Troubleshooting reports

src/submissions/__init__.py

@@ -1,4 +1,6 @@
 # __init__.py
 
 # Version of the realpython-reader package
-__version__ = "1.3.0"
+__version__ = "202302.3b"
+__author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
+__copyright__ = "2022-2023, Government of Canada"

src/submissions/backend/db/__init__.py

@@ -15,7 +15,9 @@ import json
 # from dateutil.relativedelta import relativedelta
 from getpass import getuser
 import numpy as np
-from tools import check_not_nan
+from tools import check_not_nan, check_is_power_user
+import yaml
+from pathlib import Path
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -367,7 +369,8 @@ def lookup_org_by_name(ctx:dict, name:str|None) -> models.Organization:
         models.Organization: retrieved organization
     """    
     logger.debug(f"Querying organization: {name}")
-    return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
+    # return ctx['database_session'].query(models.Organization).filter(models.Organization.name==name).first()
+    return ctx['database_session'].query(models.Organization).filter(models.Organization.name.startswith(name)).first()
 
 def submissions_to_df(ctx:dict, sub_type:str|None=None) -> pd.DataFrame:
     """
@@ -457,13 +460,10 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> dict:
     Returns:
         dict: a dictionary containing results of db addition
     """    
-    try:
+    # try:
-        power_users = ctx['power_users']
+    #     power_users = ctx['power_users']
-    except KeyError:
+    # except KeyError:
-        logger.debug("This user does not have permission to add kits.")
+    if not check_is_power_user(ctx=ctx):
-        return {'code':1,'message':"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:
@@ -499,13 +499,14 @@ def create_org_from_yaml(ctx:dict, org:dict) -> dict:
     Returns:
         dict: dictionary containing results of db addition
     """    
-    try:
+    # try:
-        power_users = ctx['power_users']
+    #     power_users = ctx['power_users']
-    except KeyError:
+    # except KeyError:
-        logger.debug("This user does not have permission to add kits.")
+    #     logger.debug("This user does not have permission to add kits.")
-        return {'code':1,'message':"This user does not have permission to add organizations."}
+    #     return {'code':1,'message':"This user does not have permission to add organizations."}
-    logger.debug(f"Adding organization for user: {getuser()}")
+    # logger.debug(f"Adding organization for user: {getuser()}")
-    if getuser() not in power_users:
+    # if getuser() not in power_users:
+    if not check_is_power_user(ctx=ctx):
         logger.debug(f"{getuser()} does not have permission to add kits.")
         return {'code':1, 'message':"This user does not have permission to add organizations."}
     for client in org:
@@ -624,3 +625,23 @@ def lookup_submission_by_rsl_num(ctx:dict, rsl_num:str):
 
 def lookup_submissions_using_reagent(ctx:dict, reagent:models.Reagent) -> list[models.BasicSubmission]:
     return ctx['database_session'].query(models.BasicSubmission).join(reagents_submissions).filter(reagents_submissions.c.reagent_id==reagent.id).all()
+
+
+def delete_submission_by_id(ctx:dict, id:int) -> None:
+    """
+    Deletes a submission and its associated samples from the database.
+
+    Args:
+        ctx (dict): settings passed down from gui
+        id (int): id of submission to be deleted.
+    """    
+    # In order to properly do this Im' going to have to delete all of the secondary table stuff as well.
+    sub = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.id==id).first()
+    backup = sub.to_dict()
+    with open(Path(ctx['backup_path']).joinpath(f"{sub.rsl_plate_num}-backup({date.today().strftime('%Y%m%d')}).yml"), "w") as f:
+        yaml.dump(backup, f)
+    sub.reagents = []
+    for sample in sub.samples:
+        ctx['database_session'].delete(sample)
+    ctx["database_session"].delete(sub)
+    ctx["database_session"].commit()

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

@@ -74,6 +74,14 @@ class BasicSubmission(Base):
             ext_info = json.loads(self.extraction_info)
         except TypeError:
             ext_info = None
+        try:
+            reagents = [item.to_sub_dict() for item in self.reagents]
+        except:
+            reagents = None
+        try:
+            samples = [item.to_sub_dict() for item in self.samples]
+        except:
+            samples = None
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
@@ -85,6 +93,8 @@ class BasicSubmission(Base):
             "Extraction Kit": ext_kit,
             "Technician": self.technician,
             "Cost": self.run_cost,
+            "reagents": reagents,
+            "samples": samples,
             "ext_info": ext_info
         }
         # logger.debug(f"{self.rsl_plate_num} extraction: {output['Extraction Status']}")

