Working new version.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202309.02
+
+- Massive restructure of app and database to allow better relationships between kits/reagenttypes & submissions/samples.
+
 ## 202308.03
 
 - Large restructure of database to allow better relationships between kits/reagenttypes & submissions/samples.

TODO.md

@@ -1,8 +1,8 @@
 - [ ] Clean up & document code... again.
     - Including paring down the logging.debugs
 - [ ] Fix Tests... again.
-- [ ] Rebuild database
+- [x] Rebuild database
-- [ ] Provide more generic names for reagenttypes in kits and move specific names to reagents.
+- [x] Provide more generic names for reagenttypes in kits and move specific names to reagents.
     - ex. Instead of "omega_e-z_96_disruptor_plate_c_plus" in reagent types, have "omega_plate" and have "omega_e-z_96_disruptor_plate_c_plus" in reagent name.
     - Maybe rename to "ReagentRoles"?
     - If I'm doing this, since the forms have a different layout for each submission type I should rewrite the parser to use the locations given in database... Which I should do anyway

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202308.1b"
+__version__ = "202309.2b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 
@@ -32,4 +32,8 @@ class bcolors:
 
 # Landon, this is your slightly less past self here. For the most part, Past Landon has not screwed us. I've been able to add in the
 # Wastewater Artic with minimal difficulties, except that the parser of the non-standard, user-generated excel sheets required slightly
-# more work.
+# more work.
+
+# Landon, this is your even more slightly less past self here. I've overhauled a lot of stuff to make things more flexible, so you should
+# hopefully be even less screwed than before... at least with regards to parsers. The addition of kits and such is another story. Putting that
+# On the todo list.

src/submissions/backend/db/functions.py

@@ -4,9 +4,6 @@ Convenience functions for interacting with the database.
 
 import pprint
 from . import models
-# from .models.kits import KitType
-# from .models.submissions import BasicSample, reagents_submissions, BasicSubmission, SubmissionSampleAssociation
-# from .models import submissions
 import pandas as pd
 import sqlalchemy.exc
 import sqlite3
@@ -34,7 +31,7 @@ def set_sqlite_pragma(dbapi_connection, connection_record):
     cursor.execute("PRAGMA foreign_keys=ON")
     cursor.close()
 
-def store_submission(ctx:Settings, base_submission:models.BasicSubmission, samples:List[dict]=[]) -> None|dict:
+def store_submission(ctx:Settings, base_submission:models.BasicSubmission) -> None|dict:
     """
     Upserts submissions into database
 
@@ -46,55 +43,19 @@ def store_submission(ctx:Settings, base_submission:models.BasicSubmission, sampl
         None|dict : object that indicates issue raised for reporting in gui
     """    
     logger.debug(f"Hello from store_submission")
-    # Add all samples to sample table
+    # Final check for proper RSL name
     typer = RSLNamer(ctx=ctx, instr=base_submission.rsl_plate_num)
     base_submission.rsl_plate_num = typer.parsed_name
-    # for sample in samples:
-    #     instance = sample['sample']
-    #     logger.debug(f"Typer: {typer.submission_type}")
-    #     logger.debug(f"sample going in: {type(sample['sample'])}\n{sample['sample'].__dict__}")
-    #     # Suuuuuper hacky way to be sure that the artic doesn't overwrite the ww plate in a ww sample
-    #     # need something more elegant
-    #     # if "_artic" not in typer.submission_type:
-    #     #     sample.rsl_plate = base_submission
-    #     # else:
-    #     #     logger.debug(f"{sample.ww_sample_full_id} is an ARTIC sample.")
-    #     #     # base_submission.samples.remove(sample)
-    #     #     # sample.rsl_plate = sample.rsl_plate
-    #     #     # sample.artic_rsl_plate = base_submission
-    #     # logger.debug(f"Attempting to add sample: {sample.to_string()}")
-    #     # try:
-    #         # ctx['database_session'].add(sample)
-    #     # ctx.database_session.add(instance)
-    #     # ctx.database_session.commit()
-    #     # logger.debug(f"Submitter id: {sample['sample'].submitter_id} and table id: {sample['sample'].id}")
-    #     logger.debug(f"Submitter id: {instance.submitter_id} and table id: {instance.id}")
-    #     assoc = SubmissionSampleAssociation(submission=base_submission, sample=instance, row=sample['row'], column=sample['column'])
-        
-    #     # except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
-    #     #     logger.debug(f"Hit an integrity error : {e}")
-    #     #     continue
-    #     try:
-    #         base_submission.submission_sample_associations.append(assoc)
-    #     except IntegrityError as e:
-    #         logger.critical(e)
-    #         continue
-        # logger.debug(f"Here is the sample to be stored in the DB: {sample.__dict__}")
-    # Add submission to submission table
-    # ctx['database_session'].add(base_submission)
     ctx.database_session.add(base_submission)
     logger.debug(f"Attempting to add submission: {base_submission.rsl_plate_num}")
     try:
-        # ctx['database_session'].commit()
         ctx.database_session.commit()
     except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
         logger.debug(f"Hit an integrity error : {e}")
-        # ctx['database_session'].rollback()
         ctx.database_session.rollback()
         return {"message":"This plate number already exists, so we can't add it.", "status":"Critical"}
     except (sqlite3.OperationalError, sqlalchemy.exc.IntegrityError) as e:
         logger.debug(f"Hit an operational error: {e}")
-        # ctx['database_session'].rollback()
         ctx.database_session.rollback()
         return {"message":"The database is locked for editing.", "status":"Critical"}
     return None
@@ -111,10 +72,8 @@ def store_reagent(ctx:Settings, reagent:models.Reagent) -> None|dict:
         None|dict: object indicating issue to be reported in the gui
     """    
     logger.debug(f"Reagent dictionary: {reagent.__dict__}")
-    # ctx['database_session'].add(reagent)
     ctx.database_session.add(reagent)
     try:
-        # ctx['database_session'].commit()
         ctx.database_session.commit()
     except (sqlite3.OperationalError, sqlalchemy.exc.OperationalError):
         return {"message":"The database is locked for editing."}
@@ -131,7 +90,6 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
     Returns:
         models.BasicSubmission: Constructed submission object
     """
-    # from tools import check_regex_match, RSLNamer
     # convert submission type into model name
     query = info_dict['submission_type'].replace(" ", "")
     # Ensure an rsl plate number exists for the plate
@@ -143,8 +101,6 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
         # enforce conventions on the rsl plate number from the form
         info_dict['rsl_plate_num'] = RSLNamer(ctx=ctx, instr=info_dict["rsl_plate_num"]).parsed_name
     # check database for existing object
-    # instance = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
-    # instance = ctx.database_session.query(models.BasicSubmission).filter(models.BasicSubmission.rsl_plate_num==info_dict['rsl_plate_num']).first()
     instance = lookup_submission_by_rsl_num(ctx=ctx, rsl_num=info_dict['rsl_plate_num'])
     # get model based on submission type converted above
     logger.debug(f"Looking at models for submission type: {query}")
@@ -166,7 +122,6 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
         # set fields based on keys in dictionary
         match item:
             case "extraction_kit":
-                # q_str = info_dict[item]
                 logger.debug(f"Looking up kit {value}")
                 try:
                     field_value = lookup_kittype_by_name(ctx=ctx, name=value)
@@ -185,13 +140,7 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
                 field_value = lookup_org_by_name(ctx=ctx, name=value)
                 logger.debug(f"Got {field_value} for organization {value}")
             case "submitter_plate_num":
-                # Because of unique constraint, there will be problems with 
-                # multiple submissions named 'None', so...
-                # Should be depreciated with use of pydantic validator
                 logger.debug(f"Submitter plate id: {value}")
-                # if info_dict[item] == None or info_dict[item] == "None" or info_dict[item] == "":
-                #     logger.debug(f"Got None as a submitter plate number, inserting random string to preserve database unique constraint.")
-                #     info_dict[item] = uuid.uuid4().hex.upper()
                 field_value = value
             case "samples":
                 for sample in value:
@@ -200,6 +149,7 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
                         sample_instance = sample['sample']
                     else:
                         logger.warning(f"Sample {sample} already exists, creating association.")
+                    logger.debug(f"Adding {sample_instance.__dict__}")
                     if sample_instance in instance.samples:
                         logger.error(f"Looks like there's a duplicate sample on this plate: {sample_instance.submitter_id}!")
                         continue
@@ -207,7 +157,7 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
                         with ctx.database_session.no_autoflush:
                             try:
                                 sample_query = sample_instance.sample_type.replace('Sample', '').strip()
-                                logger.debug(f"Here is the sample instance type: {sample_query}")
+                                logger.debug(f"Here is the sample instance type: {sample_instance}")
                                 try:
                                     assoc = getattr(models, f"{sample_query}Association")
                                 except AttributeError as e:
@@ -227,7 +177,6 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
                         continue
                 continue
             case "submission_type":
-                # item = "submission_type"
                 field_value = lookup_submissiontype_by_name(ctx=ctx, type_name=value)            
             case _:
                 field_value = value
@@ -242,14 +191,13 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
     # calculate cost of the run: immutable cost + mutable times number of columns
     # This is now attached to submission upon creation to preserve at-run costs incase of cost increase in the future.
     try:
-        # ceil(instance.sample_count / 8) will get number of columns
-        # the cost of a full run multiplied by (that number / 12) is x twelfths the cost of a full run
         logger.debug(f"Calculating costs for procedure...")
         instance.calculate_base_cost()
     except (TypeError, AttributeError) as e:
         logger.debug(f"Looks like that kit doesn't have cost breakdown yet due to: {e}, using full plate cost.")
         instance.run_cost = instance.extraction_kit.cost_per_run
     logger.debug(f"Calculated base run cost of: {instance.run_cost}")
+    # Apply any discounts that are applicable for client and kit.
     try:
         logger.debug("Checking and applying discounts...")
         discounts = [item.amount for item in lookup_discounts_by_org_and_kit(ctx=ctx, kit_id=instance.extraction_kit.id, lab_id=instance.submitting_lab.id)]
@@ -299,12 +247,6 @@ def construct_reagent(ctx:Settings, info_dict:dict) -> models.Reagent:
                     reagent.name = info_dict[item]
     # add end-of-life extension from reagent type to expiry date
     # NOTE: this will now be done only in the reporting phase to account for potential changes in end-of-life extensions
-    # try:
-    #     reagent.expiry = reagent.expiry + reagent.type.eol_ext
-    # except TypeError as e:
-    #     logger.debug(f"We got a type error: {e}.")
-    # except AttributeError:
-    #     pass
     return reagent
 
 def get_all_reagenttype_names(ctx:Settings) -> list[str]:
@@ -317,7 +259,6 @@ def get_all_reagenttype_names(ctx:Settings) -> list[str]:
     Returns:
         list[str]: reagent type names
     """    
-    # lookedup = [item.__str__() for item in ctx['database_session'].query(models.ReagentType).all()]
     lookedup = [item.__str__() for item in ctx.database_session.query(models.ReagentType).all()]
     return lookedup
 
@@ -333,12 +274,11 @@ def lookup_reagenttype_by_name(ctx:Settings, rt_name:str) -> models.ReagentType:
         models.ReagentType: looked up reagent type
     """    
     logger.debug(f"Looking up ReagentType by name: {rt_name.title()}")
-    # lookedup = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
     lookedup = ctx.database_session.query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
     logger.debug(f"Found ReagentType: {lookedup}")
     return lookedup
 
-def lookup_kittype_by_use(ctx:Settings, used_by:str|None=None) -> list[models.KitType]:
+def lookup_kittype_by_use(ctx:Settings, used_for:str|None=None) -> list[models.KitType]:
     """
     Lookup kits by a sample type its used for
 
