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Prior to major database rebuild.

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This commit is contained in:
Landon Wark
2023-07-27 08:14:04 -05:00
parent f22e697815
commit af810ae528
22 changed files with 76 additions and 696 deletions
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11
src/submissions/backend/db/functions.py
View File

@@ -49,12 +49,16 @@ def store_submission(ctx:Settings, base_submission:models.BasicSubmission) -> No
base_submission.rsl_plate_num = typer.parsed_name
for sample in base_submission.samples:
logger.debug(f"Typer: {typer.submission_type}")
logger.debug(f"sample going in: {type(sample)}\n{sample.__dict__}")
# Suuuuuper hacky way to be sure that the artic doesn't overwrite the ww plate in a ww sample
# need something more elegant
if "_artic" not in typer.submission_type.lower():
if "_artic" not in typer.submission_type:
sample.rsl_plate = base_submission
else:
sample.artic_rsl_plate = base_submission
logger.debug(f"{sample.ww_sample_full_id} is an ARTIC sample.")
# base_submission.samples.remove(sample)
# sample.rsl_plate = sample.rsl_plate
# sample.artic_rsl_plate = base_submission
logger.debug(f"Attempting to add sample: {sample.to_string()}")
try:
# ctx['database_session'].add(sample)
@@ -62,6 +66,7 @@ def store_submission(ctx:Settings, base_submission:models.BasicSubmission) -> No
except (sqlite3.IntegrityError, sqlalchemy.exc.IntegrityError) as e:
logger.debug(f"Hit an integrity error : {e}")
continue
logger.debug(f"Here is the sample to be stored in the DB: {sample.__dict__}")
# Add submission to submission table
# ctx['database_session'].add(base_submission)
ctx.database_session.add(base_submission)
@@ -650,7 +655,7 @@ def get_control_subtypes(ctx:Settings, type:str, mode:str) -> list[str]:
# Only the first control of type is necessary since they all share subtypes
try:
outs = get_all_controls_by_type(ctx=ctx, con_type=type)[0]
except TypeError:
except (TypeError, IndexError):
return []
# Get analysis mode data as dict
jsoner = json.loads(getattr(outs, mode))

36
src/submissions/backend/db/models/samples.py
View File

@@ -156,39 +156,3 @@ class BCSample(Base):
col=well_col,
positive=False)
# class ArticSample(Base):
# """
# base of artic sample
# """
# __tablename__ = "_artic_samples"
# id = Column(INTEGER, primary_key=True) #: primary key
# well_number = Column(String(8)) #: location on parent plate
# rsl_plate = relationship("WastewaterArtic", back_populates="samples") #: relationship to parent plate
# rsl_plate_id = Column(INTEGER, ForeignKey("_submissions.id", ondelete="SET NULL", name="fk_WWA_submission_id"))
# ww_sample_full_id = Column(String(64), nullable=False)
# lims_sample_id = Column(String(64), nullable=False)
# ct_1 = Column(FLOAT(2)) #: first ct value in column
# ct_2 = Column(FLOAT(2)) #: second ct value in column
# def to_string(self) -> str:
# """
# string representing sample object
# Returns:
# str: string representing location and sample id
# """
# return f"{self.well_number}: {self.ww_sample_full_id}"
# def to_sub_dict(self) -> dict:
# """
# gui friendly dictionary
# Returns:
# dict: well location and name (sample id, organism) NOTE: keys must sync with WWSample to_sub_dict above
# """
# return {
# "well": self.well_number,
# "name": self.ww_sample_full_id,
# }