prior to db rebuild

src/submissions/backend/db/functions.py

@@ -18,7 +18,7 @@ from getpass import getuser
 import numpy as np
 import yaml
 from pathlib import Path
-from tools import Settings
+from tools import Settings, check_regex_match, RSLNamer
 
 
 
@@ -43,7 +43,6 @@ def store_submission(ctx:Settings, base_submission:models.BasicSubmission) -> No
     Returns:
         None|dict : object that indicates issue raised for reporting in gui
     """    
-    from tools import RSLNamer
     logger.debug(f"Hello from store_submission")
     # Add all samples to sample table
     typer = RSLNamer(ctx=ctx, instr=base_submission.rsl_plate_num)
@@ -52,7 +51,7 @@ def store_submission(ctx:Settings, base_submission:models.BasicSubmission) -> No
         logger.debug(f"Typer: {typer.submission_type}")
         # 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:
+        if "_artic" not in typer.submission_type.lower():
             sample.rsl_plate = base_submission
         else:
             sample.artic_rsl_plate = base_submission
@@ -114,7 +113,7 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
     Returns:
         models.BasicSubmission: Constructed submission object
     """
-    from tools import check_regex_match, RSLNamer
+    # 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
@@ -127,7 +126,8 @@ def construct_submission_info(ctx:Settings, info_dict:dict) -> models.BasicSubmi
         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 = 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}")
     model = getattr(models, query)
@@ -866,8 +866,6 @@ def hitpick_plate(submission:models.BasicSubmission, plate_number:int=0) -> list
     plate_dicto = []
     for sample in submission.samples:
         # have sample report back its info if it's positive, otherwise, None
-        method_list = [func for func in dir(sample) if callable(getattr(sample, func))]
-        logger.debug(f"Method list of sample: {method_list}")
         samp = sample.to_hitpick()
         if samp == None:
             continue
@@ -963,7 +961,6 @@ def lookup_last_used_reagenttype_lot(ctx:Settings, type_name:str) -> models.Reag
     except AttributeError:
         return None
 
-
 def check_kit_integrity(sub:BasicSubmission|KitType, reagenttypes:list|None=None) -> dict|None:
     """
     Ensures all reagents expected in kit are listed in Submission

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

@@ -18,7 +18,7 @@ class WWSample(Base):
 
     id = Column(INTEGER, primary_key=True) #: primary key
     ww_processing_num = Column(String(64)) #: wastewater processing number 
-    ww_sample_full_id = Column(String(64), nullable=False)
+    ww_sample_full_id = Column(String(64), nullable=False, unique=True)
     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"))
@@ -111,7 +111,7 @@ class BCSample(Base):
 
     id = Column(INTEGER, primary_key=True) #: primary key
     well_number = Column(String(8)) #: location on parent plate
-    sample_id = Column(String(64), nullable=False) #: identification from submitter
+    sample_id = Column(String(64), nullable=False, unique=True) #: identification from submitter
     organism = Column(String(64)) #: bacterial specimen
     concentration = Column(String(16)) #:
     rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id")) #: id of parent plate