Improved generic submissions to replace viral culture addition.

alembic/versions/0746f7e2c10e_rebuild_20240723.py

@@ -33,67 +33,67 @@ def upgrade() -> None:
     )
     op.create_table('_contact',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('email', sa.String(length=64), nullable=True),
     sa.Column('phone', sa.String(length=32), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_controltype',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=255), nullable=True),
+    sa.Column('sub_type', sa.String(length=255), nullable=True),
     sa.Column('targets', sa.JSON(), nullable=True),
     sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
+    sa.UniqueConstraint('sub_type')
     )
     op.create_table('_equipment',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('nickname', sa.String(length=64), nullable=True),
     sa.Column('asset_number', sa.String(length=16), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_equipmentrole',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=32), nullable=True),
+    sa.Column('sub_type', sa.String(length=32), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_kittype',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
+    sa.UniqueConstraint('sub_type')
     )
     op.create_table('_organization',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('cost_centre', sa.String(), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_process',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
+    sa.UniqueConstraint('sub_type')
     )
     op.create_table('_reagentrole',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('eol_ext', sa.Interval(), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_submissiontype',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=128), nullable=True),
+    sa.Column('sub_type', sa.String(length=128), nullable=True),
     sa.Column('info_map', sa.JSON(), nullable=True),
     sa.Column('defaults', sa.JSON(), nullable=True),
     sa.Column('template_file', sa.LargeBinary(), nullable=True),
     sa.Column('sample_map', sa.JSON(), nullable=True),
     sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
+    sa.UniqueConstraint('sub_type')
     )
     op.create_table('_tiprole',
     sa.Column('id', sa.INTEGER(), nullable=False),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.PrimaryKeyConstraint('id')
     )
     op.create_table('_bacterialculturesample',
@@ -107,7 +107,7 @@ def upgrade() -> None:
     sa.Column('id', sa.INTEGER(), nullable=False),
     sa.Column('kit_id', sa.INTEGER(), nullable=True),
     sa.Column('client_id', sa.INTEGER(), nullable=True),
-    sa.Column('name', sa.String(length=128), nullable=True),
+    sa.Column('sub_type', sa.String(length=128), nullable=True),
     sa.Column('amount', sa.FLOAT(precision=2), nullable=True),
     sa.ForeignKeyConstraint(['client_id'], ['_organization.id'], name='fk_org_id', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['kit_id'], ['_kittype.id'], name='fk_kit_type_id', ondelete='SET NULL'),
@@ -164,7 +164,7 @@ def upgrade() -> None:
     op.create_table('_reagent',
     sa.Column('id', sa.INTEGER(), nullable=False),
     sa.Column('role_id', sa.INTEGER(), nullable=True),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('lot', sa.String(length=64), nullable=True),
     sa.Column('expiry', sa.TIMESTAMP(), nullable=True),
     sa.ForeignKeyConstraint(['role_id'], ['_reagentrole.id'], name='fk_reagent_role_id', ondelete='SET NULL'),
@@ -207,7 +207,7 @@ def upgrade() -> None:
     op.create_table('_tips',
     sa.Column('id', sa.INTEGER(), nullable=False),
     sa.Column('role_id', sa.INTEGER(), nullable=True),
-    sa.Column('name', sa.String(length=64), nullable=True),
+    sa.Column('sub_type', sa.String(length=64), nullable=True),
     sa.Column('lot', sa.String(length=64), nullable=True),
     sa.ForeignKeyConstraint(['role_id'], ['_tiprole.id'], name='fk_tip_role_id', ondelete='SET NULL'),
     sa.PrimaryKeyConstraint('id')
@@ -245,7 +245,7 @@ def upgrade() -> None:
     sa.ForeignKeyConstraint(['contact_id'], ['_contact.id'], name='fk_BS_contact_id', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['extraction_kit_id'], ['_kittype.id'], name='fk_BS_extkit_id', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['reagents_id'], ['_reagent.id'], name='fk_BS_reagents_id', ondelete='SET NULL'),
-    sa.ForeignKeyConstraint(['submission_type_name'], ['_submissiontype.name'], name='fk_BS_subtype_name', ondelete='SET NULL'),
+    sa.ForeignKeyConstraint(['submission_type_name'], ['_submissiontype.sub_type'], name='fk_BS_subtype_name', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['submitting_lab_id'], ['_organization.id'], name='fk_BS_sublab_id', ondelete='SET NULL'),
     sa.PrimaryKeyConstraint('id'),
     sa.UniqueConstraint('rsl_plate_num'),
@@ -277,7 +277,7 @@ def upgrade() -> None:
     op.create_table('_control',
     sa.Column('id', sa.INTEGER(), nullable=False),
     sa.Column('parent_id', sa.INTEGER(), nullable=True),
-    sa.Column('name', sa.String(length=255), nullable=True),
+    sa.Column('sub_type', sa.String(length=255), nullable=True),
     sa.Column('submitted_date', sa.TIMESTAMP(), nullable=True),
     sa.Column('contains', sa.JSON(), nullable=True),
     sa.Column('matches', sa.JSON(), nullable=True),
@@ -291,7 +291,7 @@ def upgrade() -> None:
     sa.ForeignKeyConstraint(['sample_id'], ['_basicsample.id'], name='cont_BCS_id', ondelete='SET NULL'),
     sa.ForeignKeyConstraint(['submission_id'], ['_basicsubmission.id'], ),
     sa.PrimaryKeyConstraint('id'),
-    sa.UniqueConstraint('name')
+    sa.UniqueConstraint('sub_type')
     )
     op.create_table('_submissionequipmentassociation',
     sa.Column('equipment_id', sa.INTEGER(), nullable=False),