src/submissions/backend/excel/parser.py

@@ -187,14 +187,18 @@ class SheetParser(object):
                 if not isinstance(row[5], float) and check_not_nan(row[5]):
                     # must be prefixed with 'lot_' to be recognized by gui
                     # regex below will remove 80% from 80% ethanol in the Wastewater kit.
-                    output_key = re.sub(r"\d{1,3}%", "", row[0].lower().strip().replace(' ', '_'))
+                    output_key = re.sub(r"^\d{1,3}%\s?", "", row[0].lower().strip().replace(' ', '_'))
+                    output_key = output_key.strip("_")
                     try:
                         output_var = row[5].upper()
                     except AttributeError:
                         logger.debug(f"Couldn't upperize {row[5]}, must be a number")
                         output_var = row[5]
                     if check_not_nan(row[7]):
+                        try:
                             expiry = row[7].date()
+                        except AttributeError:
+                            expiry = date.today()
                     else:
                         expiry = date.today()
                     self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}

src/submissions/backend/excel/reports.py

@@ -41,6 +41,9 @@ def make_report_xlsx(records:list[dict]) -> DataFrame:
     # 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 split_row_item(item:str) -> float:
+#     return item.split(" ")[-1]
+
 
 def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     
@@ -59,17 +62,23 @@ def make_report_html(df:DataFrame, start_date:date, end_date:date) -> str:
     output = []
     logger.debug(f"Report DataFrame: {df}")
     for ii, row in enumerate(df.iterrows()):
-        row = [item for item in row]
+        # row = [item for item in row]
-        logger.debug(f"Row: {row}")
+        logger.debug(f"Row {ii}: {row}")
-        
         lab = row[0][0]
+        logger.debug(type(row))
         logger.debug(f"Old lab: {old_lab}, Current lab: {lab}")
-        kit = dict(name=row[0][1], cost=row[1]['Cost'], plate_count=int(row[1]['Kit Count']), sample_count=int(row[1]['Sample Count']))
+        logger.debug(f"Name: {row[0][1]}")
+        data = [item for item in row[1]]
+        # logger.debug(data)
+        # logger.debug(f"Cost: {split_row_item(data[1])}")
+        # logger.debug(f"Kit count: {split_row_item(data[0])}")
+        # logger.debug(f"Sample Count: {split_row_item(data[2])}")
+        kit = dict(name=row[0][1], cost=data[1], plate_count=int(data[0]), sample_count=int(data[2]))
         if lab == old_lab:
-            output[ii-1]['kits'].append(kit)
+            output[-1]['kits'].append(kit)
-            output[ii-1]['total_cost'] += kit['cost']
+            output[-1]['total_cost'] += kit['cost']
-            output[ii-1]['total_samples'] += kit['sample_count']
+            output[-1]['total_samples'] += kit['sample_count']
-            output[ii-1]['total_plates'] += kit['plate_count']
+            output[-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)

src/submissions/frontend/__init__.py

@@ -52,7 +52,7 @@ class App(QMainWindow):
         super().__init__()
         self.ctx = ctx
         try:
-            self.title = f"Submissions App (v{ctx['package'].__version__})"
+            self.title = f"Submissions App (v{ctx['package'].__version__}) - {ctx['database']}"
         except AttributeError:
             self.title = f"Submissions App"
         # set initial app position and size
@@ -85,6 +85,7 @@ class App(QMainWindow):
         reportMenu = menuBar.addMenu("&Reports")
         maintenanceMenu = menuBar.addMenu("&Monthly")
         helpMenu = menuBar.addMenu("&Help")
+        helpMenu.addAction(self.helpAction)
         fileMenu.addAction(self.importAction)
         reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinControlsAction)
@@ -111,6 +112,7 @@ class App(QMainWindow):
         self.addOrgAction = QAction("Add Org", self)
         self.joinControlsAction = QAction("Link Controls")
         self.joinExtractionAction = QAction("Link Ext Logs")
+        self.helpAction = QAction("&About", self)
 
 
     def _connectActions(self):
@@ -128,6 +130,12 @@ class App(QMainWindow):
         self.table_widget.datepicker.end_date.dateChanged.connect(self._controls_getter)
         self.joinControlsAction.triggered.connect(self.linkControls)
         self.joinExtractionAction.triggered.connect(self.linkExtractions)
+        self.helpAction.triggered.connect(self.showAbout)
+
+    def showAbout(self):
+        output = f"Version: {self.ctx['package'].__version__}\n\nAuthor: {self.ctx['package'].__author__['name']} - {self.ctx['package'].__author__['email']}\n\nCopyright: {self.ctx['package'].__copyright__}"
+        about = AlertPop(message=output, status="information")
+        about.exec()
 
 
     def importSubmission(self):

src/submissions/frontend/custom_widgets/sub_details.py

@@ -2,17 +2,19 @@ from datetime import date
 from PyQt6.QtWidgets import (
     QVBoxLayout, QDialog, QTableView,
     QTextEdit, QPushButton, QScrollArea, 
-    QMessageBox, QFileDialog
+    QMessageBox, QFileDialog, QMenu
 )
 from PyQt6.QtCore import Qt, QAbstractTableModel
-from PyQt6.QtGui import QFontMetrics
+from PyQt6.QtGui import QFontMetrics, QAction, QCursor
 
