Database updates, scraping samples from excel sheets

src/submissions/backend/db/__init__.py

@@ -16,6 +16,12 @@ def get_kits_by_use( ctx:dict, kittype_str:str|None) -> list:
 
 
 def store_submission(ctx:dict, base_submission:models.BasicSubmission) -> None:
+    for sample in base_submission.samples:
+        sample.rsl_plate = base_submission
+        try:
+            ctx['database_session'].add(sample)
+        except IntegrityError:
+            continue
     ctx['database_session'].add(base_submission)
     try:
         ctx['database_session'].commit()
@@ -53,6 +59,11 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
                 # Because of unique constraint, the submitter plate number cannot be None, so...
                 if info_dict[item] == None:
                     info_dict[item] = uuid.uuid4().hex.upper()
+                field_value = info_dict[item]
+            # case "samples":
+            #     for sample in info_dict[item]:
+            #         instance.samples.append(sample)
+            #     continue
             case _:
                 field_value = info_dict[item]
         try:
@@ -60,6 +71,7 @@ def construct_submission_info(ctx:dict, info_dict:dict) -> models.BasicSubmissio
         except AttributeError:
             print(f"Could not set attribute: {item} to {info_dict[item]}")
             continue
+    # print(instance.__dict__)
     return instance
     # looked_up = []
     # for reagent in reagents:
@@ -184,7 +196,11 @@ def create_kit_from_yaml(ctx:dict, exp:dict) -> None:
     Args:
         ctx (dict): Context dictionary passed down from frontend
         exp (dict): Experiment dictionary created from yaml file
-    """    
+    """
+    try:
+        exp['password'].decode()
+    except (UnicodeDecodeError, AttributeError):
+        exp['password'] = exp['password'].encode()
     if base64.b64encode(exp['password']) != b'cnNsX3N1Ym1pNTVpb25z':
         print(f"Not the correct password.")
         return

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

@@ -8,4 +8,4 @@ from .controls import Control, ControlType
 from .kits import KitType, ReagentType, Reagent
 from .submissions import BasicSubmission, BacterialCulture, Wastewater
 from .organizations import Organization, Contact
-from .samples import Sample
+from .samples import WWSample, BCSample

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

@@ -3,15 +3,16 @@ from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKe
 from sqlalchemy.orm import relationship, relationships
 
 
-class Sample(Base):
+class WWSample(Base):
 
     __tablename__ = "_ww_samples"
 
     id = Column(INTEGER, primary_key=True) #: primary key
     ww_processing_num = Column(String(64))
-    ww_sample_full_id = Column(String(64))
+    ww_sample_full_id = Column(String(64), nullable=False)
     rsl_number = Column(String(64))
     rsl_plate = relationship("Wastewater", back_populates="samples")
+    rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWS_sample_id"))
     collection_date = Column(TIMESTAMP) #: Date submission received
     testing_type = Column(String(64))
     site_status = Column(String(64))
@@ -21,7 +22,35 @@ class Sample(Base):
     seq_submitted = Column(BOOLEAN())
     ww_seq_run_id = Column(String(64))
     sample_type = Column(String(8))
+    well_number = Column(String(8))
+
+    def to_string(self):
+        return f"{self.well_number}: {self.ww_sample_full_id}"
+
+    def to_sub_dict(self):
+        return {
+            "well": self.well_number,
+            "name": self.ww_sample_full_id,
+        }
 
 
+class BCSample(Base):
 
+    __tablename__ = "_bc_samples"
 
+    id = Column(INTEGER, primary_key=True) #: primary key
+    well_number = Column(String(8))
+    sample_id = Column(String(64), nullable=False)
+    organism = Column(String(64))
+    concentration = Column(String(16))
+    rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_BCS_sample_id"))
+    rsl_plate = relationship("BacterialCulture", back_populates="samples")
+
+    def to_string(self):
+        return f"{self.well_number}: {self.sample_id} - {self.organism}"
+
+    def to_sub_dict(self):
+        return {
+            "well": self.well_number,
+            "name": f"{self.sample_id} - ({self.organism})",
+        }

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

@@ -15,10 +15,10 @@ class BasicSubmission(Base):
     submitter_plate_num = Column(String(127), unique=True) #: The number given to the submission by the submitting lab
     submitted_date = Column(TIMESTAMP) #: Date submission received
     submitting_lab = relationship("Organization", back_populates="submissions") #: client
-    submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL"))
+    submitting_lab_id = Column(INTEGER, ForeignKey("_organizations.id", ondelete="SET NULL", name="fk_BS_sublab_id"))
     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"))
+    extraction_kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", name="fk_BS_extkit_id"))
     submission_type = Column(String(32))
     technician = Column(String(64))
     # Move this into custom types?
@@ -94,10 +94,12 @@ class BasicSubmission(Base):
 class  BacterialCulture(BasicSubmission):
     control = relationship("Control", back_populates="submissions") #: A control sample added to submission
     control_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_BC_control_id"))
+    samples = relationship("BCSample", back_populates="rsl_plate", uselist=True)
+    # bc_sample_id = Column(INTEGER, ForeignKey("_bc_samples.id", ondelete="SET NULL", name="fk_BC_sample_id"))
     __mapper_args__ = {"polymorphic_identity": "bacterial_culture", "polymorphic_load": "inline"}
     
 
 class Wastewater(BasicSubmission):
-    samples = relationship("Sample", back_populates="rsl_plate")
-    sample_id = Column(String, ForeignKey("_ww_samples.id", ondelete="SET NULL", name="fk_WW_sample_id"))
+    samples = relationship("WWSample", back_populates="rsl_plate", uselist=True)
+    # 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"}