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Merged
Ulthran merged 3 commits into from
Dec 17, 2025
Merged

Add bacteremia isolate ingestion test #42

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39a0c54
Add bacteremia isolate ingestion test
Ulthran Dec 17, 2025
824dc8f
Handle duplicate isolate rows without false conflicts
Ulthran Dec 17, 2025
074ea70
Coerce on ingest
Ulthran Dec 17, 2025
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53 changes: 45 additions & 8 deletions marc_db/ingest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,9 @@ def _ensure_required_columns(df: pd.DataFrame, required: Iterable[str]):
raise ValueError(f"Missing required column(s): {', '.join(missing)}")


def _load_dataframe(data: Optional[Union[pd.DataFrame, Path, str]]) -> Optional[pd.DataFrame]:
def _load_dataframe(
data: Optional[Union[pd.DataFrame, Path, str]]
) -> Optional[pd.DataFrame]:
if data is None or isinstance(data, pd.DataFrame):
return data
return pd.read_csv(Path(data), sep="\t")
Expand Down Expand Up @@ -66,27 +68,62 @@ def _ingest_isolates(df: pd.DataFrame, session: Session):
"received_date",
"cryobanking_date",
]
isolates["subject_id"] = pd.to_numeric(
isolates["subject_id"], errors="coerce"
).astype("Int64")
isolates["specimen_id"] = pd.to_numeric(
isolates["specimen_id"], errors="coerce"
).astype("Int64")
isolates["received_date"] = pd.to_datetime(
isolates["received_date"], errors="coerce"
).dt.date
isolates["received_date"] = isolates["received_date"].apply(
lambda x: None if pd.isna(x) else x
)
isolates["cryobanking_date"] = pd.to_datetime(
isolates["cryobanking_date"], errors="coerce"
).dt.date
isolates["cryobanking_date"] = isolates["cryobanking_date"].apply(
lambda x: None if pd.isna(x) else x
)

added = []
added = {}
for _, row in isolates.iterrows():
i = Isolate(**row.to_dict())
if i.sample_id in {iso.sample_id for iso in added}:
if i != next(iso for iso in added if iso.sample_id == i.sample_id):
print(f"Conflicting isolate data for SampleID {i.sample_id}")
isolate_kwargs = row.to_dict()
sample_id = isolate_kwargs["sample_id"]

existing = added.get(sample_id)
if existing:
if existing != isolate_kwargs:
print(f"Conflicting isolate data for SampleID {sample_id}")
continue
session.add(i)
added.append(i)

isolate = Isolate(**isolate_kwargs)
if not isinstance(isolate.subject_id, int) or not isinstance(
isolate.specimen_id, int
):
print(
f"Invalid subject_id or specimen_id for SampleID {sample_id}: {isolate.subject_id}, {isolate.specimen_id}"
)
session.add(isolate)
try:
session.flush()
except Exception as e:
print(f"Error adding isolate with SampleID {sample_id}: {e}")
session.rollback()
continue
added[sample_id] = isolate_kwargs

aliquot_df = df[["Tube Barcode", "Box-name_position", "SampleID"]].copy()
aliquot_df.columns = ["tube_barcode", "box_name", "isolate_id"]
for _, row in aliquot_df.iterrows():
session.add(Aliquot(**row.to_dict()))
try:
session.flush()
except Exception as e:
print(f"Error adding aliquot for SampleID {row.isolate_id}: {e}")
session.rollback()
continue


def _ingest_assemblies(
Expand Down
130 changes: 130 additions & 0 deletions tests/test_ingest.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,3 +73,133 @@ def test_ingest_accepts_path_strings():

session.close()
engine.dispose()


def test_duplicate_isolate_rows_do_not_warn_when_identical(capsys):
engine = create_engine("sqlite:///:memory:")
Session = sessionmaker(bind=engine)
session = Session()
Base.metadata.create_all(engine)

isolates_df = pd.read_csv(data_dir / "test_multi_aliquot.tsv", sep="\t")

ingest_from_tsvs(isolates=isolates_df, yes=True, session=session)

captured = capsys.readouterr()
assert "Conflicting isolate data" not in captured.out
assert len(get_isolates(session)) == 2
assert len(get_aliquots(session)) == 5

session.close()
engine.dispose()


def test_ingest_bacteremia_example(tmp_path):
engine = create_engine("sqlite:///:memory:")
Session = sessionmaker(bind=engine)
session = Session()
Base.metadata.create_all(engine)

