Addition of new reagent lots updated.

CHANGELOG.md

@@ -1,3 +1,7 @@
+# 202510.01
+
+- Update for Python 3.13
+
 # 202509.04
 
 - Qubit results parsing complete.

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

@@ -48,10 +48,10 @@ class BaseClass(Base):
         except AttributeError:
             return f"<{self.__class__.__name__}(Name Unavailable)>"
 
-    # @classproperty
-    @classmethod
+
     @declared_attr
-    def aliases(cls) -> List[str]:
+    @classmethod
+    def aliases(cls):
         """
         List of other names this class might be known by.
 
@@ -60,9 +60,9 @@ class BaseClass(Base):
         """
         return [cls.query_alias]
 
-    @classmethod
     @declared_attr
-    def query_alias(cls) -> str:
+    @classmethod
+    def query_alias(cls):
         """
         What to query this class as.
 
@@ -71,8 +71,8 @@ class BaseClass(Base):
         """
         return cls.__name__.lower()
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __tablename__(cls) -> str:
         """
         Sets table name to lower case class name.
@@ -82,8 +82,8 @@ class BaseClass(Base):
         """
         return f"_{cls.__name__.lower()}"
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __database_session__(cls) -> Session:
         """
         Pull db session from ctx to be used in operations
@@ -93,8 +93,8 @@ class BaseClass(Base):
         """
         return ctx.database_session
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __directory_path__(cls) -> Path:
         """
         Pull directory path from ctx to be used in operations.
@@ -104,8 +104,8 @@ class BaseClass(Base):
         """
         return ctx.directory_path
 
-    @classmethod
     @declared_attr
+    @classmethod
     def __backup_path__(cls) -> Path:
         """
         Pull backup directory path from ctx to be used in operations.
@@ -119,10 +119,9 @@ class BaseClass(Base):
         super().__init__(*args, **kwargs)
         self._misc_info = dict()
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def jsons(cls) -> List[str]:
+    @classmethod
+    def jsons(cls):
         """
         Get list of JSON db columns
 
@@ -134,10 +133,9 @@ class BaseClass(Base):
         except AttributeError:
             return []
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def timestamps(cls) -> List[str]:
+    @classmethod
+    def timestamps(cls):
         """
         Get list of TIMESTAMP columns
 
@@ -392,10 +390,9 @@ class BaseClass(Base):
             pass
         return dicto
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def pydantic_model(cls) -> BaseModel:
+    @classmethod
+    def pydantic_model(cls):
         """
         Gets the pydantic model corresponding to this object.
 
@@ -414,9 +411,9 @@ class BaseClass(Base):
         return model
 
     # @classproperty
-    @classmethod
     @declared_attr
-    def add_edit_tooltips(cls) -> dict:
+    @classmethod
+    def add_edit_tooltips(cls):
         """
         Gets tooltips for Omni-add-edit
 
@@ -425,10 +422,9 @@ class BaseClass(Base):
         """
         return dict()
 
-    # @classproperty
-    @classmethod
     @declared_attr
-    def details_template(cls) -> Template:
+    @classmethod
+    def details_template(cls):
         """
         Get the details jinja template for the correct class
 
@@ -524,6 +520,7 @@ class BaseClass(Base):
         if isinstance(field_type, InstrumentedAttribute):
             match field_type.property:
                 case ColumnProperty():
+
                     return super().__setattr__(key, value)
                 case _RelationshipDeclared():
                     if field_type.property.uselist:
@@ -660,6 +657,7 @@ class BaseClass(Base):
             pyd = getattr(pydant, pyd_model_name)
         except AttributeError:
             raise AttributeError(f"Could not get pydantic class {pyd_model_name}")
+        pyd.model_rebuild()
         return pyd(**self.details_dict(**kwargs))
 
     def show_details(self, obj):
@@ -699,6 +697,7 @@ class ConfigItem(BaseClass):
     """
     Key:JSON objects to store config settings in database. 
     """
+
     id = Column(INTEGER, primary_key=True)
     key = Column(String(32))  #: Name of the configuration item.
     value = Column(JSON)  #: Value associated with the config item.

