Moments before disaster

CHANGELOG.md

@@ -1,3 +1,8 @@
+## 202403.01
+
+- Added navigation in submission details to sample details.
+- Updated cost calculations.
+
 ## 202402.04
 
 - Addition of comments to gel box.

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

@@ -4,6 +4,7 @@ Contains all models for sqlalchemy
 import sys
 from sqlalchemy.orm import DeclarativeMeta, declarative_base, Query
 from sqlalchemy.ext.declarative import declared_attr
+# Load testing environment
 if 'pytest' in sys.modules:
     from pathlib import Path
     sys.path.append(Path(__file__).parents[4].absolute().joinpath("tests").__str__())

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

@@ -3,7 +3,7 @@ Models for the main submission types.
 '''
 from __future__ import annotations
 from getpass import getuser
-import math, json, logging, uuid, tempfile, re, yaml, base64
+import json, logging, uuid, tempfile, re, yaml, base64
 from zipfile import ZipFile
 from tempfile import TemporaryDirectory
 from reportlab.graphics.barcode import createBarcodeImageInMemory
@@ -237,6 +237,7 @@ class BasicSubmission(BaseClass):
                 self.run_cost = assoc.constant_cost + (assoc.mutable_cost_column * cols_count_96) + (assoc.mutable_cost_sample * int(self.sample_count))
             except Exception as e:
                 logger.error(f"Calculation error: {e}")
+        self.run_cost = round(self.run_cost, 2)
 
     def calculate_column_count(self) -> int:
         """
@@ -338,7 +339,7 @@ class BasicSubmission(BaseClass):
         logger.debug(f"Got {len(subs)} submissions.")
         df = pd.DataFrame.from_records(subs)
         # Exclude sub information
-        for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number']:
+        for item in ['controls', 'extraction_info', 'pcr_info', 'comment', 'comments', 'samples', 'reagents', 'equipment', 'gel_info', 'gel_image', 'dna_core_submission_number', 'source_plates']:
             try:
                 df = df.drop(item, axis=1)
             except:
@@ -873,8 +874,8 @@ class BasicSubmission(BaseClass):
         Returns:
             dict: dictionary of functions
         """        
-        names = ["Delete", "Details", "Add Comment", "Add Equipment", "Export"]
+        names = ["Delete", "Details", "Edit", "Add Comment", "Add Equipment", "Export"]
-        funcs = [self.delete, self.show_details, self.add_comment, self.add_equipment, self.backup]
+        funcs = [self.delete, self.show_details, self.edit, self.add_comment, self.add_equipment, self.backup]
         dicto = {item[0]:item[1] for item in zip(names, funcs)}
         return dicto
     
@@ -915,6 +916,15 @@ class BasicSubmission(BaseClass):
         if dlg.exec():
             pass
 
+    def edit(self, obj):
+        from frontend.widgets.submission_widget import SubmissionFormWidget
+        for widg in obj.app.table_widget.formwidget.findChildren(SubmissionFormWidget):
+            logger.debug(widg)
+            widg.setParent(None)
+        pyd = self.to_pydantic(backup=True)
+        form = pyd.toForm(parent=obj)
+        obj.app.table_widget.formwidget.layout().addWidget(form)
+
     def add_comment(self, obj):
         """
         Creates widget for adding comments to submissions
@@ -1300,25 +1310,6 @@ class WastewaterArtic(BasicSubmission):
                            polymorphic_load="inline", 
                            inherit_condition=(id == BasicSubmission.id))
 
-    def calculate_base_cost(self):
-        """
-        This method overrides parent method due to multiple output plates from a single submission
-        """        
-        logger.debug(f"Hello from calculate base cost in WWArtic")
-        try:
-            cols_count_96 = math.ceil(int(self.sample_count) / 8)
-        except Exception as e:
-            logger.error(f"Column count error: {e}")
-        assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type][0]
-        # Since we have multiple output plates per submission form, the constant cost will have to reflect this.
-        output_plate_count = math.ceil(int(self.sample_count) / 16)
-        logger.debug(f"Looks like we have {output_plate_count} output plates.")
-        const_cost = assoc.constant_cost * output_plate_count
-        try:
-            self.run_cost = const_cost + (assoc.mutable_cost_column * cols_count_96) + (assoc.mutable_cost_sample * int(self.sample_count))
-        except Exception as e:
-            logger.error(f"Calculation error: {e}")
-
     def to_dict(self, full_data:bool=False, backup:bool=False) -> dict:
         """
         Extends parent class method to add controls to dict
@@ -1859,7 +1850,7 @@ class BasicSample(BaseClass):
         Returns:
             Tuple(dict, Template): (Updated dictionary, Template to be rendered)
         """        
-        base_dict['excluded'] = ['submissions', 'excluded']
+        base_dict['excluded'] = ['submissions', 'excluded', 'colour', 'tooltip']
         env = jinja_template_loading()
         temp_name = f"{cls.__name__.lower()}_details.html"
         logger.debug(f"Returning template: {temp_name}")

