Update to autofill.

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 202309.03
+
+- Autofill now adds name of reagent instead of type.
+
 ## 202309.02
 
 - Massive restructure of app and database to allow better relationships between kits/reagenttypes & submissions/samples.

TODO.md

@@ -1,5 +1,7 @@
+- [ ] Make kits easier to add.
 - [ ] Clean up & document code... again.
     - Including paring down the logging.debugs
+    - Also including reducing number of functions in db.functions
 - [ ] Fix Tests... again.
 - [x] Rebuild database
 - [x] Provide more generic names for reagenttypes in kits and move specific names to reagents.

src/submissions/__init__.py

@@ -4,7 +4,7 @@ from pathlib import Path
 
 # Version of the realpython-reader package
 __project__ = "submissions"
-__version__ = "202309.2b"
+__version__ = "202309.3b"
 __author__ = {"name":"Landon Wark", "email":"Landon.Wark@phac-aspc.gc.ca"}
 __copyright__ = "2022-2023, Government of Canada"
 

src/submissions/backend/db/functions.py

@@ -18,7 +18,7 @@ import numpy as np
 import yaml
 from pathlib import Path
 from tools import Settings, check_regex_match, RSLNamer
-from typing import List
+from typing import List, Tuple
 
 
 
@@ -27,6 +27,14 @@ logger = logging.getLogger(f"submissions.{__name__}")
 # The below _should_ allow automatic creation of foreign keys in the database
 @event.listens_for(Engine, "connect")
 def set_sqlite_pragma(dbapi_connection, connection_record):
+    """
+    *should* allow automatic creation of foreign keys in the database
+    I have no idea how it actually works.
+
+    Args:
+        dbapi_connection (_type_): _description_
+        connection_record (_type_): _description_
+    """    
     cursor = dbapi_connection.cursor()
     cursor.execute("PRAGMA foreign_keys=ON")
     cursor.close()
@@ -79,7 +87,7 @@ def store_reagent(ctx:Settings, reagent:models.Reagent) -> None|dict:
         return {"message":"The database is locked for editing."}
     return None
 
-def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmission:
+def construct_submission_info(ctx:Settings, info_dict:dict) -> Tuple[models.BasicSubmission, dict]:
     """
     Construct submission object from dictionary
 
@@ -273,7 +281,7 @@ def lookup_reagenttype_by_name(ctx:Settings, rt_name:str) -> models.ReagentType:
     Returns:
         models.ReagentType: looked up reagent type
     """    
-    logger.debug(f"Looking up ReagentType by name: {rt_name.title()}")
+    logger.debug(f"Looking up ReagentType by name: {rt_name}")
     lookedup = ctx.database_session.query(models.ReagentType).filter(models.ReagentType.name==rt_name).first()
     logger.debug(f"Found ReagentType: {lookedup}")
     return lookedup
@@ -302,7 +310,7 @@ def lookup_kittype_by_name(ctx:Settings, name:str|dict) -> models.KitType:
 
     Args:
         ctx (Settings): settings object passed from bui
-        name (str): name of kit to query
+        name (str|dict): name of kit to query, or parsed object containing value=name
 
     Returns:
         models.KitType: retrieved kittype
@@ -989,25 +997,6 @@ def lookup_reagent(ctx:Settings, reagent_lot:str, type_name:str|None=None) -> mo
         # return ctx['database_session'].query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
         return ctx.database_session.query(models.Reagent).filter(models.Reagent.lot==reagent_lot).first()
     
-def lookup_last_used_reagenttype_lot(ctx:Settings, type_name:str) -> models.Reagent:
-    """
-    Look up the last used reagent of the reagent type
-
-    Args:
-        ctx (Settings): Settings object passed down from gui
-        type_name (str): Name of reagent type
-
-    Returns:
-        models.Reagent: Reagent object with last used lot.
-    """    
-    # rt = ctx['database_session'].query(models.ReagentType).filter(models.ReagentType.name==type_name).first()
-    rt = ctx.database_session.query(models.ReagentType).filter(models.ReagentType.name==type_name).first()
-    logger.debug(f"Reagent type looked up for {type_name}: {rt.__str__()}")
-    try:
-        return lookup_reagent(ctx=ctx, reagent_lot=rt.last_used, type_name=type_name)
-    except AttributeError:
-        return None
-
 def check_kit_integrity(sub:models.BasicSubmission|models.KitType, reagenttypes:list|None=None) -> dict|None:
     """
     Ensures all reagents expected in kit are listed in Submission
@@ -1120,7 +1109,7 @@ 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:
+def lookup_sub_samp_association_by_plate_sample(ctx:Settings, rsl_plate_num:str|models.BasicSample, rsl_sample_num:str|models.BasicSubmission) -> models.WastewaterAssociation:
     """
     _summary_
 
