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[FIX] Ensure pipeline variables are returned from the graph in an aggregate query #349

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merged 2 commits into from
Oct 10, 2024
Merged

[FIX] Ensure pipeline variables are returned from the graph in an aggregate query #349

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82f3259
ensure pipeline metadata is returned in agg results
alyssadai Oct 9, 2024
598cd05
update mocked response from graph in tests
alyssadai Oct 10, 2024
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17 changes: 7 additions & 10 deletions app/api/crud.py
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,6 @@ async def get(

response_obj = []
dataset_cols = ["dataset_uuid", "dataset_name"]
dataset_available_pipeline_info = {}
if not results_df.empty:
for (dataset_uuid, dataset_name), group in results_df.groupby(
by=dataset_cols
Expand Down Expand Up @@ -259,13 +258,11 @@ async def get(

subject_data = list(subject_data.to_dict("records"))

dataset_available_pipeline_info = (
group.groupby("pipeline_name", dropna=True)[
"pipeline_version"
]
.apply(lambda x: list(x.dropna().unique()))
.to_dict()
)
dataset_available_pipelines = (
group.groupby("pipeline_name", dropna=True)["pipeline_version"]
.apply(lambda x: list(x.dropna().unique()))
.to_dict()
)

response_obj.append(
CohortQueryResponse(
Expand All @@ -276,7 +273,7 @@ async def get(
],
dataset_portal_uri=(
group["dataset_portal_uri"].iloc[0]
if group["dataset_portal_uri"].notna().all()
if not group["dataset_portal_uri"].isna().any()
else None
),
num_matching_subjects=group["sub_id"].nunique(),
Expand All @@ -287,7 +284,7 @@ async def get(
group["image_modal"].notna()
].unique()
),
available_pipelines=dataset_available_pipeline_info,
available_pipelines=dataset_available_pipelines,
)
)

Expand Down
4 changes: 2 additions & 2 deletions app/api/utility.py
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Original file line number Diff line number Diff line change
Expand Up @@ -307,11 +307,11 @@ def create_query(
query_string = (
textwrap.dedent(
"""
SELECT ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?image_modal
SELECT ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?image_modal ?pipeline_version ?pipeline_name
WHERE {"""
)
+ textwrap.indent(query_string, " ")
+ "} GROUP BY ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?image_modal"
+ "} GROUP BY ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?image_modal ?pipeline_version ?pipeline_name"
)

return "\n".join([create_context(), query_string])
Expand Down
27 changes: 24 additions & 3 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,7 +74,11 @@ def test_data():
"http://purl.org/nidash/nidm#T2Weighted",
],
"available_pipelines": {
"freesurfer": ["7.3.2", "2.8.2", "8.7.0-rc"]
"https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer": [
"7.3.2",
"2.8.2",
"8.7.0-rc",
]
},
},
{
Expand All @@ -90,8 +94,15 @@ def test_data():
"http://purl.org/nidash/nidm#T1Weighted",
],
"available_pipelines": {
"freesurfer": ["7.3.2", "2.1.2"],
"fmriprep": ["23.1.3", "22.1.4", "v2.0.1"],
"https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer": [
"7.3.2",
"2.1.2",
],
"https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep": [
"23.1.3",
"22.1.4",
"v2.0.1",
],
},
},
]
Expand All @@ -110,6 +121,8 @@ def mockreturn(query, timeout=5.0):
"dataset_portal_uri",
"sub_id",
"image_modal",
"pipeline_name",
"pipeline_version",
]
},
"results": {
Expand Down Expand Up @@ -141,6 +154,14 @@ def mockreturn(query, timeout=5.0):
"type": "uri",
"value": "http://purl.org/nidash/nidm#T1Weighted",
},
"pipeline_version": {
"type": "literal",
"value": "7.3.2",
},
"pipeline_name": {
"type": "uri",
"value": "https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer",
},
},
]
},
Expand Down