@@ -349,10 +289,9 @@ def lookup_kittype_by_use(ctx:Settings, used_by:str|None=None) -> list[models.Ki
     Returns:
         list[models.KitType]: list of kittypes that have that sample type in their uses
     """    
-    if used_by != None:
+    if used_for != None:
-        # return ctx['database_session'].query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
+        # Get kittypes whose 'used_for' name is used_for. 
-        # return ctx.database_session.query(models.KitType).filter(models.KitType.used_for.contains(used_by)).all()
+        return ctx.database_session.query(models.KitType).filter(models.KitType.used_for.any(name=used_for)).all()
-        return ctx.database_session.query(models.KitType).filter(models.KitType.used_for.any(name=used_by)).all()
     else:
         # return ctx['database_session'].query(models.KitType).all()
         return ctx.database_session.query(models.KitType).all()
@@ -371,11 +310,20 @@ def lookup_kittype_by_name(ctx:Settings, name:str|dict) -> models.KitType:
     if isinstance(name, dict):
         name = name['value']
     logger.debug(f"Querying kittype: {name}")
-    # return ctx['database_session'].query(models.KitType).filter(models.KitType.name==name).first()
     with ctx.database_session.no_autoflush:
         return ctx.database_session.query(models.KitType).filter(models.KitType.name==name).first()
     
 def lookup_kittype_by_id(ctx:Settings, id:int) -> models.KitType:
+    """
+    Find a kit by its id integer
+
+    Args:
+        ctx (Settings): Settings passed down from gui
+        id (int): id number of the kit.
+
+    Returns:
+        models.KitType: Kit.
+    """    
     return ctx.database_session.query(models.KitType).filter(models.KitType.id==id).first()
 
 def lookup_regent_by_type_name(ctx:Settings, type_name:str) -> list[models.Reagent]:
@@ -389,7 +337,6 @@ def lookup_regent_by_type_name(ctx:Settings, type_name:str) -> list[models.Reage
     Returns:
         list[models.Reagent]: list of retrieved reagents
     """    
-    # return ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
     return ctx.database_session.query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name==type_name).all()
 
 def lookup_regent_by_type_name_and_kit_name(ctx:Settings, type_name:str, kit_name:str) -> list[models.Reagent]:
@@ -406,8 +353,6 @@ def lookup_regent_by_type_name_and_kit_name(ctx:Settings, type_name:str, kit_nam
     """    
     # What I want to do is get the reagent type by name 
     # Hang on, this is going to be a long one.
-    # by_type = ctx['database_session'].query(models.Reagent).join(models.Reagent.type, aliased=True).filter(models.ReagentType.name.endswith(type_name)).all()
-    # rt_types = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name.endswith(type_name))
     rt_types = ctx.database_session.query(models.ReagentType).filter(models.ReagentType.name.endswith(type_name))
     # add filter for kit name... 
     try:
@@ -440,7 +385,7 @@ def lookup_all_submissions_by_type(ctx:Settings, sub_type:str|None=None, chronol
         subs = ctx.database_session.query(models.BasicSubmission)
     else:
         # subs = ctx['database_session'].query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_")).all()
-        subs = ctx.database_session.query(models.BasicSubmission).filter(models.BasicSubmission.submission_type==sub_type.lower().replace(" ", "_"))
+        subs = ctx.database_session.query(models.BasicSubmission).filter(models.BasicSubmission.submission_type_name==sub_type)
     if chronologic:
         subs.order_by(models.BasicSubmission.submitted_date)
     return subs.all()
@@ -1172,6 +1117,25 @@ def lookup_subsamp_association_by_plate_sample(ctx:Settings, rsl_plate_num:str,
                 .filter(models.BasicSample.submitter_id==rsl_sample_num)\
                 .first()
 
+def lookup_sub_wwsamp_association_by_plate_sample(ctx:Settings, rsl_plate_num:str, rsl_sample_num:str) -> models.WastewaterAssociation:
+    """
+    _summary_
+
+    Args:
+        ctx (Settings): _description_
+        rsl_plate_num (str): _description_
+        sample_submitter_id (_type_): _description_
+
+    Returns:
+        models.SubmissionSampleAssociation: _description_
+    """    
+    return ctx.database_session.query(models.WastewaterAssociation)\
+                .join(models.Wastewater)\
+                .join(models.WastewaterSample)\
+                .filter(models.BasicSubmission.rsl_plate_num==rsl_plate_num)\
+                .filter(models.BasicSample.submitter_id==rsl_sample_num)\
+                .first()
+
 def lookup_all_reagent_names_by_role(ctx:Settings, role_name:str) -> List[str]:
     """
     _summary_
@@ -1222,4 +1186,18 @@ def add_reagenttype_to_kit(ctx:Settings, rt_name:str, kit_name:str, eol:int=0):
     kit.kit_reagenttype_associations.append(assoc)
     ctx.database_session.add(kit)
     ctx.database_session.commit()
-    
+
+def lookup_subsamp_association_by_models(ctx:Settings, submission:models.BasicSubmission, sample:models.BasicSample) -> models.SubmissionSampleAssociation:
+    return ctx.database_session.query(models.SubmissionSampleAssociation) \
+        .filter(models.SubmissionSampleAssociation.submission==submission) \
+        .filter(models.SubmissionSampleAssociation.sample==sample).first()
+
+def update_subsampassoc_with_pcr(ctx:Settings, submission:models.BasicSubmission, sample:models.BasicSample, input_dict:dict):
+    assoc = lookup_subsamp_association_by_models(ctx, submission=submission, sample=sample)
+    for k,v in input_dict.items():
+        try:
+            setattr(assoc, k, v)
+        except AttributeError:
+            logger.error(f"Can't set {k} to {v}")
+    ctx.database_session.add(assoc)
+    ctx.database_session.commit()

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

@@ -9,5 +9,4 @@ metadata = Base.metadata
 from .controls import Control, ControlType
 from .kits import KitType, ReagentType, Reagent, Discount, KitTypeReagentTypeAssociation, SubmissionType, SubmissionTypeKitTypeAssociation
 from .organizations import Organization, Contact
-# from .samples import WWSample, BCSample, BasicSample
 from .submissions import BasicSubmission, BacterialCulture, Wastewater, WastewaterArtic, WastewaterSample, BacterialCultureSample, BasicSample, SubmissionSampleAssociation, WastewaterAssociation

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

@@ -12,16 +12,6 @@ import logging
 logger = logging.getLogger(f'submissions.{__name__}')
 
 
-# # Table containing reagenttype-kittype relationships
-# reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, 
-#                               Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), 
-#                               Column("kits_id", INTEGER, ForeignKey("_kits.id")),
-#                             #   The entry will look like ["Bacteria Culture":{"row":1, "column":4}]
-#                               Column("uses", JSON),
-#                             #   is the reagent required for that kit?
-#                               Column("required", INTEGER)
-#                               )
-
 reagenttypes_reagents = Table("_reagenttypes_reagents", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("reagenttype_id", INTEGER, ForeignKey("_reagent_types.id")))
 
 
@@ -34,13 +24,7 @@ class KitType(Base):
     id = Column(INTEGER, primary_key=True) #: primary key  
     name = Column(String(64), unique=True) #: name of kit
     submissions = relationship("BasicSubmission", back_populates="extraction_kit") #: submissions this kit was used for
-    # used_for = Column(JSON) #: list of names of sample types this kit can process
+    
-    # used_for = relationship("SubmissionType", back_populates="extraction_kits", uselist=True, secondary=submissiontype_kittypes)
-    # cost_per_run = Column(FLOAT(2)) #: dollar amount for each full run of this kit NOTE: depreciated, use the constant and mutable costs instead
-    # reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes) #: reagent types this kit contains
-    # reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id")) #: joined reagent type id
-    # kit_reagenttype_association = 
-
     kit_reagenttype_associations = relationship(
         "KitTypeReagentTypeAssociation",
         back_populates="kit_type",
@@ -51,7 +35,6 @@ class KitType(Base):
     # to "keyword" attribute
     reagent_types = association_proxy("kit_reagenttype_associations", "reagent_type")
 
-
     kit_submissiontype_associations = relationship(
         "SubmissionTypeKitTypeAssociation",
         back_populates="kit_type",
@@ -60,7 +43,6 @@ class KitType(Base):
 
     used_for = association_proxy("kit_submissiontype_associations", "submission_type")
 
-
     def __repr__(self) -> str:
         return f"<KitType({self.name})>"
     
@@ -74,6 +56,15 @@ class KitType(Base):
         return self.name
     
     def get_reagents(self, required:bool=False) -> list:
+        """
+        Return ReagentTypes linked to kit through KitTypeReagentTypeAssociation.
+
+        Args:
+            required (bool, optional): If true only return required types. Defaults to False.
+
+        Returns:
+            list: List of ReagentTypes
+        """        
         if required:
             return [item.reagent_type for item in self.kit_reagenttype_associations if item.required == 1]
         else:
@@ -81,14 +72,24 @@ class KitType(Base):
     
 
     def construct_xl_map_for_use(self, use:str) -> dict:
-        # map = self.used_for[use]
+        """
+        Creates map of locations in excel workbook for a SubmissionType
+
+        Args:
+            use (str): Submissiontype.name
+
+        Returns:
+            dict: Dictionary containing information locations.
+        """        
         map = {}
+        # Get all KitTypeReagentTypeAssociation for SubmissionType
         assocs = [item for item in self.kit_reagenttype_associations if use in item.uses]
         for assoc in assocs:
             try:
                 map[assoc.reagent_type.name] = assoc.uses[use]
             except TypeError:
                 continue
+        # Get SubmissionType info map
         try:
             st_assoc = [item for item in self.used_for if use == item.name][0]
             map['info'] = st_assoc.info_map
@@ -106,7 +107,6 @@ class KitTypeReagentTypeAssociation(Base):
     kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
     uses = Column(JSON)
     required = Column(INTEGER)
-    # reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
 
     kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
 
@@ -139,11 +139,8 @@ class ReagentType(Base):
 
     id = Column(INTEGER, primary_key=True) #: primary key  
     name = Column(String(64)) #: name of reagent type
-    # kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id")) #: id of joined kit type
-    # kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id]) #: kits this reagent is used in
     instances = relationship("Reagent", back_populates="type", secondary=reagenttypes_reagents) #: concrete instances of this reagent type
     eol_ext = Column(Interval()) #: extension of life interval
-    # required = Column(INTEGER, server_default="1") #: sqlite boolean to determine if reagent type is essential for the kit
     last_used = Column(String(32)) #: last used lot number of this type of reagent
 
     @validates('required')
@@ -202,8 +199,10 @@ class Reagent(Base):
             dict: gui friendly dictionary
         """        
         if extraction_kit != None:
+            # Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
             try:
                 reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
+            # Most will be able to fall back to first ReagentType in itself because most will only have 1.
             except:
                 reagent_role = self.type[0]
         else:
@@ -212,9 +211,9 @@ class Reagent(Base):
             rtype = reagent_role.name.replace("_", " ").title()
         except AttributeError:
             rtype = "Unknown"
+        # Calculate expiry with EOL from ReagentType
         try:
             place_holder = self.expiry + reagent_role.eol_ext
-            # logger.debug(f"EOL_ext for {self.lot} -- {self.expiry} + {self.type.eol_ext} = {place_holder}")
         except TypeError as e:
             place_holder = date.today()
             logger.debug(f"We got a type error setting {self.lot} expiry: {e}. setting to today for testing")
@@ -227,9 +226,28 @@ class Reagent(Base):
             "expiry": place_holder.strftime("%Y-%m-%d")
         }
     
