Automated Control lot retrieval

TODO.md

@@ -1,3 +1,5 @@
+- [ ] Fix Parsed/Missing mix ups.
+- [x] Have sample parser check for controls and add to reagents?
 - [x] Update controls to NestedMutableJson
 - [x] Appending of qPCR results to WW not saving. Find out why.
     - Possibly due to immutable JSON? But... it's worked before... Right?

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

@@ -5,7 +5,7 @@ from __future__ import annotations
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey
 from sqlalchemy.orm import relationship, Query
 from sqlalchemy_json import NestedMutableJson
-import logging
+import logging, re
 from operator import itemgetter
 from . import BaseClass
 from tools import setup_lookup
@@ -25,6 +25,9 @@ class ControlType(BaseClass):
     targets = Column(JSON) #: organisms checked for
     instances = relationship("Control", back_populates="controltype") #: control samples created of this type.
 
+    def __repr__(self) -> str:
+        return f"<ControlType({self.name})>"
+
     @classmethod
     @setup_lookup
     def query(cls, 
@@ -74,6 +77,16 @@ class ControlType(BaseClass):
         subtypes = [item for item in jsoner[genera] if "_hashes" not in item and "_ratio" not in item]
         return subtypes
           
+    @classmethod
+    def get_positive_control_types(cls):
+        return [item for item in cls.query() if item.targets != []]
+    
+    @classmethod
+    def build_positive_regex(cls):
+        strings = list(set([item.name.split("-")[0] for item in cls.get_positive_control_types()]))
+        return re.compile(rf"(^{'|^'.join(strings)})-.*", flags=re.IGNORECASE)
+
+
 class Control(BaseClass):
     """
     Base class of a control sample.

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

@@ -1117,6 +1117,39 @@ class BacterialCulture(BasicSubmission):
     #     input_dict['submitted_date']['missing'] = True
     #     return input_dict
 
