sample_full_id, row=well_row, col=well_col)
+        else:
+            return None
+
 
 class BCSample(Base):
     """

src/submissions/backend/excel/parser.py

@@ -132,7 +132,10 @@ class SheetParser(object):
                         try:
                             expiry = row[3].date()
                         except AttributeError as e:
+                            try:
                                 expiry = datetime.strptime(row[3], "%Y-%m-%d")
+                            except TypeError as e:
+                                expiry = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + row[3] - 2)
                     else:
                         logger.debug(f"Date: {row[3]}")
                         expiry = date.today()
@@ -378,7 +381,7 @@ class PCRParser(object):
             self.samples_df['Assessment'] = well_call_df.values
         except ValueError:
             logger.error("Well call number doesn't match sample number")
-        logger.debug(f"Well call dr: {well_call_df}")
+        logger.debug(f"Well call df: {well_call_df}")
         # iloc is [row][column]
         for ii, row in self.samples_df.iterrows():
             try:
@@ -387,7 +390,7 @@ class PCRParser(object):
                 sample_obj = dict(
                     sample = row['Sample'],
                     plate_rsl = self.plate_num,
-                    well_num = row['Well Position']
+                    elution_well = row['Well Position']
                 )
             logger.debug(f"Got sample obj: {sample_obj}") 
             # logger.debug(f"row: {row}")

src/submissions/backend/excel/reports.py

@@ -213,3 +213,7 @@ def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
     return df
     # else:
     #     return df
+
+
+def make_hitpicks(input:list) -> DataFrame:
+    return DataFrame.from_records(input)

src/submissions/frontend/__init__.py

@@ -135,6 +135,7 @@ class App(QMainWindow):
         logger.debug(f"Attempting to open {url}")
         webbrowser.get('windows-default').open(f"file://{url.__str__()}")
 