-    def to_reagent_dict(self) -> dict:
+    def to_reagent_dict(self, extraction_kit:KitType=None) -> dict:
+        """
+        Returns basic reagent dictionary.
+
+        Returns:
+            dict: Basic reagent dictionary of 'type', 'lot', 'expiry' 
+        """        
+        if extraction_kit != None:
+            # Get the intersection of this reagent's ReagentType and all ReagentTypes in KitType
+            try:
+                reagent_role = list(set(self.type).intersection(extraction_kit.reagent_types))[0]
+            # Most will be able to fall back to first ReagentType in itself because most will only have 1.
+            except:
+                reagent_role = self.type[0]
+        else:
+            reagent_role = self.type[0]
+        try:
+            rtype = reagent_role.name
+        except AttributeError:
+            rtype = "Unknown"
         return {
-            "type": type,
+            "type": rtype,
             "lot": self.lot,
             "expiry": self.expiry.strftime("%Y-%m-%d")
         }
@@ -249,12 +267,14 @@ class Discount(Base):
     amount = Column(FLOAT(2))
 
 class SubmissionType(Base):
-
+    """
+    Abstract of types of submissions.
+    """    
     __tablename__ = "_submission_types"
 
     id = Column(INTEGER, primary_key=True) #: primary key
     name = Column(String(128), unique=True) #: name of submission type
-    info_map = Column(JSON)
+    info_map = Column(JSON) #: Where basic information is found in the excel workbook corresponding to this type.
     instances = relationship("BasicSubmission", backref="submission_type")
     
     submissiontype_kit_associations = relationship(
@@ -269,14 +289,15 @@ class SubmissionType(Base):
         return f"<SubmissionType({self.name})>"
     
 class SubmissionTypeKitTypeAssociation(Base):
-
+    """
+    Abstract of relationship between kits and their submission type.
+    """    
     __tablename__ = "_submissiontypes_kittypes"
     submission_types_id = Column(INTEGER, ForeignKey("_submission_types.id"), primary_key=True)
     kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
     mutable_cost_column = Column(FLOAT(2)) #: dollar amount per 96 well plate that can change with number of columns (reagents, tips, etc)
     mutable_cost_sample = Column(FLOAT(2)) #: dollar amount that can change with number of samples (reagents, tips, etc)
     constant_cost = Column(FLOAT(2)) #: dollar amount per plate that will remain constant (plates, man hours, etc)
-    # reagent_type_name = Column(INTEGER, ForeignKey("_reagent_types.name"))
 
     kit_type = relationship(KitType, back_populates="kit_submissiontype_associations")
 

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

@@ -21,7 +21,6 @@ class Organization(Base):
     submissions = relationship("BasicSubmission", back_populates="submitting_lab") #: submissions this organization has submitted
     cost_centre = Column(String()) #: cost centre used by org for payment
     contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts) #: contacts involved with this org
-    # contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id")) #: contact ids of this organization
 
     def __str__(self) -> str:
         """
@@ -47,5 +46,4 @@ class Contact(Base):
     email = Column(String(64)) #: contact email
     phone = Column(String(32)) #: contact phone number
     organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
-    # organization_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_contact_org_id")) #: joined organization ids
 

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

@@ -3,7 +3,7 @@ Models for the main submission types.
 '''
 import math
 from . import Base
-from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT
+from sqlalchemy import Column, String, TIMESTAMP, INTEGER, ForeignKey, Table, JSON, FLOAT, case
 from sqlalchemy.orm import relationship, validates
 import logging
 import json
@@ -11,10 +11,10 @@ from json.decoder import JSONDecodeError
 from math import ceil
 from sqlalchemy.ext.associationproxy import association_proxy
 import uuid
-from . import Base
 from pandas import Timestamp
 from dateutil.parser import parse
 import pprint
+from tools import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -23,7 +23,7 @@ reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("rea
 
 class BasicSubmission(Base):
     """
-    Base of basic submission which polymorphs into BacterialCulture and Wastewater
+    Concrete of basic submission which polymorphs into BacterialCulture and Wastewater
     """
     __tablename__ = "_submissions"
 
@@ -36,7 +36,6 @@ class BasicSubmission(Base):
     sample_count = Column(INTEGER) #: Number of samples in the submission
     extraction_kit = relationship("KitType", back_populates="submissions") #: The extraction kit used
     extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
-    # submission_type = Column(String(32)) #: submission type (should be string in D3 of excel sheet)
     submission_type_name = Column(String, ForeignKey("_submission_types.name", ondelete="SET NULL", name="fk_BS_subtype_name"))
     technician = Column(String(64)) #: initials of processing tech(s)
     # Move this into custom types?
@@ -83,7 +82,6 @@ class BasicSubmission(Base):
             dict: dictionary used in submissions summary
         """        
         # get lab from nested organization object
-        
         try:
             sub_lab = self.submitting_lab.name
         except AttributeError:
@@ -105,24 +103,16 @@ class BasicSubmission(Base):
         except JSONDecodeError as e:
             ext_info = None
             logger.debug(f"Json error in {self.rsl_plate_num}: {e}")
+        # Updated 2023-09 to use the extraction kit to pull reagents.
         try:
             reagents = [item.to_sub_dict(extraction_kit=self.extraction_kit) for item in self.reagents]
         except Exception as e:
             logger.error(f"We got an error retrieving reagents: {e}")
             reagents = None
-        # try:
-        #     samples = [item.sample.to_sub_dict(item.__dict__()) for item in self.submission_sample_associations]
-        # except Exception as e:
-        #     logger.error(f"Problem making list of samples: {e}")
-        #     samples = None
         samples = []
+        # Updated 2023-09 to get sample association with plate number
         for item in self.submission_sample_associations:
             sample = item.sample.to_sub_dict(submission_rsl=self.rsl_plate_num)
-            # try:
-            #     sample['well'] = f"{row_map[item.row]}{item.column}"
-            # except KeyError as e:
-            #     logger.error(f"Unable to find row {item.row} in row_map.")
-            #     sample['well'] = None
             samples.append(sample)
         try:
             comments = self.comment
@@ -171,7 +161,7 @@ class BasicSubmission(Base):
         output = {
             "id": self.id,
             "Plate Number": self.rsl_plate_num,
-            "Submission Type": self.submission_type.replace("_", " ").title(),
+            "Submission Type": self.submission_type_name.replace("_", " ").title(),
             "Submitter Plate Number": self.submitter_plate_num,
             "Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
             "Submitting Lab": sub_lab,
@@ -182,16 +172,18 @@ class BasicSubmission(Base):
         return output
     
     def calculate_base_cost(self):
+        """
+        Calculates cost of the plate
+        """        
+        # Calculate number of columns based on largest column number
         try:
-            # cols_count_96 = ceil(int(self.sample_count) / 8)
             cols_count_96 = self.calculate_column_count()
         except Exception as e:
             logger.error(f"Column count error: {e}")
-        # cols_count_24 = ceil(int(self.sample_count) / 3)
+        # Get kit associated with this submission
-        logger.debug(f"Pre-association check. {pprint.pformat(self.__dict__)}")
         assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type][0]
         logger.debug(f"Came up with association: {assoc}")
-        # if all(item == 0.0 for item in [self.extraction_kit.constant_cost, self.extraction_kit.mutable_cost_column, self.extraction_kit.mutable_cost_sample]):
+        # If every individual cost is 0 this is probably an old plate.
         if all(item == 0.0 for item in [assoc.constant_cost, assoc.mutable_cost_column, assoc.mutable_cost_sample]):
             try:
                 self.run_cost = self.extraction_kit.cost_per_run
@@ -203,14 +195,28 @@ class BasicSubmission(Base):
             except Exception as e:
                 logger.error(f"Calculation error: {e}")
 
-    def calculate_column_count(self):
+    def calculate_column_count(self) -> int:
+        """
+        Calculate the number of columns in this submission 
+
+        Returns:
+            int: largest column number
+        """           
         logger.debug(f"Here's the samples: {self.samples}")
-        # columns = [int(sample.well_number[-2:]) for sample in self.samples]
         columns = [assoc.column for assoc in self.submission_sample_associations]
         logger.debug(f"Here are the columns for {self.rsl_plate_num}: {columns}")
         return max(columns)
     
     def hitpick_plate(self, plate_number:int|None=None) -> list:
+        """
+        Returns positve sample locations for plate
+
+        Args:
+            plate_number (int | None, optional): Plate id. Defaults to None.
+
+        Returns:
+            list: list of htipick dictionaries for each sample
+        """        
         output_list = []
         for assoc in self.submission_sample_associations:
             samp = assoc.sample.to_hitpick(submission_rsl=self.rsl_plate_num)
@@ -232,7 +238,6 @@ class BacterialCulture(BasicSubmission):
     derivative submission type from BasicSubmission
     """    
     controls = relationship("Control", back_populates="submission", uselist=True) #: A control sample added to submission
-    # samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
     __mapper_args__ = {"polymorphic_identity": "Bacterial Culture", "polymorphic_load": "inline"}
 
     def to_dict(self) -> dict:
@@ -250,11 +255,9 @@ class Wastewater(BasicSubmission):
     """
     derivative submission type from BasicSubmission
     """    
-    # samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
     pcr_info = Column(JSON)
     ext_technician = Column(String(64))
     pcr_technician = Column(String(64))
-    # ww_sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "Wastewater", "polymorphic_load": "inline"}
 
     def to_dict(self) -> dict:
@@ -276,10 +279,7 @@ class WastewaterArtic(BasicSubmission):
     """
     derivative submission type for artic wastewater
     """    
-    # samples = relationship("WWSample", back_populates="artic_rsl_plate", uselist=True)
+    __mapper_args__ = {"polymorphic_identity": "Wastewater Artic", "polymorphic_load": "inline"}
-    # Can it use the pcr_info from the wastewater? Cause I can't define pcr_info here due to conflicts with that
-    # Not necessary because we don't get any results for this procedure.
-    __mapper_args__ = {"polymorphic_identity": "wastewater_artic", "polymorphic_load": "inline"}
 
     def calculate_base_cost(self):
         """
@@ -290,12 +290,13 @@ class WastewaterArtic(BasicSubmission):
             cols_count_96 = ceil(int(self.sample_count) / 8)
         except Exception as e:
             logger.error(f"Column count error: {e}")
+        assoc = [item for item in self.extraction_kit.kit_submissiontype_associations if item.submission_type == self.submission_type][0]
         # Since we have multiple output plates per submission form, the constant cost will have to reflect this.
         output_plate_count = math.ceil(int(self.sample_count) / 16)
         logger.debug(f"Looks like we have {output_plate_count} output plates.")
-        const_cost = self.extraction_kit.constant_cost * output_plate_count
+        const_cost = assoc.constant_cost * output_plate_count
         try:
-            self.run_cost = const_cost + (self.extraction_kit.mutable_cost_column * cols_count_96) + (self.extraction_kit.mutable_cost_sample * int(self.sample_count))
+            self.run_cost = const_cost + (assoc.mutable_cost_column * cols_count_96) + (assoc.mutable_cost_sample * int(self.sample_count))
         except Exception as e:
             logger.error(f"Calculation error: {e}")
 
@@ -318,7 +319,15 @@ class BasicSample(Base):
 
     __mapper_args__ = {
         "polymorphic_identity": "basic_sample",
-        "polymorphic_on": sample_type,
+        # "polymorphic_on": sample_type,
+        "polymorphic_on": case(
+            [
+                (sample_type == "Wastewater Sample", "Wastewater Sample"),
+                (sample_type == "Wastewater Artic Sample", "Wastewater Sample"),
+                (sample_type == "Bacterial Culture Sample", "Bacterial Culture Sample"),
+            ],
+            else_="basic_sample"
+         ),
         "with_polymorphic": "*",
     }
 
@@ -335,7 +344,23 @@ class BasicSample(Base):
     def __repr__(self) -> str:
         return f"<{self.sample_type.replace('_', ' ').title(). replace(' ', '')}({self.submitter_id})>"
     
+    def set_attribute(self, name, value):
+        # logger.debug(f"Setting {name} to {value}")
+        try:
+            setattr(self, name, value)
+        except AttributeError:
+            logger.error(f"Attribute {name} not found")
+    
     def to_sub_dict(self, submission_rsl:str) -> dict:
+        """
+        Returns a dictionary of locations.
+
+        Args:
+            submission_rsl (str): Submission RSL number.
+
+        Returns:
+            dict: 'well' and sample submitter_id as 'name'
+        """        
         row_map = {1:"A", 2:"B", 3:"C", 4:"D", 5:"E", 6:"F", 7:"G", 8:"H"}
         self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
         sample = {}
@@ -347,73 +372,30 @@ class BasicSample(Base):
         sample['name'] = self.submitter_id
         return sample
     