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

@@ -346,6 +346,7 @@ class Reagent(BaseClass, LogMixin):
         return [dict(name=self.name, lot=lot.lot, expiry=lot.expiry + self.eol_ext) for lot in self.reagentlot]
 
 
+
 class ReagentLot(BaseClass):
 
     pyd_model_name = "Reagent"
@@ -445,6 +446,7 @@ class ReagentLot(BaseClass):
         output['reagent'] = output['reagent'].name
         return output
 
+
 class Discount(BaseClass):
     """
     Relationship table for client labs for certain kits.
@@ -929,7 +931,7 @@ class Procedure(BaseClass):
         logger.info(f"Add Results! {resultstype_name}")
         from backend.managers import results
         results_manager = getattr(results, f"{resultstype_name}Manager")
-        rs = results_manager(procedure=self, parent=obj, fname=Path("C:\\Users\lwark\Documents\Submission_Forms\QubitData_18-09-2025_13-43-53.csv"))
+        rs = results_manager(procedure=self, parent=obj)#, fname=Path("C:\\Users\lwark\Documents\Submission_Forms\QubitData_18-09-2025_13-43-53.csv"))
         procedure = rs.procedure_to_pydantic()
         samples = rs.samples_to_pydantic()
         if procedure:

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

@@ -43,7 +43,7 @@ class ClientSubmission(BaseClass, LogMixin):
     submission_category = Column(String(64))  #: i.e. Surveillance
     sample_count = Column(INTEGER)  #: Number of sample in the procedure
     full_batch_size = Column(INTEGER)  #: Number of wells in provided plate. 0 if no plate.
-    comment = Column(JSON)  #: comment objects from users.
+    comments = Column(JSON)  #: comment objects from users.
     run = relationship("Run", back_populates="clientsubmission")  #: many-to-one relationship
     contact = relationship("Contact", back_populates="clientsubmission")  #: contact representing submitting lab.
     contact_id = Column(INTEGER, ForeignKey("_contact.id", ondelete="SET NULL",
@@ -240,9 +240,9 @@ class ClientSubmission(BaseClass, LogMixin):
             custom = None
             runs = None
         try:
-            comments = self.comment
+            comments = self.comments
         except Exception as e:
-            logger.error(f"Error setting comment: {self.comment}, {e}")
+            logger.error(f"Error setting comment: {self.comments}, {e}")
             comments = None
         try:
             contact = self.contact.name
@@ -1926,7 +1926,7 @@ class ProcedureSampleAssociation(BaseClass):
         # NOTE: Figure out how to merge the misc_info if doing .update instead.
         relevant = {k: v for k, v in output.items() if k not in ['sample']}
         output = output['sample'].details_dict()
-        logger.debug(output)
+        # logger.debug(output)
         misc = output['misc_info']
         output.update(relevant)
         output['misc_info'] = misc
@@ -1937,6 +1937,8 @@ class ProcedureSampleAssociation(BaseClass):
 
     def to_pydantic(self, **kwargs):
         output = super().to_pydantic(pyd_model_name="PydSample")
+        # from backend.validators.pydant import PydSample
+        # output = PydSample(**self.details_dict(**kwargs))
         try:
             output.submission_rank = output.misc_info['submission_rank']
         except KeyError:

src/submissions/backend/excel/parsers/__init__.py

@@ -62,7 +62,7 @@ class DefaultParser(object):
         self.sheet = sheet
         if not start_row:
             start_row = self.__class__.start_row
-        if self.filepath.suffix == ".xslx":
+        if self.filepath.suffix == ".xlsx":
             self.workbook = load_workbook(self.filepath, data_only=True)
             self.worksheet = self.workbook[self.sheet]
         elif self.filepath.suffix == ".csv":

src/submissions/backend/excel/parsers/clientsubmission_parser.py

@@ -3,6 +3,8 @@ Module for clientsubmission parsing
 """
 from __future__ import annotations
 import logging
+import sys
+from datetime import datetime
 from pathlib import Path
 from string import ascii_lowercase
 from typing import Generator, TYPE_CHECKING
@@ -135,6 +137,9 @@ class ClientSubmissionInfoParser(DefaultKEYVALUEParser, SubmissionTyperMixin):
             output['submissiontype']['value'] = self.submissiontype.name.title()
         except KeyError:
             pass
+        if isinstance(output['submitted_date']['value'], datetime):
+            output['submitted_date']['value'] = output['submitted_date']['value'].date()
+
         return output
 