alembic/versions/ef1a0222b882_adding_viral_cultures.py

@@ -24,7 +24,7 @@ def upgrade() -> None:
     sa.PrimaryKeyConstraint('id')
     )
     # with op.batch_alter_table('_process', schema=None) as batch_op:
-    #     batch_op.create_unique_constraint("process_uni", ['name'])
+    #     batch_op.create_unique_constraint("process_uni", ['sub_type'])
     #
     # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
     #     batch_op.create_unique_constraint("subsamp_uni", ['id'])
@@ -40,17 +40,17 @@ def upgrade() -> None:
 
 def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
-    with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
+    # with op.batch_alter_table('_wastewaterarticassociation', schema=None) as batch_op:
-        batch_op.alter_column('source_plate',
+    #     batch_op.alter_column('source_plate',
-               existing_type=sa.String(length=32),
+    #            existing_type=sa.String(length=32),
-               type_=sa.VARCHAR(length=16),
+    #            type_=sa.VARCHAR(length=16),
-               existing_nullable=True)
+    #            existing_nullable=True)
-
+    #
-    with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
+    # with op.batch_alter_table('_submissionsampleassociation', schema=None) as batch_op:
-        batch_op.drop_constraint("subsamp_uni", type_='unique')
+    #     batch_op.drop_constraint("subsamp_uni", type_='unique')
-
+    #
-    with op.batch_alter_table('_process', schema=None) as batch_op:
+    # with op.batch_alter_table('_process', schema=None) as batch_op:
-        batch_op.drop_constraint("process_uni", type_='unique')
+    #     batch_op.drop_constraint("process_uni", type_='unique')
 
     op.drop_table('_viralculture')
     # ### end Alembic commands ###

docs/source/conf.py

@@ -13,7 +13,7 @@ from submissions import __version__, __copyright__, __author__
 
 project = 'RSL Submissions'
 copyright = __copyright__
-author = f"{__author__['name']} - {__author__['email']}"
+author = f"{__author__['sub_type']} - {__author__['email']}"
 release = __version__
 
 # -- General configuration ---------------------------------------------------

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

@@ -58,7 +58,7 @@ class ControlType(BaseClass):
         Get subtypes associated with this controltype (currently used only for Kraken)
 
         Args:
-            mode (str): analysis mode name
+            mode (str): analysis mode sub_type
 
         Returns:
             List[str]: list of subtypes available

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

@@ -5,7 +5,7 @@ from __future__ import annotations
 
 import datetime
 import json
-from pprint import pprint
+from pprint import pprint, pformat
 
 from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT, BLOB
 from sqlalchemy.orm import relationship, validates, Query
@@ -846,7 +846,7 @@ class SubmissionType(BaseClass):
                 pass
         return cls.execute_query(query=query, limit=limit)
 