-    def to_hitpick(self, submission_rsl:str) -> dict|None:
+    def to_hitpick(self, submission_rsl:str|None=None) -> dict|None:
         """
         Outputs a dictionary of locations
 
         Returns:
             dict: dictionary of sample id, row and column in elution plate
         """        
-        self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
+        # self.assoc = [item for item in self.sample_submission_associations if item.submission.rsl_plate_num==submission_rsl][0]
-        # dictionary to translate row letters into numbers
+        # Since there is no PCR, negliable result is necessary.
-        # row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
+        return dict(name=self.submitter_id, positive=False)
-        # if either n1 or n2 is positive, include this sample
-        # well_row = row_dict[self.well_number[0]]
-        # The remaining charagers are the columns
-        # well_col = self.well_number[1:]
-        return dict(name=self.submitter_id, 
-                    # row=well_row, 
-                    # col=well_col, 
-                    positive=False)
 
 class WastewaterSample(BasicSample):
     """
-    Base wastewater sample
+    Derivative wastewater sample
     """
-    # __tablename__ = "_ww_samples"
-
-    # id = Column(INTEGER, primary_key=True) #: primary key
     ww_processing_num = Column(String(64)) #: wastewater processing number 
-    ww_sample_full_id = Column(String(64))
+    ww_full_sample_id = Column(String(64))
     rsl_number = Column(String(64)) #: rsl plate identification number
-    # rsl_plate = relationship("Wastewater", back_populates="samples") #: relationship to parent plate
-    # rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_submission_id"))
     collection_date = Column(TIMESTAMP) #: Date sample collected
     received_date = Column(TIMESTAMP) #: Date sample received
-    # well_number = Column(String(8)) #: location on 96 well plate
-    # The following are fields from the sample tracking excel sheet Ruth put together.
-    # I have no idea when they will be implemented or how.
-    # testing_type = Column(String(64)) 
-    # site_status = Column(String(64))
     notes = Column(String(2000))
-    # ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
-    # ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
-    # n1_status = Column(String(32))
-    # n2_status = Column(String(32))
-    # seq_submitted = Column(BOOLEAN())
-    # ww_seq_run_id = Column(String(64))
-    # sample_type = Column(String(16))
-    # pcr_results = Column(JSON)
     sample_location = Column(String(8)) #: location on 24 well plate
-    # artic_rsl_plate = relationship("WastewaterArtic", back_populates="samples")
-    # artic_well_number = Column(String(8))
-    
     __mapper_args__ = {"polymorphic_identity": "Wastewater Sample", "polymorphic_load": "inline"}
 
-    # def to_string(self) -> str:
-    #     """
-    #     string representing sample object
-
-    #     Returns:
-    #         str: string representing location and sample id
-    #     """        
-    #     return f"{self.well_number}: {self.ww_sample_full_id}"
-
-    # @validates("received-date")
-    # def convert_rdate_time(self, key, value):
-    #     if isinstance(value, Timestamp):
-    #         return value.date()
-    #     return value
         
     @validates("collected-date")
     def convert_cdate_time(self, key, value):
@@ -423,31 +405,68 @@ class WastewaterSample(BasicSample):
         if isinstance(value, str):
             return parse(value)
         return value
+    
+    @validates("rsl_number")
+    def use_submitter_id(self, key, value):
+        logger.debug(f"Validating {key}: {value}")
+        return value or self.submitter_id
 
-    # @collection_date.setter
+    # def __init__(self, **kwargs):
-    # def collection_date(self, value):
+    #     # Had a problem getting collection date from excel as text only.
-    #     match value:
+    #     if 'collection_date' in kwargs.keys():
-    #         case Timestamp():
+    #         logger.debug(f"Got collection_date: {kwargs['collection_date']}. Attempting parse.")
-    #             self.collection_date = value.date()
+    #         if isinstance(kwargs['collection_date'], str):
-    #         case str():
+    #             logger.debug(f"collection_date is a string...")
-    #             self.collection_date = parse(value)
+    #             kwargs['collection_date'] = parse(kwargs['collection_date'])
-    #         case _:
+    #             logger.debug(f"output is {kwargs['collection_date']}")
-    #             self.collection_date = value
+    #     # Due to the plate map being populated with RSL numbers, we have to do some shuffling.
-        
+    #     try:
+    #         kwargs['rsl_number'] = kwargs['submitter_id']
+    #     except KeyError as e:
+    #         logger.error(f"Error using {kwargs} for submitter_id")
+    #     try:
+    #         check = check_not_nan(kwargs['ww_full_sample_id'])
+    #     except KeyError:
+    #         logger.error(f"Error using {kwargs} for ww_full_sample_id")
+    #         check = False
+    #     if check:
+    #         kwargs['submitter_id'] = kwargs["ww_full_sample_id"]
+    #     super().__init__(**kwargs)
 
-    def __init__(self, **kwargs):
+    def set_attribute(self, name:str, value):
-        if 'collection_date' in kwargs.keys():
+        """
-            logger.debug(f"Got collection_date: {kwargs['collection_date']}. Attempting parse.")
+        Set an attribute of this object. Extends parent.
-            if isinstance(kwargs['collection_date'], str):
+
-                logger.debug(f"collection_date is a string...")
+        Args:
-                kwargs['collection_date'] = parse(kwargs['collection_date'])
+            name (str): _description_
-                logger.debug(f"output is {kwargs['collection_date']}")
+            value (_type_): _description_
-        super().__init__(**kwargs)
+        """        
+        # Due to the plate map being populated with RSL numbers, we have to do some shuffling. 
+        # logger.debug(f"Input - {name}:{value}")
+        match name:
+            case "submitter_id":
+                if self.submitter_id != None:
+                    return
+                else:
+                    super().set_attribute("rsl_number", value)
+            case "ww_full_sample_id":
+                if value != None:
+                    super().set_attribute(name, value)
+                    name = "submitter_id"
+            case 'collection_date':
+                if isinstance(value, str):
+                    logger.debug(f"collection_date {value} is a string. Attempting parse...")
+                    value = parse(value)
+            case "rsl_number":
+                if value == None:
+                    value = self.submitter_id
+        # logger.debug(f"Output - {name}:{value}")
+        super().set_attribute(name, value)
 
 
     def to_sub_dict(self, submission_rsl:str) -> dict:
         """
-        Gui friendly dictionary. Inherited from BasicSample
+        Gui friendly dictionary. Extends parent method.
         This version will include PCR status.
 
         Args:
@@ -458,15 +477,13 @@ class WastewaterSample(BasicSample):
         """        
         # Get the relevant submission association for this sample
         sample = super().to_sub_dict(submission_rsl=submission_rsl)
+        # check if PCR data exists.
         try:
             check = self.assoc.ct_n1 != None and self.assoc.ct_n2 != None
         except AttributeError as e:
             check = False
         if check:
-            # logger.debug(f"Using well info in name.")
             sample['name'] = f"{self.submitter_id}\n\t- ct N1: {'{:.2f}'.format(self.assoc.ct_n1)} ({self.assoc.n1_status})\n\t- ct N2: {'{:.2f}'.format(self.assoc.ct_n2)} ({self.assoc.n2_status})"
-        # else:
-            # logger.error(f"Couldn't get the pcr info")
         return sample
     
     def to_hitpick(self, submission_rsl:str) -> dict|None:
@@ -477,67 +494,30 @@ class WastewaterSample(BasicSample):
             dict: dictionary of sample id, row and column in elution plate
         """       
         sample = super().to_hitpick(submission_rsl=submission_rsl)
-        # dictionary to translate row letters into numbers
-        # row_dict = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
         # if either n1 or n2 is positive, include this sample
         try:
             sample['positive'] = any(["positive" in item for item in [self.assoc.n1_status, self.assoc.n2_status]])
         except (TypeError, AttributeError) as e:
             logger.error(f"Couldn't check positives for {self.rsl_number}. Looks like there isn't PCR data.")
-            # return None
-            # positive = False
-        # well_row = row_dict[self.well_number[0]]
-        # well_col = self.well_number[1:]
-        # if positive:
-        #     try:
-        #         # The first character of the elution well is the row
-        #         well_row = row_dict[self.elution_well[0]]
-        #         # The remaining charagers are the columns
-        #         well_col = self.elution_well[1:]
-        #     except TypeError as e:
-        #         logger.error(f"This sample doesn't have elution plate info.")
-        #         return None
         return sample
         
 class BacterialCultureSample(BasicSample):
     """
     base of bacterial culture sample
     """
-    # __tablename__ = "_bc_samples"
-
-    # id = Column(INTEGER, primary_key=True) #: primary key
-    # well_number = Column(String(8)) #: location on parent plate
-    # sample_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
     organism = Column(String(64)) #: bacterial specimen
-    concentration = Column(String(16)) #:
+    concentration = Column(String(16)) #: sample concentration
-    # sample_type = Column(String(16))
-    # rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate
-    # rsl_plate = relationship("BacterialCulture", back_populates="samples") #: relationship to parent plate
-
     __mapper_args__ = {"polymorphic_identity": "Bacterial Culture Sample", "polymorphic_load": "inline"}
 
-    # def to_string(self) -> str:
-    #     """
-    #     string representing object
-
-    #     Returns:
-    #         str: string representing well location, sample id and organism
-    #     """        
-    #     return f"{self.well_number}: {self.sample_id} - {self.organism}"
-
     def to_sub_dict(self, submission_rsl:str) -> dict:
         """
-        gui friendly dictionary
+        gui friendly dictionary, extends parent method.
 
         Returns:
             dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
         """
         sample = super().to_sub_dict(submission_rsl=submission_rsl)
         sample['name'] = f"{self.submitter_id} - ({self.organism})"
-        # return {
-        #     # "well": self.well_number,
-        #     "name": f"{self.submitter_id} - ({self.organism})",
-        # }
         return sample
 
 class SubmissionSampleAssociation(Base):
@@ -548,18 +528,19 @@ class SubmissionSampleAssociation(Base):
     __tablename__ = "_submission_sample"
     sample_id = Column(INTEGER, ForeignKey("_samples.id"), nullable=False)
     submission_id = Column(INTEGER, ForeignKey("_submissions.id"), primary_key=True)
-    row = Column(INTEGER, primary_key=True)
+    row = Column(INTEGER, primary_key=True) #: row on the 96 well plate
-    column = Column(INTEGER, primary_key=True)
+    column = Column(INTEGER, primary_key=True) #: column on the 96 well plate
 
+    # reference to the Submission object
     submission = relationship(BasicSubmission, back_populates="submission_sample_associations")
 
-    # reference to the "ReagentType" object
+    # reference to the Sample object
-    # sample = relationship("BasicSample")
     sample = relationship(BasicSample, back_populates="sample_submission_associations")
 
     base_sub_type = Column(String)
-    # """Refers to the type of parent."""
+    
-
+    # Refers to the type of parent.
+    # Hooooooo boy, polymorphic association type, now we're getting into the weeds!
     __mapper_args__ = {
         "polymorphic_identity": "basic_association",
         "polymorphic_on": base_sub_type,
@@ -576,11 +557,14 @@ class SubmissionSampleAssociation(Base):
         return f"<SubmissionSampleAssociation({self.submission.rsl_plate_num} & {self.sample.submitter_id})"
 
 class WastewaterAssociation(SubmissionSampleAssociation):
-
+    """
+    Derivative custom Wastewater/Submission Association... fancy.
+    """    
     ct_n1 = Column(FLOAT(2)) #: AKA ct for N1
     ct_n2 = Column(FLOAT(2)) #: AKA ct for N2
-    n1_status = Column(String(32))
+    n1_status = Column(String(32)) #: positive or negative for N1
-    n2_status = Column(String(32))
+    n2_status = Column(String(32)) #: positive or negative for N2
-    pcr_results = Column(JSON)
+    pcr_results = Column(JSON) #: imported PCR status from QuantStudio
+
+    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}
 