+    # All main window functions return a result which is reported here, unless it is None
     def result_reporter(self, result:dict|None=None):
         if result != None:
             msg = AlertPop(message=result['message'], status=result['status'])
@@ -147,128 +148,6 @@ class App(QMainWindow):
         self, result = import_submission_function(self)
         logger.debug(f"Import result: {result}")
         self.result_reporter(result)
-        # logger.debug(self.ctx)
-        # # initialize samples
-        # self.samples = []
-        # self.reagents = {}
-        # # set file dialog
-        # home_dir = str(Path(self.ctx["directory_path"]))
-        # fname = Path(QFileDialog.getOpenFileName(self, 'Open file', home_dir)[0])
-        # logger.debug(f"Attempting to parse file: {fname}")
-        # assert fname.exists()
-        # # create sheetparser using excel sheet and context from gui
-        # try:
-        #     prsr = SheetParser(fname, **self.ctx)
-        # except PermissionError:
-        #     logger.error(f"Couldn't get permission to access file: {fname}")
-        #     return
-        # if prsr.sub['rsl_plate_num'] == None:
-        #     prsr.sub['rsl_plate_num'] = RSLNamer(fname.__str__()).parsed_name
-        # logger.debug(f"prsr.sub = {prsr.sub}")
-        # # destroy any widgets from previous imports
-        # for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
-        #     item.setParent(None)
-        # # regex to parser out different variable types for decision making
-        # variable_parser = re.compile(r"""
-        #     # (?x)
-        #     (?P<extraction_kit>^extraction_kit$) |
-        #     (?P<submitted_date>^submitted_date$) |
-        #     (?P<submitting_lab>)^submitting_lab$ |
-        #     (?P<samples>)^samples$ |
-        #     (?P<reagent>^lot_.*$) |
-        #     (?P<csv>^csv$)
-        # """, re.VERBOSE)
-        # for item in prsr.sub:
-        #     logger.debug(f"Item: {item}")
-        #     # attempt to match variable name to regex group
-        #     try:
-        #         mo = variable_parser.fullmatch(item).lastgroup
-        #     except AttributeError:
-        #         mo = "other"
-        #     logger.debug(f"Mo: {mo}")
-        #     match mo:
-        #         case 'submitting_lab':
-        #             # create label
-        #             self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-        #             logger.debug(f"{item}: {prsr.sub[item]}")
-        #             # create combobox to hold looked up submitting labs
-        #             add_widget = QComboBox()
-        #             labs = [item.__str__() for item in lookup_all_orgs(ctx=self.ctx)]
-        #             # try to set closest match to top of list
-        #             try:
-        #                 labs = difflib.get_close_matches(prsr.sub[item], labs, len(labs), 0)
-        #             except (TypeError, ValueError):
-        #                 pass
-        #             # set combobox values to lookedup values
-        #             add_widget.addItems(labs)
-        #         case 'extraction_kit':
-        #             # create label
-        #             self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-        #             # if extraction kit not available, all other values fail
-        #             if not check_not_nan(prsr.sub[item]):
-        #                 msg = AlertPop(message="Make sure to check your extraction kit in the excel sheet!", status="warning")
-        #                 msg.exec()
-        #             # create combobox to hold looked up kits
-        #             # add_widget = KitSelector(ctx=self.ctx, submission_type=prsr.sub['submission_type'], parent=self)
-        #             add_widget = QComboBox()
-        #             # add_widget.currentTextChanged.connect(self.kit_reload)
-        #             # lookup existing kits by 'submission_type' decided on by sheetparser
-        #             uses = [item.__str__() for item in lookup_kittype_by_use(ctx=self.ctx, used_by=prsr.sub['submission_type'])]
-        #             # if len(uses) > 0:
-        #             add_widget.addItems(uses)
-        #             # else:
-        #                 # add_widget.addItems(['bacterial_culture'])
-        #             if check_not_nan(prsr.sub[item]):
-        #                 self.ext_kit = prsr.sub[item]
-        #             else:
-        #                 self.ext_kit = add_widget.currentText()
-        #         case 'submitted_date':
-        #             # create label
-        #             self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-        #             # uses base calendar
-        #             add_widget = QDateEdit(calendarPopup=True)
-        #             # sets submitted date based on date found in excel sheet
-        #             try:
-        #                 add_widget.setDate(prsr.sub[item])
-        #             # if not found, use today
-        #             except:
-        #                 add_widget.setDate(date.today())
-        #         case 'reagent':
-        #             # create label
-        #             reg_label = QLabel(item.replace("_", " ").title())
-        #             reg_label.setObjectName(f"lot_{item}_label")
-        #             self.table_widget.formlayout.addWidget(reg_label)
-        #             # create reagent choice widget
-        #             add_widget = ImportReagent(ctx=self.ctx, item=item, prsr=prsr)
-        #             self.reagents[item] = prsr.sub[item]
-        #         case 'samples':
-        #             # hold samples in 'self' until form submitted
-        #             logger.debug(f"{item}: {prsr.sub[item]}")
-        #             self.samples = prsr.sub[item]
-        #             add_widget = None
-        #         case 'csv':
-        #             self.csv = prsr.sub[item]
-        #         case _:
-        #             # anything else gets added in as a line edit
-        #             self.table_widget.formlayout.addWidget(QLabel(item.replace("_", " ").title()))
-        #             add_widget = QLineEdit()
-        #             logger.debug(f"Setting widget text to {str(prsr.sub[item]).replace('_', ' ')}")
-        #             add_widget.setText(str(prsr.sub[item]).replace("_", " "))
-        #     try:
-        #         add_widget.setObjectName(item)
-        #         logger.debug(f"Widget name set to: {add_widget.objectName()}")
-        #         self.table_widget.formlayout.addWidget(add_widget)
-        #     except AttributeError as e:
-        #         logger.error(e)
-        # # compare self.reagents with expected reagents in kit
-        # if hasattr(self, 'ext_kit'):
-        #     self.kit_integrity_completion()
-        # # create submission button
-        # # submit_btn = QPushButton("Submit")
-        # # submit_btn.setObjectName("submit_btn")
-        # # self.table_widget.formlayout.addWidget(submit_btn)
-        # # submit_btn.clicked.connect(self.submit_new_sample)
-        # logger.debug(f"Imported reagents: {self.reagents}")
 
 
     def kit_reload(self):
@@ -277,16 +156,6 @@ class App(QMainWindow):
         """        
         self, result = kit_reload_function(self)
         self.result_reporter(result)
-        # for item in self.table_widget.formlayout.parentWidget().findChildren(QWidget):
-        #     # item.setParent(None)
-        #     if isinstance(item, QLabel):
-        #         if item.text().startswith("Lot"):
-        #             item.setParent(None)
-        #     else:
-        #         logger.debug(f"Type of {item.objectName()} is {type(item)}")
-        #         if item.objectName().startswith("lot_"):
-        #             item.setParent(None)
-        # self.kit_integrity_completion()
             