@@ -1132,12 +1121,36 @@ def lookup_sub_wwsamp_association_by_plate_sample(ctx:Settings, rsl_plate_num:st
     Returns:
         models.SubmissionSampleAssociation: _description_
     """    
-    return ctx.database_session.query(models.WastewaterAssociation)\
+    # logger.debug(f"{type(rsl_plate_num)}, {type(rsl_sample_num)}")
-                .join(models.Wastewater)\
+    match rsl_plate_num:
-                .join(models.WastewaterSample)\
+        case models.BasicSubmission()|models.Wastewater():
-                .filter(models.BasicSubmission.rsl_plate_num==rsl_plate_num)\
+            # logger.debug(f"Model for rsl_plate_num: {rsl_plate_num}")
-                .filter(models.BasicSample.submitter_id==rsl_sample_num)\
+            first_query = ctx.database_session.query(models.SubmissionSampleAssociation)\
-                .first()
+                .filter(models.SubmissionSampleAssociation.submission==rsl_plate_num)
+        case str():
+            # logger.debug(f"String for rsl_plate_num: {rsl_plate_num}")
+            first_query = ctx.database_session.query(models.SubmissionSampleAssociation)\
+                .join(models.BasicSubmission)\
+                .filter(models.BasicSubmission.rsl_plate_num==rsl_plate_num)
+        case _:
+            logger.error(f"Unknown case for rsl_plate_num {rsl_plate_num}")
+    match rsl_sample_num:
+        case models.BasicSample()|models.WastewaterSample():
+            # logger.debug(f"Model for rsl_sample_num: {rsl_sample_num}")
+            second_query = first_query.filter(models.SubmissionSampleAssociation.sample==rsl_sample_num)
+        # case models.WastewaterSample:
+        #     second_query = first_query.filter(models.SubmissionSampleAssociation.sample==rsl_sample_num)
+        case str():
+            # logger.debug(f"String for rsl_sample_num: {rsl_sample_num}")
+            second_query = first_query.join(models.BasicSample)\
+                .filter(models.BasicSample.submitter_id==rsl_sample_num)
+        case _:
+            logger.error(f"Unknown case for rsl_sample_num {rsl_sample_num}")
+    try:
+        return second_query.first()
+    except UnboundLocalError:
+        logger.error(f"Couldn't construct second query")
+        return None
 
 def lookup_all_reagent_names_by_role(ctx:Settings, role_name:str) -> List[str]:
     """
@@ -1183,7 +1196,7 @@ def add_reagenttype_to_kit(ctx:Settings, rt_name:str, kit_name:str, eol:int=0):
     kit = lookup_kittype_by_name(ctx=ctx, name=kit_name)
     rt = lookup_reagenttype_by_name(ctx=ctx, rt_name=rt_name)
     if rt == None:
-        rt = models.ReagentType(name=rt_name.strip(), eol_ext=timedelta(30*eol), last_used="")
+        rt = models.ReagentType(name=rt_name.strip(), eol_ext=timedelta(30*eol))
         ctx.database_session.add(rt)
     assoc = models.KitTypeReagentTypeAssociation(kit_type=kit, reagent_type=rt, uses={})
     kit.kit_reagenttype_associations.append(assoc)
@@ -1204,3 +1217,68 @@ def update_subsampassoc_with_pcr(ctx:Settings, submission:models.BasicSubmission
             logger.error(f"Can't set {k} to {v}")
     ctx.database_session.add(assoc)
     ctx.database_session.commit()
+
+def lookup_ww_sample_by_processing_number(ctx:Settings, processing_number:str):
+    return ctx.database_session.query(models.WastewaterSample).filter(models.WastewaterSample.ww_processing_num==processing_number).first()
+
+def lookup_kitreagentassoc_by_kit_and_reagent(ctx:Settings, kit:models.KitType|str, reagent_type:models.ReagentType|str) -> models.KitTypeReagentTypeAssociation:
+    """
+    _summary_
+
+    Args:
+        ctx (Settings): _description_
+        kit (models.KitType | str): _description_
+        reagent_type (models.ReagentType | str): _description_
+
+    Returns:
+        models.KitTypeReagentTypeAssociation: _description_
+    """    
+    base_query = ctx.database_session.query(models.KitTypeReagentTypeAssociation)
+    match kit:
+        case models.KitType():
+            query1 = base_query.filter(models.KitTypeReagentTypeAssociation.kit_type==kit)
+        case str():
+            query1 = base_query.join(models.KitType).filter(models.KitType.name==kit)
+        case _:
+            query1 = base_query
+    match reagent_type:
+        case models.ReagentType():
+            query2 = query1.filter(models.KitTypeReagentTypeAssociation.reagent_type==reagent_type)
+        case str():
+            query2 = query1.join(models.ReagentType).filter(models.ReagentType.name==reagent_type)
+        case _:
+            query2 = query1
+    return query2.first()
+
+def lookup_last_used_reagenttype_lot(ctx:Settings, type_name:str, extraction_kit:str|None=None) -> models.Reagent:
+    """
+    Look up the last used reagent of the reagent type
+
+    Args:
+        ctx (Settings): Settings object passed down from gui
+        type_name (str): Name of reagent type
+
+    Returns:
+        models.Reagent: Reagent object with last used lot.
+    """    
+    assoc = lookup_kitreagentassoc_by_kit_and_reagent(ctx=ctx, kit=extraction_kit, reagent_type=type_name)
+    return lookup_reagent(ctx=ctx, reagent_lot=assoc.last_used)
+    
+def update_last_used(ctx:Settings, reagent:models.Reagent, kit:models.KitType):
+    """
+    _summary_
+
+    Args:
+        ctx (Settings): _description_
+        reagent (models.ReagentType): _description_
+        reagent_lot (str): _description_
+    """    
+    rt = list(set(reagent.type).intersection(kit.reagent_types))[0]
+    if rt != None:
+        assoc = lookup_kitreagentassoc_by_kit_and_reagent(ctx=ctx, kit=kit, reagent_type=rt)
+        if assoc != None:
+            if assoc.last_used != reagent.lot:
+                logger.debug(f"Updating {assoc} last used to {reagent.lot}")
+                assoc.last_used = reagent.lot
+                ctx.database_session.merge(assoc)
+                ctx.database_session.commit()