-    def to_dict(self):
+    def to_export_dict(self):
         base_dict = dict(name=self.name)
         base_dict['info'] = self.construct_info_map(mode='export')
         base_dict['defaults'] = self.defaults
@@ -874,6 +874,7 @@ class SubmissionType(BaseClass):
             return None
         with open(filepath, "r") as f:
             import_dict = json.load(fp=f)
+        logger.debug(pformat(import_dict))
         submission_type = cls.query(name=import_dict['name'])
         if submission_type:
             return submission_type

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

@@ -113,15 +113,6 @@ class BasicSubmission(BaseClass):
     __mapper_args__ = {
         "polymorphic_identity": "Basic Submission",
         "polymorphic_on": submission_type_name,
-        # "polymorphic_on": case(
-        #
-        #     (submission_type_name == "Bacterial Culture", "Bacterial Culture"),
-        #     (submission_type_name == "Wastewater Artic", "Wastewater Artic"),
-        #     (submission_type_name == "Wastewater", "Wastewater"),
-        #     (submission_type_name == "Viral Culture", "Bacterial Culture"),
-        #
-        #     else_="Basic Sample"
-        # ),
         "with_polymorphic": "*",
     }
 
@@ -160,7 +151,7 @@ class BasicSubmission(BaseClass):
         return output
 
     @classmethod
-    def get_default_info(cls, *args):
+    def get_default_info(cls, *args, submission_type: SubmissionType | None = None):
         # NOTE: Create defaults for all submission_types
         parent_defs = super().get_default_info()
         recover = ['filepath', 'samples', 'csv', 'comment', 'equipment']
@@ -185,7 +176,10 @@ class BasicSubmission(BaseClass):
                 continue
             else:
                 output[k] = v
-        st = cls.get_submission_type()
+        if isinstance(submission_type, SubmissionType):
+            st = submission_type
+        else:
+            st = cls.get_submission_type(submission_type)
         if st is None:
             logger.error("No default info for BasicSubmission.")
         else:
@@ -205,18 +199,23 @@ class BasicSubmission(BaseClass):
         return output
 
     @classmethod
-    def get_submission_type(cls) -> SubmissionType:
+    def get_submission_type(cls, sub_type: str | SubmissionType | None = None) -> SubmissionType:
         """
         Gets the SubmissionType associated with this class
 
         Returns:
             SubmissionType: SubmissionType with name equal to this polymorphic identity
         """
-        name = cls.__mapper_args__['polymorphic_identity']
+        match sub_type:
-        return SubmissionType.query(name=name)
+            case str():
+                return SubmissionType.query(name=sub_type)
+            case SubmissionType():
+                return sub_type
+            case _:
+                return SubmissionType.query(cls.__mapper_args__['polymorphic_identity'])
 
     @classmethod
-    def construct_info_map(cls, mode: Literal["read", "write"]) -> dict:
+    def construct_info_map(cls, submission_type:SubmissionType|None=None, mode: Literal["read", "write"]="read") -> dict:
         """
         Method to call submission type's construct info map.
 
@@ -226,17 +225,17 @@ class BasicSubmission(BaseClass):
         Returns:
             dict: Map of info locations.
         """
-        return cls.get_submission_type().construct_info_map(mode=mode)
+        return cls.get_submission_type(submission_type).construct_info_map(mode=mode)
 
     @classmethod
-    def construct_sample_map(cls) -> dict:
+    def construct_sample_map(cls, submission_type:SubmissionType|None=None) -> dict:
         """
         Method to call submission type's construct_sample_map
 
         Returns:
             dict: sample location map
         """
-        return cls.get_submission_type().construct_sample_map()
+        return cls.get_submission_type(submission_type).construct_sample_map()
 
     @classmethod
     def finalize_details(cls, input_dict: dict) -> dict:
@@ -466,7 +465,7 @@ class BasicSubmission(BaseClass):
         Returns:
             pd.DataFrame: Pandas Dataframe of all relevant submissions
         """
-        # logger.debug(f"Querying Type: {submission_type}")
+        logger.debug(f"Querying Type: {submission_type}")
         # logger.debug(f"Using limit: {limit}")
         # NOTE: use lookup function to create list of dicts
         subs = [item.to_dict() for item in
@@ -635,14 +634,13 @@ class BasicSubmission(BaseClass):
         super().save()
 