 

src/submissions/backend/excel/writers/results_writers/__init__.py

@@ -1,6 +1,8 @@
 """
 
 """
+from openpyxl import Workbook
+
 from backend.excel.writers import DefaultKEYVALUEWriter, DefaultTABLEWriter
 from backend.db.models import ProcedureType
 from tools import flatten_list
@@ -16,6 +18,15 @@ class DefaultResultsSampleWriter(DefaultTABLEWriter):
         super().__init__(pydant_obj=pydant_obj, proceduretype=proceduretype, *args, **kwargs)
         self.pydant_obj = flatten_list([sample.results for sample in pydant_obj.sample])
 
+    def write_to_workbook(self, workbook: Workbook, sheet: str | None = None,
+                          start_row: int | None = None, *args, **kwargs) -> Workbook:
+        try:
+            self.worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        except KeyError:
+            self.worksheet = workbook.create_sheet(f"{self.proceduretype.name[:15]} Results")
+            # worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        return workbook
+
 
 from .qubit_results_writer import QubitInfoWriter, QubitSampleWriter
 from .pcr_results_writer import PCRInfoWriter, PCRSampleWriter

src/submissions/backend/excel/writers/results_writers/qubit_results_writer.py

@@ -1,16 +1,13 @@
 """
-Writers for PCR results from Design and Analysis Software
+Writers for PCR results from Qubit device
 """
 from __future__ import annotations
 import logging
 from pprint import pformat
-from typing import Generator, TYPE_CHECKING
 from openpyxl import Workbook
 from openpyxl.styles import Alignment
 from . import DefaultResultsInfoWriter, DefaultResultsSampleWriter
-from tools import flatten_list
-if TYPE_CHECKING:
-    from backend.db.models import ProcedureType
+
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -24,16 +21,12 @@ class QubitInfoWriter(DefaultResultsInfoWriter):
 class QubitSampleWriter(DefaultResultsSampleWriter):
 
     def write_to_workbook(self, workbook: Workbook, *args, **kwargs) -> Workbook:
-        try:
-            self.worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
-        except KeyError:
-            self.worksheet = workbook.create_sheet(f"{self.proceduretype.name[:15]} Results")
-            # worksheet = workbook[f"{self.proceduretype.name[:15]} Results"]
+        workbook = super().write_to_workbook(workbook=workbook, *args, **kwargs)
         header_row = self.proceduretype.allowed_result_methods['Qubit']['sample']['start_row']
         for iii, header in enumerate(self.column_headers, start=1):
-            logger.debug(f"Row: {header_row}, column: {iii}")
+            # logger.debug(f"Row: {header_row}, column: {iii}")
             self.worksheet.cell(row=header_row, column=iii, value=header.replace("_", " ").title())
-        logger.debug(f"Column headers: {self.column_headers}")
+        # logger.debug(f"Column headers: {self.column_headers}")
         for iii, result in enumerate(self.pydant_obj, start = 1):
             row = header_row + iii
             for k, v in result.result.items():
@@ -42,7 +35,7 @@ class QubitSampleWriter(DefaultResultsSampleWriter):
                 except StopIteration:
                     print(f"fail for {k.replace('_', ' ').title()}")
                     continue
-                logger.debug(f"Writing to row: {row}, column {column}")
+                # logger.debug(f"Writing to row: {row}, column {column}")
                 cell = self.worksheet.cell(row=row, column=column)
                 cell.value = v
                 cell.alignment = Alignment(horizontal='left')
@@ -56,6 +49,3 @@ class QubitSampleWriter(DefaultResultsSampleWriter):
             for k, value in result.result.items():
                 output.append(k)
         return sorted(list(set(output)))
-
-
-

src/submissions/backend/managers/__init__.py

@@ -15,7 +15,7 @@ class DefaultManager(object):
 
     def __init__(self, parent, input_object: Path | str | None = None):
         self.parent = parent
-        logger.debug(f"Input object: {pformat(input_object.__dict__)}")
+
         match input_object:
             case str():
                 self.input_object = Path(input_object)

src/submissions/backend/validators/__init__.py

@@ -1,15 +1,18 @@
 """
 Contains all validators
 """
+from __future__ import annotations
 import logging, re
 import sys
 from pathlib import Path
 from openpyxl import load_workbook
-from backend.db.models import Run, SubmissionType
 from tools import jinja_template_loading
 from jinja2 import Template
 from dateutil.parser import parse
 from datetime import datetime
+from typing import TYPE_CHECKING
+if TYPE_CHECKING:
+    from backend.db.models import SubmissionType
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -27,15 +30,17 @@ class DefaultNamer(object):
 
 class ClientSubmissionNamer(DefaultNamer):
 