 
     def kit_integrity_completion(self):
@@ -297,26 +166,6 @@ class App(QMainWindow):
         """        
         self, result = kit_integrity_completion_function(self)
         self.result_reporter(result)
-        # logger.debug(inspect.currentframe().f_back.f_code.co_name)
-        # kit_widget = self.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
-        # logger.debug(f"Kit selector: {kit_widget}")
-        # self.ext_kit = kit_widget.currentText()
-        # logger.debug(f"Checking integrity of {self.ext_kit}")
-        # kit = lookup_kittype_by_name(ctx=self.ctx, name=self.ext_kit)
-        # reagents_to_lookup = [item.replace("lot_", "") for item in self.reagents]
-        # logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
-        # kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
-        # 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 = ImportReagent(ctx=self.ctx, item=item)
-        #         self.table_widget.formlayout.addWidget(add_widget)
-        # submit_btn = QPushButton("Submit")
-        # submit_btn.setObjectName("lot_submit_btn")
-        # self.table_widget.formlayout.addWidget(submit_btn)
-        # submit_btn.clicked.connect(self.submit_new_sample)
         
 
     def submit_new_sample(self):

src/submissions/frontend/custom_widgets/sub_details.py

@@ -3,6 +3,8 @@ Contains widgets specific to the submission summary and submission details.
 '''
 import base64
 from datetime import datetime
+from io import BytesIO
+import math
 from PyQt6 import QtPrintSupport
 from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QTableView,
@@ -10,16 +12,18 @@ from PyQt6.QtWidgets import (
     QMessageBox, QFileDialog, QMenu, QLabel,
     QDialogButtonBox, QToolBar, QMainWindow
 )
-from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
+from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel, QItemSelectionModel
 from PyQt6.QtGui import QFontMetrics, QAction, QCursor, QPixmap, QPainter
-from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num
+from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
+# from backend.misc import hitpick_plate
+from backend.excel import make_hitpicks
 from jinja2 import Environment, FileSystemLoader
 from xhtml2pdf import pisa
 import sys
 from pathlib import Path
 import logging
-from .pop_ups import QuestionAsker
+from .pop_ups import QuestionAsker, AlertPop
-from ..visualizations import make_plate_barcode
+from ..visualizations import make_plate_barcode, make_plate_map
 from getpass import getuser
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -92,6 +96,7 @@ class SubmissionsSheet(QTableView):
         self.resizeColumnsToContents()
         self.resizeRowsToContents()
         self.setSortingEnabled(True)
+        
         self.doubleClicked.connect(self.show_details)
  
     def setData(self) -> None: 
@@ -111,10 +116,8 @@ class SubmissionsSheet(QTableView):
             pass
         proxyModel = QSortFilterProxyModel()
         proxyModel.setSourceModel(pandasModel(self.data))
-        # self.model = pandasModel(self.data)
-        # self.setModel(self.model)
         self.setModel(proxyModel)
-        # self.resize(800,600)
+        
 
     def show_details(self) -> None:
         """
@@ -155,14 +158,17 @@ class SubmissionsSheet(QTableView):
         detailsAction = QAction('Details', self)
         barcodeAction = QAction("Print Barcode", self)
         commentAction = QAction("Add Comment", self)
+        hitpickAction = QAction("Hitpicks", self)
         renameAction.triggered.connect(lambda: self.delete_item(event))
         detailsAction.triggered.connect(lambda: self.show_details())
         barcodeAction.triggered.connect(lambda: self.create_barcode())
         commentAction.triggered.connect(lambda: self.add_comment())
+        hitpickAction.triggered.connect(lambda: self.hit_pick())
         self.menu.addAction(detailsAction)
         self.menu.addAction(renameAction)
         self.menu.addAction(barcodeAction)
         self.menu.addAction(commentAction)
+        self.menu.addAction(hitpickAction)
         # add other required actions
         self.menu.popup(QCursor.pos())
 
@@ -185,6 +191,62 @@ class SubmissionsSheet(QTableView):
         self.setData()
 