-    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}

src/submissions/backend/excel/parser.py

@@ -6,7 +6,7 @@ import pprint
 from typing import List
 import pandas as pd
 from pathlib import Path
-from backend.db import lookup_ww_sample_by_ww_sample_num, lookup_sample_by_submitter_id, get_reagents_in_extkit, lookup_kittype_by_name, lookup_submissiontype_by_name, models
+from backend.db import lookup_sample_by_submitter_id, get_reagents_in_extkit, lookup_kittype_by_name, lookup_submissiontype_by_name, models
 from backend.pydant import PydSubmission, PydReagent
 import logging
 from collections import OrderedDict
@@ -14,8 +14,6 @@ import re
 import numpy as np
 from datetime import date
 from dateutil.parser import parse, ParserError
-import uuid
-# from submissions.backend.db.functions import 
 from tools import check_not_nan, RSLNamer, convert_nans_to_nones, Settings
 from frontend.custom_widgets.pop_ups import SubmissionTypeSelector, KitSelector
 
@@ -69,7 +67,7 @@ class SheetParser(object):
         # Check metadata for category, return first category
         if self.xl.book.properties.category != None:
             logger.debug("Using file properties to find type...")
-            categories = [item.strip().title() for item in self.xl.book.properties.category.split(";")]
+            categories = [item.strip().replace("_", " ").title() for item in self.xl.book.properties.category.split(";")]
             return dict(value=categories[0], parsed=False)
         else:
             # This code is going to be depreciated once there is full adoption of the client sheets
@@ -95,7 +93,13 @@ class SheetParser(object):
         """
         _summary_
         """        
-        info = InfoParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']).parse_info()
+        info = InfoParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_info()
+        parser_query = f"parse_{self.sub['submission_type']['value'].replace(' ', '_').lower()}"
+        try:
+            custom_parser = getattr(self, parser_query)
+            info = custom_parser(info)
+        except AttributeError:
+            logger.error(f"Couldn't find submission parser: {parser_query}")
         for k,v in info.items():
             if k != "sample":
                 self.sub[k] = v
@@ -107,288 +111,41 @@ class SheetParser(object):
     def parse_samples(self):
         self.sample_result, self.sub['samples'] = SampleParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_samples()
 
-    def parse_bacterial_culture(self) -> None:
+    def parse_bacterial_culture(self, input_dict) -> dict:
-        """
-        pulls info specific to bacterial culture sample type
         """
+        Update submission dictionary with type specific information
 
-        # def parse_reagents(df:pd.DataFrame) -> None:
+        Args:
-        #     """
+            input_dict (dict): Input sample dictionary
-        #     Pulls reagents from the bacterial sub-dataframe
 
-        #     Args:
+        Returns:
-        #         df (pd.DataFrame): input sub dataframe
+            dict: Updated sample dictionary
-        #     """            
-        #     for ii, row in df.iterrows():
-        #         # skip positive control
-        #         logger.debug(f"Running reagent parse for {row[1]} with type {type(row[1])} and value: {row[2]} with type {type(row[2])}")
-        #         # if the lot number isn't a float and the reagent type isn't blank
-        #         # if not isinstance(row[2], float) and check_not_nan(row[1]):
-        #         if check_not_nan(row[1]):
-        #             # must be prefixed with 'lot_' to be recognized by gui
-        #             # This is no longer true since reagents are loaded into their own key in dictionary
-        #             try:
-        #                 reagent_type = row[1].replace(' ', '_').lower().strip()
-        #             except AttributeError:
-        #                 pass
-        #             # If there is a double slash in the type field, such as ethanol/iso
-        #             # Use the cell to the left for reagent type.
-        #             if reagent_type == "//":
-        #                 if check_not_nan(row[2]):
-        #                     reagent_type = row[0].replace(' ', '_').lower().strip()
-        #                 else:
-        #                     continue
-        #             try:
-        #                 output_var = convert_nans_to_nones(str(row[2]).upper())
-        #             except AttributeError:
-        #                 logger.debug(f"Couldn't upperize {row[2]}, must be a number")
-        #                 output_var = convert_nans_to_nones(str(row[2]))
-        #             logger.debug(f"Output variable is {output_var}")
-        #             logger.debug(f"Expiry date for imported reagent: {row[3]}")
-        #             if check_not_nan(row[3]):
-        #                 try:
-        #                     expiry = row[3].date()
-        #                 except AttributeError as e:
-        #                     try:
-        #                         expiry = datetime.strptime(row[3], "%Y-%m-%d")
-        #                     except TypeError as e:
-        #                         expiry = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + row[3] - 2)
-        #             else:
-        #                 logger.debug(f"Date: {row[3]}")
-        #                 # expiry = date.today()
-        #                 expiry = date(year=1970, month=1, day=1)
-        #             # self.sub[f"lot_{reagent_type}"] = {'lot':output_var, 'exp':expiry}
-        #             # self.sub['reagents'].append(dict(type=reagent_type, lot=output_var, exp=expiry))
-        #             self.sub['reagents'].append(PydReagent(type=reagent_type, lot=output_var, exp=expiry))
-        # submission_info = self.xl.parse(sheet_name="Sample List", dtype=object)
-        # self.sub['extraction_kit'] = submission_info.iloc[3][3]
-        # submission_info = self.parse_generic("Sample List")
-        # # iloc is [row][column] and the first row is set as header row so -2
-        # self.sub['technician'] = str(submission_info.iloc[11][1])
-        # # reagents
-        # # must be prefixed with 'lot_' to be recognized by gui
-        # # This is no longer true wince the creation of self.sub['reagents']
-        # self.sub['reagents'] = []
-        # reagent_range = submission_info.iloc[1:14, 4:8]
-        # logger.debug(reagent_range)
-        # parse_reagents(reagent_range)
-        # get individual sample info
-        sample_parser = SampleParser(self.ctx, submission_info.iloc[16:112])
-        logger.debug(f"Sample type: {self.sub['submission_type']}")
-        if isinstance(self.sub['submission_type'], dict):
-            getter = self.sub['submission_type']['value']
-        else:
-            getter = self.sub['submission_type']
-        sample_parse = getattr(sample_parser, f"parse_{getter.replace(' ', '_').lower()}_samples")
-        logger.debug(f"Parser result: {self.sub}")
-        self.sample_result, self.sub['samples'] = sample_parse()
-
-    def parse_wastewater(self) -> None:
-        """
-        pulls info specific to wastewater sample type
         """        
-        def retrieve_elution_map():
+        return input_dict
-            full = self.xl.parse("Extraction Worksheet")
+        
-            elu_map = full.iloc[9:18, 5:]
+    def parse_wastewater(self, input_dict) -> dict:
-            elu_map.set_index(elu_map.columns[0], inplace=True)
-            elu_map.columns = elu_map.iloc[0]
-            elu_map = elu_map.tail(-1)
-            return elu_map
-        # def parse_reagents(df:pd.DataFrame) -> None:
-        #     """
-        #     Pulls reagents from the bacterial sub-dataframe
-
-        #     Args:
-        #         df (pd.DataFrame): input sub dataframe
-        #     """
-        #     # iterate through sub-df rows
-        #     for ii, row in df.iterrows():
-        #         # logger.debug(f"Parsing this row for reagents: {row}")
-        #         if check_not_nan(row[5]):
-        #             # must be prefixed with 'lot_' to be recognized by gui
-        #             # regex below will remove 80% from 80% ethanol in the Wastewater kit.
-        #             output_key = re.sub(r"^\d{1,3}%\s?", "", row[0].lower().strip().replace(' ', '_'))
-        #             output_key = output_key.strip("_")
-        #             # output_var is the lot number
-        #             try:
-        #                 output_var = convert_nans_to_nones(str(row[5].upper()))
-        #             except AttributeError:
-        #                 logger.debug(f"Couldn't upperize {row[5]}, must be a number")
-        #                 output_var = convert_nans_to_nones(str(row[5]))
-        #             if check_not_nan(row[7]):
-        #                 try:
-        #                     expiry = row[7].date()
-        #                 except AttributeError:
-        #                     expiry = date.today()
-        #             else:
-        #                 expiry = date.today()
-        #             logger.debug(f"Expiry date for {output_key}: {expiry} of type {type(expiry)}")
-        #             # self.sub[f"lot_{output_key}"] = {'lot':output_var, 'exp':expiry}
-        #             # self.sub['reagents'].append(dict(type=output_key, lot=output_var, exp=expiry))
-        #             reagent = PydReagent(type=output_key, lot=output_var, exp=expiry)
-        #             logger.debug(f"Here is the created reagent: {reagent}")
-        #             self.sub['reagents'].append(reagent)
-        # parse submission sheet
-        submission_info = self.parse_generic("WW Submissions (ENTER HERE)")
-        # parse enrichment sheet
-        enrichment_info = self.xl.parse("Enrichment Worksheet", dtype=object)
-        # set enrichment reagent range
-        enr_reagent_range = enrichment_info.iloc[0:4, 9:20]
-        # parse extraction sheet
-        extraction_info = self.xl.parse("Extraction Worksheet", dtype=object)
-        # set extraction reagent range 
-        ext_reagent_range = extraction_info.iloc[0:5, 9:20]
-        # parse qpcr sheet
-        qprc_info = self.xl.parse("qPCR Worksheet", dtype=object)
-        # set qpcr reagent range
-        pcr_reagent_range = qprc_info.iloc[0:5, 9:20]
-        # compile technician info from all sheets
-        if all(map(check_not_nan, [enrichment_info.columns[2], extraction_info.columns[2], qprc_info.columns[2]])):
-            parsed = True
-        else:
-            parsed = False
-        self.sub['technician'] = dict(value=f"Enr: {enrichment_info.columns[2]}, Ext: {extraction_info.columns[2]}, PCR: {qprc_info.columns[2]}", parsed=parsed)
-        self.sub['reagents'] = []
-        # parse_reagents(enr_reagent_range)
-        # parse_reagents(ext_reagent_range)
-        # parse_reagents(pcr_reagent_range)
-        # parse samples
-        sample_parser = SampleParser(self.ctx, submission_info.iloc[16:], elution_map=retrieve_elution_map())
-        sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type']['value'].lower()}_samples")
-        self.sample_result, self.sub['samples'] = sample_parse()
-        self.sub['csv'] = self.xl.parse("Copy to import file", dtype=object)
-
-    def parse_wastewater_artic(self) -> None:
         """
-        pulls info specific to wastewater_arctic submission type
+        Update submission dictionary with type specific information
+
+        Args:
+            input_dict (dict): Input sample dictionary
+
+        Returns:
+            dict: Updated sample dictionary
+        """        
+        return input_dict
+
+    def parse_wastewater_artic(self, input_dict:dict) -> dict:
         """
-        if isinstance(self.sub['submission_type'], str):
+        Update submission dictionary with type specific information
-            self.sub['submission_type'] = dict(value=self.sub['submission_type'], parsed=True)
-        # def parse_reagents(df:pd.DataFrame):
-        #     logger.debug(df)
-        #     for ii, row in df.iterrows():
-        #         if check_not_nan(row[1]):
-        #             try:
-        #                 output_key = re.sub(r"\(.+?\)", "", row[0].lower().strip().replace(' ', '_'))
-        #             except AttributeError:
-        #                 continue
-        #             output_key = output_key.strip("_")
-        #             output_key = massage_common_reagents(output_key)
-        #             try:
-        #                 output_var = convert_nans_to_nones(str(row[1].upper()))
-        #             except AttributeError:
-        #                 logger.debug(f"Couldn't upperize {row[1]}, must be a number")
-        #                 output_var = convert_nans_to_nones(str(row[1]))
-        #             logger.debug(f"Output variable is {output_var}")
-        #             logger.debug(f"Expiry date for imported reagent: {row[2]}")
-        #             if check_not_nan(row[2]):
-        #                 try:
-        #                     expiry = row[2].date()
-        #                 except AttributeError as e:
-        #                     try:
-        #                         expiry = datetime.strptime(row[2], "%Y-%m-%d")
-        #                     except TypeError as e:
-        #                         expiry = datetime.fromordinal(datetime(1900, 1, 1).toordinal() + row[2] - 2)
-        #                     except ValueError as e:
-        #                         continue
-        #             else:
-        #                 logger.debug(f"Date: {row[2]}")
-        #                 expiry = date.today()
-        #             # self.sub['reagents'].append(dict(type=output_key, lot=output_var, exp=expiry))
-        #             self.sub['reagents'].append(PydReagent(type=output_key, lot=output_var, exp=expiry))
-        #         else:
-        #             continue
-        def massage_samples(df:pd.DataFrame, lookup_table:pd.DataFrame) -> pd.DataFrame:
-            """
-            Takes sample info from Artic sheet format and converts to regular formate
 
-            Args:
+        Args:
-                df (pd.DataFrame): Elution plate map
+            input_dict (dict): Input sample dictionary
-                lookup_table (pd.DataFrame): Sample submission form map.
 