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

@@ -97,39 +97,7 @@ class KitType(Base):
             map['info'] = {}
         return map
     
-class KitTypeReagentTypeAssociation(Base):
-    """
-    table containing reagenttype/kittype associations
-    DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
-    """    
-    __tablename__ = "_reagenttypes_kittypes"
-    reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True)
-    kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
-    uses = Column(JSON)
-    required = Column(INTEGER)
 
-    kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
-
-    # reference to the "ReagentType" object
-    reagent_type = relationship("ReagentType")
-
-    def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
-        self.kit_type = kit_type
-        self.reagent_type = reagent_type
-        self.uses = uses
-        self.required = required
-
-    @validates('required')
-    def validate_age(self, key, value):
-        if not 0 <= value < 2:
-            raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
-        return value
-    
-    @validates('reagenttype')
-    def validate_reagenttype(self, key, value):
-        if not isinstance(value, ReagentType):
-            raise ValueError(f'{value} is not a reagenttype')
-        return value
 
 class ReagentType(Base):
     """
@@ -141,7 +109,16 @@ class ReagentType(Base):
     name = Column(String(64)) #: name of reagent type
     instances = relationship("Reagent", back_populates="type", secondary=reagenttypes_reagents) #: concrete instances of this reagent type
     eol_ext = Column(Interval()) #: extension of life interval
-    last_used = Column(String(32)) #: last used lot number of this type of reagent
+    
+    reagenttype_kit_associations = relationship(
+        "KitTypeReagentTypeAssociation",
+        back_populates="reagent_type",
+        cascade="all, delete-orphan",
+    )
+
+    # association proxy of "user_keyword_associations" collection
+    # to "keyword" attribute
+    kit_types = association_proxy("kit_reagenttype_associations", "kit_type")
 
     @validates('required')
     def validate_age(self, key, value):
@@ -161,6 +138,44 @@ class ReagentType(Base):
     def __repr__(self):
         return f"ReagentType({self.name})"
     
+class KitTypeReagentTypeAssociation(Base):
+    """
+    table containing reagenttype/kittype associations
+    DOC: https://docs.sqlalchemy.org/en/14/orm/extensions/associationproxy.html
+    """    
+    __tablename__ = "_reagenttypes_kittypes"
+    reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id"), primary_key=True)
+    kits_id = Column(INTEGER, ForeignKey("_kits.id"), primary_key=True)
+    uses = Column(JSON)
+    required = Column(INTEGER)
+    last_used = Column(String(32)) #: last used lot number of this type of reagent
+
+    kit_type = relationship(KitType, back_populates="kit_reagenttype_associations")
+
+    # reference to the "ReagentType" object
+    reagent_type = relationship(ReagentType, back_populates="reagenttype_kit_associations")
+
+    def __init__(self, kit_type=None, reagent_type=None, uses=None, required=1):
+        self.kit_type = kit_type
+        self.reagent_type = reagent_type
+        self.uses = uses
+        self.required = required
+
+    def __repr__(self) -> str:
+        return f"<KitTypeReagentTypeAssociation({self.kit_type} & {self.reagent_type})>"
+
+    @validates('required')
+    def validate_age(self, key, value):
+        if not 0 <= value < 2:
+            raise ValueError(f'Invalid required value {value}. Must be 0 or 1.')
+        return value
+    
+    @validates('reagenttype')
+    def validate_reagenttype(self, key, value):
+        if not isinstance(value, ReagentType):
+            raise ValueError(f'{value} is not a reagenttype')
+        return value
+
 class Reagent(Base):
     """
     Concrete reagent instance
@@ -247,11 +262,13 @@ class Reagent(Base):
         except AttributeError:
             rtype = "Unknown"
         return {
+            "name":self.name,
             "type": rtype,
             "lot": self.lot,
             "expiry": self.expiry.strftime("%Y-%m-%d")
         }
 
+    
 class Discount(Base):
     """
     Relationship table for client labs for certain kits.
@@ -266,6 +283,9 @@ class Discount(Base):
     name = Column(String(128))
     amount = Column(FLOAT(2))
 
+    def __repr__(self) -> str:
+        return f"<Discount({self.name})>"
+
 class SubmissionType(Base):
     """
     Abstract of types of submissions.

