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Add findings to study-summary endpoint #349

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merged 5 commits into from
Aug 23, 2024
Merged

Add findings to study-summary endpoint #349

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f420826
Quickfix version upgrade
jimmymathews Aug 13, 2024
5108ee1
Add findings to study-summary endpoint
franciscouzo Aug 14, 2024
ab01c6f
Update test data artifact
jimmymathews Aug 23, 2024
3754130
Version bump
jimmymathews Aug 23, 2024
f034337
Merge branch 'main' into summary-findings
jimmymathews Aug 23, 2024
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2 changes: 1 addition & 1 deletion build/apiserver/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ RUN python -m pip install scikit-learn==1.5.0
RUN python -m pip install Pillow==9.5.0
RUN python -m pip install pydantic==2.7.2
RUN python -m pip install secure==0.3.0
RUN python -m pip install matplotlib==3.9.0
RUN python -m pip install matplotlib==3.9.2
RUN python -m pip install squidpy==1.5.0
ARG version
ARG service_name
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6 changes: 3 additions & 3 deletions pyproject.toml.unversioned
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Expand Up @@ -31,7 +31,7 @@ repository = "https://github.com/nadeemlab/SPT"

[project.optional-dependencies]
apiserver = [
"matplotlib==3.9.0",
"matplotlib==3.9.2",
"fastapi==0.111.0",
"uvicorn==0.30.0",
"pandas==2.2.2",
Expand Down Expand Up @@ -66,7 +66,7 @@ ondemand = [
"squidpy==1.5.0",
]
workflow = [
"matplotlib==3.9.0",
"matplotlib==3.9.2",
"umap-learn==0.5.6",
"numpy==1.26.4",
"scipy==1.13.1",
Expand All @@ -82,7 +82,7 @@ workflow = [
all = [
"bokeh==3.4.1",
"h5py==3.10.0",
"matplotlib==3.9.0",
"matplotlib==3.9.2",
"umap-learn==0.5.6",
"uvicorn==0.30.0",
"Jinja2==3.1.4",
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2 changes: 2 additions & 0 deletions spatialprofilingtoolbox/db/accessors/study.py
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Expand Up @@ -43,11 +43,13 @@ def get_study_summary(self, study: str) -> StudySummary:
publication = self._get_publication(study)
assay = self._get_assay(components.measurement)
sample_cohorts = get_sample_cohorts(self.cursor, study)
findings = self.get_study_findings()
return StudySummary(
context=Context(institution=institution, assay=assay, contact=contact),
products=Products(data_release=data_release, publication=publication),
counts=counts_summary,
cohorts=sample_cohorts,
findings=findings,
)

def get_study_components(self, study: str) -> StudyComponents:
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1 change: 1 addition & 0 deletions spatialprofilingtoolbox/db/exchange_data_formats/study.py
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Expand Up @@ -97,3 +97,4 @@ class StudySummary(BaseModel):
products: Products
counts: CountsSummary
cohorts: SampleCohorts
findings: list[str]
7 changes: 6 additions & 1 deletion test/apiserver/module_tests/expected_study_summary_structured.json
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Expand Up @@ -87,5 +87,10 @@
"result": "Extreme responder"
}
]
}
},
"findings": [
"Finding 1.",
"Finding 2.",
"Finding 3."
]
}
2 changes: 1 addition & 1 deletion version.txt
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@@ -1 +1 @@
0.28.0
0.29.0
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