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[REF] Update SessionPath -> SessionFilePath #242

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[REF] Update SessionPath -> SessionFilePath #242

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6 changes: 3 additions & 3 deletions cohort_creator/_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def create_tsv_participant_session_in_datasets(output_dir: Path, dataset_paths:
"DatasetID": [],
"SubjectID": [],
"SessionID": [],
"SessionPath": [],
"SessionFilePath": [],
}

for dataset in dataset_paths:
Expand All @@ -60,7 +60,7 @@ def create_tsv_participant_session_in_datasets(output_dir: Path, dataset_paths:
ses += "/"
else:
ses = ""
content["SessionPath"].append(f"{dataset.name}/sub-{sub}/{ses}")
content["SessionFilePath"].append(f"{dataset.name}/sub-{sub}/{ses}")

df = pd.DataFrame(content)
output_file = output_dir.parent / "code" / "participants.tsv"
Expand Down Expand Up @@ -153,7 +153,7 @@ def check_tsv_content(tsv_file: Path | str) -> pd.DataFrame:


def check_participant_listing(participant_listing: pd.DataFrame) -> None:
for col in ["SubjectID", "SessionPath"]:
for col in ["SubjectID", "SessionFilePath"]:
if col not in participant_listing.columns:
raise ValueError(
f"Column '{col}' not found in participants listing data.\n"
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2 changes: 1 addition & 1 deletion docs/visualize_neurobagel.py
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Expand Up @@ -54,7 +54,7 @@ def wrangle(df: pd.DataFrame) -> pd.DataFrame:
present.append(i)
df = df[mask]

df["dataset_name"] = df["SessionPath"].apply(lambda x: x.split("/")[1])
df["dataset_name"] = df["SessionFilePath"].apply(lambda x: x.split("/")[1])

df["missing_age"] = df["Age"].isnull()

Expand Down
2 changes: 1 addition & 1 deletion inputs/participant-results.tsv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
DatasetID SubjectID Age Sex Diagnosis Assessment SessionID SessionPath NumSessions Modality
DatasetID SubjectID Age Sex Diagnosis Assessment SessionID SessionFilePath NumSessions Modality
http://neurobagel.org/vocab/0f2f957a-7979-442c-92fc-b1f68c0d3b50 sub-01 38.0 http://purl.bioontology.org/ontology/SNOMEDCT/248153007 , , ses-1 /ds001454/sub-01/ses-1 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted
http://neurobagel.org/vocab/0f2f957a-7979-442c-92fc-b1f68c0d3b50 sub-01 38.0 http://purl.bioontology.org/ontology/SNOMEDCT/248153007 , , ses-2 /ds001454/sub-01/ses-2 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted
http://neurobagel.org/vocab/15abcd42-0f61-4b44-81bf-7b51ba15b14e sub-control05 36.0 http://purl.bioontology.org/ontology/SNOMEDCT/248153007 , , ses-1preEEG /ds001408/sub-control05/ses-1preEEG 2 http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted
Expand Down
2 changes: 1 addition & 1 deletion tests/data/participants.tsv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
DatasetID SubjectID Age Sex Diagnosis SessionID SessionPath NumSessions Modality
DatasetID SubjectID Age Sex Diagnosis SessionID SessionFilePath NumSessions Modality
ds000001 sub-03 26 Female PD n/a 1 [T1,T2,bold]
ds000001 sub-17 25 Female CTL n/a 1 [T1,T2,bold]
ds000002 sub-12 25 Female n/a 1 [T1,T2,bold]
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2 changes: 1 addition & 1 deletion tests/test_utils.py
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Expand Up @@ -64,7 +64,7 @@ def test_create_tsv_participant_session_in_datasets(bids_examples, tmp_path):
assert tsv_file.exists()
df = pd.read_csv(tsv_file, sep="\t")

assert df.columns.tolist() == ["DatasetID", "SubjectID", "SessionID", "SessionPath"]
assert df.columns.tolist() == ["DatasetID", "SubjectID", "SessionID", "SessionFilePath"]

assert df["DatasetID"].unique().tolist() == ["ds001", "ds006"]

Expand Down
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