From 3c63b19f13737bca5a2c6379cab200f862973b0d Mon Sep 17 00:00:00 2001
From: Francisco Couzo <franciscouzo@gmail.com>
Date: Fri, 23 Aug 2024 17:21:19 -0300
Subject: [PATCH] Add findings to study-summary endpoint (#349)

* Quickfix version upgrade

* Add findings to study-summary endpoint

* Update test data artifact

* Version bump

---------

Co-authored-by: James Mathews <mail@jmath.read-books.org>
---
 build/apiserver/Dockerfile                                 | 2 +-
 pyproject.toml.unversioned                                 | 6 +++---
 spatialprofilingtoolbox/db/accessors/study.py              | 2 ++
 spatialprofilingtoolbox/db/exchange_data_formats/study.py  | 1 +
 .../module_tests/expected_study_summary_structured.json    | 7 ++++++-
 version.txt                                                | 2 +-
 6 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/build/apiserver/Dockerfile b/build/apiserver/Dockerfile
index 7d3db8161..0d1aba451 100644
--- a/build/apiserver/Dockerfile
+++ b/build/apiserver/Dockerfile
@@ -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
diff --git a/pyproject.toml.unversioned b/pyproject.toml.unversioned
index 855c32f41..316872506 100644
--- a/pyproject.toml.unversioned
+++ b/pyproject.toml.unversioned
@@ -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",
@@ -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",
@@ -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",
diff --git a/spatialprofilingtoolbox/db/accessors/study.py b/spatialprofilingtoolbox/db/accessors/study.py
index eedffe35d..2054d021d 100644
--- a/spatialprofilingtoolbox/db/accessors/study.py
+++ b/spatialprofilingtoolbox/db/accessors/study.py
@@ -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:
diff --git a/spatialprofilingtoolbox/db/exchange_data_formats/study.py b/spatialprofilingtoolbox/db/exchange_data_formats/study.py
index 7bd5c0bde..ac0c3f293 100644
--- a/spatialprofilingtoolbox/db/exchange_data_formats/study.py
+++ b/spatialprofilingtoolbox/db/exchange_data_formats/study.py
@@ -97,3 +97,4 @@ class StudySummary(BaseModel):
     products: Products
     counts: CountsSummary
     cohorts: SampleCohorts
+    findings: list[str]
diff --git a/test/apiserver/module_tests/expected_study_summary_structured.json b/test/apiserver/module_tests/expected_study_summary_structured.json
index 20804dcf6..1a6d21243 100644
--- a/test/apiserver/module_tests/expected_study_summary_structured.json
+++ b/test/apiserver/module_tests/expected_study_summary_structured.json
@@ -87,5 +87,10 @@
                 "result": "Extreme responder"
             }
         ]
-    }
+    },
+    "findings": [
+        "Finding 1.",
+        "Finding 2.",
+        "Finding 3."
+    ]
 }
diff --git a/version.txt b/version.txt
index 022a03374..beb3a3f6f 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-0.28.0
\ No newline at end of file
+0.29.0
\ No newline at end of file