Debugged upgrades.

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

@@ -116,7 +116,7 @@ class BaseClass(Base):
             query: Query = cls.__database_session__.query(model)
         # logger.debug(f"Grabbing singles using {model.get_default_info}")
         singles = model.get_default_info('singles')
-        logger.debug(f"Querying: {model}, singles: {singles}")
+        logger.debug(f"Querying: {model}, with kwargs: {kwargs}")
         for k, v in kwargs.items():
             logger.debug(f"Using key: {k} with value: {v}")
             # logger.debug(f"That key found attribute: {attr} with type: {attr}")

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

@@ -629,6 +629,7 @@ class SubmissionType(BaseClass):
                 output = {k:v[mode] for k,v in info.items() if v[mode]}
             case "write":
                 output = {k:v[mode] + v['read'] for k,v in info.items() if v[mode] or v['read']}
+                output = {k:v for k, v in output.items() if all([isinstance(item, dict) for item in v])}
         return output
 
     def construct_sample_map(self):
@@ -935,6 +936,9 @@ class SubmissionReagentAssociation(BaseClass):
         return f"<{self.submission.rsl_plate_num}&{self.reagent.lot}>"
 
     def __init__(self, reagent=None, submission=None):
+        if isinstance(reagent, list):
+            logger.warning(f"Got list for reagent. Likely no lot was provided. Using {reagent[0]}")
+            reagent = reagent[0]
         self.reagent = reagent
         self.submission = submission
         self.comments = ""

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

@@ -67,7 +67,8 @@ class Organization(BaseClass):
             case _:
                 pass
         return cls.execute_query(query=query, limit=limit)
-    
+        # return query.first()
+
     @check_authorization
     def save(self):
         super().save()

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

@@ -21,7 +21,7 @@ from openpyxl.worksheet.worksheet import Worksheet
 from openpyxl.drawing.image import Image as OpenpyxlImage
 from tools import check_not_nan, row_map, setup_lookup, jinja_template_loading, rreplace
 from datetime import datetime, date
-from typing import List, Any, Tuple
+from typing import List, Any, Tuple, Literal
 from dateutil.parser import parse
 from dateutil.parser import ParserError
 from pathlib import Path
@@ -418,11 +418,11 @@ class BasicSubmission(BaseClass):
             case "samples":
                 for sample in value:
                     # logger.debug(f"Parsing {sample} to sql.")
-                    sample, _ = sample.toSQL(submission=self)
+                    sample, _ = sample.to_sql(submission=self)
                 return
             case "reagents":
                 logger.debug(f"Reagents coming into SQL: {value}")
-                field_value = [reagent['value'].toSQL()[0] if isinstance(reagent, dict) else reagent.toSQL()[0] for
+                field_value = [reagent['value'].to_sql()[0] if isinstance(reagent, dict) else reagent.to_sql()[0] for
                                reagent in value]
                 logger.debug(f"Reagents coming out of SQL: {field_value}")
             case "submission_type":
@@ -620,7 +620,7 @@ class BasicSubmission(BaseClass):
         return plate_map
 
     @classmethod
-    def parse_info(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
         """
         Update submission dictionary with type specific information
 
@@ -666,7 +666,7 @@ class BasicSubmission(BaseClass):
         return input_dict
 
     @classmethod
-    def custom_autofill(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
+    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
         """
         Adds custom autofill methods for submission
 
@@ -730,7 +730,9 @@ class BasicSubmission(BaseClass):
                 repeat = "1"
         except AttributeError as e:
             repeat = ""
-        return re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
+        outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
+        abb = cls.get_default_info('abbreviation')
+        return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
         # return outstr
 
     @classmethod
@@ -1045,7 +1047,7 @@ class BasicSubmission(BaseClass):
             logger.debug(widg)
             widg.setParent(None)
         pyd = self.to_pydantic(backup=True)
-        form = pyd.toForm(parent=obj)
+        form = pyd.to_form(parent=obj)
         obj.app.table_widget.formwidget.layout().addWidget(form)
 
     def add_comment(self, obj):
@@ -1112,7 +1114,7 @@ class BasicSubmission(BaseClass):
         # wb = pyd.autofill_excel()
         # wb = pyd.autofill_samples(wb)
         # wb = pyd.autofill_equipment(wb)
-        writer = pyd.toWriter()
+        writer = pyd.to_writer()
         # wb.save(filename=fname.with_suffix(".xlsx"))
         writer.xl.save(filename=fname.with_suffix(".xlsx"))
 
