Database updates, scraping samples from excel sheets

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})",
+        }