-            Returns:
+        Returns:
-                pd.DataFrame: _description_
+            dict: Updated sample dictionary
-            """            
+        """        
-            lookup_table.set_index(lookup_table.columns[0], inplace=True)
+        return input_dict
-            lookup_table.columns = lookup_table.iloc[0]
-            logger.debug(f"Massaging samples from {lookup_table}")
-            df.set_index(df.columns[0], inplace=True)
-            df.columns = df.iloc[0]
-            logger.debug(f"df to massage\n: {df}")
-            return_list = []
-            for _, ii in df.iloc[1:,1:].iterrows():
-                for c in df.columns.to_list():
-                    if not check_not_nan(c):
-                        continue
-                    logger.debug(f"Checking {ii.name}{c}")
-                    if check_not_nan(df.loc[ii.name, int(c)]) and df.loc[ii.name, int(c)] != "EMPTY":
-                        sample_name = df.loc[ii.name, int(c)]
-                        row = lookup_table.loc[lookup_table['Sample Name (WW)'] == sample_name]
-                        logger.debug(f"Looking up {row['Sample Name (LIMS)'][-1]}")
-                        try:
-                            return_list.append(dict(submitter_id=re.sub(r"\s?\(.*\)", "", df.loc[ii.name, int(c)]), \
-                                                # well=f"{ii.name}{c}",
-                                                row = row_keys[ii.name],
-                                                column = c,
-                                                artic_plate=self.sub['rsl_plate_num'],
-                                                sample_name=row['Sample Name (LIMS)'][-1]
-                                                ))
-                        except TypeError as e:
-                            logger.error(f"Got an int for {c}, skipping.")
-                            continue
-            logger.debug(f"massaged sample list for {self.sub['rsl_plate_num']}: {pprint.pprint(return_list)}")
-            return return_list
-        submission_info = self.xl.parse("First Strand", dtype=object)
-        biomek_info = self.xl.parse("ArticV4 Biomek", dtype=object)
-        sub_reagent_range = submission_info.iloc[56:, 1:4].dropna(how='all')
-        biomek_reagent_range = biomek_info.iloc[60:, 0:3].dropna(how='all')
-        # submission_info = self.xl.parse("cDNA", dtype=object)
-        # biomek_info = self.xl.parse("ArticV4_1 Biomek", dtype=object)
-        # # Reminder that the iloc uses row, column ordering
-        # # sub_reagent_range = submission_info.iloc[56:, 1:4].dropna(how='all')
-        # sub_reagent_range = submission_info.iloc[7:15, 5:9].dropna(how='all')
-        # biomek_reagent_range = biomek_info.iloc[62:, 0:3].dropna(how='all')
-        self.sub['submitter_plate_num'] = ""
-        self.sub['rsl_plate_num'] =  RSLNamer(ctx=self.ctx, instr=self.filepath.__str__()).parsed_name
-        self.sub['submitted_date'] = biomek_info.iloc[1][1]
-        self.sub['submitting_lab'] = "Enterics Wastewater Genomics"
-        self.sub['sample_count'] = submission_info.iloc[4][6]
-        # self.sub['sample_count'] = submission_info.iloc[34][6]
-        self.sub['extraction_kit'] = "ArticV4.1"
-        self.sub['technician'] = f"MM: {biomek_info.iloc[2][1]}, Bio: {biomek_info.iloc[3][1]}"
-        self.sub['reagents'] = []
-        # parse_reagents(sub_reagent_range)
-        # parse_reagents(biomek_reagent_range)
-        samples = massage_samples(biomek_info.iloc[22:31, 0:], submission_info.iloc[4:37, 1:5])
-        # samples = massage_samples(biomek_info.iloc[25:33, 0:])
-        sample_parser = SampleParser(self.ctx, pd.DataFrame.from_records(samples))
-        sample_parse = getattr(sample_parser, f"parse_{self.sub['submission_type']['value'].lower()}_samples")
-        self.sample_result, self.sub['samples'] = sample_parse()
-
-    # def parse_reagents(self):
-    #     ext_kit = lookup_kittype_by_name(ctx=self.ctx, name=self.sub['extraction_kit'])
-    #     if ext_kit != None:
-    #         logger.debug(f"Querying extraction kit: {self.sub['submission_type']}")
-    #         reagent_map = ext_kit.construct_xl_map_for_use(use=self.sub['submission_type']['value'])
-    #         logger.debug(f"Reagent map: {pprint.pformat(reagent_map)}")
-    #     else:
-    #         raise AttributeError("No extraction kit found, unable to parse reagents")
-    #     for sheet in self.xl.sheet_names:
-    #         df = self.xl.parse(sheet)
-    #         relevant = {k:v for k,v in reagent_map.items() if sheet in reagent_map[k]['sheet']}
-    #         logger.debug(f"relevant map for {sheet}: {pprint.pformat(relevant)}")
-    #         if relevant == {}:
-    #             continue
-    #         for item in relevant:
-    #             try:
-    #             # role = item
-    #                 name = df.iat[relevant[item]['name']['row']-2, relevant[item]['name']['column']-1]
-    #                 lot = df.iat[relevant[item]['lot']['row']-2, relevant[item]['lot']['column']-1]
-    #                 expiry = df.iat[relevant[item]['expiry']['row']-2, relevant[item]['expiry']['column']-1]
-    #             except (KeyError, IndexError):
-    #                 continue
-    #             # self.sub['reagents'].append(dict(name=name, lot=lot, expiry=expiry, role=role))
-    #             self.sub['reagents'].append(PydReagent(type=item, lot=lot, exp=expiry, name=name))
 
 
     def import_kit_validation_check(self):
@@ -411,9 +168,6 @@ class SheetParser(object):
         else:
             if isinstance(self.sub['extraction_kit'], str):
                 self.sub['extraction_kit'] = dict(value=self.sub['extraction_kit'], parsed=False)
-        
-        # logger.debug(f"Here is the validated parser dictionary:\n\n{pprint.pformat(self.sub)}\n\n")
-        # return parser_sub
 
     def import_reagent_validation_check(self):
         """
@@ -439,20 +193,16 @@ class InfoParser(object):
 
     def __init__(self, ctx:Settings, xl:pd.ExcelFile, submission_type:str):
         self.ctx = ctx
-        # self.submission_type = submission_type
-        # self.extraction_kit = extraction_kit
         self.map = self.fetch_submission_info_map(submission_type=submission_type)
         self.xl = xl
         logger.debug(f"Info map for InfoParser: {pprint.pformat(self.map)}")
 
     def fetch_submission_info_map(self, submission_type:dict) -> dict:
+        if isinstance(submission_type, str):
+            submission_type = dict(value=submission_type, parsed=False)
         logger.debug(f"Looking up submission type: {submission_type['value']}")
         submission_type = lookup_submissiontype_by_name(ctx=self.ctx, type_name=submission_type['value'])
         info_map = submission_type.info_map
-        # try:
-        #     del info_map['samples']
-        # except KeyError:
-        #     pass
         return info_map
 
     def parse_info(self) -> dict:
@@ -461,11 +211,13 @@ class InfoParser(object):
             df = self.xl.parse(sheet, header=None)
             relevant = {}
             for k, v in self.map.items():
+                if isinstance(v, str):
+                    dicto[k] = dict(value=v, parsed=True)
+                    continue
                 if k == "samples":
                     continue
                 if sheet in self.map[k]['sheets']:
                     relevant[k] = v
-            # relevant = {k:v for k,v in self.map.items() if sheet in self.map[k]['sheets']}
             logger.debug(f"relevant map for {sheet}: {pprint.pformat(relevant)}")
             if relevant == {}:
                 continue
@@ -485,8 +237,6 @@ class InfoParser(object):
                             continue
                 else:
                     dicto[item] = dict(value=convert_nans_to_nones(value), parsed=False)
-        # if "submitter_plate_num" not in dicto.keys():
-        #     dicto['submitter_plate_num'] = dict(value=None, parsed=False)
         return dicto
                 
 class ReagentParser(object):
@@ -515,7 +265,6 @@ class ReagentParser(object):
             for item in relevant:
                 logger.debug(f"Attempting to scrape: {item}")
                 try:
-                # role = item
                     name = df.iat[relevant[item]['name']['row']-1, relevant[item]['name']['column']-1]
                     lot = df.iat[relevant[item]['lot']['row']-1, relevant[item]['lot']['column']-1]
                     expiry = df.iat[relevant[item]['expiry']['row']-1, relevant[item]['expiry']['column']-1]
@@ -526,7 +275,6 @@ class ReagentParser(object):
                     parsed = True
                 else:
                     parsed = False
-                # self.sub['reagents'].append(dict(name=name, lot=lot, expiry=expiry, role=role))
                 logger.debug(f"Got lot for {item}-{name}: {lot} as {type(lot)}")
                 lot = str(lot)
                 listo.append(dict(value=PydReagent(type=item.strip(), lot=lot, exp=expiry, name=name), parsed=parsed))
@@ -556,8 +304,9 @@ class SampleParser(object):
         self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
         self.excel_to_db_map = sample_info_map['xl_db_translation']
         self.create_basic_dictionaries_from_plate_map()
-        self.parse_lookup_table()
+        if isinstance(self.lookup_table, pd.DataFrame):
-
+            self.parse_lookup_table()
+        
     def fetch_sample_info_map(self, submission_type:dict) -> dict:
         logger.debug(f"Looking up submission type: {submission_type}")
         submission_type = lookup_submissiontype_by_name(ctx=self.ctx, type_name=submission_type)
@@ -575,7 +324,10 @@ class SampleParser(object):
         return df
     
     def construct_lookup_table(self, lookup_table_location) -> pd.DataFrame:
-        df = self.xl.parse(lookup_table_location['sheet'], header=None, dtype=object)
+        try:
+            df = self.xl.parse(lookup_table_location['sheet'], header=None, dtype=object)
+        except KeyError:
+            return None
         df = df.iloc[lookup_table_location['start_row']-1:lookup_table_location['end_row']]
         df = pd.DataFrame(df.values[1:], columns=df.iloc[0])
         df = df.reset_index(drop=True)
@@ -583,12 +335,16 @@ class SampleParser(object):
         return df
     