@@ -1166,25 +1168,25 @@ class BacterialCulture(BasicSubmission):
             plate_map.iloc[6, 0] = num2
         return plate_map
 
-    @classmethod
-    def custom_autofill(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
-        """
-        Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
-
-        Args:
-            input_excel (Workbook): Input openpyxl workbook
-
-        Returns:
-            Workbook: Updated openpyxl workbook
-        """
-        input_excel = super().custom_autofill(input_excel)
-        sheet = input_excel['Plate Map']
-        if sheet.cell(12, 2).value == None:
-            sheet.cell(row=12, column=2, value="=IF(ISBLANK('Sample List'!$B42),\"\",'Sample List'!$B42)")
-        if sheet.cell(13, 2).value == None:
-            sheet.cell(row=13, column=2, value="=IF(ISBLANK('Sample List'!$B43),\"\",'Sample List'!$B43)")
-        input_excel["Sample List"].cell(row=15, column=2, value=getuser())
-        return input_excel
+    # @classmethod
+    # def custom_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
+    #     """
+    #     Stupid stopgap solution to there being an issue with the Bacterial Culture plate map. Extends parent.
+    #
+    #     Args:
+    #         input_excel (Workbook): Input openpyxl workbook
+    #
+    #     Returns:
+    #         Workbook: Updated openpyxl workbook
+    #     """
+    #     input_excel = super().custom_writer(input_excel)
+    #     sheet = input_excel['Plate Map']
+    #     if sheet.cell(12, 2).value == None:
+    #         sheet.cell(row=12, column=2, value="=IF(ISBLANK('Sample List'!$B42),\"\",'Sample List'!$B42)")
+    #     if sheet.cell(13, 2).value == None:
+    #         sheet.cell(row=13, column=2, value="=IF(ISBLANK('Sample List'!$B43),\"\",'Sample List'!$B43)")
+    #     input_excel["Sample List"].cell(row=15, column=2, value=getuser())
+    #     return input_excel
 
     @classmethod
     def get_regex(cls) -> str:
@@ -1297,7 +1299,7 @@ class Wastewater(BasicSubmission):
         return output
 
     @classmethod
-    def parse_info(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
         """
         Update submission dictionary with type specific information. Extends parent
 
@@ -1307,7 +1309,7 @@ class Wastewater(BasicSubmission):
         Returns:
             dict: Updated sample dictionary
         """
-        input_dict = super().parse_info(input_dict)
+        input_dict = super().custom_info_parser(input_dict)
         if xl != None:
             input_dict['csv'] = xl["Copy to import file"]
         return input_dict
@@ -1458,7 +1460,7 @@ class WastewaterArtic(BasicSubmission):
         return output
 
     @classmethod
-    def parse_info(cls, input_dict: dict, xl: pd.ExcelFile | None = None) -> dict:
+    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None) -> dict:
         """
         Update submission dictionary with type specific information
 
@@ -1469,17 +1471,23 @@ class WastewaterArtic(BasicSubmission):
         Returns:
             dict: Updated sample dictionary
         """
-        input_dict = super().parse_info(input_dict)
-        workbook = load_workbook(xl.io, data_only=True)
-        ws = workbook['Egel results']
+        input_dict = super().custom_info_parser(input_dict)
+        # workbook = load_workbook(xl.io, data_only=True)
+        ws = xl['Egel results']
         data = [ws.cell(row=ii, column=jj) for jj in range(15, 27) for ii in range(10, 18)]
         data = [cell for cell in data if cell.value is not None and "NTC" in cell.value]
         input_dict['gel_controls'] = [
             dict(sample_id=cell.value, location=f"{row_map[cell.row - 9]}{str(cell.column - 14).zfill(2)}") for cell in
             data]
-        ws = workbook['First Strand List']
+        ws = xl['First Strand List']
         data = [dict(plate=ws.cell(row=ii, column=3).value, starting_sample=ws.cell(row=ii, column=4).value) for ii in
                 range(8, 11)]
+        for datum in data:
+            if datum['plate'] in ["None", None, ""]:
+                continue
+            else:
+                from backend.validators import RSLNamer
+                datum['plate'] = RSLNamer(filename=datum['plate'], sub_type="Wastewater").parsed_name
         input_dict['source_plates'] = data
         return input_dict
 