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

@@ -47,3 +47,6 @@ class Contact(Base):
     phone = Column(String(32)) #: contact phone number
     organization = relationship("Organization", back_populates="contacts", uselist=True, secondary=orgs_contacts) #: relationship to joined organization
 
+    def __repr__(self) -> str:
+        return f"<Contact({self.name})>"
+

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

@@ -13,8 +13,6 @@ from sqlalchemy.ext.associationproxy import association_proxy
 import uuid
 from pandas import Timestamp
 from dateutil.parser import parse
-import pprint
-from tools import check_not_nan
 
 logger = logging.getLogger(f"submissions.{__name__}")
 
@@ -348,7 +346,7 @@ class BasicSample(Base):
             return value
         
     def __repr__(self) -> str:
-        return f"<{self.sample_type.replace('_', ' ').title(). replace(' ', '')}({self.submitter_id})>"
+        return f"<{self.sample_type.replace('_', ' ').title().replace(' ', '')}({self.submitter_id})>"
     
     def set_attribute(self, name, value):
         # logger.debug(f"Setting {name} to {value}")
@@ -417,56 +415,36 @@ class WastewaterSample(BasicSample):
         logger.debug(f"Validating {key}: {value}")
         return value or self.submitter_id
 
-    # def __init__(self, **kwargs):
-    #     # Had a problem getting collection date from excel as text only.
-    #     if 'collection_date' in kwargs.keys():
-    #         logger.debug(f"Got collection_date: {kwargs['collection_date']}. Attempting parse.")
-    #         if isinstance(kwargs['collection_date'], str):
-    #             logger.debug(f"collection_date is a string...")
-    #             kwargs['collection_date'] = parse(kwargs['collection_date'])
-    #             logger.debug(f"output is {kwargs['collection_date']}")
-    #     # 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 set_attribute(self, name:str, value):
         """
         Set an attribute of this object. Extends parent.
 
         Args:
-            name (str): _description_
+            name (str): name of the attribute
-            value (_type_): _description_
+            value (_type_): value to be set
         """        
         # 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 submitter_id already has a value, stop
                 if self.submitter_id != None:
                     return
+                # otherwise also set rsl_number to the same value
                 else:
                     super().set_attribute("rsl_number", value)
             case "ww_full_sample_id":
+                # If value present, set ww_full_sample_id and make this the submitter_id
                 if value != None:
                     super().set_attribute(name, value)
                     name = "submitter_id"
             case 'collection_date':
+                # If this is a string use dateutils to parse into 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)
 
 

src/submissions/backend/excel/parser.py

@@ -14,7 +14,7 @@ import re
 import numpy as np
 from datetime import date
 from dateutil.parser import parse, ParserError
-from tools import check_not_nan, RSLNamer, convert_nans_to_nones, Settings
+from tools import check_not_nan, RSLNamer, convert_nans_to_nones, Settings, convert_well_to_row_column
 from frontend.custom_widgets.pop_ups import SubmissionTypeSelector, KitSelector
 
 logger = logging.getLogger(f"submissions.{__name__}")
@@ -48,13 +48,11 @@ class SheetParser(object):
         # make decision about type of sample we have
         self.sub['submission_type'] = self.type_decider()
         # # grab the info map from the submission type in database
-        # self.info_map = self.fetch_kit_info_map()
         self.parse_info()
         self.import_kit_validation_check()
         self.parse_reagents()
         self.import_reagent_validation_check()
         self.parse_samples()
-        # self.sub['sample_count'] = len(self.sub['samples'])
        
 
     def type_decider(self) -> str:
@@ -91,7 +89,7 @@ class SheetParser(object):
                 
     def parse_info(self):
         """
-        _summary_
+        Pulls basic information from the excel sheet
         """        
         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()}"
@@ -101,14 +99,23 @@ class SheetParser(object):
         except AttributeError:
             logger.error(f"Couldn't find submission parser: {parser_query}")
         for k,v in info.items():
-            if k != "sample":
+            match k:
+                case "sample":
+                    pass
+                case _:
                     self.sub[k] = v
         logger.debug(f"Parser.sub after info scrape: {pprint.pformat(self.sub)}")
 
     def parse_reagents(self):
+        """
+        Pulls reagent info from the excel sheet
+        """        
         self.sub['reagents'] = ReagentParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type'], extraction_kit=self.sub['extraction_kit']).parse_reagents()
 
     def parse_samples(self):
+        """
+        Pulls sample info from the excel sheet
+        """        
         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, input_dict) -> dict:
@@ -159,7 +166,7 @@ class SheetParser(object):
         Returns:
             List[PydReagent]: List of reagents
         """    
-        if not check_not_nan(self.sub['extraction_kit']):
+        if not check_not_nan(self.sub['extraction_kit']['value']):
             dlg = KitSelector(ctx=self.ctx, title="Kit Needed", message="At minimum a kit is needed. Please select one.")
             if dlg.exec():
                 self.sub['extraction_kit'] = dict(value=dlg.getValues(), parsed=False)
@@ -197,7 +204,16 @@ class InfoParser(object):
         self.xl = xl
         logger.debug(f"Info map for InfoParser: {pprint.pformat(self.map)}")
 