     def create_basic_dictionaries_from_plate_map(self):
+        invalids = [0, "0"]
         new_df = self.plate_map.dropna(axis=1, how='all')
         columns = new_df.columns.tolist()
         for _, iii in new_df.iterrows():
             for c in columns:
                 # logger.debug(f"Checking sample {iii[c]}")
                 if check_not_nan(iii[c]):
+                    if iii[c] in invalids:
+                        logger.debug(f"Invalid sample name: {iii[c]}, skipping.")
+                        continue
                     id = iii[c]
                     logger.debug(f"Adding sample {iii[c]}")
                     try:
@@ -600,8 +356,9 @@ class SampleParser(object):
     def parse_lookup_table(self):
         def determine_if_date(input_str) -> str|date:
             # logger.debug(f"Looks like we have a str: {input_str}")
-            regex = re.compile(r"\d{4}-?\d{2}-?\d{2}")
+            regex = re.compile(r"^\d{4}-?\d{2}-?\d{2}")
             if bool(regex.search(input_str)):
+                logger.warning(f"{input_str} is a date!")
                 try:
                     return parse(input_str)
                 except ParserError:
@@ -610,6 +367,7 @@ class SampleParser(object):
                 return input_str
         for sample in self.samples:
             addition = self.lookup_table[self.lookup_table.isin([sample['submitter_id']]).any(axis=1)].squeeze().to_dict()
+            logger.debug(f"Lookuptable info: {addition}")
             for k,v in addition.items():
                 # logger.debug(f"Checking {k} in lookup table.")
                 if check_not_nan(k) and isinstance(k, str):
@@ -645,193 +403,89 @@ class SampleParser(object):
                     case _:
                         v = v
                 try:
-                    translated_dict[self.excel_to_db_map[k]] = v
+                    translated_dict[self.excel_to_db_map[k]] = convert_nans_to_nones(v)
                 except KeyError:
                     translated_dict[k] = convert_nans_to_nones(v)
-            # translated_dict['sample_type'] = f"{self.submission_type.replace(' ', '_').lower()}_sample"
             translated_dict['sample_type'] = f"{self.submission_type} Sample"
+            parser_query = f"parse_{translated_dict['sample_type'].replace(' ', '_').lower()}"
             # logger.debug(f"New sample dictionary going into object creation:\n{translated_dict}")
+            try:
+                custom_parser = getattr(self, parser_query)
+                translated_dict = custom_parser(translated_dict)
+            except AttributeError:
+                logger.error(f"Couldn't get custom parser: {parser_query}")
             new_samples.append(self.generate_sample_object(translated_dict))
         return result, new_samples
 
     def generate_sample_object(self, input_dict) -> models.BasicSample:
-        # query = input_dict['sample_type'].replace('_sample', '').replace("_", " ").title().replace(" ", "")
         query = input_dict['sample_type'].replace(" ", "")
-        database_obj = getattr(models, query)
+        try:
+            database_obj = getattr(models, query)
+        except AttributeError as e:
+            logger.error(f"Could not find the model {query}. Using generic.")
+            database_obj = models.BasicSample
+        logger.debug(f"Searching database for {input_dict['submitter_id']}...")
         instance = lookup_sample_by_submitter_id(ctx=self.ctx, submitter_id=input_dict['submitter_id'])
         if instance == None:
+            logger.debug(f"Couldn't find sample {input_dict['submitter_id']}. Creating new sample.")
             instance = database_obj()
             for k,v in input_dict.items():
                 try:
-                    setattr(instance, k, v)
+                    # setattr(instance, k, v)
+                    instance.set_attribute(k, v)
                 except Exception as e:
                     logger.error(f"Failed to set {k} due to {type(e).__name__}: {e}")
         else:
-            logger.debug(f"Sample already exists, will run update.")
+            logger.debug(f"Sample {instance.submitter_id} already exists, will run update.")
         return dict(sample=instance, row=input_dict['row'], column=input_dict['column'])
 
 
-    # def parse_bacterial_culture_samples(self) -> Tuple[str|None, list[dict]]:
+    def parse_bacterial_culture_sample(self, input_dict:dict) -> dict:
         """
-        construct bacterial culture specific sample objects
+        Update sample dictionary with bacterial culture specific information
+
+        Args:
+            input_dict (dict): Input sample dictionary
 
         Returns:
-            list[BCSample]: list of sample objects
+            dict: Updated sample dictionary
-        """       
-        # logger.debug(f"Samples: {self.samples}")
-        
-        new_list = []
-        for sample in self.samples:
-            logger.debug(f"Well info: {sample['This section to be filled in completely by submittor']}")
-            instance = lookup_sample_by_submitter_id(ctx=self.ctx, submitter_id=sample['Unnamed: 1'])
-            if instance == None:
-                instance = BacterialCultureSample()
-            well_number = sample['This section to be filled in completely by submittor']
-            row = row_keys[well_number[0]]
-            column = int(well_number[1:])
-            instance.submitter_id = sample['Unnamed: 1']
-            instance.organism = sample['Unnamed: 2']
-            instance.concentration = sample['Unnamed: 3']
-            # logger.debug(f"Sample object: {new.sample_id} = {type(new.sample_id)}")
-            logger.debug(f"Got sample_id: {instance.submitter_id}")
-            # need to exclude empties and blanks
-            if check_not_nan(instance.submitter_id):
-                new_list.append(dict(sample=instance, row=row, column=column))
-        return None, new_list
-
-    # def parse_wastewater_samples(self) -> Tuple[str|None, list[dict]]:
-        """
-        construct wastewater specific sample objects
-
-        Returns:
-            list[WWSample]: list of sample objects
         """        
-        def search_df_for_sample(sample_rsl:str):
+        logger.debug("Called bacterial culture sample parser")
-            # logger.debug(f"Attempting to find sample {sample_rsl} in \n {self.elution_map}")
+        return input_dict
-            well = self.elution_map.where(self.elution_map==sample_rsl)
+
-            # logger.debug(f"Well: {well}")
+    def parse_wastewater_sample(self, input_dict:dict) -> dict:
-            well = well.dropna(how='all').dropna(axis=1, how="all")
+        """
-            if well.size > 1:
+        Update sample dictionary with wastewater specific information
-                well = well.iloc[0].to_frame().dropna().T
+
-            logger.debug(f"well {sample_rsl} post processing: {well.size}: {type(well)}")#, {well.index[0]}, {well.columns[0]}")
+        Args:
-            try:
+            input_dict (dict): Input sample dictionary
-                self.elution_map.at[well.index[0], well.columns[0]] = np.nan
+
-            except IndexError as e:
+        Returns:
-                logger.error(f"Couldn't find the well for {sample_rsl}")
+            dict: Updated sample dictionary
-                return 0, 0
+        """        
-            try:
+        logger.debug(f"Called wastewater sample parser")
-                column = int(well.columns[0])
-            except TypeError as e:
-                logger.error(f"Problem parsing out column number for {well}:\n {e}")
-            row = row_keys[well.index[0]]
-            return row, column
-        new_list = []
-        return_val = None
-        for sample in self.samples:
-            logger.debug(f"Sample: {sample}")
-            instance = lookup_ww_sample_by_ww_sample_num(ctx=self.ctx, sample_number=sample['Unnamed: 3'])
-            if instance == None:
-                instance = WastewaterSample()
-                if check_not_nan(sample["Unnamed: 7"]):
-                    if sample["Unnamed: 7"] != "Fixed" and sample['Unnamed: 7'] != "Flex":
-                        instance.rsl_number = sample['Unnamed: 7'] # previously Unnamed: 9
-                    elif check_not_nan(sample['Unnamed: 9']):
-                        instance.rsl_number = sample['Unnamed: 9'] # previously Unnamed: 9
-                    else:
-                        logger.error(f"No RSL sample number found for this sample.")
-                        continue
-                else:
-                    logger.error(f"No RSL sample number found for this sample.")
-                    continue
-                instance.ww_processing_num = sample['Unnamed: 2']
-                # need to ensure we have a sample id for database integrity
-                # if we don't have a sample full id, make one up
-                if check_not_nan(sample['Unnamed: 3']):
-                    logger.debug(f"Sample name: {sample['Unnamed: 3']}")
-                    instance.submitter_id = sample['Unnamed: 3']
-                else:
-                    instance.submitter_id = uuid.uuid4().hex.upper()
-                # logger.debug(f"The Submitter sample id is: {instance.submitter_id}")
-                # need to ensure we get a collection date
-                if check_not_nan(sample['Unnamed: 5']):
-                    instance.collection_date = sample['Unnamed: 5']
-                else:
-                    instance.collection_date = date.today()
-                # new.testing_type = sample['Unnamed: 6']
-                # new.site_status = sample['Unnamed: 7']
-                instance.notes = str(sample['Unnamed: 6']) # previously Unnamed: 8
-                instance.well_24 = sample['Unnamed: 1']
-            else:
-                # What to do if the sample already exists 
-                assert isinstance(instance, WastewaterSample)
-                if instance.rsl_number == None:
-                    if check_not_nan(sample["Unnamed: 7"]):
-                        if sample["Unnamed: 7"] != "Fixed" and sample['Unnamed: 7'] != "Flex":
-                            instance.rsl_number = sample['Unnamed: 7'] # previously Unnamed: 9
-                        elif check_not_nan(sample['Unnamed: 9']):
-                            instance.rsl_number = sample['Unnamed: 9'] # previously Unnamed: 9
-                    else:
-                        logger.error(f"No RSL sample number found for this sample.")
-                if instance.collection_date == None:
-                    if check_not_nan(sample['Unnamed: 5']):
-                        instance.collection_date = sample['Unnamed: 5']
-                    else:
-                        instance.collection_date = date.today()
-                if instance.notes == None:
-                    instance.notes = str(sample['Unnamed: 6']) # previously Unnamed: 8
-                if instance.well_24 == None:
-                    instance.well_24 = sample['Unnamed: 1']
-                logger.debug(f"Already have that sample, going to add association to this plate.")
-            row, column = search_df_for_sample(instance.rsl_number)
-            # if elu_well != None:
-            #     row = elu_well[0]
-            #     col = elu_well[1:].zfill(2)
-            #     # new.well_number = f"{row}{col}"
-            # else:
-            #     # try:
-            #     return_val += f"{new.rsl_number}\n"
-            #     # except TypeError:
-            #         # return_val = f"{new.rsl_number}\n"
-            new_list.append(dict(sample=instance, row=row, column=column))
-        return return_val, new_list
     
-    # def parse_wastewater_artic_samples(self) -> Tuple[str|None, list[WastewaterSample]]:
+    def parse_wastewater_artic_sample(self, input_dict:dict) -> dict:
         """
-        The artic samples are the wastewater samples that are to be sequenced
+        Update sample dictionary with artic specific information
-        So we will need to lookup existing ww samples and append Artic well # and plate relation
+
+        Args:
+            input_dict (dict): Input sample dictionary
 
         Returns:
-            list[WWSample]: list of wastewater samples to be updated
+            dict: Updated sample dictionary
         """        
+        logger.debug("Called wastewater artic sample parser")
+        input_dict['sample_type'] = "Wastewater Sample"
+        # Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
+        # at the end, this has to be done here. No moving to sqlalchemy object :(
+        input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
+        return input_dict
         
-        new_list = []
-        missed_samples = []
-        for sample in self.samples:
-            with self.ctx.database_session.no_autoflush:
-                instance = lookup_ww_sample_by_ww_sample_num(ctx=self.ctx, sample_number=sample['sample_name'])
-            logger.debug(f"Checking: {sample}")
-            if instance == None:
-                logger.error(f"Unable to find match for: {sample['sample_name']}. Making new instance using {sample['submitter_id']}.")
-                instance = WastewaterSample()
-                instance.ww_processing_num = sample['sample_name']
-                instance.submitter_id = sample['submitter_id']
-                missed_samples.append(sample['sample_name'])
-                # continue
-            logger.debug(f"Got instance: {instance.submitter_id}")
-            # if sample['row'] != None:
-            #     row = int(row_keys[sample['well'][0]])
-            # if sample['column'] != None:                
-            #     column = int(sample['well'][1:])
-                # sample['well'] = f"{row}{col}"
-            # instance.artic_well_number = sample['well']
-            if instance.submitter_id != "NTC1" and instance.submitter_id != "NTC2":
-                new_list.append(dict(sample=instance, row=sample['row'], column=sample['column']))
-        missed_str = "\n\t".join(missed_samples)
-        return f"Could not find matches for the following samples:\n\t {missed_str}", new_list
-
 class PCRParser(object):
     """
     Object to pull data from Design and Analysis PCR export file.
+    TODO: Generify this object.
     """    
     def __init__(self, ctx:dict, filepath:Path|None = None) -> None:
         """

src/submissions/backend/pydant/__init__.py

@@ -1,5 +1,5 @@
 import uuid
-from pydantic import BaseModel, field_validator, Extra
+from pydantic import BaseModel, field_validator, Extra, Field
 from datetime import date, datetime
 from dateutil.parser import parse
 from dateutil.parser._parser import ParserError
@@ -32,10 +32,17 @@ class PydReagent(BaseModel):
 