@@ -1493,10 +1501,13 @@ class WastewaterArtic(BasicSubmission):
             instr = re.sub(r"Artic", "", instr, flags=re.IGNORECASE)
         except (AttributeError, TypeError) as e:
             logger.error(f"Problem using regex: {e}")
-        # logger.debug(f"Before RSL addition: {instr}")
-        instr = instr.replace("-", "")
+        logger.debug(f"Before RSL addition: {instr}")
+        try:
+            instr = instr.replace("-", "")
+        except AttributeError:
+            instr = date.today().strftime("%Y%m%d")
         instr = re.sub(r"^(\d{6})", f"RSL-AR-\\1", instr)
-        # logger.debug(f"name coming out of Artic namer: {instr}")
+        logger.debug(f"name coming out of Artic namer: {instr}")
         outstr = super().enforce_name(instr=instr, data=data)
 
         return outstr
@@ -1527,8 +1538,12 @@ class WastewaterArtic(BasicSubmission):
             del input_dict['sample_name_(ww)']
         except KeyError:
             logger.error(f"Unable to set ww_processing_num for sample {input_dict['submitter_id']}")
-        if "ENC" in input_dict['submitter_id']:
-            input_dict['submitter_id'] = cls.en_adapter(input_str=input_dict['submitter_id'])
+        year = str(date.today().year)[-2:]
+        # if "ENC" in input_dict['submitter_id']:
+        if re.search(rf"^{year}-(ENC)", input_dict['submitter_id']):
+            input_dict['rsl_number'] = cls.en_adapter(input_str=input_dict['submitter_id'])
+        if re.search(rf"^{year}-(RSL)", input_dict['submitter_id']):
+            input_dict['rsl_number'] = cls.pbs_adapter(input_str=input_dict['submitter_id'])
         return input_dict
 
     @classmethod
@@ -1543,8 +1558,10 @@ class WastewaterArtic(BasicSubmission):
             str: output name
         """
         logger.debug(f"input string raw: {input_str}")
-        # Remove letters. 
-        processed = re.sub(r"[A-QS-Z]+\d*", "", input_str)
+        # Remove letters.
+        processed = input_str.replace("RSL", "")
+        processed = re.sub(r"\(.*\)$", "", processed).strip()
+        processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
         # Remove trailing '-' if any
         processed = processed.strip("-")
         logger.debug(f"Processed after stripping letters: {processed}")
@@ -1554,7 +1571,7 @@ class WastewaterArtic(BasicSubmission):
         except AttributeError:
             en_num = "1"
         en_num = en_num.strip("-")
-        logger.debug(f"Processed after en-num: {processed}")
+        logger.debug(f"Processed after en_num: {processed}")
         try:
             plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
             processed = rreplace(processed, plate_num, "")
@@ -1571,7 +1588,58 @@ class WastewaterArtic(BasicSubmission):
         logger.debug(f"Processed after month: {processed}")
         year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
         year = f"20{year}"
-        final_en_name = f"EN{year}{month}{day}-{en_num}"
+        final_en_name = f"EN{en_num}-{year}{month}{day}"
+        logger.debug(f"Final EN name: {final_en_name}")
+        return final_en_name
+
+    @classmethod
+    def pbs_adapter(cls, input_str):
+        """
+                Stopgap solution because WW names their ENs different
+
+                Args:
+                    input_str (str): input name
+
+                Returns:
+                    str: output name
+                """
+        logger.debug(f"input string raw: {input_str}")
+        # Remove letters.
+        processed = input_str.replace("RSL", "")
+        processed = re.sub(r"\(.*\)$", "", processed).strip()
+        processed = re.sub(r"[A-QS-Z]+\d*", "", processed)
+        # Remove trailing '-' if any
+        processed = processed.strip("-")
+        logger.debug(f"Processed after stripping letters: {processed}")
+        # try:
+        #     en_num = re.search(r"\-\d{1}$", processed).group()
+        #     processed = rreplace(processed, en_num, "")
+        # except AttributeError:
+        #     en_num = "1"
+        # en_num = en_num.strip("-")
+        # logger.debug(f"Processed after en_num: {processed}")
+        try:
+            plate_num = re.search(r"\-\d{1}R?\d?$", processed).group()
+            processed = rreplace(processed, plate_num, "")
+        except AttributeError:
+            plate_num = "1"
+        plate_num = plate_num.strip("-")
+        logger.debug(f"Plate num: {plate_num}")
+        repeat_num = re.search(r"R(?P<repeat>\d)?$", "PBS20240426-2R").groups()[0]
+        if repeat_num is None and "R" in plate_num:
+            repeat_num = "1"
+        plate_num = re.sub(r"R", rf"R{repeat_num}", plate_num)
+        logger.debug(f"Processed after plate-num: {processed}")
+        day = re.search(r"\d{2}$", processed).group()
+        processed = rreplace(processed, day, "")
+        logger.debug(f"Processed after day: {processed}")
+        month = re.search(r"\d{2}$", processed).group()
+        processed = rreplace(processed, month, "")
+        processed = processed.replace("--", "")
+        logger.debug(f"Processed after month: {processed}")
+        year = re.search(r'^(?:\d{2})?\d{2}', processed).group()
+        year = f"20{year}"
+        final_en_name = f"PBS{year}{month}{day}-{plate_num}"
         logger.debug(f"Final EN name: {final_en_name}")
         return final_en_name
 