-    def fetch_submission_info_map(self, submission_type:dict) -> dict:
+    def fetch_submission_info_map(self, submission_type:str|dict) -> dict:
+        """
+        Gets location of basic info from the submission_type object in the database.
+
+        Args:
+            submission_type (str|dict): name of the submission type or parsed object with value=submission_type
+
+        Returns:
+            dict: Location map of all info for this submission type
+        """        
         if isinstance(submission_type, str):
             submission_type = dict(value=submission_type, parsed=False)
         logger.debug(f"Looking up submission type: {submission_type['value']}")
@@ -206,6 +222,12 @@ class InfoParser(object):
         return info_map
 
     def parse_info(self) -> dict:
+        """
+        Pulls basic info from the excel sheet.
+
+        Returns:
+            dict: key:value of basic info
+        """        
         dicto = {}
         for sheet in self.xl.sheet_names:
             df = self.xl.parse(sheet, header=None)
@@ -302,6 +324,8 @@ class SampleParser(object):
         sample_info_map = self.fetch_sample_info_map(submission_type=submission_type)
         self.plate_map = self.construct_plate_map(plate_map_location=sample_info_map['plate_map'])
         self.lookup_table = self.construct_lookup_table(lookup_table_location=sample_info_map['lookup_table'])
+        if "plates" in sample_info_map:
+            self.plates = sample_info_map['plates']
         self.excel_to_db_map = sample_info_map['xl_db_translation']
         self.create_basic_dictionaries_from_plate_map()
         if isinstance(self.lookup_table, pd.DataFrame):
@@ -383,7 +407,7 @@ class SampleParser(object):
                                 sample[k] = v
             logger.debug(f"Output sample dict: {sample}")
 
-    def parse_samples(self) -> List[dict]:
+    def parse_samples(self, generate:bool=True) -> List[dict]:
         result = None
         new_samples = []
         for ii, sample in enumerate(self.samples):
@@ -414,7 +438,10 @@ class SampleParser(object):
                 translated_dict = custom_parser(translated_dict)
             except AttributeError:
                 logger.error(f"Couldn't get custom parser: {parser_query}")
+            if generate:
                 new_samples.append(self.generate_sample_object(translated_dict))
+            else:
+                new_samples.append(translated_dict)
         return result, new_samples
 
     def generate_sample_object(self, input_dict) -> models.BasicSample:
@@ -464,6 +491,7 @@ class SampleParser(object):
             dict: Updated sample dictionary
         """        
         logger.debug(f"Called wastewater sample parser")
+        return input_dict
     
     def parse_wastewater_artic_sample(self, input_dict:dict) -> dict:
         """
@@ -482,6 +510,24 @@ class SampleParser(object):
         input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
         return input_dict
     
+    def parse_first_strand_sample(self, input_dict:dict) -> dict:
+        logger.debug("Called first strand sample parser")
+        input_dict['well'] = re.search(r"\s\((.*)\)$", input_dict['submitter_id']).groups()[0]
+        input_dict['submitter_id'] = re.sub(r"\s\(.*\)$", "", str(input_dict['submitter_id'])).strip()
+        return input_dict
+    
+    def grab_plates(self):
+        plates = []
+        for plate in self.plates:
+            df = self.xl.parse(plate['sheet'], header=None)
+            if isinstance(df.iat[plate['row']-1, plate['column']-1], str):
+                output = RSLNamer(ctx=self.ctx, instr=df.iat[plate['row']-1, plate['column']-1]).parsed_name
+            else:
+                continue
+            plates.append(output)
+        return plates
+
+        
 class PCRParser(object):
     """
     Object to pull data from Design and Analysis PCR export file.

src/submissions/backend/pydant/__init__.py

@@ -200,18 +200,26 @@ class PydSubmission(BaseModel, extra=Extra.allow):
     @field_validator("extraction_kit", mode='before')
     @classmethod
     def rescue_kit(cls, value):
-        # from frontend.custom_widgets.pop_ups import KitSelector
+        
-        # if check_not_nan(value):
+        if check_not_nan(value):
-        #     if isinstance(value, str):
+            if isinstance(value, str):
-        #         return dict(value=value, parsed=True)
+                return dict(value=value, parsed=True)
-        #     elif isinstance(value, dict):
+            elif isinstance(value, dict):
-        #         return value
+                return value
-        # else:
+        else:
-        #     raise ValueError(f"No extraction kit found.")
+            raise ValueError(f"No extraction kit found.")
         if value == None:
             return dict(value=None, parsed=False)
         return value
     