 
+    def hit_pick(self):
+        """
+        Extract positive samples from submissions with PCR results and export to csv.
+        NOTE: For this to work for arbitrary samples, positive samples must have 'positive' in their name
+        """        
+        # Get all selected rows
+        indices = self.selectionModel().selectedIndexes()
+        # convert to id numbers
+        indices = [index.sibling(index.row(), 0).data() for index in indices]
+        # biomek can handle 4 plates maximum
+        if len(indices) > 4:
+            logger.error(f"Error: Had to truncate number of plates to 4.")
+            indices = indices[:4]
+        # lookup ids in the database
+        subs = [lookup_submission_by_id(self.ctx, id) for id in indices]
+        # full list of samples
+        dicto = []
+        # list to contain plate images
+        images = []
+        for iii, sub in enumerate(subs):
+            # second check to make sure there aren't too many plates
+            if iii > 3: 
+                logger.error(f"Error: Had to truncate number of plates to 4.")
+                continue
+            plate_dicto = hitpick_plate(submission=sub, plate_number=iii+1)
+            if plate_dicto == None:
+                continue
+            image = make_plate_map(plate_dicto)
+            images.append(image)
+            for item in plate_dicto:
+                if len(dicto) < 94:
+                    dicto.append(item)
+                else:
+                    logger.error(f"We had to truncate the number of samples to 94.")
+        logger.debug(f"We found {len(dicto)} to hitpick")
+        msg = AlertPop(message=f"We found {len(dicto)} samples to hitpick", status="INFORMATION")
+        msg.exec()
+        # convert all samples to dataframe
+        df = make_hitpicks(dicto)
+        logger.debug(f"Size of the dataframe: {df.size}")
+        if df.size == 0:
+            return
+        date = datetime.strftime(datetime.today(), "%Y-%m-%d")
+        # ask for filename and save as csv.
+        home_dir = Path(self.ctx["directory_path"]).joinpath(f"Hitpicks_{date}.csv").resolve().__str__()
+        fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".csv")[0])
+        if fname.__str__() == ".":
+            logger.debug("Saving csv was cancelled.")
+            return
+        df.to_csv(fname.__str__(), index=False)
+        # show plate maps
+        for image in images:
+            try:
+                image.show()
+            except Exception as e:
+                logger.error(f"Could not show image: {e}.")
         
     
 class SubmissionDetails(QDialog):
@@ -239,7 +301,17 @@ class SubmissionDetails(QDialog):
         Renders submission to html, then creates and saves .pdf file to user selected file.
         """        
         template = env.get_template("submission_details.html")
+        # make barcode because, reasons
         self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
+        sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
+        plate_dicto = hitpick_plate(sub)
+        platemap = make_plate_map(plate_dicto)
+        logger.debug(f"platemap: {platemap}")
+        image_io = BytesIO()
+        platemap.save(image_io, 'JPEG')
+        platemap.save("test.jpg", 'JPEG')
+        self.base_dict['platemap'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
+        logger.debug(self.base_dict)
         html = template.render(sub=self.base_dict)
         home_dir = Path(self.ctx["directory_path"]).joinpath(f"Submission_Details_{self.base_dict['Plate Number']}.pdf").resolve().__str__()
         fname = Path(QFileDialog.getSaveFileName(self, "Save File", home_dir, filter=".pdf")[0])
@@ -269,18 +341,10 @@ class BarcodeWindow(QDialog):
         # creating label
         self.label = QLabel()
         self.img = make_plate_barcode(rsl_num)
-        # logger.debug(dir(img), img.contents[0])
-        # fp = BytesIO().read()
-        # img.save(formats=['png'], fnRoot=fp)
-        # pixmap = QPixmap("C:\\Users\\lwark\\Documents\\python\\submissions\\src\\Drawing000.png")
         self.pixmap = QPixmap()
-        # self.pixmap.loadFromData(self.img.asString("bmp"))
         self.pixmap.loadFromData(self.img)
         # adding image to label
         self.label.setPixmap(self.pixmap)
-        # Optional, resize label to image size
-        # self.label.resize(self.pixmap.width(), self.pixmap.height())
-        # self.label.resize(200, 200)
         # show all the widgets]
         QBtn = QDialogButtonBox.StandardButton.Ok | QDialogButtonBox.StandardButton.Cancel
         self.buttonBox = QDialogButtonBox(QBtn)
@@ -300,8 +364,6 @@ class BarcodeWindow(QDialog):
         adds items to menu bar
         """    
         toolbar = QToolBar("My main toolbar")
-        # self.addToolBar(toolbar)  
-        # self.layout.setToolBar(toolbar)  
         toolbar.addAction(self.printAction)
         