-from backend.db import submissions_to_df, lookup_submission_by_id, lookup_all_sample_types, create_kit_from_yaml
+from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id
 from jinja2 import Environment, FileSystemLoader
 from xhtml2pdf import pisa
 import sys
 from pathlib import Path
 import logging
+from .pop_ups import AlertPop, QuestionAsker
+from tools import check_is_power_user
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -91,6 +93,14 @@ class SubmissionsSheet(QTableView):
         sets data in model
         """        
         self.data = submissions_to_df(ctx=self.ctx)
+        try:
+            del self.data['samples']
+        except KeyError:
+            pass
+        try:
+            del self.data['reagents']
+        except KeyError:
+            pass
         self.model = pandasModel(self.data)
         self.setModel(self.model)
         # self.resize(800,600)
@@ -108,6 +118,34 @@ class SubmissionsSheet(QTableView):
             pass
 
 
+    def contextMenuEvent(self, event):
+        self.menu = QMenu(self)
+        renameAction = QAction('Delete', self)
+        detailsAction = QAction('Details', self)
+        # Originally I intended to limit deletions to power users.
+        # renameAction.setEnabled(False)
+        # if check_is_power_user(ctx=self.ctx):
+        #     renameAction.setEnabled(True)
+        renameAction.triggered.connect(lambda: self.delete_item(event))
+        detailsAction.triggered.connect(lambda: self.show_details())
+        self.menu.addAction(detailsAction)
+        self.menu.addAction(renameAction)
+        # add other required actions
+        self.menu.popup(QCursor.pos())
+
+
+    def delete_item(self, event):
+        index = (self.selectionModel().currentIndex())
+        value = index.sibling(index.row(),0).data()
+        logger.debug(index)
+        msg = QuestionAsker(title="Delete?", message=f"Are you sure you want to delete {index.sibling(index.row(),1).data()}?\n")
+        if msg.exec():
+            delete_submission_by_id(ctx=self.ctx, id=value)
+        else:
+            return
+        self.setData()
+
+
 
     
 class SubmissionDetails(QDialog):
@@ -130,8 +168,8 @@ class SubmissionDetails(QDialog):
         # don't want id
         del self.base_dict['id']
         # convert sub objects to dicts
-        self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
+        # self.base_dict['reagents'] = [item.to_sub_dict() for item in data.reagents]
-        self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
+        # self.base_dict['samples'] = [item.to_sub_dict() for item in data.samples]
         # retrieve jinja template
         template = env.get_template("submission_details.txt")
         # render using object dict

src/submissions/templates/submission_details.html

@@ -20,6 +20,7 @@
                 &nbsp;&nbsp;&nbsp;&nbsp;{{ item['type'] }}: {{ item['lot'] }} (EXP: {{ item['expiry'] }})<br>
             {% endif %}
         {% endfor %}</p>
+        {% if sub['samples'] %}
         <h3><u>Samples:</u></h3>
         <p>{% for item in sub['samples'] %}
             {% if loop.index == 1 %}
@@ -28,6 +29,7 @@
                 &nbsp;&nbsp;&nbsp;&nbsp;{{ item['well'] }}: {{ item['name'] }}<br>
             {% endif %}
         {% endfor %}</p>
+        {% endif %}
         {% if sub['controls'] %}
         <h3><u>Attached Controls:</u></h3>
         {% for item in sub['controls'] %}

src/submissions/templates/submission_details.txt

@@ -6,10 +6,10 @@
 Reagents:
 {% for item in sub['reagents'] %}
     {{ item['type'] }}: {{ item['lot'] }} (EXP: {{ item['expiry'] }}){% endfor %}
-    
+{% if sub['samples']%}
 Samples:
 {% for item in sub['samples'] %}
-    {{ item['well'] }}: {{ item['name'] }}{% endfor %}
+    {{ item['well'] }}: {{ item['name'] }}{% endfor %}{% endif %}
 {% if sub['controls'] %}
 Attached Controls:
 {% for item in sub['controls'] %}

src/submissions/tools/__init__.py

@@ -1,5 +1,6 @@
 import numpy as np
 import logging
+import getpass
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -11,3 +12,14 @@ def check_not_nan(cell_contents) -> bool:
     except Exception as e:
         logger.debug(f"Check encounteded unknown error: {type(e).__name__} - {e}")
         return False
+
+
+def check_is_power_user(ctx:dict) -> bool:
+    try:
+        check = getpass.getuser() in ctx['power_users']
+    except KeyError as e:
+        check = False
+    except Exception as e:
+        logger.debug(f"Check encounteded unknown error: {type(e).__name__} - {e}")
+        check = False
+    return check