Updating AddEdit to hopefully include ReagentAdd

CHANGELOG.md

@@ -1,3 +1,11 @@
+# 202501.02
+
+- Fixed bug where Wastewater ENs were not receiving rsl_number and therefore not getting PCR data.
+
+# 202501.01
+
+- Created Client Manager to be run by super users.
+
 # 202412.06
 
 - Switched startup/teardown scripts to importlib/getattr addition to ctx.

TODO.md

@@ -1,3 +1,4 @@
+- [ ] Find a way to merge AddEdit with ReagentAdder
 - [x] Find a way to merge omni_search and sample_search
 - [x] Allow parsing of custom fields to a json 'custom' field in _basicsubmissions
 - [x] Upgrade to generators when returning lists.

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

@@ -608,7 +608,7 @@ class Reagent(BaseClass, LogMixin):
                         if isinstance(value, str):
                             field_value = datetime.strptime(value, "%Y-%m-%d")
                         elif isinstance(value, date):
-                            field_value = datetime.combine(value, datetime.min.time())
+                            field_value = datetime.combine(value, datetime.max.time())
                         else:
                             field_value = value
                         field_value.replace(tzinfo=timezone)

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

@@ -1502,6 +1502,25 @@ class Wastewater(BasicSubmission):
                     logger.error(f"Error handling couldn't get csv due to: {e}")
         return input_dict
 
+    @classmethod
+    def parse_samples(cls, input_dict: dict) -> dict:
+        """
+        Update sample dictionary with type specific information. Extends parent
+
+        Args:
+            input_dict (dict): Input sample dictionary
+
+        Returns:
+            dict: Updated sample dictionary
+        """
+        input_dict = super().parse_samples(input_dict=input_dict)
+        # NOTE: Had to put in this section due to ENs not having rsl_number and therefore not getting PCR results.
+        check = check_key_or_attr("rsl_number", input_dict)
+        if not check:
+            input_dict['rsl_number'] = input_dict['submitter_id']
+        # logger.debug(pformat(input_dict, indent=4))
+        return input_dict
+
     @classmethod
     def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> Generator[dict, None, None]:
         """
@@ -1633,6 +1652,7 @@ class Wastewater(BasicSubmission):
         self.save(original=False)
         for sample in self.samples:
             try:
+                # NOTE: Fix for ENs which have no rsl_number...
                 sample_dict = next(item for item in pcr_samples if item['sample'] == sample.rsl_number)
             except StopIteration:
                 continue
@@ -2539,7 +2559,7 @@ class WastewaterSample(BasicSample):
         Custom sample parser. Extends parent
 
         Args:
-            input_dict (dict): Basic parser results.
+            input_dict (dict): Basic parser results for this sample.
 
         Returns:
             dict: Updated parser results.
@@ -2554,6 +2574,8 @@ class WastewaterSample(BasicSample):
             output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_num']
         if output_dict['ww_full_sample_id'] is not None and output_dict["submitter_id"] in disallowed:
             output_dict["submitter_id"] = output_dict['ww_full_sample_id']
+        check = check_key_or_attr("rsl_number", output_dict, check_none=True)
+        # logger.debug(pformat(output_dict, indent=4))
         return output_dict
 
     @classmethod

src/submissions/backend/validators/pydant.py

@@ -144,7 +144,9 @@ class PydReagent(BaseModel):
                     case "expiry":
                         if isinstance(value, str):
                             value = date(year=1970, month=1, day=1)
-                        value = datetime.combine(value, datetime.min.time())
+                        # NOTE: if min time is used, any reagent set to expire today (Bac postive control, eg) will have expired at midnight and therefore be flagged.
+                        # NOTE: Make expiry at date given, plus now time + 1 hour
+                        value = datetime.combine(value, datetime.max.time())
                         reagent.expiry = value.replace(tzinfo=timezone)
                     case _:
                         try:
@@ -826,7 +828,7 @@ class PydSubmission(BaseModel, extra='allow'):
                 case item if item in instance.timestamps():
                     logger.warning(f"Incoming timestamp key: {item}, with value: {value}")
                     if isinstance(value, date):
-                        value = datetime.combine(value, datetime.min.time())
+                        value = datetime.combine(value, datetime.max.time())
                         value = value.replace(tzinfo=timezone)
                     elif isinstance(value, str):
                         value: datetime = datetime.strptime(value, "%Y-%m-%d")
@@ -961,7 +963,7 @@ class PydSubmission(BaseModel, extra='allow'):
             if reagent not in exempt:
                 role_expiry = ReagentRole.query(name=reagent.role).eol_ext
                 try:
-                    dt = datetime.combine(reagent.expiry, datetime.min.time())
+                    dt = datetime.combine(reagent.expiry, datetime.max.time())
                 except TypeError:
                     continue
                 if datetime.now() > dt + role_expiry:

src/submissions/frontend/widgets/app.py

@@ -117,7 +117,7 @@ class App(QMainWindow):
         connect menu and tool bar item to functions
         """
         self.importAction.triggered.connect(self.table_widget.formwidget.importSubmission)
-        self.addReagentAction.triggered.connect(self.table_widget.formwidget.add_reagent)
+        self.addReagentAction.triggered.connect(self.table_widget.formwidget.new_add_reagent)
         self.joinExtractionAction.triggered.connect(self.table_widget.sub_wid.link_extractions)
         self.joinPCRAction.triggered.connect(self.table_widget.sub_wid.link_pcr)
         self.helpAction.triggered.connect(self.showAbout)

src/submissions/frontend/widgets/omni_add_edit.py

@@ -1,3 +1,4 @@
+from datetime import date
 from typing import Any
 
 from PyQt6.QtWidgets import (
@@ -12,7 +13,7 @@ logger = logging.getLogger(f"submissions.{__name__}")
 
 class AddEdit(QDialog):
 
-    def __init__(self, parent, instance: Any):
+    def __init__(self, parent, instance: Any|None=None):
         super().__init__(parent)
         self.instance = instance
         self.object_type = instance.__class__
@@ -22,13 +23,16 @@ class AddEdit(QDialog):
         self.buttonBox = QDialogButtonBox(QBtn)
         self.buttonBox.accepted.connect(self.accept)
         self.buttonBox.rejected.connect(self.reject)
-        fields = {k: v for k, v in self.object_type.__dict__.items() if
+        # fields = {k: v for k, v in self.object_type.__dict__.items() if
-                  isinstance(v, InstrumentedAttribute) and k != "id"}
+        #           isinstance(v, InstrumentedAttribute) and k != "id"}
+        fields = {k: v for k, v in self.object_type.__dict__.items() if k != "id"}
         for key, field in fields.items():
+            logger.debug(f"")
             try:
                 widget = EditProperty(self, key=key, column_type=field.property.expression.type,
                                           value=getattr(self.instance, key))
-            except AttributeError:
+            except AttributeError as e:
+                logger.error(f"Problem setting widget {key}: {e}")
                 continue
             self.layout.addWidget(widget, self.layout.rowCount(), 0)
         self.layout.addWidget(self.buttonBox)
@@ -62,14 +66,19 @@ class EditProperty(QWidget):
         self.setObjectName(key)
         match column_type:
             case String():
+                if not value:
+                    value = ""
                 self.widget = QLineEdit(self)
                 self.widget.setText(value)
             case TIMESTAMP():
-                self.widget = QDateEdit(self)
+                self.widget = QDateEdit(self, calendarPopup=True)
+                if not value:
+                    value = date.today()
                 self.widget.setDate(value)
             case _:
                 logger.error(f"{column_type} not a supported type.")
                 self.widget = None
+                return
         self.layout.addWidget(self.widget, 0, 1, 1, 3)
         self.setLayout(self.layout)
 

src/submissions/frontend/widgets/submission_widget.py

@@ -19,6 +19,7 @@ from backend.db import (
 from pprint import pformat
 from .pop_ups import QuestionAsker, AlertPop
 from .misc import AddReagentForm
+from .omni_add_edit import AddEdit
 from typing import List, Tuple
 from datetime import date
 
@@ -139,6 +140,15 @@ class SubmissionFormContainer(QWidget):
         self.layout().addWidget(self.form)
         return report
 
+
+    def new_add_reagent(self):
+        instance = Reagent()
+        dlg = AddEdit(parent=self, instance=instance)
+        if dlg.exec():
+            obj = dlg.parse_form()
+            print(obj)
+
+
     @report_result
     def add_reagent(self, reagent_lot: str | None = None, reagent_role: str | None = None, expiry: date | None = None,
                     name: str | None = None, kit: str | KitType | None = None) -> Tuple[PydReagent, Report]:

src/submissions/tools/__init__.py

@@ -449,7 +449,10 @@ class Settings(BaseSettings, extra="allow"):
 
     def set_from_db(self):
         if 'pytest' in sys.modules:
-            output = dict(power_users=['lwark', 'styson', 'ruwang'])
+            output = dict(power_users=['lwark', 'styson', 'ruwang'],
+                          startup_scripts=dict(hello=None),
+                          teardown_scripts=dict(goodbye=None)
+                          )
         else:
             # print(f"Hello from database settings getter.")
             # print(self.__dict__)