 
@@ -321,7 +383,6 @@ class BarcodeWindow(QDialog):
 
     def print_barcode(self):
         printer = QtPrintSupport.QPrinter()
-        
         dialog = QtPrintSupport.QPrintDialog(printer)
         if dialog.exec():
             self.handle_paint_request(printer, self.pixmap.toImage())

src/submissions/frontend/main_window_functions.py

@@ -41,15 +41,11 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]:
     result = None
-    # from .custom_widgets.misc import ImportReagent
-    # from .custom_widgets.pop_ups import AlertPop
     logger.debug(obj.ctx)
     # initialize samples
     obj.samples = []
     obj.reagents = {}
     # set file dialog
-    # home_dir = str(Path(obj.ctx["directory_path"]))
-    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir)[0])
     fname = select_open_file(obj, extension="xlsx")
     logger.debug(f"Attempting to parse file: {fname}")
     if not fname.exists():
@@ -69,7 +65,6 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
         item.setParent(None)
     # regex to parser out different variable types for decision making
     variable_parser = re.compile(r"""
-        # (?x)
         (?P<extraction_kit>^extraction_kit$) |
         (?P<submitted_date>^submitted_date$) |
         (?P<submitting_lab>)^submitting_lab$ |
@@ -161,13 +156,11 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
     if hasattr(obj, 'ext_kit'):
         obj.kit_integrity_completion()
     logger.debug(f"Imported reagents: {obj.reagents}")
-    
     return obj, result
 
 def kit_reload_function(obj:QMainWindow) -> QMainWindow:
     result = None
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
-        # item.setParent(None)
         if isinstance(item, QLabel):
             if item.text().startswith("Lot"):
                 item.setParent(None)
@@ -180,20 +173,22 @@ def kit_reload_function(obj:QMainWindow) -> QMainWindow:
 
 def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
     result = None
-    # from .custom_widgets.misc import ImportReagent
-    # from .custom_widgets.pop_ups import AlertPop
     logger.debug(inspect.currentframe().f_back.f_code.co_name)
+    # find the widget that contains lit info
     kit_widget = obj.table_widget.formlayout.parentWidget().findChild(QComboBox, 'extraction_kit')
     logger.debug(f"Kit selector: {kit_widget}")
+    # get current kit info
     obj.ext_kit = kit_widget.currentText()
     logger.debug(f"Checking integrity of {obj.ext_kit}")
+    # get the kit from database using current kit info
     kit = lookup_kittype_by_name(ctx=obj.ctx, name=obj.ext_kit)
+    # get all reagents stored in the QWindow object
     reagents_to_lookup = [item.replace("lot_", "") for item in obj.reagents]
     logger.debug(f"Reagents for lookup for {kit.name}: {reagents_to_lookup}")
+    # make sure kit contains all necessary info
     kit_integrity = check_kit_integrity(kit, reagents_to_lookup)
+    # if kit integrity comes back with an error, make widgets with missing reagents using default info
     if kit_integrity != None:
-        # msg = AlertPop(message=kit_integrity['message'], status="critical")
-        # msg.exec()
         result = dict(message=kit_integrity['message'], status="Warning")
         for item in kit_integrity['missing']:
             obj.table_widget.formlayout.addWidget(QLabel(f"Lot {item.replace('_', ' ').title()}"))
@@ -207,9 +202,9 @@ def kit_integrity_completion_function(obj:QMainWindow) -> QMainWindow:
 