@@ -1600,11 +1668,17 @@ class WastewaterArtic(BasicSubmission):
             dict: Updated parser product.
         """
         input_dict = super().finalize_parse(input_dict, xl, info_map)
-        input_dict['csv'] = xl.parse("hitpicks_csv_to_export")
+        logger.debug(f"Incoming input_dict: {pformat(input_dict)}")
+        # TODO: Move to validator?
+        for sample in input_dict['samples']:
+            logger.debug(f"Sample: {sample}")
+            if re.search(r"^NTC", sample['submitter_id']):
+                sample['submitter_id'] = sample['submitter_id'] + "-WWG-" + input_dict['rsl_plate_num']['value']
+        input_dict['csv'] = xl["hitpicks_csv_to_export"]
         return input_dict
 
     @classmethod
-    def custom_autofill(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
+    def custom_info_writer(cls, input_excel: Workbook, info: dict | None = None, backup: bool = False) -> Workbook:
         """
         Adds custom autofill methods for submission. Extends Parent
 
@@ -1616,10 +1690,10 @@ class WastewaterArtic(BasicSubmission):
         Returns:
             Workbook: Updated workbook
         """
-        input_excel = super().custom_autofill(input_excel, info, backup)
-        worksheet = input_excel["First Strand List"]
-        samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
-        samples = sorted(samples, key=attrgetter('column', 'row'))
+        input_excel = super().custom_info_writer(input_excel, info, backup)
+        # worksheet = input_excel["First Strand List"]
+        # samples = cls.query(rsl_number=info['rsl_plate_num']['value']).submission_sample_associations
+        # samples = sorted(samples, key=attrgetter('column', 'row'))
         logger.debug(f"Info:\n{pformat(info)}")
         check = 'source_plates' in info.keys() and info['source_plates'] is not None
         if check:
@@ -1708,15 +1782,22 @@ class WastewaterArtic(BasicSubmission):
         """
         logger.debug(f"Hello from {self.__class__.__name__} dictionary sample adjuster.")
         output = []
+        set_plate = None
         for assoc in self.submission_sample_associations:
             dicto = assoc.to_sub_dict()
-            old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
-            try:
-                dicto['plate_name'] = old_sub.rsl_plate_num
-            except AttributeError:
-                dicto['plate_name'] = ""
-            old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
-            dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
+            # old_sub = assoc.sample.get_previous_ww_submission(current_artic_submission=self)
+            # try:
+            #     dicto['plate_name'] = old_sub.rsl_plate_num
+            # except AttributeError:
+            #     dicto['plate_name'] = ""
+            # old_assoc = WastewaterAssociation.query(submission=old_sub, sample=assoc.sample, limit=1)
+            # dicto['well'] = f"{row_map[old_assoc.row]}{old_assoc.column}"
+            for item in self.source_plates:
+                old_plate = WastewaterAssociation.query(submission=item['plate'], sample=assoc.sample, limit=1)
+                if old_plate is not None:
+                    set_plate = old_plate.submission.rsl_plate_num
+                    break
+            dicto['plate_name'] = set_plate
             output.append(dicto)
         return output
 
@@ -1892,6 +1973,10 @@ class BasicSample(BaseClass):
         logger.info(f"Recruiting model: {model}")
         return model
 