+    # @field_validator("extraction_kit")
+    # @classmethod
+    # def enforce_kit(cls, value, values):
+    #     from frontend.custom_widgets.pop_ups import KitSelector
+    #     if value['value'] == None:
+    #         return dict(value=KitSelector(values.data['ctx'], title="Select Extraction Kit", message="No extraction kit was found, please select from below."))
+    #     return value
+            
     @field_validator("submission_type", mode='before')
     @classmethod
     def make_submission_type(cls, value, values):

src/submissions/frontend/__init__.py

@@ -64,6 +64,7 @@ class App(QMainWindow):
         fileMenu = menuBar.addMenu("&File")
         # Creating menus using a title
         editMenu = menuBar.addMenu("&Edit")
+        methodsMenu = menuBar.addMenu("&Methods")
         reportMenu = menuBar.addMenu("&Reports")
         maintenanceMenu = menuBar.addMenu("&Monthly")
         helpMenu = menuBar.addMenu("&Help")
@@ -71,6 +72,7 @@ class App(QMainWindow):
         helpMenu.addAction(self.docsAction)
         fileMenu.addAction(self.importAction)
         fileMenu.addAction(self.importPCRAction)
+        methodsMenu.addAction(self.constructFS)
         reportMenu.addAction(self.generateReportAction)
         maintenanceMenu.addAction(self.joinControlsAction)
         maintenanceMenu.addAction(self.joinExtractionAction)
@@ -103,6 +105,7 @@ class App(QMainWindow):
         self.joinPCRAction = QAction("Link PCR Logs")
         self.helpAction = QAction("&About", self)
         self.docsAction = QAction("&Docs", self)
+        self.constructFS = QAction("Make First Strand", self)
 
 
     def _connectActions(self):
@@ -125,6 +128,7 @@ class App(QMainWindow):
         self.joinPCRAction.triggered.connect(self.linkPCR)
         self.helpAction.triggered.connect(self.showAbout)
         self.docsAction.triggered.connect(self.openDocs)
+        self.constructFS.triggered.connect(self.construct_first_strand)
 
     def showAbout(self):
         """
@@ -290,6 +294,14 @@ class App(QMainWindow):
         self, result = import_pcr_results_function(self)
         self.result_reporter(result)
 
+    def construct_first_strand(self):
+        """
+        Converts first strand excel sheet to Biomek CSV
+        """        
+        from .main_window_functions import construct_first_strand_function
+        self, result = construct_first_strand_function(self)
+        self.result_reporter(result)
+
 class AddSubForm(QWidget):
     
     def __init__(self, parent):

src/submissions/frontend/custom_widgets/misc.py

@@ -31,7 +31,7 @@ class AddReagentForm(QDialog):
         super().__init__()
         self.ctx = ctx
         if reagent_lot == None:
-            reagent_lot = ""
+            reagent_lot = reagent_type
 
         self.setWindowTitle("Add Reagent")
 
@@ -257,7 +257,7 @@ class ControlsDatePicker(QWidget):
 
 class ImportReagent(QComboBox):
 
-    def __init__(self, ctx:dict, reagent:PydReagent):
+    def __init__(self, ctx:dict, reagent:PydReagent, extraction_kit:str):
         super().__init__()
         self.setEditable(True)
         # Ensure that all reagenttypes have a name that matches the items in the excel parser
@@ -289,7 +289,7 @@ class ImportReagent(QComboBox):
                 relevant_reagents.insert(0, str(reagent.lot))
             else:
                 # TODO: look up the last used reagent of this type in the database
-                looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type)
+                looked_up_reg = lookup_last_used_reagenttype_lot(ctx=ctx, type_name=reagent.type, extraction_kit=extraction_kit)
                 logger.debug(f"Because there was no reagent listed for {reagent}, we will insert the last lot used: {looked_up_reg}")
                 if looked_up_reg != None:
                     relevant_reagents.remove(str(looked_up_reg.lot))