 def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
     result = None
-    # from .custom_widgets.misc import ImportReagent
+    # extract info from the form widgets
-    # from .custom_widgets.pop_ups import AlertPop, QuestionAsker
     info = extract_form_info(obj.table_widget.tab1)
+    # seperate out reagents
     reagents = {k:v for k,v in info.items() if k.startswith("lot_")}
     info = {k:v for k,v in info.items() if not k.startswith("lot_")}
     logger.debug(f"Info: {info}")
@@ -268,12 +263,9 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
     # reset form
     for item in obj.table_widget.formlayout.parentWidget().findChildren(QWidget):
         item.setParent(None)
-    # print(dir(obj))
     if hasattr(obj, 'csv'):
         dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
         if dlg.exec():
-            # home_dir = Path(obj.ctx["directory_path"]).joinpath(f"{base_submission.rsl_plate_num}.csv").resolve().__str__()
-            # fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter=".csv")[0])
             fname = select_save_file(obj, f"{base_submission.rsl_plate_num}.csv", extension="csv")
             try:
                 obj.csv.to_csv(fname.__str__(), index=False)
@@ -282,8 +274,8 @@ def submit_new_sample_function(obj:QMainWindow) -> QMainWindow:
     return obj, result
 
 def generate_report_function(obj:QMainWindow) -> QMainWindow:
-    # from .custom_widgets import ReportDatePicker
     result = None
+    # ask for date ranges
     dlg = ReportDatePicker()
     if dlg.exec():
         info = extract_form_info(dlg)
@@ -324,8 +316,6 @@ def generate_report_function(obj:QMainWindow) -> QMainWindow:
 def add_kit_function(obj:QMainWindow) -> QMainWindow:
     result = None
     # setup file dialog to find yaml flie
-    # home_dir = str(Path(obj.ctx["directory_path"]))
-    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
     fname = select_open_file(obj, extension="yml")
     assert fname.exists()
     # read yaml file
@@ -340,19 +330,11 @@ def add_kit_function(obj:QMainWindow) -> QMainWindow:
         return
     # send to kit creator function
     result = create_kit_from_yaml(ctx=obj.ctx, exp=exp)
-    # match result['code']:
-    #     case 0:
-    #         msg = AlertPop(message=result['message'], status='info')
-    #     case 1:
-    #         msg = AlertPop(message=result['message'], status='critical')
-    # msg.exec()
     return obj, result
 
 def add_org_function(obj:QMainWindow) -> QMainWindow:
     result = None
     # setup file dialog to find yaml flie
-    # home_dir = str(Path(obj.ctx["directory_path"]))
-    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = "yml(*.yml)")[0])
     fname = select_open_file(obj, extension="yml")
     assert fname.exists()
     # read yaml file
@@ -367,12 +349,6 @@ def add_org_function(obj:QMainWindow) -> QMainWindow:
         return obj, result
     # send to kit creator function
     result = create_org_from_yaml(ctx=obj.ctx, org=org)
-    # match result['code']:
-    #     case 0:
-    #         msg = AlertPop(message=result['message'], status='information')
-    #     case 1:
-    #         msg = AlertPop(message=result['message'], status='critical')
-    # msg.exec()
     return obj, result
 
 def controls_getter_function(obj:QMainWindow) -> QMainWindow:
@@ -412,8 +388,18 @@ def controls_getter_function(obj:QMainWindow) -> QMainWindow:
     return obj, result
 
 def chart_maker_function(obj:QMainWindow) -> QMainWindow:
+    """
+    create html chart for controls reporting
+
+    Args:
+        obj (QMainWindow): original MainWindow
+
+    Returns:
+        QMainWindow: MainWindow with control display updates
+    """    
     result = None
     logger.debug(f"Control getter context: \n\tControl type: {obj.con_type}\n\tMode: {obj.mode}\n\tStart Date: {obj.start_date}\n\tEnd Date: {obj.end_date}")
+    # set the subtype for kraken
     if obj.table_widget.sub_typer.currentText() == "":
         obj.subtype = None
     else:
@@ -425,7 +411,7 @@ def chart_maker_function(obj:QMainWindow) -> QMainWindow:
     if controls == None:
         fig = None
     else:
-        # change each control to list of dicts
+        # change each control to list of dictionaries
         data = [control.convert_by_mode(mode=obj.mode) for control in controls]
         # flatten data to one dimensional list
         data = [item for sublist in data for item in sublist]
@@ -646,7 +632,8 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
     logger.debug(f"Existing {type(sub.pcr_info)}: {sub.pcr_info}")
     logger.debug(f"Inserting {type(json.dumps(parser.pcr))}: {json.dumps(parser.pcr)}")
     obj.ctx["database_session"].commit()
-    logger.debug(f"Got {len(parser.samples)} to update!")
+    logger.debug(f"Got {len(parser.samples)} samples to update!")
+    logger.debug(f"Parser samples: {parser.samples}")
     for sample in parser.samples:
         logger.debug(f"Running update on: {sample['sample']}")
         sample['plate_rsl'] = sub.rsl_plate_num
@@ -655,11 +642,3 @@ def import_pcr_results_function(obj:QMainWindow) -> QMainWindow:
     return obj, result
     # dlg.exec()    
 