     @classmethod
-    def get_regex(cls) -> str:
+    def get_regex(cls, submission_type:SubmissionType|str|None=None):
-        """
+        # logger.debug(f"Attempting to get regex for {cls.__mapper_args__['polymorphic_identity']}")
-        Dummy for inheritence.
+        logger.debug(f"Attempting to get regex for {submission_type}")
-
+        try:
-        Returns:
+            return cls.get_submission_type(submission_type).defaults['regex']
-            str: Regex for submission type.
+        except AttributeError as e:
-        """
+            raise AttributeError(f"Couldn't get submission type for {cls.__mapper_args__['polymorphic_identity']}")
-        return cls.construct_regex()
 
     # Polymorphic functions
 
@@ -654,7 +652,8 @@ class BasicSubmission(BaseClass):
         Returns:
             re.Pattern: Regular expression pattern to discriminate between submission types.
         """
-        rstring = rf'{"|".join([item.get_regex() for item in cls.__subclasses__()])}'
+        # rstring = rf'{"|".join([item.get_regex() for item in cls.__subclasses__()])}'
+        rstring = rf'{"|".join([item.defaults["regex"] for item in SubmissionType.query()])}'
         regex = re.compile(rstring, flags=re.IGNORECASE | re.VERBOSE)
         return regex
 
@@ -685,7 +684,7 @@ class BasicSubmission(BaseClass):
                     #          item.__mapper_args__['polymorphic_identity'] == polymorphic_identity][0]
                     model = cls.__mapper__.polymorphic_map[polymorphic_identity].class_
                 except Exception as e:
-                    logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}")
+                    logger.error(f"Could not get polymorph {polymorphic_identity} of {cls} due to {e}, falling back to BasicSubmission")
             case _:
                 pass
         if attrs is None or len(attrs) == 0:
@@ -796,11 +795,13 @@ class BasicSubmission(BaseClass):
         # logger.info(f"Hello from {cls.__mapper_args__['polymorphic_identity']} Enforcer!")
         from backend.validators import RSLNamer
         # logger.debug(f"instr coming into {cls}: {instr}")
-        # logger.debug(f"data coming into {cls}: {data}")
+        logger.debug(f"data coming into {cls}: {data}")
-        defaults = cls.get_default_info("abbreviation", "submission_type")
+        # defaults = cls.get_default_info("abbreviation", "submission_type")
-        data['abbreviation'] = defaults['abbreviation']
+        data['abbreviation'] = cls.get_default_info("abbreviation", submission_type=data['submission_type'])
-        if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
+        # logger.debug(f"Default info: {defaults}")
-            data['submission_type'] = defaults['submission_type']
+        # data['abbreviation'] = defaults['abbreviation']
+        # if 'submission_type' not in data.keys() or data['submission_type'] in [None, ""]:
+        #     data['submission_type'] = defaults['submission_type']
         if instr in [None, ""]:
             # logger.debug("Sending to RSLNamer to make new plate name.")
             outstr = RSLNamer.construct_new_plate_name(data=data)
@@ -829,9 +830,11 @@ class BasicSubmission(BaseClass):
         except AttributeError as e:
             repeat = ""
         outstr = re.sub(r"(-\dR)\d?", rf"\1 {repeat}", outstr).replace(" ", "")
-        abb = cls.get_default_info('abbreviation')
+        # abb = cls.get_default_info('abbreviation')
-        outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
+        # outstr = re.sub(rf"RSL{abb}", rf"RSL-{abb}", outstr)
-        return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
+        # return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
+        outstr = re.sub(rf"RSL{data['abbreviation']}", rf"RSL-{data['abbreviation']}", outstr)
+        return re.sub(rf"{data['abbreviation']}(\d)", rf"{data['abbreviation']}-\1", outstr)
 
     @classmethod
     def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
@@ -1261,15 +1264,15 @@ class BacterialCulture(BasicSubmission):
             output['controls'] = [item.to_sub_dict() for item in self.controls]
         return output
 
-    @classmethod
+    # @classmethod
-    def get_regex(cls) -> str:
+    # def get_regex(cls) -> str:
-        """
+    #     """
-        Retrieves string for regex construction.
+    #     Retrieves string for regex construction.
-
+    #
-        Returns:
+    #     Returns:
-            str: string for regex construction
+    #         str: string for regex construction
-        """
+    #     """
-        return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    #     return "(?P<Bacterial_Culture>RSL(?:-|_)?BC(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
 