src/submissions/frontend/widgets/submission_details.py

@@ -33,21 +33,10 @@ class SubmissionDetails(QDialog):
             self.app = parent.parent().parent().parent().parent().parent().parent()
         except AttributeError:
             self.app = None
-        self.setWindowTitle(f"Submission Details - {sub.rsl_plate_num}")
+        # self.setWindowTitle(f"Submission Details - {sub.rsl_plate_num}")
         # create scrollable interior
         interior = QScrollArea()
         interior.setParent(self)
-        # self.base_dict = sub.to_dict(full_data=True)
-        # logger.debug(f"Submission details data:\n{pformat({k:v for k,v in self.base_dict.items() if k != 'samples'})}")
-        # # don't want id
-        # del self.base_dict['id']
-        # logger.debug(f"Creating barcode.")
-        # if not check_if_app():
-        #     self.base_dict['barcode'] = base64.b64encode(sub.make_plate_barcode(width=120, height=30)).decode('utf-8')
-        # logger.debug(f"Making platemap...")
-        # self.base_dict['platemap'] = sub.make_plate_map()
-        # self.base_dict, self.template = sub.get_details_template(base_dict=self.base_dict)
-        # self.html = self.template.render(sub=self.base_dict)
         self.webview = QWebEngineView(parent=self)
         self.webview.setMinimumSize(900, 500)
         self.webview.setMaximumSize(900, 500)
@@ -80,6 +69,7 @@ class SubmissionDetails(QDialog):
         base_dict, template = sample.get_details_template(base_dict=base_dict)
         html = template.render(sample=base_dict)
         self.webview.setHtml(html)
+        self.setWindowTitle(f"Sample Details - {sample.submitter_id}")
         
     @pyqtSlot(str)
     def submission_details(self, submission:str|BasicSubmission):
@@ -104,6 +94,7 @@ class SubmissionDetails(QDialog):
         self.base_dict, self.template = submission.get_details_template(base_dict=self.base_dict)
         self.html = self.template.render(sub=self.base_dict)
         self.webview.setHtml(self.html)
+        self.setWindowTitle(f"Submission Details - {submission.rsl_plate_num}")
 
     def export(self):
         """
@@ -124,8 +115,6 @@ class SubmissionDetails(QDialog):
         self.base_dict['export_map'] = base64.b64encode(image_io.getvalue()).decode('utf-8')
         del self.base_dict['platemap']
         self.html2 = self.template.render(sub=self.base_dict)
-        with open("test.html", "w") as fw:
-            fw.write(self.html2)
         try:
             with open(fname, "w+b") as f:
                 pisa.CreatePDF(self.html2, dest=f)

src/submissions/frontend/widgets/submission_widget.py

@@ -148,11 +148,11 @@ class SubmissionFormContainer(QWidget):
         logger.debug(f"Pydantic result: \n\n{pformat(self.pyd)}\n\n")
         self.form = self.pyd.toForm(parent=self)
         self.layout().addWidget(self.form)
-        kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
+        # kit_widget = self.form.find_widgets(object_name="extraction_kit")[0].input
-        logger.debug(f"Kitwidget {kit_widget}")
+        # logger.debug(f"Kitwidget {kit_widget}")
-        self.scrape_reagents(kit_widget.currentText())
+        # self.scrape_reagents(kit_widget.currentText())
-        kit_widget.currentTextChanged.connect(self.scrape_reagents)
+        # kit_widget.currentTextChanged.connect(self.scrape_reagents)
-        # compare obj.reagents with expected reagents in kit
+        # # compare obj.reagents with expected reagents in kit
         if self.prsr.sample_result != None:
             report.add_result(msg=self.prsr.sample_result, status="Warning")
         self.report.add_result(report)
@@ -220,7 +220,8 @@ class SubmissionFormContainer(QWidget):
         for reagent in self.form.reagents:
             logger.debug(f"Creating widget for {reagent}")
             add_widget = ReagentFormWidget(parent=self, reagent=reagent, extraction_kit=self.ext_kit)
-            self.form.layout().addWidget(add_widget)
+            # self.form.layout().addWidget(add_widget)
+            self.form.layout.addWidget(add_widget)
             if reagent.missing:
                 missing_reagents.append(reagent)
         logger.debug(f"Checking integrity of {self.ext_kit}")
@@ -397,15 +398,15 @@ class SubmissionFormWidget(QWidget):
         super().__init__(parent)
         self.ignore = ['filepath', 'samples', 'reagents', 'csv', 'ctx', 'comment', 'equipment', 'source_plates']
         self.recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
-        layout = QVBoxLayout()
+        self.layout = QVBoxLayout()
         for k, v in kwargs.items():
             if k not in self.ignore:
                 add_widget = self.create_widget(key=k, value=v, submission_type=kwargs['submission_type'])
                 if add_widget != None:
-                    layout.addWidget(add_widget)
+                    self.layout.addWidget(add_widget)
             else:
                 setattr(self, k, v)
-        self.setLayout(layout)
+        self.setLayout(self.layout)
 
     def create_widget(self, key:str, value:dict, submission_type:str|None=None) -> "self.InfoItem":
         """
@@ -420,7 +421,15 @@ class SubmissionFormWidget(QWidget):
             self.InfoItem: Form widget to hold name:value
         """        
         if key not in self.ignore:
-            return self.InfoItem(self, key=key, value=value, submission_type=submission_type)
+            widget = self.InfoItem(self, key=key, value=value, submission_type=submission_type)
+            # match key:
+            #     case "extraction_kit":
+            #         # compare obj.reagents with expected reagents in kit
+            #         self.scrape_reagents(widget.currentText())
+            #         widget.currentTextChanged.connect(self.scrape_reagents)
+            #     case _:
+            #         pass
+            return widget
         return None
         
     def clear_form(self):