+    @classmethod
+    def sql_enforcer(cls, pyd_sample:"PydSample"):
+        return pyd_sample
+
     @classmethod
     def parse_sample(cls, input_dict: dict) -> dict:
         f"""
@@ -1996,15 +2081,16 @@ class BasicSample(BaseClass):
         disallowed = ["id"]
         if kwargs == {}:
             raise ValueError("Need to narrow down query or the first available instance will be returned.")
-        for key in kwargs.keys():
-            if key in disallowed:
-                raise ValueError(
-                    f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects.")
+        # for key in kwargs.keys():
+        #     if key in disallowed:
+        #         raise ValueError(
+        #             f"{key} is not allowed as a query argument as it could lead to creation of duplicate objects.")
+        sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in disallowed}
         instance = cls.query(sample_type=sample_type, limit=1, **kwargs)
         logger.debug(f"Retrieved instance: {instance}")
-        if instance == None:
-            used_class = cls.find_polymorphic_subclass(attrs=kwargs, polymorphic_identity=sample_type)
-            instance = used_class(**kwargs)
+        if instance is None:
+            used_class = cls.find_polymorphic_subclass(attrs=sanitized_kwargs, polymorphic_identity=sample_type)
+            instance = used_class(**sanitized_kwargs)
             instance.sample_type = sample_type
             logger.debug(f"Creating instance: {instance}")
         return instance
@@ -2061,7 +2147,7 @@ class WastewaterSample(BasicSample):
             dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
         """
         sample = super().to_sub_dict(full_data=full_data)
-        sample['WW Processing Number'] = self.ww_processing_num
+        sample['WW Processing Num'] = self.ww_processing_num
         sample['Sample Location'] = self.sample_location
         sample['Received Date'] = self.received_date
         sample['Collection Date'] = self.collection_date
@@ -2080,14 +2166,17 @@ class WastewaterSample(BasicSample):
         """
         output_dict = super().parse_sample(input_dict)
         logger.debug(f"Initial sample dict: {pformat(output_dict)}")
+        disallowed = ["", None, "None"]
         try:
             check = output_dict['rsl_number'] in [None, "None"]
         except KeyError:
             check = True
         if check:
-            output_dict['rsl_number'] = "RSL-WW-" + output_dict['ww_processing_number']
-        if output_dict['ww_full_sample_id'] is not None:
+            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']
+        # if re.search(r"^NTC", output_dict['submitter_id']):
+        #     output_dict['submitter_id'] = "Artic-" + output_dict['submitter_id']
         # Ad hoc repair method for WW (or possibly upstream) not formatting some dates properly.
         # NOTE: Should be handled by validator.
         # match output_dict['collection_date']:
@@ -2166,7 +2255,7 @@ class SubmissionSampleAssociation(BaseClass):
     submission_id = Column(INTEGER, ForeignKey("_basicsubmission.id"), primary_key=True)  #: id of associated submission
     row = Column(INTEGER, primary_key=True)  #: row on the 96 well plate
     column = Column(INTEGER, primary_key=True)  #: column on the 96 well plate
-    submission_rank = Column(INTEGER, nullable=False, default=1) #: Location in sample list
+    submission_rank = Column(INTEGER, nullable=False, default=0) #: Location in sample list
 
     # reference to the Submission object
     submission = relationship(BasicSubmission,
@@ -2186,12 +2275,13 @@ class SubmissionSampleAssociation(BaseClass):
     }
 
     def __init__(self, submission: BasicSubmission = None, sample: BasicSample = None, row: int = 1, column: int = 1,
-                 id: int | None = None):
+                 id: int | None = None, submission_rank: int = 0):
         self.submission = submission
         self.sample = sample
         self.row = row
         self.column = column
-        if id != None:
+        self.submission_rank = submission_rank
+        if id is not None:
             self.id = id
         else:
             self.id = self.__class__.autoincrement_id()
@@ -2257,6 +2347,7 @@ class SubmissionSampleAssociation(BaseClass):
         Returns:
             int: incremented id
         """
+
         try:
             return max([item.id for item in cls.query()]) + 1
         except ValueError as e:
@@ -2360,7 +2451,7 @@ class SubmissionSampleAssociation(BaseClass):
                         association_type: str = "Basic Association",
                         submission: BasicSubmission | str | None = None,
                         sample: BasicSample | str | None = None,
-                        # id:int|None=None,
+                        id:int|None=None,
                         **kwargs) -> SubmissionSampleAssociation:
         """
         Queries for an association, if none exists creates a new one.
@@ -2401,10 +2492,11 @@ class SubmissionSampleAssociation(BaseClass):
             instance = cls.query(submission=submission, sample=sample, row=row, column=column, limit=1)
         except StatementError:
             instance = None
-        if instance == None:
+        if instance is None:
+            # sanitized_kwargs = {k:v for k,v in kwargs.items() if k not in ['id']}
             used_cls = cls.find_polymorphic_subclass(polymorphic_identity=association_type)
             # instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
-            instance = used_cls(submission=submission, sample=sample, **kwargs)
+            instance = used_cls(submission=submission, sample=sample, id=id, **kwargs)
         return instance
 
     def delete(self):