src/submissions/frontend/main_window_functions.py

@@ -26,12 +26,13 @@ from backend.db.functions import (
     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_subsampassoc_with_pcr,
-    check_kit_integrity
+    check_kit_integrity, lookup_sub_samp_association_by_plate_sample, lookup_ww_sample_by_processing_number,
+    lookup_sample_by_submitter_id, update_last_used
 )
-from backend.excel.parser import SheetParser, PCRParser
+from backend.excel.parser import SheetParser, PCRParser, SampleParser
 from backend.excel.reports import make_report_html, make_report_xlsx, convert_data_list_to_df
 from backend.pydant import PydReagent
-from tools import check_not_nan
+from tools import check_not_nan, convert_well_to_row_column
 from .custom_widgets.pop_ups import AlertPop, QuestionAsker
 from .custom_widgets import ReportDatePicker
 from .custom_widgets.misc import ImportReagent, ParsedQLabel
@@ -182,7 +183,7 @@ def import_submission_function(obj:QMainWindow) -> Tuple[QMainWindow, dict|None]
                     # reg_label.setObjectName(f"lot_{reagent['type']}_label")
                     reg_label.setObjectName(f"lot_{reagent['value'].type}_label")
                     # create reagent choice widget
-                    add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent['value'])
+                    add_widget = ImportReagent(ctx=obj.ctx, reagent=reagent['value'], extraction_kit=pyd.extraction_kit['value'])
                     add_widget.setObjectName(f"lot_{reagent['value'].type}")
                     logger.debug(f"Widget name set to: {add_widget.objectName()}")
                     obj.table_widget.formlayout.addWidget(reg_label)
@@ -277,7 +278,7 @@ def kit_integrity_completion_function(obj:QMainWindow) -> Tuple[QMainWindow, dic
     for item in obj.missing_reagents:
         obj.table_widget.formlayout.addWidget(ParsedQLabel({'parsed':False}, item.type, title=False))
         reagent = dict(type=item.type, lot=None, exp=date.today(), name=None)
-        add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent))#item=item)
+        add_widget = ImportReagent(ctx=obj.ctx, reagent=PydReagent(**reagent), extraction_kit=obj.ext_kit)#item=item)
         obj.table_widget.formlayout.addWidget(add_widget)
     submit_btn = QPushButton("Submit")
     submit_btn.setObjectName("lot_submit_btn")
@@ -310,7 +311,6 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         # Lookup any existing reagent of this type with this lot number
         wanted_reagent = lookup_reagent(ctx=obj.ctx, reagent_lot=reagents[reagent], type_name=reagent)
         logger.debug(f"Looked up reagent: {wanted_reagent}")
-        # logger.debug(f"\n\nLooking for {reagent} in {obj.reagents}\n\n")
         # if reagent not found offer to add to database
         if wanted_reagent == None:
             r_lot = reagents[reagent]
@@ -328,15 +328,11 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
             else:
                 # In this case we will have an empty reagent and the submission will fail kit integrity check
                 logger.debug("Will not add reagent.")
-                # obj.ctx.database_session.rollback()
                 return obj, dict(message="Failed integrity check", status="critical")
-        # if wanted_reagent != None:
         parsed_reagents.append(wanted_reagent)
-        wanted_reagent.type.last_used = reagents[reagent]
     # move samples into preliminary submission dict
     info['samples'] = obj.samples
     info['uploaded_by'] = getuser()
-    # info['columns'] = obj.column_count
     # construct submission object
     logger.debug(f"Here is the info_dict: {pprint.pformat(info)}")
     base_submission, result = construct_submission_info(ctx=obj.ctx, info_dict=info)
@@ -359,6 +355,7 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
     # add reagents to submission object
     for reagent in parsed_reagents:
         base_submission.reagents.append(reagent)
+        update_last_used(ctx=obj.ctx, reagent=reagent, kit=base_submission.extraction_kit)
     logger.debug(f"Parsed reagents: {pprint.pformat(parsed_reagents)}")
     logger.debug("Checking kit integrity...")
     kit_integrity = check_kit_integrity(base_submission)
@@ -377,12 +374,8 @@ def submit_new_sample_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
         logger.debug(f"We have blank reagents in the excel sheet.\n\tLet's try to fill them in.") 
         extraction_kit = lookup_kittype_by_name(obj.ctx, name=obj.ext_kit)
         logger.debug(f"We have the extraction kit: {extraction_kit.name}")
-        
-        # TODO replace below with function in KitType object. Update Kittype associations.
-        # excel_map = extraction_kit.used_for[obj.current_submission_type.replace('_', ' ')]
         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(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)
@@ -881,17 +874,8 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
     # 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()
     # pare down info to just what's missing
     relevant_info_map = {k:v for k,v in xl_map['info'].items() if k in missing_info and k != 'samples'}
     relevant_info = {k:v for k,v in info.items() if k in missing_info}
@@ -910,9 +894,9 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
         # name is only present for Bacterial Culture
         try:
             new_reagent['name'] = relevant_reagent_map[new_reagent['type']]['name']
-            new_reagent['name']['value'] = reagent['type']
+            new_reagent['name']['value'] = reagent['name']
-        except:
+        except Exception as e:
-            pass
+            logger.error(f"Couldn't get name due to {e}")
         new_reagents.append(new_reagent)
     # construct new info objects to put into excel sheets
     new_info = []
@@ -936,21 +920,98 @@ def autofill_excel(obj:QMainWindow, xl_map:dict, reagents:List[dict], missing_re
         # Get relevant reagents for that sheet
         sheet_reagents = [item for item in new_reagents if sheet in item['sheet']]
         for reagent in sheet_reagents:
-            logger.debug(f"Attempting: {reagent['type']}:")
+            logger.debug(f"Attempting to write lot {reagent['lot']['value']} in: row {reagent['lot']['row']}, column {reagent['lot']['column']}")
             worksheet.cell(row=reagent['lot']['row'], column=reagent['lot']['column'], value=reagent['lot']['value'])
+            logger.debug(f"Attempting to write expiry {reagent['expiry']['value']} in: row {reagent['expiry']['row']}, column {reagent['expiry']['column']}")
             worksheet.cell(row=reagent['expiry']['row'], column=reagent['expiry']['column'], value=reagent['expiry']['value'])
             try:
-                worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'].replace("_", " ").upper())
+                logger.debug(f"Attempting to write name {reagent['name']['value']} in: row {reagent['name']['row']}, column {reagent['name']['column']}")
-            except:
+                worksheet.cell(row=reagent['name']['row'], column=reagent['name']['column'], value=reagent['name']['value'])
-                pass
+            except Exception as e:
+                logger.error(f"Could not write name {reagent['name']['value']} due to {e}")
         # Get relevant info for that sheet
         sheet_info = [item for item in new_info if sheet in item['location']['sheets']]
         for item in sheet_info:
             logger.debug(f"Attempting: {item['type']}")
             worksheet.cell(row=item['location']['row'], column=item['location']['column'], value=item['value'])
-        # Hacky way to 
+        # Hacky way to pop in 'signed by'
         if info['submission_type'] == "Bacterial Culture":
             workbook["Sample List"].cell(row=14, column=2, value=getuser()[0:2].upper())
     fname = select_save_file(obj=obj, default_name=info['rsl_plate_num'], extension="xlsx")
     workbook.save(filename=fname.__str__())
 