-    def __init__(self, filepath: str | Path, submissiontype: str|SubmissionType|None=None,
+    def __init__(self, filepath: str | Path, submissiontype: str|"SubmissionType"|None=None,
                  data: dict | None = None, **kwargs):
+        from backend.db.models import SubmissionType
         super().__init__(filepath=filepath)
         if not submissiontype:
-            submissiontype = self.retrieve_submissiontype(filepath=self.filepath)
+            self.submissiontype = self.retrieve_submissiontype(filepath=self.filepath)
         if isinstance(submissiontype, str):
-            submissiontype = SubmissionType.query(name=submissiontype)
+            self.submissiontype = SubmissionType.query(name=submissiontype)
 
-    def retrieve_submissiontype(self, filepath: str | Path):
+    def retrieve_submissiontype(self):
+        from backend.db.models import SubmissionType
         # NOTE: Attempt 1, get from form properties:
         sub_type = self.get_subtype_from_properties()
         if not sub_type:
@@ -51,6 +56,7 @@ class ClientSubmissionNamer(DefaultNamer):
         return sub_type
 
     def get_subtype_from_regex(self) -> SubmissionType:
+        from backend.db.models import SubmissionType
         regex = SubmissionType.regex
         m = regex.search(self.filepath.__str__())
         try:
@@ -64,6 +70,7 @@ class ClientSubmissionNamer(DefaultNamer):
 
     def get_subtype_from_preparse(self) -> SubmissionType:
         from backend.excel.parsers.clientsubmission_parser import ClientSubmissionInfoParser
+        from backend.db.models import SubmissionType
         parser = ClientSubmissionInfoParser(self.filepath)
         sub_type = next((value for k, value in parser.parsed_info.items() if k == "submissiontype"), None)
         sub_type = SubmissionType.query(name=sub_type)
@@ -72,6 +79,7 @@ class ClientSubmissionNamer(DefaultNamer):
         return sub_type
 
     def get_subtype_from_properties(self) -> SubmissionType:
+        from backend.db.models import SubmissionType
         wb = load_workbook(self.filepath)
         # NOTE: Gets first category in the metadata.
         categories = wb.properties.category.split(";")
@@ -88,6 +96,7 @@ class RSLNamer(object):
     """
 
     def __init__(self, filename: str, submission_type: str | None = None, data: dict | None = None):
+        from backend.db.models import SubmissionType
         # NOTE: Preferred method is path retrieval, but might also need validation for just string.
         filename = Path(filename) if Path(filename).exists() else filename
         self.submission_type = submission_type
@@ -113,7 +122,7 @@ class RSLNamer(object):
         Returns:
             str: parsed procedure type
         """
-
+        from backend.db.models import SubmissionType
         def st_from_path(filepath: Path) -> str:
             """
             Sub def to get proceduretype from a file path
@@ -186,8 +195,9 @@ class RSLNamer(object):
             regex (str): string to construct pattern
             filename (str): string to be parsed
         """
+        from backend.db.models import Run
         if regex is None:
-            regex = BasicRun.regex
+            regex = Run.regex
         match filename:
             case Path():
                 m = regex.search(filename.stem)
@@ -215,6 +225,7 @@ class RSLNamer(object):
         Returns:
             str: Output filename
         """
+        from backend.db.models import Run
         if "submitted_date" in data.keys():
             if isinstance(data['submitted_date'], dict):
                 if data['submitted_date']['value'] is not None:

src/submissions/backend/validators/pydant.py

@@ -37,6 +37,8 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
     def prevalidate(cls, data):
         sql_fields = [k for k, v in cls._sql_object.__dict__.items() if isinstance(v, InstrumentedAttribute)]
         output = {}
+        match data:
+            case dict():
                 try:
                     items = data.items()
                 except AttributeError as e:
@@ -48,6 +50,8 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
                         output[new_key] = value
                     else:
                         output[key] = value
+            case _:
+                output = data
         return output
 