     @field_validator("lot", mode='before')
     @classmethod
-    def enforce_lot_string(cls, value):
+    def rescue_lot_string(cls, value):
         if value != None:
             return convert_nans_to_nones(str(value))
         return value
+    
+    @field_validator("lot")
+    @classmethod
+    def enforce_lot_string(cls, value):
+        if value != None:
+            return value.upper()
+        return value
             
     @field_validator("exp", mode="before")
     @classmethod
@@ -66,8 +73,9 @@ class PydSubmission(BaseModel, extra=Extra.allow):
     ctx: Settings
     filepath: Path
     submission_type: dict|None
-    submitter_plate_num: dict|None
+    # For defaults
-    rsl_plate_num: dict|None
+    submitter_plate_num: dict|None = Field(default=dict(value=None, parsed=False), validate_default=True)
+    rsl_plate_num: dict|None = Field(default=dict(value=None, parsed=False), validate_default=True)
     submitted_date: dict|None
     submitting_lab: dict|None
     sample_count: dict|None
@@ -77,12 +85,12 @@ class PydSubmission(BaseModel, extra=Extra.allow):
     samples: List[Any]
     # missing_fields: List[str] = []
     
-    @field_validator("submitter_plate_num")
+    # @field_validator("submitter_plate_num", mode="before")
-    @classmethod
+    # @classmethod
-    def rescue_submitter_id(cls, value):
+    # def rescue_submitter_id(cls, value):
-        if value == None:
+    #     if value == None:
-            return dict(value=None, parsed=False)
+    #         return dict(value=None, parsed=False)
-        return value
+    #     return value
 
     @field_validator("submitter_plate_num")
     @classmethod

src/submissions/frontend/all_window_functions.py

@@ -28,6 +28,8 @@ def select_open_file(obj:QMainWindow, file_extension:str) -> Path:
     except FileNotFoundError:
         home_dir = Path.home().resolve().__str__()
     fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', home_dir, filter = f"{file_extension}(*.{file_extension})")[0])
+    # fname = Path(QFileDialog.getOpenFileName(obj, 'Open file', filter = f"{file_extension}(*.{file_extension})")[0])
+
     return fname
 
 def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
@@ -48,6 +50,8 @@ def select_save_file(obj:QMainWindow, default_name:str, extension:str) -> Path:
     except FileNotFoundError:
         home_dir = Path.home().joinpath(default_name).resolve().__str__()
     fname = Path(QFileDialog.getSaveFileName(obj, "Save File", home_dir, filter = f"{extension}(*.{extension})")[0])
+    # fname = Path(QFileDialog.getSaveFileName(obj, "Save File", filter = f"{extension}(*.{extension})")[0])
+
     return fname
 
 def extract_form_info(object) -> dict:

src/submissions/frontend/custom_widgets/sub_details.py

@@ -17,6 +17,7 @@ from PyQt6.QtCore import Qt, QAbstractTableModel, QSortFilterProxyModel
 from PyQt6.QtGui import QAction, QCursor, QPixmap, QPainter
 from backend.db import submissions_to_df, lookup_submission_by_id, delete_submission_by_id, lookup_submission_by_rsl_num, hitpick_plate
 from backend.excel import make_hitpicks
+from tools import check_if_app
 from tools import jinja_template_loading
 from xhtml2pdf import pisa
 from pathlib import Path
@@ -291,10 +292,14 @@ class SubmissionDetails(QDialog):
         # interior.resize(w,900)
         # txt_editor.setText(text)
         # interior.setWidget(txt_editor)
-        self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
+        logger.debug(f"Creating barcode.")
+        if not check_if_app():
+            self.base_dict['barcode'] = base64.b64encode(make_plate_barcode(self.base_dict['Plate Number'], width=120, height=30)).decode('utf-8')
         sub = lookup_submission_by_rsl_num(ctx=self.ctx, rsl_num=self.base_dict['Plate Number'])
         # plate_dicto = hitpick_plate(sub)
+        logger.debug(f"Hitpicking plate...")
         plate_dicto = sub.hitpick_plate()
+        logger.debug(f"Making platemap...")
         platemap = make_plate_map(plate_dicto)
         logger.debug(f"platemap: {platemap}")
         image_io = BytesIO()

src/submissions/frontend/main_window_functions.py

@@ -25,7 +25,7 @@ from backend.db.functions import (
     lookup_all_orgs, lookup_kittype_by_use, lookup_kittype_by_name, 
     construct_submission_info, lookup_reagent, store_submission, lookup_submissions_by_date_range, 
     create_kit_from_yaml, create_org_from_yaml, get_control_subtypes, get_all_controls_by_type,
-    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_ww_sample,
+    lookup_all_submissions_by_type, get_all_controls, lookup_submission_by_rsl_num, update_subsampassoc_with_pcr,
     check_kit_integrity
 )
 from backend.excel.parser import SheetParser, PCRParser
@@ -133,7 +133,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                 # lookup existing kits by 'submission_type' decided on by sheetparser
                 # uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'].lower())]
                 logger.debug(f"Looking up kits used for {pyd.submission_type['value']}")
-                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_by=pyd.submission_type['value'])]
+                uses = [item.__str__() for item in lookup_kittype_by_use(ctx=obj.ctx, used_for=pyd.submission_type['value'])]
                 logger.debug(f"Kits received for {pyd.submission_type['value']}: {uses}")
                 if check_not_nan(value['value']):
                     logger.debug(f"The extraction kit in parser was: {value['value']}")
@@ -365,7 +365,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     if kit_integrity != None:
         return obj, dict(message=kit_integrity['message'], status="critical")
     logger.debug(f"Sending submission: {base_submission.rsl_plate_num} to database.")
-    result = store_submission(ctx=obj.ctx, base_submission=base_submission, samples=obj.samples)
+    result = store_submission(ctx=obj.ctx, base_submission=base_submission)
     # check result of storing for issues
     # update summary sheet
     obj.table_widget.sub_wid.setData()
@@ -383,7 +383,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         excel_map = extraction_kit.construct_xl_map_for_use(obj.current_submission_type)
         logger.debug(f"Extraction kit map:\n\n{pprint.pformat(excel_map)}")
         # excel_map.update(extraction_kit.used_for[obj.current_submission_type.replace('_', ' ').title()])
-        input_reagents = [item.to_reagent_dict() for item in parsed_reagents]
+        input_reagents = [item.to_reagent_dict(extraction_kit=base_submission.extraction_kit) for item in parsed_reagents]
+        logger.debug(f"Parsed reagents going into autofile: {pprint.pformat(input_reagents)}")
         autofill_excel(obj=obj, xl_map=excel_map, reagents=input_reagents, missing_reagents=obj.missing_reagents, info=info, missing_info=obj.missing_info)
     if hasattr(obj, 'csv'):
         dlg = QuestionAsker("Export CSV?", "Would you like to export the csv file?")
@@ -844,10 +845,16 @@ def import_pcr_results_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     obj.ctx.database_session.commit()
     logger.debug(f"Got {len(parser.samples)} samples to update!")
     logger.debug(f"Parser samples: {parser.samples}")
-    for sample in parser.samples:
+    for sample in sub.samples:
-        logger.debug(f"Running update on: {sample['sample']}")
+        logger.debug(f"Running update on: {sample}")
-        sample['plate_rsl'] = sub.rsl_plate_num
+        try:
-        update_ww_sample(ctx=obj.ctx, sample_obj=sample)
+            sample_dict = [item for item in parser.samples if item['sample']==sample.rsl_number][0]
+        except IndexError:
+            continue
+        # sample['plate_rsl'] = sub.rsl_plate_num
+        # update_ww_sample(ctx=obj.ctx, sample_obj=sample)
+        update_subsampassoc_with_pcr(ctx=obj.ctx, submission=sub, sample=sample, input_dict=sample_dict)
+
     result = dict(message=f"We added PCR info to {sub.rsl_plate_num}.", status='information')
     return obj, result
 
@@ -872,7 +879,16 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
     # pare down the xl map to only the missing data.
     relevant_reagent_map = {k:v for k,v in xl_map.items() if k in [reagent.type for reagent in missing_reagents]}
     # pare down reagents to only what's missing
+    logger.debug(f"Checking {[item['type'] for item in reagents]} against {[reagent.type for reagent in missing_reagents]}")
     relevant_reagents = [item for item in reagents if item['type'] in [reagent.type for reagent in missing_reagents]]
+    # relevant_reagents = []
+    # for item in reagents:
+    #     logger.debug(f"Checking {item['type']} in {[reagent.type for reagent in missing_reagents]}")
+    #     if item['type'] in [reagent.type for reagent in missing_reagents]:
+    #         logger.debug("Hit!")
+    #         relevant_reagents.append(item)
+    #     else:
+    #         logger.debug('Miss.')
     logger.debug(f"Here are the relevant reagents: {pprint.pformat(relevant_reagents)}")
     # hacky manipulation of submission type so it looks better.
     # info['submission_type'] = info['submission_type'].replace("_", " ").title()

src/submissions/templates/submission_details.html

@@ -5,7 +5,7 @@
     </head>
     {% set excluded = ['reagents', 'samples', 'controls', 'ext_info', 'pcr_info', 'comments', 'barcode', 'platemap'] %}
     <body>
-        <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">
+        <h2><u>Submission Details for {{ sub['Plate Number'] }}</u></h2>&nbsp;&nbsp;&nbsp;{% if sub['barcode'] %}<img align='right' height="30px" width="120px" src="data:image/jpeg;base64,{{ sub['barcode'] | safe }}">{% endif %}
         <p>{% for key, value in sub.items() if key not in excluded %}
             &nbsp;&nbsp;&nbsp;&nbsp;<b>{{ key }}: </b>{% if key=='Cost' %} {{ "${:,.2f}".format(value) }}{% else %}{{ value }}{% endif %}<br>
         {% endfor %}</p>

src/submissions/tools/__init__.py

@@ -195,7 +195,7 @@ class RSLNamer(object):
                 # (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(?:_|-)\d?((?!\d)|R)?\d(?!\d))?)|
                 (?P<wastewater>RSL(?:-|_)?WW(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?)|
                 (?P<bacterial_culture>RSL-?\d{2}-?\d{4})|
-                (?P<wastewater_artic>(\d{4}-\d{2}-\d{2}_(?:\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?))
+                (?P<wastewater_artic>(\d{4}-\d{2}-\d{2}(?:-|_)(?:\d_)?artic)|(RSL(?:-|_)?AR(?:-|_)?20\d{2}-?\d{2}-?\d{2}(?:(_|-)\d?(\D|$)R?\d?)?))
                 """, flags = re.IGNORECASE | re.VERBOSE)
         m = regex.search(self.out_str)
         if m != None:
@@ -308,10 +308,10 @@ class RSLNamer(object):
         except AttributeError:
             self.parsed_name = construct()
         try:
-            plate_number = int(re.search(r"_\d?_", self.parsed_name).group().strip("_"))
+            plate_number = int(re.search(r"_|-\d?_", self.parsed_name).group().strip("_").strip("-"))
-        except AttributeError as e:
+        except (AttributeError, ValueError) as e:
             plate_number = 1
-        self.parsed_name = re.sub(r"(_\d)?_ARTIC", f"-{plate_number}", self.parsed_name)
+        self.parsed_name = re.sub(r"(_|-\d)?_ARTIC", f"-{plate_number}", self.parsed_name)
 
 class GroupWriteRotatingFileHandler(handlers.RotatingFileHandler):
 
@@ -611,7 +611,6 @@ def jinja_template_loading():
         loader_path = Path(sys._MEIPASS).joinpath("files", "templates")
     else:
         loader_path = Path(__file__).parents[1].joinpath('templates').absolute().__str__()
-
     # jinja template loading
     loader = FileSystemLoader(loader_path)
     env = Environment(loader=loader)