     @classmethod
     def filename_template(cls):
@@ -1339,47 +1342,47 @@ class BacterialCulture(BasicSubmission):
         return input_dict
 
 
-class ViralCulture(BasicSubmission):
+# class ViralCulture(BasicSubmission):
-
+#
-    id = Column(INTEGER, ForeignKey('_basicsubmission.id'), primary_key=True)
+#     id = Column(INTEGER, ForeignKey('_basicsubmission.id'), primary_key=True)
-    __mapper_args__ = dict(polymorphic_identity="Viral Culture",
+#     __mapper_args__ = dict(polymorphic_identity="Viral Culture",
-                           polymorphic_load="inline",
+#                            polymorphic_load="inline",
-                           inherit_condition=(id == BasicSubmission.id))
+#                            inherit_condition=(id == BasicSubmission.id))
-
+#
-    @classmethod
+#     # @classmethod
-    def get_regex(cls) -> str:
+#     # def get_regex(cls) -> str:
-        """
+#     #     """
-        Retrieves string for regex construction.
+#     #     Retrieves string for regex construction.
-
+#     #
-        Returns:
+#     #     Returns:
-            str: string for regex construction
+#     #         str: string for regex construction
-        """
+#     #     """
-        return "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+#     #     return "(?P<Viral_Culture>RSL(?:-|_)?VE(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
-
+#
-    @classmethod
+#     @classmethod
-    def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
+#     def custom_sample_autofill_row(cls, sample, worksheet: Worksheet) -> int:
-        """
+#         """
-        Extends parent
+#         Extends parent
-        """
+#         """
-        # logger.debug(f"Checking {sample.well}")
+#         # logger.debug(f"Checking {sample.well}")
-        # logger.debug(f"here's the worksheet: {worksheet}")
+#         # logger.debug(f"here's the worksheet: {worksheet}")
-        row = super().custom_sample_autofill_row(sample, worksheet)
+#         row = super().custom_sample_autofill_row(sample, worksheet)
-        df = pd.DataFrame(list(worksheet.values))
+#         df = pd.DataFrame(list(worksheet.values))
-        # logger.debug(f"Here's the dataframe: {df}")
+#         # logger.debug(f"Here's the dataframe: {df}")
-        idx = df[df[0] == sample.well]
+#         idx = df[df[0] == sample.well]
-        if idx.empty:
+#         if idx.empty:
-            new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
+#             new = f"{sample.well[0]}{sample.well[1:].zfill(2)}"
-            # logger.debug(f"Checking: {new}")
+#             # logger.debug(f"Checking: {new}")
-            idx = df[df[0] == new]
+#             idx = df[df[0] == new]
-        # logger.debug(f"Here is the row: {idx}")
+#         # logger.debug(f"Here is the row: {idx}")
-        row = idx.index.to_list()[0]
+#         row = idx.index.to_list()[0]
-        return row + 1
+#         return row + 1
-
+#
-    @classmethod
+#     @classmethod
-    def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
+#     def custom_info_parser(cls, input_dict: dict, xl: Workbook | None = None, custom_fields: dict = {}) -> dict:
-        input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
+#         input_dict = super().custom_info_parser(input_dict=input_dict, xl=xl, custom_fields=custom_fields)
-        logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
+#         logger.debug(f"\n\nInfo dictionary:\n\n{pformat(input_dict)}\n\n")
-        return input_dict
+#         return input_dict
 
 
 class Wastewater(BasicSubmission):
@@ -1499,15 +1502,15 @@ class Wastewater(BasicSubmission):
         outstr = super().enforce_name(instr=instr, data=data)
         return outstr
 
-    @classmethod
+    # @classmethod
-    def get_regex(cls) -> str:
+    # def get_regex(cls) -> str:
-        """
+    #     """
-        Retrieves string for regex construction
+    #     Retrieves string for regex construction
-
+    #
-        Returns:
+    #     Returns:
-            str: String for regex construction
+    #         str: String for regex construction
-        """
+    #     """
-        return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
+    #     return "(?P<Wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)?\d?([^_0123456789\sA-QS-Z]|$)?R?\d?)?)"
 