+    @classmethod
+    def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None, plate_map: dict | None = None) -> dict:
+        """
+        Extends parent. Currently finds control sample and adds to reagents.
+
+        Args:
+            input_dict (dict): _description_
+            xl (pd.ExcelFile | None, optional): _description_. Defaults to None.
+            info_map (dict | None, optional): _description_. Defaults to None.
+            plate_map (dict | None, optional): _description_. Defaults to None.
+
+        Returns:
+            dict: _description_
+        """        
+        from . import ControlType
+        input_dict = super().finalize_parse(input_dict, xl, info_map, plate_map)
+        # build regex for all control types that have targets
+        regex = ControlType.build_positive_regex()
+        # search samples for match
+        for sample in input_dict['samples']:
+            matched = regex.match(sample.submitter_id)
+            if bool(matched):
+                logger.debug(f"Control match found: {sample.submitter_id}")
+                new_lot = matched.group()
+                try:
+                    pos_control_reg = [reg for reg in input_dict['reagents'] if reg.type=="Bacterial-Positive Control"][0]
+                except IndexError:
+                    logger.error(f"No positive control reagent listed")
+                    return input_dict
+                pos_control_reg.lot = new_lot
+                pos_control_reg.missing = False
+        return input_dict
+
     @classmethod
     def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
         """
@@ -1505,53 +1538,53 @@ class WastewaterArtic(BasicSubmission):
         # logger.debug(pformat(input_dict))
         # logger.debug(pformat(info_map))
         # logger.debug(pformat(plate_map))
-        samples = []
+        # samples = []
-        for sample in input_dict['samples']:
+        # for sample in input_dict['samples']:
-            logger.debug(f"Input sample: {pformat(sample.__dict__)}")
+        #     logger.debug(f"Input sample: {pformat(sample.__dict__)}")
-            if sample.submitter_id == "NTC1":
+        #     if sample.submitter_id == "NTC1":
-                samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=2, source_row=0, source_column=0, plate_number='control', plate=None))
+        #         samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=2, source_row=0, source_column=0, plate_number='control', plate=None))
-                continue
+        #         continue
-            elif sample.submitter_id == "NTC2":
+        #     elif sample.submitter_id == "NTC2":
-                samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=5, source_row=0, source_column=0, plate_number='control', plate=None))
+        #         samples.append(dict(sample=sample.submitter_id, destination_row=8, destination_column=5, source_row=0, source_column=0, plate_number='control', plate=None))
-                continue
+        #         continue
-            destination_row = sample.row[0]
+        #     destination_row = sample.row[0]
-            destination_column = sample.column[0]
+        #     destination_column = sample.column[0]
-            # logger.debug(f"Looking up: {sample.submitter_id} friend.")
+        #     # logger.debug(f"Looking up: {sample.submitter_id} friend.")
-            lookup_sample = BasicSample.query(submitter_id=sample.submitter_id)
+        #     lookup_sample = BasicSample.query(submitter_id=sample.submitter_id)
-            lookup_ssa = SubmissionSampleAssociation.query(sample=lookup_sample, exclude_submission_type=cls.__mapper_args__['polymorphic_identity'] , chronologic=True, reverse=True, limit=1)
+        #     lookup_ssa = SubmissionSampleAssociation.query(sample=lookup_sample, exclude_submission_type=cls.__mapper_args__['polymorphic_identity'] , chronologic=True, reverse=True, limit=1)
-            try:
+        #     try:
-                plate = lookup_ssa.submission.rsl_plate_num
+        #         plate = lookup_ssa.submission.rsl_plate_num
-                source_row = lookup_ssa.row
+        #         source_row = lookup_ssa.row
-                source_column = lookup_ssa.column
+        #         source_column = lookup_ssa.column
-            except AttributeError as e:
+        #     except AttributeError as e:
-                logger.error(f"Problem with lookup: {e}")
+        #         logger.error(f"Problem with lookup: {e}")
-                plate = "Error"
+        #         plate = "Error"
-                source_row = 0
+        #         source_row = 0
-                source_column = 0
+        #         source_column = 0
-                # continue
+        #         # continue
-            output_sample = dict(
+        #     output_sample = dict(
-                sample=sample.submitter_id,
+        #         sample=sample.submitter_id,
-                destination_column=destination_column, 
+        #         destination_column=destination_column, 
-                destination_row=destination_row,
+        #         destination_row=destination_row,
-                plate=plate,
+        #         plate=plate,
-                source_column=source_column,
+        #         source_column=source_column,
-                source_row = source_row
+        #         source_row = source_row
-                )
+        #         )
-            logger.debug(f"output sample: {pformat(output_sample)}")
+        #     logger.debug(f"output sample: {pformat(output_sample)}")
-            samples.append(output_sample)
+        #     samples.append(output_sample)
-        plates = sorted(list(set([sample['plate'] for sample in samples if sample['plate'] != None and sample['plate'] != "Error"])))
+        # plates = sorted(list(set([sample['plate'] for sample in samples if sample['plate'] != None and sample['plate'] != "Error"])))
-        logger.debug(f"Here's what I got for plates: {plates}")
+        # logger.debug(f"Here's what I got for plates: {plates}")
-        for iii, plate in enumerate(plates):
+        # for iii, plate in enumerate(plates):
-            for sample in samples:
+        #     for sample in samples:
-                if sample['plate'] == plate:
+        #         if sample['plate'] == plate:
-                    sample['plate_number'] = iii + 1
+        #             sample['plate_number'] = iii + 1
-        df = pd.DataFrame.from_records(samples).fillna(value="")
+        # df = pd.DataFrame.from_records(samples).fillna(value="")
-        try:
+        # try:
-            df.source_row = df.source_row.astype(int)
+        #     df.source_row = df.source_row.astype(int)
-            df.source_column = df.source_column.astype(int)
+        #     df.source_column = df.source_column.astype(int)
-            df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
+        #     df.sort_values(by=['destination_column', 'destination_row'], inplace=True)
-        except AttributeError as e:
+        # except AttributeError as e:
-            logger.error(f"Couldn't construct df due to {e}")
+        #     logger.error(f"Couldn't construct df due to {e}")
         # input_dict['csv'] = df
         input_dict['csv'] = xl.parse("hitpicks_csv_to_export")
         return input_dict

src/submissions/backend/validators/pydant.py

@@ -809,8 +809,8 @@ class PydSubmission(BaseModel, extra='allow'):
         # # what reagent types are in both lists?
         # missing = list(set(ext_kit_rtypes).difference(reagenttypes))
         missing = []
-        # output_reagents = self.reagents
+        output_reagents = self.reagents
-        output_reagents = ext_kit_rtypes
+        # output_reagents = ext_kit_rtypes
         logger.debug(f"Already have these reagent types: {reagenttypes}")
         for rt in ext_kit_rtypes:
             if rt.type not in reagenttypes:

src/submissions/frontend/widgets/submission_widget.py

@@ -369,7 +369,7 @@ class SubmissionFormWidget(QWidget):
         match result.code:
             # code 0: everything is fine.
             case 0:
-                self.report.add_result(None)
+                report.add_result(None)
             # code 1: ask for overwrite
             case 1:
                 dlg = QuestionAsker(title=f"Review {base_submission.rsl_plate_num}?", message=result.msg)
@@ -379,11 +379,11 @@ class SubmissionFormWidget(QWidget):
                     result = None
                 else:
                     self.app.ctx.database_session.rollback()
-                    self.report.add_result(Result(msg="Overwrite cancelled", status="Information"))
+                    report.add_result(Result(msg="Overwrite cancelled", status="Information"))
                     return
             # code 2: No RSL plate number given
             case 2:
-                self.report.add_result(result)
+                report.add_result(result)
                 return
             case _:
                 pass
@@ -457,7 +457,8 @@ class SubmissionFormWidget(QWidget):
         for k,v in info.items():
             self.pyd.set_attribute(key=k, value=v)
         # return submission
-        self.report.add_result(report)
+        report.add_result(report)
+        return report
     
     class InfoItem(QWidget):