bacteremia_tsv = """SampleID\tsample species\tReceived by mARC\tCryobanking\tsample_source\tNote\tTechnician\tspecial_collection\tTube Type\tTube Barcode\tBox-name_position\tSubject ID\tSpecimen ID
marc.bacteremia.1\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164439\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.2\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164431\tmARC Bacteremia Isolates Box 1\t2.0\t2.0
marc.bacteremia.3\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164460\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.4\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164429\tmARC Bacteremia Isolates Box 1\t3.0\t3.0
marc.bacteremia.5\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164455\tmARC Bacteremia Isolates Box 1\t4.0\t4.0
marc.bacteremia.6\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164452\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.7\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164446\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.8\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164454\tmARC Bacteremia Isolates Box 1\t5.0\t6.0
marc.bacteremia.9\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164472\tmARC Bacteremia Isolates Box 1\t6.0\t7.0
marc.bacteremia.10\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164444\tmARC Bacteremia Isolates Box 1\t6.0\t8.0
marc.bacteremia.11\tKlebsiella pneumoniae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164428\tmARC Bacteremia Isolates Box 1\t7.0\t9.0
marc.bacteremia.12\tEscherichia coli\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164468\tmARC Bacteremia Isolates Box 1\t8.0\t10.0
marc.bacteremia.13\tEnterobacter cloacae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164462\tmARC Bacteremia Isolates Box 1\t9.0\t11.0
marc.bacteremia.14\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164450\tmARC Bacteremia Isolates Box 1\t10.0\t12.0
marc.bacteremia.15\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113164467\tmARC Bacteremia Isolates Box 1\t11.0\t13.0
marc.bacteremia.16\tPseudomonas aeruginosa\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165151\tmARC Bacteremia Isolates Box 1\t12.0\t14.0
marc.bacteremia.17\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165140\tmARC Bacteremia Isolates Box 1\t13.0\t15.0
marc.bacteremia.18\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165159\tmARC Bacteremia Isolates Box 1\t14.0\t16.0
marc.bacteremia.19\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165166\tmARC Bacteremia Isolates Box 1\t14.0\t17.0
marc.bacteremia.20\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165167\tmARC Bacteremia Isolates Box 1\t14.0\t18.0
marc.bacteremia.21\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165144\tmARC Bacteremia Isolates Box 1\t15.0\t19.0
marc.bacteremia.22\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165158\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.23\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165182\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.24\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165177\tmARC Bacteremia Isolates Box 1\t15.0\t21.0
marc.bacteremia.25\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165181\tmARC Bacteremia Isolates Box 1\t15.0\t22.0
marc.bacteremia.26\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165162\tmARC Bacteremia Isolates Box 1\t14.0\t23.0
marc.bacteremia.27\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165180\tmARC Bacteremia Isolates Box 1\t14.0\t24.0
marc.bacteremia.28\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165161\tmARC Bacteremia Isolates Box 1\t15.0\t25.0
marc.bacteremia.29\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165153\tmARC Bacteremia Isolates Box 1\t14.0\t26.0
marc.bacteremia.30\tUnknown\t2022-03-16 00:00:00\t2022-03-16 00:00:00\tblood culture\t\tT'Nia\tBacteremia\ta\tNA2113165169\tmARC Bacteremia Isolates Box 1\t17.0\t27.0
marc.bacteremia.1\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164442\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.2\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164449\tmARC Bacteremia Isolates Box 1\t2.0\t2.0
marc.bacteremia.3\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164427\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.4\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113163791\tmARC Bacteremia Isolates Box 1\t3.0\t3.0
marc.bacteremia.5\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164465\tmARC Bacteremia Isolates Box 1\t4.0\t4.0
marc.bacteremia.6\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164435\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.7\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164456\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.8\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164445\tmARC Bacteremia Isolates Box 1\t5.0\t6.0
marc.bacteremia.9\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164447\tmARC Bacteremia Isolates Box 1\t6.0\t7.0
marc.bacteremia.10\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164457\tmARC Bacteremia Isolates Box 1\t6.0\t8.0
marc.bacteremia.11\tKlebsiella pneumoniae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164463\tmARC Bacteremia Isolates Box 1\t7.0\t9.0
marc.bacteremia.12\tEscherichia coli\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164434\tmARC Bacteremia Isolates Box 1\t8.0\t10.0
marc.bacteremia.13\tEnterobacter cloacae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164470\tmARC Bacteremia Isolates Box 1\t9.0\t11.0
marc.bacteremia.14\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164432\tmARC Bacteremia Isolates Box 1\t10.0\t12.0
marc.bacteremia.15\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113164453\tmARC Bacteremia Isolates Box 1\t11.0\t13.0
marc.bacteremia.16\tPseudomonas aeruginosa\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165142\tmARC Bacteremia Isolates Box 1\t12.0\t14.0
marc.bacteremia.17\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165147\tmARC Bacteremia Isolates Box 1\t13.0\t15.0
