[REF] Make session count names clearer in query response (#282)

* update session count variable names in response * update default SPARQL query file * better highlight default query file in README * Update README.md Co-authored-by: Sebastian Urchs <[email protected]> --------- Co-authored-by: Sebastian Urchs <[email protected]>
neurobagel · Feb 28, 2024 · 2b1377b · 2b1377b
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diff --git a/README.md b/README.md
@@ -29,6 +29,7 @@ Please refer to our [**official documentation**](https://neurobagel.org/api/) fo
     - [Docker (recommended)](#docker)
     - [Python](#python)
 - [Testing](#testing)
+- [The default Neurobagel SPARQL query](#the-default-neurobagel-sparql-query)
 - [License](#license)
 
 
@@ -180,7 +181,7 @@ pytest tests
 
 ## The default Neurobagel SPARQL query
 
-`docs/default_neurobagel_query.rq` contains a sample default SPARQL query sent by the Neurobagel API to a graph database to retrieve all available phenotypic and imaging data.
+[`docs/default_neurobagel_query.rq`](docs/default_neurobagel_query.rq) contains a sample default SPARQL query sent by the Neurobagel API to a graph database to retrieve all available phenotypic and imaging data.
 This file is mainly intended for reference because in normal operations, 
 the API will always talk to the graph on behalf of the user.
 

diff --git a/app/api/crud.py b/app/api/crud.py
@@ -175,8 +175,8 @@ async def get(
                         {
                             "sub_id": "first",
                             "session_id": "first",
-                            "num_phenotypic_sessions": "first",
-                            "num_imaging_sessions": "first",
+                            "num_matching_phenotypic_sessions": "first",
+                            "num_matching_imaging_sessions": "first",
                             "session_type": "first",
                             "age": "first",
                             "sex": "first",

diff --git a/app/api/models.py b/app/api/models.py
@@ -57,8 +57,8 @@ class SessionResponse(BaseModel):
 
     sub_id: str
     session_id: str
-    num_phenotypic_sessions: int
-    num_imaging_sessions: int
+    num_matching_phenotypic_sessions: int
+    num_matching_imaging_sessions: int
     session_type: str
     age: Optional[float]
     sex: Optional[str]

diff --git a/app/api/utility.py b/app/api/utility.py
@@ -141,12 +141,12 @@ def create_query(
     if min_num_phenotypic_sessions is not None:
         subject_level_filters += (
             "\n"
-            + f"FILTER (?num_phenotypic_sessions >= {min_num_phenotypic_sessions})."
+            + f"FILTER (?num_matching_phenotypic_sessions >= {min_num_phenotypic_sessions})."
         )
     if min_num_imaging_sessions is not None:
         subject_level_filters += (
             "\n"
-            + f"FILTER (?num_imaging_sessions >= {min_num_imaging_sessions})."
+            + f"FILTER (?num_matching_imaging_sessions >= {min_num_imaging_sessions})."
         )
 
     phenotypic_session_level_filters = ""
@@ -194,7 +194,7 @@ def create_query(
     query_string = textwrap.dedent(
         f"""
         SELECT DISTINCT ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?age ?sex
-        ?diagnosis ?subject_group ?num_phenotypic_sessions ?num_imaging_sessions ?session_id ?session_type ?assessment ?image_modal ?session_file_path
+        ?diagnosis ?subject_group ?num_matching_phenotypic_sessions ?num_matching_imaging_sessions ?session_id ?session_type ?assessment ?image_modal ?session_file_path
         WHERE {{
             ?dataset_uuid a nb:Dataset;
                     nb:hasLabel ?dataset_name;
@@ -229,7 +229,7 @@ def create_query(
                 ?session nb:hasAssessment ?assessment.
             }}
             {{
-                SELECT ?subject (count(distinct ?phenotypic_session) as ?num_phenotypic_sessions)
+                SELECT ?subject (count(distinct ?phenotypic_session) as ?num_matching_phenotypic_sessions)
                 WHERE {{
                     ?subject a nb:Subject.
                     OPTIONAL {{
@@ -255,7 +255,7 @@ def create_query(
                 }} GROUP BY ?subject
             }}
             {{
-                SELECT ?subject (count(distinct ?imaging_session) as ?num_imaging_sessions)
+                SELECT ?subject (count(distinct ?imaging_session) as ?num_matching_imaging_sessions)
                 WHERE {{
                     ?subject a nb:Subject.
                     OPTIONAL {{

diff --git a/docs/default_neurobagel_query.rq b/docs/default_neurobagel_query.rq
@@ -6,7 +6,7 @@ PREFIX nidm: <http://purl.org/nidash/nidm#>
 PREFIX snomed: <http://purl.bioontology.org/ontology/SNOMEDCT/>
 
 SELECT DISTINCT ?dataset_uuid ?dataset_name ?dataset_portal_uri ?sub_id ?age ?sex
-?diagnosis ?subject_group ?num_phenotypic_sessions ?num_imaging_sessions ?session_id ?session_type ?assessment ?image_modal ?session_file_path
+?diagnosis ?subject_group ?num_matching_phenotypic_sessions ?num_matching_imaging_sessions ?session_id ?session_type ?assessment ?image_modal ?session_file_path
 WHERE {
     ?dataset_uuid a nb:Dataset;
             nb:hasLabel ?dataset_name;
@@ -15,7 +15,7 @@ WHERE {
             nb:hasLabel ?sub_id;
             nb:hasSession ?session.
     ?session a ?session_type;
-                nb:hasLabel ?session_id.
+             nb:hasLabel ?session_id.
     OPTIONAL {
         ?session nb:hasAcquisition/nb:hasContrastType ?image_modal.
         OPTIONAL {
@@ -41,7 +41,7 @@ WHERE {
         ?session nb:hasAssessment ?assessment.
     }
     {
-        SELECT ?subject (count(distinct ?phenotypic_session) as ?num_phenotypic_sessions)
+        SELECT ?subject (count(distinct ?phenotypic_session) as ?num_matching_phenotypic_sessions)
         WHERE {
             ?subject a nb:Subject.
             OPTIONAL {
@@ -67,7 +67,7 @@ WHERE {
         } GROUP BY ?subject
     }
     {
-        SELECT ?subject (count(distinct ?imaging_session) as ?num_imaging_sessions)
+        SELECT ?subject (count(distinct ?imaging_session) as ?num_matching_imaging_sessions)
         WHERE {
             ?subject a nb:Subject.
             OPTIONAL {
@@ -78,4 +78,4 @@ WHERE {
         } GROUP BY ?subject
     }
 
-}
+}