-
-
-
-
-
-
-
-

src/submissions/frontend/visualizations/__init__.py

@@ -3,3 +3,4 @@ Contains all operations for creating charts, graphs and visual effects.
 '''
 from .control_charts import *
 from .barcode import *
+from .plate_map import *

src/submissions/frontend/visualizations/plate_map.py

@@ -0,0 +1,80 @@
+from pathlib import Path
+import sys
+from PIL import Image, ImageDraw, ImageFont
+import numpy as np
+from tools import check_if_app
+import logging
+
+logger = logging.getLogger(f"submissions.{__name__}")
+
+def make_plate_map(sample_list:list) -> Image:
+    """
+    Makes a pillow image of a plate from hitpicks 
+
+    Args:
+        sample_list (list): list of positive sample dictionaries from the hitpicks
+
+    Returns:
+        Image: Image of the 96 well plate with positive samples in red.
+    """  
+    # If we can't get a plate number, do nothing  
+    try:
+        plate_num = sample_list[0]['plate_name']
+    except IndexError as e:
+        logger.error(f"Couldn't get a plate number. Will not make plate.")
+        return None
+    except TypeError as e:
+        logger.error(f"No samples for this plate. Nothing to do.")
+        return None
+    # Make a 8 row, 12 column, 3 color ints array, filled with white by default
+    grid = np.full((8,12,3),255, dtype=np.uint8)
+    # Go through samples and change its row/column to red
+    for sample in sample_list:
+        grid[int(sample['row'])-1][int(sample['column'])-1] = [255,0,0]
+    # Create image from the grid
+    img = Image.fromarray(grid).resize((1200, 800), resample=Image.NEAREST)
+    # create a drawer over the image
+    draw = ImageDraw.Draw(img)
+    # draw grid over the image
+    y_start = 0
+    y_end = img.height
+    step_size = int(img.width / 12)
+    for x in range(0, img.width, step_size):
+        line = ((x, y_start), (x, y_end))
+        draw.line(line, fill=128)
+    x_start = 0
+    x_end = img.width
+    step_size = int(img.height / 8)
+    for y in range(0, img.height, step_size):
+        line = ((x_start, y), (x_end, y))
+        draw.line(line, fill=128)
+    del draw
+    old_size = img.size
+    new_size = (1300, 900)
+    # create a new, larger white image to hold the annotations
+    new_img = Image.new("RGB", new_size, "White")
+    box = tuple((n - o) // 2 for n, o in zip(new_size, old_size))
+    # paste plate map into the new image
+    new_img.paste(img, box)
+    # create drawer over the new image
+    draw = ImageDraw.Draw(new_img)
+    # font = ImageFont.truetype("sans-serif.ttf", 16)
+    if check_if_app():
+        font_path = Path(sys._MEIPASS).joinpath("files", "resources")
+    else:
+        font_path = Path(__file__).parents[2].joinpath('resources').absolute()
+        logger.debug(f"Font path: {font_path}")
+    font = ImageFont.truetype(font_path.joinpath('arial.ttf').__str__(), 32)
+    row_dict = ["A", "B", "C", "D", "E", "F", "G", "H"]
+    # write the plate number on the image
+    draw.text((100, 850),plate_num,(0,0,0),font=font)
+    # write column numbers
+    for num in range(1,13):
+        x = (num * 100) - 10
+        draw.text((x, 0), str(num), (0,0,0),font=font)
+    # write row letters
+    for num in range(1,9):
+        letter = row_dict[num-1]
+        y = (num * 100) - 10
+        draw.text((10, y), letter, (0,0,0),font=font)
+    return new_img

src/submissions/templates/submission_details.html

@@ -3,7 +3,7 @@
     <head>
         <title>Submission Details for {{ sub['Plate Number'] }}</title>
     </head>
-    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode'] %}
+    {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap'] %}
     <body>
         <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">
         <p>{% for key, value in sub.items() if key not in excluded %}
@@ -93,5 +93,9 @@
             {% endif %}
         {% endfor %}</p>
         {% endif %}
+        {% if sub['platemap'] %}
+        <h3><u>>Plate map:</u></h3>
+        <img height="300px" width="650px" src="data:image/jpeg;base64,{{ sub['platemap'] | safe }}">
+        {% endif %}
     </body>
 </html>