     @model_validator(mode='after')
@@ -136,6 +140,48 @@ class PydBaseClass(BaseModel, extra='allow', validate_assignment=True):
         return list(set(output))
 
 
+class PydResults(PydBaseClass, arbitrary_types_allowed=True):
+    result: dict = Field(default={})
+    result_type: str = Field(default="NA")
+    img: None | bytes = Field(default=None)
+    # parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
+    parent: Any | None = Field(default=None)
+    date_analyzed: datetime | None = Field(default=None)
+
+    @field_validator("date_analyzed")
+    @classmethod
+    def set_today(cls, value):
+        match value:
+            case str():
+                value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
+            case datetime():
+                pass
+            case date():
+                value = datetime.combine(value, datetime.max.time())
+            case _:
+                value = datetime.now()
+        return value
+
+    def to_sql(self):
+        sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
+        try:
+            check = sql.image
+        except FileNotFoundError:
+            check = False
+        if not check:
+            sql.image = self.img
+        if not sql.date_analyzed:
+            sql.date_analyzed = self.date_analyzed
+        match self.parent:
+            case ProcedureSampleAssociation():
+                sql.sampleprocedureassociation = self.parent
+            case Procedure():
+                sql.procedure = self.parent
+            case _:
+                logger.error("Improper association found.")
+        return sql
+
+
 class PydReagentLot(PydBaseClass):
     lot: str | None
     name: str | None = Field(default=None)
@@ -145,9 +191,9 @@ class PydReagentLot(PydBaseClass):
 
 
 class PydReagent(PydBaseClass):
-    lot: str | None
+    # lot: str | None
     reagentrole: str | None
-    expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
+    # expiry: date | datetime | Literal['NA'] | None = Field(default=None, validate_default=True)
     name: str | None = Field(default=None, validate_default=True)
     missing: bool = Field(default=True)
     comment: str | None = Field(default="", validate_default=True)
@@ -178,47 +224,47 @@ class PydReagent(PydBaseClass):
                 return value
         return value
 
-    @field_validator("lot", mode='before')
-    @classmethod
-    def rescue_lot_string(cls, value):
-        if value is not None:
-            return convert_nans_to_nones(str(value).strip())
-        return value
-
-    @field_validator("lot")
-    @classmethod
-    def enforce_lot_string(cls, value):
-        if value is not None:
-            return value.upper().strip()
-        return value
-
-    @field_validator("expiry", mode="before")
-    @classmethod
-    def enforce_date(cls, value):
-        if value is not None:
-            match value:
-                case int():
-                    return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
-                case 'NA':
-                    return value
-                case str():
-                    return parse(value)
-                case date():
-                    return datetime.combine(value, datetime.max.time())
-                case datetime():
-                    return value
-                case _:
-                    return convert_nans_to_nones(str(value))
-        if value is None:
-            value = datetime.combine(date.today(), datetime.max.time())
-        return value
-
-    @field_validator("expiry")
-    @classmethod
-    def date_na(cls, value):
-        if isinstance(value, date) and value.year == 1970:
-            value = "NA"
-        return value
+    # @field_validator("lot", mode='before')
+    # @classmethod
+    # def rescue_lot_string(cls, value):
+    #     if value is not None:
+    #         return convert_nans_to_nones(str(value).strip())
+    #     return value
+    #
+    # @field_validator("lot")
+    # @classmethod
+    # def enforce_lot_string(cls, value):
+    #     if value is not None:
+    #         return value.upper().strip()
+    #     return value
+    #
+    # @field_validator("expiry", mode="before")
+    # @classmethod
+    # def enforce_date(cls, value):
+    #     if value is not None:
+    #         match value:
+    #             case int():
+    #                 return datetime.fromordinal(datetime(1900, 1, 1).toordinal() + value - 2)
+    #             case 'NA':
+    #                 return value
+    #             case str():
+    #                 return parse(value)
+    #             case date():
+    #                 return datetime.combine(value, datetime.max.time())
+    #             case datetime():
+    #                 return value
+    #             case _:
+    #                 return convert_nans_to_nones(str(value))
+    #     if value is None:
+    #         value = datetime.combine(date.today(), datetime.max.time())
+    #     return value
+    #
+    # @field_validator("expiry")
+    # @classmethod
+    # def date_na(cls, value):
+    #     if isinstance(value, date) and value.year == 1970:
+    #         value = "NA"
+    #     return value
 
