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Database updates, scraping samples from excel sheets

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This commit is contained in:
Landon Wark
2023-01-19 11:22:57 -06:00
parent e763e7273d
commit d17ee5862d
10 changed files with 206 additions and 53 deletions
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10
src/submissions/backend/db/models/submissions.py
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@@ -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"}