     @classmethod
     def adjust_autofill_samples(cls, samples: List[Any]) -> List[Any]:
@@ -1919,15 +1922,15 @@ class WastewaterArtic(BasicSubmission):
         # logger.debug(f"Final EN name: {final_en_name}")
         return final_en_name
 
-    @classmethod
+    # @classmethod
-    def get_regex(cls) -> str:
+    # def get_regex(cls) -> str:
-        """
+    #     """
-        Retrieves string for regex construction
+    #     Retrieves string for regex construction
-
+    #
-        Returns:
+    #     Returns:
-            str: string for regex construction.
+    #         str: string for regex construction.
-        """
+    #     """
-        return "(?P<Wastewater_Artic>(\\d{4}-\\d{2}-\\d{2}(?:-|_)(?:\\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)\\d?(\\D|$)R?\\d?)?))"
+    #     return "(?P<Wastewater_Artic>(\\d{4}-\\d{2}-\\d{2}(?:-|_)(?:\\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\\d{2}-?\\d{2}-?\\d{2}(?:(_|-)\\d?(\\D|$)R?\\d?)?))"
 
     @classmethod
     def finalize_parse(cls, input_dict: dict, xl: pd.ExcelFile | None = None, info_map: dict | None = None) -> dict:

src/submissions/backend/excel/parser.py

@@ -76,6 +76,7 @@ class SheetParser(object):
                     # NOTE: Rescue submission type using scraped values to be used in Sample, Reagents, etc.
                     if v not in [None, "None", "", " "]:
                         self.submission_type = SubmissionType.query(name=v)
+                        logger.debug(f"Updated self.submission_type to {self.submission_type}")
                 case _:
                     self.sub[k] = v
 
@@ -202,7 +203,7 @@ class InfoParser(object):
         """
         self.submission_type = dict(value=self.submission_type_obj.name, missing=True)
         # logger.debug(f"Looking up submission type: {self.submission_type['value']}")
-        info_map = self.sub_object.construct_info_map("read")
+        info_map = self.sub_object.construct_info_map(submission_type=self.submission_type_obj, mode="read")
         # NOTE: Get the parse_info method from the submission type specified
         return info_map
 
@@ -385,10 +386,12 @@ class SampleParser(object):
         self.xl = xl
         if isinstance(submission_type, str):
             submission_type = SubmissionType.query(name=submission_type)
+        logger.debug(f"Sample parser is using submission type: {submission_type}")
         self.submission_type = submission_type.name
         self.submission_type_obj = submission_type
         if sub_object is None:
-            sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type_obj.name)
+            logger.warning(f"Sample parser attempting to fetch submission class with polymorphic identity: {self.submission_type}")
+            sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
         self.sub_object = sub_object
         self.sample_info_map = self.fetch_sample_info_map(submission_type=submission_type, sample_map=sample_map)
         # logger.debug(f"sample_info_map: {self.sample_info_map}")
@@ -406,12 +409,12 @@ class SampleParser(object):
             dict: Info locations.
         """
         # logger.debug(f"Looking up submission type: {submission_type}")
-        self.sample_type = self.sub_object.get_default_info("sample_type")
+        self.sample_type = self.sub_object.get_default_info("sample_type", submission_type=submission_type)
         self.samp_object = BasicSample.find_polymorphic_subclass(polymorphic_identity=self.sample_type)
         # logger.debug(f"Got sample class: {self.samp_object.__name__}")
         # logger.debug(f"info_map: {pformat(se)}")
         if sample_map is None:
-            sample_info_map = self.sub_object.construct_sample_map()
+            sample_info_map = self.sub_object.construct_sample_map(submission_type=self.submission_type_obj)
         else:
             sample_info_map = sample_map
         return sample_info_map

