initial commit

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

@@ -0,0 +1,103 @@
+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint, Table
+from sqlalchemy.orm import relationship, relationships
+from datetime import datetime as dt
+
+reagents_submissions = Table("_reagents_submissions", Base.metadata, Column("reagent_id", INTEGER, ForeignKey("_reagents.id")), Column("submission_id", INTEGER, ForeignKey("_submissions.id")))
+
+class BasicSubmission(Base):
+
+    # TODO: Figure out if I want seperate tables for different sample types.
+    __tablename__ = "_submissions"
+
+    id = Column(INTEGER, primary_key=True) #: primary key   
+    rsl_plate_num = Column(String(32), unique=True) #: RSL name (e.g. RSL-22-0012)
+    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"))
+    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"))
+    submission_type = Column(String(32))
+    technician = Column(String(64))
+    # Move this into custom types?
+    reagents = relationship("Reagent", back_populates="submissions", secondary=reagents_submissions)
+    reagents_id = Column(String, ForeignKey("_reagents.id", ondelete="SET NULL", name="fk_BS_reagents_id"))
+
+    __mapper_args__ = {
+        "polymorphic_identity": "basic_submission",
+        "polymorphic_on": submission_type,
+        "with_polymorphic": "*",
+    }
+
+    def to_dict(self):
+        print(self.submitting_lab)
+        try:
+            sub_lab = self.submitting_lab.name
+        except AttributeError:
+            sub_lab = None
+        try:
+            sub_lab = sub_lab.replace("_", " ").title()
+        except AttributeError:
+            pass
+        try:
+            ext_kit = self.extraction_kit.name
+        except AttributeError:
+            ext_kit = None
+        output = {
+            "id": self.id,
+            "Plate Number": self.rsl_plate_num,
+            "Submission Type": self.submission_type.replace("_", " ").title(),
+            "Submitter Plate Number": self.submitter_plate_num,
+            "Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
+            "Submitting Lab": sub_lab,
+            "Sample Count": self.sample_count,
+            "Extraction Kit": ext_kit,
+            "Technician": self.technician,
+        }
+        return output
+
+
+    def report_dict(self):
+        try:
+            sub_lab = self.submitting_lab.name
+        except AttributeError:
+            sub_lab = None
+        try:
+            sub_lab = sub_lab.replace("_", " ").title()
+        except AttributeError:
+            pass
+        try:
+            ext_kit = self.extraction_kit.name
+        except AttributeError:
+            ext_kit = None
+        try:
+            cost = self.extraction_kit.cost_per_run
+        except AttributeError:
+            cost = None
+        output = {
+            "id": self.id,
+            "Plate Number": self.rsl_plate_num,
+            "Submission Type": self.submission_type.replace("_", " ").title(),
+            "Submitter Plate Number": self.submitter_plate_num,
+            "Submitted Date": self.submitted_date.strftime("%Y-%m-%d"),
+            "Submitting Lab": sub_lab,
+            "Sample Count": self.sample_count,
+            "Extraction Kit": ext_kit,
+            "Cost": cost
+        }
+        return output
+
+# Below are the custom submission 
+
+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"))
+    __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"))
+    __mapper_args__ = {"polymorphic_identity": "wastewater", "polymorphic_load": "inline"}