+def construct_first_strand_function(obj:QMainWindow) -> Tuple[QMainWindow, dict]:
+
+    def get_plates(input_sample_number:str, plates:list) -> Tuple[int, str]:
+        logger.debug(f"Looking up {input_sample_number} in {plates}")
+        samp = lookup_ww_sample_by_processing_number(ctx=obj.ctx, processing_number=input_sample_number)
+        if samp ==  None:
+            samp = lookup_sample_by_submitter_id(ctx=obj.ctx, submitter_id=input_sample_number)
+        logger.debug(f"Got sample: {samp}")
+        # if samp != None:
+        new_plates = [(iii+1, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate))) for iii, plate in enumerate(plates)]
+            # for iii, plate in enumerate(plates):
+            #     lplate = lookup_submission_by_rsl_num(ctx=obj.ctx, rsl_num=plate)
+            #     if lplate == None:
+            #         continue
+            #     else:
+            #         logger.debug(f"Got a plate: {lplate}")
+            #         new_plates.append((iii, lookup_sub_samp_association_by_plate_sample(ctx=obj.ctx, rsl_sample_num=samp, rsl_plate_num=lplate)))
+        logger.debug(f"Associations: {pprint.pformat(new_plates)}")
+        try:
+            plate_num, plate = next(assoc for assoc in new_plates if assoc[1] is not None)
+        except StopIteration:
+            plate_num, plate = None, None
+        logger.debug(f"Plate number {plate_num} is {plate}")
+        return plate_num, plate
+        
+        
+    fname = select_open_file(obj=obj, file_extension="xlsx")
+    xl = pd.ExcelFile(fname)
+    sprsr = SampleParser(ctx=obj.ctx, xl=xl, submission_type="First Strand")
+    _, samples = sprsr.parse_samples(generate=False)
+    plates = sprsr.grab_plates()
+    output_samples = []
+    logger.debug(f"Samples: {pprint.pformat(samples)}")
+    old_plate_number = 1
+    for item in samples:
+        new_dict = {}
+        new_dict['sample'] = item['submitter_id']
+        if item['submitter_id'] == "NTC1":
+            new_dict['destination_row'] = 8
+            new_dict['destination_column'] = 2
+            new_dict['plate_number'] = 'control'
+        elif item['submitter_id'] == "NTC2":
+            new_dict['destination_row'] = 8
+            new_dict['destination_column'] = 5
+            new_dict['plate_number'] = 'control'
+        else:
+            new_dict['destination_row'] = item['row']
+            new_dict['destination_column'] = item['column']
+        # assocs = [(iii, lookup_ww_sample_by_processing_number_and_plate(ctx=obj.ctx, processing_number=new_dict['sample'], plate_number=plate)) for iii, plate in enumerate(plates)]
+        plate_num, plate = get_plates(input_sample_number=new_dict['sample'], plates=plates)
+        if plate_num == None:
+            plate_num = str(old_plate_number) + "*"
+        else:
+            old_plate_number = plate_num
+        logger.debug(f"Got plate number: {plate_num}, plate: {plate}")
+        if plate == None:
+            try:
+                new_dict['source_row'], new_dict['source_column'] = convert_well_to_row_column(item['well'])
+                new_dict['plate_number'] = plate_num
+            except KeyError:
+                pass
+        else:
+            new_dict['plate_number'] = plate_num
+            new_dict['plate'] = plate.submission.rsl_plate_num
+            new_dict['source_row'] = plate.row
+            new_dict['source_column'] = plate.column
+        output_samples.append(new_dict)
+    df = pd.DataFrame.from_records(output_samples)
+    df.sort_values(by=['destination_column', 'destination_row'], ascending=True, inplace=True)
+    columnsTitles = ['sample', 'destination_column', 'destination_row', 'plate_number', 'plate', "source_column", 'source_row']
+    df = df.reindex(columns=columnsTitles)
+    ofname = select_save_file(obj=obj, default_name=f"First Strand {date.today()}", extension="csv")
+    df.to_csv(ofname, index=False)
+    return obj, None
+

src/submissions/tools/__init__.py

@@ -622,3 +622,20 @@ def check_if_app(ctx:Settings=None) -> bool:
     else:
         return False
     
+def convert_well_to_row_column(input_str:str) -> Tuple[int, int]:
+    """
+    Converts typical alphanumeric (i.e. "A2") to row, column
+
+    Args:
+        input_str (str): Input string. Ex. "A2"
+
+    Returns:
+        Tuple[int, int]: row, column
+    """    
+    row_keys = dict(A=1, B=2, C=3, D=4, E=5, F=6, G=7, H=8)
+    try:
+        row = int(row_keys[input_str[0].upper()])
+        column = int(input_str[1:]) 
+    except IndexError:
+        return None, None
+    return row, column