marc.bacteremia.18\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165143\tmARC Bacteremia Isolates Box 1\t14.0\t16.0
marc.bacteremia.19\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165174\tmARC Bacteremia Isolates Box 1\t14.0\t17.0
marc.bacteremia.20\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165173\tmARC Bacteremia Isolates Box 1\t14.0\t18.0
marc.bacteremia.21\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165183\tmARC Bacteremia Isolates Box 1\t15.0\t19.0
marc.bacteremia.22\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165179\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.23\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165165\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.24\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165178\tmARC Bacteremia Isolates Box 1\t15.0\t21.0
marc.bacteremia.25\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165172\tmARC Bacteremia Isolates Box 1\t15.0\t22.0
marc.bacteremia.26\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165171\tmARC Bacteremia Isolates Box 1\t14.0\t23.0
marc.bacteremia.27\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165163\tmARC Bacteremia Isolates Box 1\t14.0\t24.0
marc.bacteremia.28\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165152\tmARC Bacteremia Isolates Box 1\t15.0\t25.0
marc.bacteremia.29\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165164\tmARC Bacteremia Isolates Box 1\t14.0\t26.0
marc.bacteremia.30\tUnknown\t2022-03-16 00:00:00\t2022-03-16 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tb\tNA2113165157\tmARC Bacteremia Isolates Box 1\t17.0\t27.0
marc.bacteremia.1\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113159912\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.2\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164461\tmARC Bacteremia Isolates Box 1\t2.0\t2.0
marc.bacteremia.3\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164458\tmARC Bacteremia Isolates Box 1\t1.0\t1.0
marc.bacteremia.4\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164471\tmARC Bacteremia Isolates Box 1\t3.0\t3.0
marc.bacteremia.5\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164466\tmARC Bacteremia Isolates Box 1\t4.0\t4.0
marc.bacteremia.6\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113161266\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.7\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164451\tmARC Bacteremia Isolates Box 1\t2.0\t5.0
marc.bacteremia.8\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164464\tmARC Bacteremia Isolates Box 1\t5.0\t6.0
marc.bacteremia.9\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164436\tmARC Bacteremia Isolates Box 1\t6.0\t7.0
marc.bacteremia.10\tUnknown\t2022-03-04 00:00:00\t2022-03-04 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113163803\tmARC Bacteremia Isolates Box 1\t6.0\t8.0
marc.bacteremia.11\tKlebsiella pneumoniae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164440\tmARC Bacteremia Isolates Box 1\t7.0\t9.0
marc.bacteremia.12\tEscherichia coli\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164473\tmARC Bacteremia Isolates Box 1\t8.0\t10.0
marc.bacteremia.13\tEnterobacter cloacae\t2022-03-07 00:00:00\t2022-03-07 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164430\tmARC Bacteremia Isolates Box 1\t9.0\t11.0
marc.bacteremia.14\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164433\tmARC Bacteremia Isolates Box 1\t10.0\t12.0
marc.bacteremia.15\tUnknown\t2022-03-09 00:00:00\t2022-03-09 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113164437\tmARC Bacteremia Isolates Box 1\t11.0\t13.0
marc.bacteremia.16\tPseudomonas aeruginosa\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165146\tmARC Bacteremia Isolates Box 1\t12.0\t14.0
marc.bacteremia.17\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165139\tmARC Bacteremia Isolates Box 1\t13.0\t15.0
marc.bacteremia.18\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165148\tmARC Bacteremia Isolates Box 1\t14.0\t16.0
marc.bacteremia.19\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165149\tmARC Bacteremia Isolates Box 1\t14.0\t17.0
marc.bacteremia.20\tStaphylococcus epidermidis\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165170\tmARC Bacteremia Isolates Box 1\t14.0\t18.0
marc.bacteremia.21\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165176\tmARC Bacteremia Isolates Box 1\t15.0\t19.0
marc.bacteremia.22\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165138\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.23\tEscherichia coli\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165185\tmARC Bacteremia Isolates Box 1\t16.0\t20.0
marc.bacteremia.24\tStaphylococcus aureus\t2022-03-11 00:00:00\t2022-03-11 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165156\tmARC Bacteremia Isolates Box 1\t15.0\t21.0
marc.bacteremia.25\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165154\tmARC Bacteremia Isolates Box 1\t15.0\t22.0
marc.bacteremia.26\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165184\tmARC Bacteremia Isolates Box 1\t14.0\t23.0
marc.bacteremia.27\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165160\tmARC Bacteremia Isolates Box 1\t14.0\t24.0
marc.bacteremia.28\tStaphylococcus aureus\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165175\tmARC Bacteremia Isolates Box 1\t15.0\t25.0
marc.bacteremia.29\tUnknown\t2022-03-14 00:00:00\t2022-03-14 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165150\tmARC Bacteremia Isolates Box 1\t14.0\t26.0
marc.bacteremia.30\tUnknown\t2022-03-16 00:00:00\t2022-03-16 00:00:00\tblood culture\t\tT'Nia\tBacteremia\tc\tNA2113165168\tmARC Bacteremia Isolates Box 1\t17.0\t27.0
"""

tsv_path = tmp_path / "bacteremia.tsv"
tsv_path.write_text(bacteremia_tsv)

ingest_from_tsvs(isolates=str(tsv_path), yes=True, session=session)

assert len(get_isolates(session)) == 30
assert len(get_aliquots(session)) == 90

session.close()
engine.dispose()