src/submissions/backend/validators/__init__.py

@@ -26,11 +26,11 @@ class RSLNamer(object):
         if self.submission_type is None:
             # logger.debug("Creating submission type because none exists")
             self.submission_type = self.retrieve_submission_type(filename=filename)
-        # logger.debug(f"got submission type: {self.submission_type}")
+        logger.debug(f"got submission type: {self.submission_type}")
         if self.submission_type is not None:
             # logger.debug("Retrieving BasicSubmission subclass")
             self.sub_object = BasicSubmission.find_polymorphic_subclass(polymorphic_identity=self.submission_type)
-            self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex())
+            self.parsed_name = self.retrieve_rsl_number(filename=filename, regex=self.sub_object.get_regex(submission_type=sub_type))
             if data is None:
                 data = dict(submission_type=self.submission_type)
             if "submission_type" not in data.keys():
@@ -50,7 +50,7 @@ class RSLNamer(object):
         """
         match filename:
             case Path():
-                # logger.debug(f"Using path method for {filename}.")
+                logger.debug(f"Using path method for {filename}.")
                 if filename.exists():
                     wb = load_workbook(filename)
                     try:
@@ -70,12 +70,14 @@ class RSLNamer(object):
                     submission_type = cls.retrieve_submission_type(filename=filename.stem.__str__())
             case str():
                 regex = BasicSubmission.construct_regex()
-                # logger.debug(f"Using string method for {filename}.")
+                logger.debug(f"Using string method for {filename}.")
+                logger.debug(f"Using regex: {regex}")
                 m = regex.search(filename)
                 try:
                     submission_type = m.lastgroup
+                    logger.debug(f"Got submission type: {submission_type}")
                 except AttributeError as e:
-                    logger.critical(f"No RSL plate number found or submission type found!: {e}")
+                    logger.critical(f"No submission type found or submission type found!: {e}")
             case _:
                 submission_type = None
         try:
@@ -112,7 +114,7 @@ class RSLNamer(object):
                 regex = re.compile(rf'{regex}', re.IGNORECASE | re.VERBOSE)
             except re.error as e:
                 regex = BasicSubmission.construct_regex()
-        # logger.debug(f"Using regex: {regex}")
+        logger.debug(f"Using regex: {regex}")
         match filename:
             case Path():
                 m = regex.search(filename.stem)

src/submissions/backend/validators/pydant.py

@@ -509,7 +509,7 @@ class PydSubmission(BaseModel, extra='allow'):
         if check_not_nan(value['value']):
             return value
         else:
-            # logger.debug("Constructing plate name.")
+            # logger.debug("Constructing plate sub_type.")
             if "pytest" in sys.modules and sub_type.replace(" ", "") == "BasicSubmission":
                 output = "RSL-BS-Test001"
             else:
@@ -642,7 +642,7 @@ class PydSubmission(BaseModel, extra='allow'):
         # this could also be done with default_factory
         self.submission_object = BasicSubmission.find_polymorphic_subclass(
             polymorphic_identity=self.submission_type['value'])
-        self.namer = RSLNamer(self.rsl_plate_num['value'])
+        self.namer = RSLNamer(self.rsl_plate_num['value'], sub_type=self.submission_type['value'])
 
     def set_attribute(self, key: str, value):
         """

src/submissions/frontend/widgets/controls_chart.py

@@ -170,7 +170,7 @@ class ControlsViewer(QWidget):
         Args:
             ctx (dict): settings passed from gui
             input_df (list[dict]): list of dictionaries containing records
-            subtype (str | None, optional): name of submission type. Defaults to None.
+            subtype (str | None, optional): sub_type of submission type. Defaults to None.
 
         Returns:
             DataFrame: dataframe of controls

src/submissions/frontend/widgets/submission_widget.py

@@ -185,7 +185,7 @@ class SubmissionFormWidget(QWidget):
         self.pyd = submission
         self.missing_info = []
         st = SubmissionType.query(name=self.pyd.submission_type['value']).get_submission_class()
-        defaults = st.get_default_info("form_recover", "form_ignore")
+        defaults = st.get_default_info("form_recover", "form_ignore", submission_type=self.pyd.submission_type['value'])
         self.recover = defaults['form_recover']
         self.ignore = defaults['form_ignore']
         # logger.debug(f"Attempting to extend ignore list with {self.pyd.submission_type['value']}")
@@ -554,6 +554,8 @@ class SubmissionFormWidget(QWidget):
                     add_widget.addItems(cats)
                     add_widget.setToolTip("Enter submission category or select from list.")
                 case _:
+                    # if key in sub_obj.get_default_info("form_ignore", submission_type=submission_type):
+                    #     return None
                     if key in sub_obj.timestamps():
                         add_widget = MyQDateEdit(calendarPopup=True, scrollWidget=parent)
                         # NOTE: sets submitted date based on date found in excel sheet