initial commit

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

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+from sqlalchemy.ext.declarative import declarative_base
+from sqlalchemy.orm import relationship
+
+Base = declarative_base()
+metadata = Base.metadata
+
+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

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

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+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, UniqueConstraint
+from sqlalchemy.orm import relationship
+
+class ControlType(Base):
+    """
+    Base class of a control archetype.
+    """    
+    __tablename__ = '_control_types'
+    
+    id = Column(INTEGER, primary_key=True) #: primary key   
+    name = Column(String(255), unique=True) #: controltype name (e.g. MCS)
+    targets = Column(JSON) #: organisms checked for
+    # instances_id = Column(INTEGER, ForeignKey("_control_samples.id", ondelete="SET NULL", name="fk_ctype_instances_id"))
+    instances = relationship("Control", back_populates="controltype") #: control samples created of this type.
+    # UniqueConstraint('name', name='uq_controltype_name')
+
+
+class Control(Base):
+    """
+    Base class of a control sample.
+    """    
+
+    __tablename__ = '_control_samples'
+    
+    id = Column(INTEGER, primary_key=True) #: primary key
+    parent_id = Column(String, ForeignKey("_control_types.id", name="fk_control_parent_id")) #: primary key of control type
+    controltype = relationship("ControlType", back_populates="instances", foreign_keys=[parent_id]) #: reference to parent control type
+    name = Column(String(255), unique=True) #: Sample ID
+    submitted_date = Column(TIMESTAMP) #: Date submitted to Robotics
+    contains = Column(JSON) #: unstructured hashes in contains.tsv for each organism
+    matches = Column(JSON) #: unstructured hashes in matches.tsv for each organism
+    kraken = Column(JSON) #: unstructured output from kraken_report
+    # UniqueConstraint('name', name='uq_control_name')
+    submissions = relationship("BacterialCulture", back_populates="control")
+

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

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+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, JSON, INTEGER, ForeignKey, Interval, Table, FLOAT
+from sqlalchemy.orm import relationship
+
+
+reagenttypes_kittypes = Table("_reagentstypes_kittypes", Base.metadata, Column("reagent_types_id", INTEGER, ForeignKey("_reagent_types.id")), Column("kits_id", INTEGER, ForeignKey("_kits.id")))
+
+
+class KitType(Base):
+
+    __tablename__ = "_kits"
+
+    id = Column(INTEGER, primary_key=True) #: primary key  
+    name = Column(String(64), unique=True)
+    submissions = relationship("BasicSubmission", back_populates="extraction_kit")
+    used_for = Column(JSON)
+    cost_per_run = Column(FLOAT(2))
+    reagent_types = relationship("ReagentType", back_populates="kits", uselist=True, secondary=reagenttypes_kittypes)
+    reagent_types_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', use_alter=True, name="fk_KT_reagentstype_id"))
+    
+    def __str__(self):
+        return self.name
+    
+
+class ReagentType(Base):
+
+    __tablename__ = "_reagent_types"
+
+    id = Column(INTEGER, primary_key=True) #: primary key  
+    name = Column(String(64))
+    kit_id = Column(INTEGER, ForeignKey("_kits.id", ondelete="SET NULL", use_alter=True, name="fk_RT_kits_id"))
+    kits = relationship("KitType", back_populates="reagent_types", uselist=True, foreign_keys=[kit_id])
+    instances = relationship("Reagent", back_populates="type")
+    # instances_id = Column(INTEGER, ForeignKey("_reagents.id", ondelete='SET NULL'))
+    eol_ext = Column(Interval())
+
+    def __str__(self):
+        return self.name
+
+
+class Reagent(Base):
+
+    __tablename__ = "_reagents"
+
+    id = Column(INTEGER, primary_key=True) #: primary key
+    type = relationship("ReagentType", back_populates="instances")
+    type_id = Column(INTEGER, ForeignKey("_reagent_types.id", ondelete='SET NULL', name="fk_reagent_type_id"))
+    name = Column(String(64))
+    lot = Column(String(64))
+    expiry = Column(TIMESTAMP)
+    submissions = relationship("BasicSubmission", back_populates="reagents", uselist=True)
+
+    def __str__(self):
+        return self.lot
+
+    def to_sub_dict(self):
+        try:
+            type = self.type.name.replace("_", " ").title()
+        except AttributeError:
+            type = "Unknown"
+        return {
+            "type": type,
+            "lot": self.lot,
+            "expiry": self.expiry.strftime("%Y-%m-%d")
+        }
+
+    
+    

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

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+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, JSON, Float, INTEGER, ForeignKey, UniqueConstraint, Table
+from sqlalchemy.orm import relationship, validates
+
+
+orgs_contacts = Table("_orgs_contacts", Base.metadata, Column("org_id", INTEGER, ForeignKey("_organizations.id")), Column("contact_id", INTEGER, ForeignKey("_contacts.id")))
+
+
+class Organization(Base):
+
+    __tablename__ = "_organizations"
+
+    id = Column(INTEGER, primary_key=True) #: primary key  
+    name = Column(String(64))
+    submissions = relationship("BasicSubmission", back_populates="submitting_lab")
+    cost_centre = Column(String())
+    contacts = relationship("Contact", back_populates="organization", secondary=orgs_contacts)
+    contact_ids = Column(INTEGER, ForeignKey("_contacts.id", ondelete="SET NULL", name="fk_org_contact_id"))
+
+    def __str__(self):
+        return self.name.replace("_", " ").title()
+
+
+class Contact(Base):
+
+    __tablename__ = "_contacts"
+
+    id = id = Column(INTEGER, primary_key=True) #: primary key  
+    name = Column(String(64))
+    email = Column(String(64))
+    phone = Column(String(32))
+    organization = relationship("Organization", back_populates="contacts", uselist=True)
+    # organization_id = Column(INTEGER, ForeignKey("_organizations.id"))
+

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

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+from . import Base
+from sqlalchemy import Column, String, TIMESTAMP, text, JSON, INTEGER, ForeignKey, FLOAT, BOOLEAN
+from sqlalchemy.orm import relationship, relationships
+
+
+class Sample(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))
+    rsl_number = Column(String(64))
+    rsl_plate = relationship("Wastewater", back_populates="samples")
+    collection_date = Column(TIMESTAMP) #: Date submission received
+    testing_type = Column(String(64))
+    site_status = Column(String(64))
+    notes = Column(String(2000))
+    ct_n1 = Column(FLOAT(2))
+    ct_n2 = Column(FLOAT(2))
+    seq_submitted = Column(BOOLEAN())
+    ww_seq_run_id = Column(String(64))
+    sample_type = Column(String(8))
+
+
+
+

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

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+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"}