     @field_validator("name", mode="before")
     @classmethod
@@ -228,7 +274,6 @@ class PydReagent(PydBaseClass):
         else:
             return values.data['reagentrole'].strip()
 
-
     def improved_dict(self) -> dict:
         """
         Constructs a dictionary consisting of model.fields and model.extras
@@ -251,15 +296,18 @@ class PydReagent(PydBaseClass):
         Returns:
             Tuple[Reagent, Report]: Reagent instance and result of function
         """
+        from backend.db.models import ReagentLot, Reagent
         report = Report()
         if self.model_extra is not None:
             self.__dict__.update(self.model_extra)
-        reagent, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
+        reagentlot, new = ReagentLot.query_or_create(lot=self.lot, name=self.name)
         if new:
-            reagentrole = ReagentRole.query(name=self.reagentrole)
-            reagent.reagentrole = reagentrole
-            reagent.expiry = self.expiry
-        return reagent, report
+            reagent = Reagent.query(name=self.name, limit=1)
+            reagentlot.reagent = reagent
+            reagentlot.expiry = self.expiry
+            if isinstance(reagentlot.expiry, str):
+                reagentlot.expiry = datetime.combine(datetime.strptime(reagentlot.expiry, "%Y-%m-%d"), datetime.max.time())
+        return reagentlot, report
 
 
 class PydSample(PydBaseClass):
@@ -330,6 +378,7 @@ class PydTips(PydBaseClass):
         Returns:
             SubmissionTipsAssociation: Association between queried tips and procedure
         """
+        from backend.db.models import TipsLot
         report = Report()
         tips = TipsLot.query(lot=self.lot, limit=1)
         return tips, report
@@ -347,6 +396,7 @@ class PydEquipment(PydBaseClass):
     @field_validator('equipmentrole', mode='before')
     @classmethod
     def get_role_name(cls, value):
+        from backend.db.models import EquipmentRole
         match value:
             case list():
                 value = value[0]
@@ -361,6 +411,7 @@ class PydEquipment(PydBaseClass):
     @field_validator('processes', mode='before')
     @classmethod
     def process_to_pydantic(cls, value, values):
+        from backend.db.models import ProcessVersion, Process
         if isinstance(value, GeneratorType):
             value = [item for item in value]
         value = convert_nans_to_nones(value)
@@ -390,6 +441,7 @@ class PydEquipment(PydBaseClass):
     @field_validator('tips', mode='before')
     @classmethod
     def tips_to_pydantic(cls, value, values):
+        from backend.db.models import TipsLot
         if isinstance(value, GeneratorType):
             value = [item for item in value]
         value = convert_nans_to_nones(value)
@@ -426,6 +478,7 @@ class PydEquipment(PydBaseClass):
         Returns:
             Tuple[Equipment, RunEquipmentAssociation]: SQL objects
         """
+        from backend.db.models import Equipment, ProcedureEquipmentAssociation, Process
         report = Report()
         if isinstance(procedure, str):
             procedure = Procedure.query(name=procedure)
@@ -639,6 +692,7 @@ class PydProcess(PydBaseClass, extra="allow"):
 
     @report_result
     def to_sql(self):
+        from backend.db.models import ProcessVersion
         report = Report()
         name = self.name.split("-")[0]
         # NOTE: can't use query_or_create due to name not being part of ProcessVersion
@@ -684,12 +738,12 @@ class PydElastic(BaseModel, extra="allow", arbitrary_types_allowed=True):
 # NOTE: Generified objects below:
 
 class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
-    proceduretype: ProcedureType | None = Field(default=None)
-    run: Run | str | None = Field(default=None)
+    proceduretype: Any | None = Field(default=None)
+    run: Any | str | None = Field(default=None)
     name: dict = Field(default=dict(value="NA", missing=True), validate_default=True)
     technician: dict = Field(default=dict(value="NA", missing=True))
     repeat: bool = Field(default=False)
-    repeat_of: Procedure | None = Field(default=None)
+    repeat_of: Any | None = Field(default=None)
     plate_map: str | None = Field(default=None)
     reagent: list | None = Field(default=[])
     reagentrole: dict | None = Field(default={}, validate_default=True)
@@ -878,7 +932,10 @@ class PydProcedure(PydBaseClass, arbitrary_types_allowed=True):
         reg.save()
 