src/submissions/tools/__init__.py

@@ -92,14 +92,12 @@ def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None
     check = set(ext_kit_rtypes) == set(reagenttypes)
     logger.debug(f"Checking if reagents match kit contents: {check}")
     # what reagent types are in both lists?
-    # common = list(set(ext_kit_rtypes).intersection(reagenttypes))
     missing = list(set(ext_kit_rtypes).difference(reagenttypes))
     logger.debug(f"Missing reagents types: {missing}")
     # if lists are equal return no problem
     if len(missing)==0:
         result = None
     else:
-        # missing = [x for x in ext_kit_rtypes if x not in common]
         result = {'message' : f"The submission you are importing is missing some reagents expected by the kit.\n\nIt looks like you are missing: {[item.upper() for item in missing]}\n\nAlternatively, you may have set the wrong extraction kit.\n\nThe program will populate lists using existing reagents.\n\nPlease make sure you check the lots carefully!", 'missing': missing}
     return result
 
@@ -168,7 +166,6 @@ class RSLNamer(object):
     Object that will enforce proper formatting on RSL plate names.
     """
     def __init__(self, instr:str):
-        # self.parsed_name, self.submission_type = self.retrieve_rsl_number(instr)
         self.retrieve_rsl_number(in_str=instr)
         if self.submission_type != None:
             parser = getattr(self, f"enforce_{self.submission_type}")
@@ -195,12 +192,13 @@ class RSLNamer(object):
             return
         logger.debug(f"Attempting match of {in_str}")
         regex = re.compile(r"""
-            (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)R?\d(?!\d))?)|
+            (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?(?!\d)R?\d(?!\d))?)|
             (?P<bacterial_culture>RSL-?\d{2}-?\d{4})
             """, flags = re.IGNORECASE | re.VERBOSE)
         m = regex.search(in_str)
         try:
             self.parsed_name = m.group().upper()
+            logger.debug(f"Got parsed submission name: {self.parsed_name}")
             self.submission_type = m.lastgroup
         except AttributeError as e:
             logger.critical("No RSL plate number found or submission type found!")
@@ -210,11 +208,8 @@ class RSLNamer(object):
         """
         Uses regex to enforce proper formatting of wastewater samples
         """        
-        # self.parsed_name = re.sub(r"(\d)-(\d)", "\1\2", self.parsed_name)
-        # year = str(date.today().year)[:2]
         self.parsed_name = re.sub(r"PCR(-|_)", "", self.parsed_name)
         self.parsed_name = self.parsed_name.replace("RSLWW", "RSL-WW")
-            # .replace(f"WW{year}", f"WW-{year}")
         self.parsed_name = re.sub(r"WW(\d{4})", r"WW-\1", self.parsed_name, flags=re.IGNORECASE)
         self.parsed_name = re.sub(r"(\d{4})-(\d{2})-(\d{2})", r"\1\2\3", self.parsed_name)
 
@@ -222,14 +217,6 @@ class RSLNamer(object):
         """
         Uses regex to enforce proper formatting of bacterial culture samples
         """        
-        # year = str(date.today().year)[2:]
-        # self.parsed_name = self.parsed_name.replace(f"RSL{year}", f"RSL-{year}")
-        # reg_year = re.compile(fr"{year}(?P<rsl>\d\d\d\d)")
         self.parsed_name = re.sub(r"RSL(\d{2})", r"RSL-\1", self.parsed_name, flags=re.IGNORECASE)
         self.parsed_name = re.sub(r"RSL-(\d{2})(\d{4})", r"RSL-\1-\2", self.parsed_name, flags=re.IGNORECASE)
-        # year = regex.group('year')
+        
-        # rsl = regex.group('rsl')
-        # self.parsed_name = re.sub(fr"{year}(\d\d\d\d)", fr"{year}-\1", self.parsed_name)
-        # plate_search = reg_year.search(self.parsed_name)
-        # if plate_search != None:
-        #     self.parsed_name = re.sub(reg_year, f"{year}-{plate_search.group('rsl')}", self.parsed_name)