     def to_sql(self, new: bool = False):
-        from backend.db.models import RunSampleAssociation, ProcedureSampleAssociation
+        from backend.db.models import (
+            RunSampleAssociation, ProcedureSampleAssociation, Procedure, ProcedureReagentLotAssociation,
+            ProcedureEquipmentAssociation
+        )
         logger.debug(f"incoming pyd: {pformat([item.__dict__ for item in self.equipment])}")
         if new:
             sql = Procedure()
@@ -1001,9 +1058,11 @@ class PydClientSubmission(PydBaseClass):
     def enforce_submitted_date(cls, value):
         match value:
             case str():
-                value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S"), missing=False)
-            case date() | datetime():
+                value = dict(value=datetime.strptime(value, "%Y-%m-%d %H:%M:%S").date(), missing=False)
+            case date():
                 value = dict(value=value, missing=False)
+            case datetime():
+                value = dict(value=value.date(), missing=False)
             case _:
                 pass
         return value
@@ -1121,6 +1180,7 @@ class PydClientSubmission(PydBaseClass):
 
     def to_sql(self):
         sql = super().to_sql()
+        from backend.db.models import SubmissionType
         assert not any([isinstance(item, PydSample) for item in sql.sample])
         sql.sample = []
         if not sql.submissiontype:
@@ -1621,44 +1681,3 @@ class PydRun(PydBaseClass):  #, extra='allow'):
             samples.append(sample)
         samples = sorted(samples, key=itemgetter("submission_rank"))
         return samples
-
-
-class PydResults(PydBaseClass, arbitrary_types_allowed=True):
-    result: dict = Field(default={})
-    result_type: str = Field(default="NA")
-    img: None | bytes = Field(default=None)
-    parent: Procedure | ProcedureSampleAssociation | None = Field(default=None)
-    date_analyzed: datetime | None = Field(default=None)
-
-    @field_validator("date_analyzed")
-    @classmethod
-    def set_today(cls, value):
-        match value:
-            case str():
-                value = datetime.strptime(value, "%Y-%m-%d %H:%M:%S")
-            case datetime():
-                pass
-            case date():
-                value = datetime.combine(value, datetime.max.time())
-            case _:
-                value = datetime.now()
-        return value
-
-    def to_sql(self):
-        sql, _ = Results.query_or_create(result_type=self.result_type, result=self.results)
-        try:
-            check = sql.image
-        except FileNotFoundError:
-            check = False
-        if not check:
-            sql.image = self.img
-        if not sql.date_analyzed:
-            sql.date_analyzed = self.date_analyzed
-        match self.parent:
-            case ProcedureSampleAssociation():
-                sql.sampleprocedureassociation = self.parent
-            case Procedure():
-                sql.procedure = self.parent
-            case _:
-                logger.error("Improper association found.")
-        return sql

src/submissions/frontend/widgets/procedure_creation.py

@@ -56,6 +56,14 @@ class ProcedureCreation(QDialog):
         proceduretype_dict = self.proceduretype.details_dict()
         # NOTE: Add --New-- as an option for reagents.
         for key, value in self.procedure.reagentrole.items():
+            try:
+                check = "--New--" in [v['name'] for v in value]
+            except TypeError:
+                try:
+                    check = "--New--" in [v.name for v in value]
+                except (TypeError, AttributeError):
+                    check = True
+            if not check:
                 value.append(dict(name="--New--"))
         if self.procedure.equipment:
             for equipmentrole in proceduretype_dict['equipment']:
@@ -72,7 +80,6 @@ class ProcedureCreation(QDialog):
         proceduretype_dict['equipment'] = [sanitize_object_for_json(object) for object in proceduretype_dict['equipment']]
         regex = re.compile(r".*R\d$")
         proceduretype_dict['previous'] = [""] + [item.name for item in self.run.procedure if item.proceduretype == self.proceduretype and not bool(regex.match(item.name))]
-        # sys.exit(f"ProcedureDict:\n{pformat(proceduretype_dict)}")
         html = render_details_template(
             template_name="procedure_creation",
             js_in=["procedure_form", "grid_drag", "context_menu"],
@@ -82,12 +89,13 @@ class ProcedureCreation(QDialog):
             plate_map=self.plate_map,
             edit=self.edit
         )
+        # with open("procedure_creation.html", "w") as f:
+        #     f.write(html)
         self.webview.setHtml(html)
 
     @pyqtSlot(str, str, str, str)
     def update_equipment(self, equipmentrole: str, equipment: str, processversion: str, tips: str):
         from backend.db.models import Equipment, ProcessVersion, TipsLot
-        logger.debug(f"\n\nEquipmentRole: {equipmentrole}, Equipment: {equipment}, Process: {processversion}, Tips: {tips}\n\n")
         try:
             equipment_of_interest = next(
                 (item for item in self.procedure.equipment if item.equipmentrole == equipmentrole))
@@ -148,9 +156,10 @@ class ProcedureCreation(QDialog):
 
     @pyqtSlot(str, str, str, str)
     def add_new_reagent(self, reagentrole: str, name: str, lot: str, expiry: str):
-        from backend.validators.pydant import PydReagent
+        from backend.validators.pydant import PydReagentLot
         expiry = datetime.datetime.strptime(expiry, "%Y-%m-%d")
-        pyd = PydReagent(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
+        logger.debug(f"{reagentrole}, {name}, {lot}, {expiry}")
+        pyd = PydReagentLot(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
         self.procedure.reagentrole[reagentrole].insert(0, pyd)
         self.set_html()
 
@@ -162,6 +171,12 @@ class ProcedureCreation(QDialog):
             return
         self.procedure.update_reagents(reagentrole=reagentrole, name=name, lot=lot, expiry=expiry)
 
+    @pyqtSlot(str, result=list)
+    def get_reagent_names(self, reagentrole_name: str):
+        from backend.db.models import ReagentRole
+        reagentrole = ReagentRole.query(name=reagentrole_name)
+        return [item.name for item in reagentrole.get_reagents(proceduretype=self.procedure.proceduretype)]
+
     def return_sql(self, new: bool = False):
         output = self.procedure.to_sql(new=new)
         return output

src/submissions/templates/js/context_menu.js

@@ -194,7 +194,7 @@ function contextListener() {
 function clickListener() {
     document.addEventListener( "click", function(e) {
         var clickeElIsLink = clickInsideElement( e, contextMenuLinkClassName );
-        backend.log(e.target.id)
+
         if ( clickeElIsLink ) {
             e.preventDefault();
             menuItemListener( clickeElIsLink );

src/submissions/templates/js/procedure_form.js

@@ -42,7 +42,7 @@ var changed_it = new Event('change');
 var reagentRoles = document.getElementsByClassName("reagentrole");
 
 for(let i = 0; i < reagentRoles.length; i++) {
-  reagentRoles[i].addEventListener("change", function() {
+  reagentRoles[i].addEventListener("change", async function() {
     if (reagentRoles[i].value.includes("--New--")) {
 //        alert("Create new reagent.")
         var br = document.createElement("br");
@@ -50,9 +50,15 @@ for(let i = 0; i < reagentRoles.length; i++) {
         var new_form = document.createElement("form");
         new_form.setAttribute("class", "new_reagent_form")
         new_form.setAttribute("id", reagentRoles[i].id + "_addition")
-        var rr_name = document.createElement("input");
-        rr_name.setAttribute("type", "text");
+        var rr_name = document.createElement("select");
         rr_name.setAttribute("id", "new_" + reagentRoles[i].id + "_name");
+        var rr_options = await backend.get_reagent_names(reagentRoles[i].id).then(
+            function(result) {
+                result.forEach( function(item) {
+                    rr_name.options.add( new Option(item));
+                });
+            }
+        );
         var rr_name_label = document.createElement("label");
         rr_name_label.setAttribute("for", "new_" + reagentRoles[i].id + "_name");
         rr_name_label.innerHTML = "Name:";

src/submissions/tools/__init__.py

@@ -782,7 +782,8 @@ def yaml_regex_creator(loader, node):
     nodes = loader.construct_sequence(node)
     name = nodes[0].replace(" ", "_")
     abbr = nodes[1]
-    return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    # return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    return f"(?P<{name}>RSL(?:-|_)?{abbr}(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)?\\d?([^_0123456789\\sA-QS-Z]|$)?R?\\d?)?)"
 
 
 def super_splitter(ins_str: str, substring: str, idx: int) -> str: