Merge branch 'neurobagel:main' into switch-to-lifespan-events

.autorc

@@ -12,9 +12,9 @@
         [
             "omit-commits",
             {
-                "username": "dependabot[bot]",
+                "username": ["dependabot[bot]", "pre-commit-ci[bot]"],
                 "subject": "[pre-commit.ci]",
-                "labels": "_bot"
+                "labels": ["_bot", "skip-release"]
             }
         ]
     ],

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.4.0
     hooks:
       - id: black
         args:
@@ -22,7 +22,7 @@ repos:
           - --per-file-ignores=./app/api/models.py:F722
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: pretty-format-json

CHANGELOG.md

@@ -0,0 +1,58 @@
+# v0.2.1 (Tue Apr 16 2024)
+
+#### 🐛 Bug Fixes
+
+- [FIX] Address performance issues in SPARQL query [#308](https://github.com/neurobagel/api/pull/308) ([@surchs](https://github.com/surchs))
+- [FIX] Disable timeout for request to graph [#305](https://github.com/neurobagel/api/pull/305) ([@alyssadai](https://github.com/alyssadai))
+
+#### Authors: 2
+
+- Alyssa Dai ([@alyssadai](https://github.com/alyssadai))
+- Sebastian Urchs ([@surchs](https://github.com/surchs))
+
+---
+
+# v0.2.0 (Thu Apr 11 2024)
+
+:tada: This release contains work from a new contributor! :tada:
+
+Thank you, Abdul Samad Siddiqui ([@samadpls](https://github.com/samadpls)), for all your work!
+
+### Release Notes
+
+#### [MNT] Release new data model ([#300](https://github.com/neurobagel/api/pull/300))
+
+We have updated the Neurobagel data model to allow users to specify phenotypic information at the session level (https://github.com/neurobagel/planning/issues/83). This release updates the node API so it can understand the new graph data.
+
+---
+
+#### 💥 Breaking Changes
+
+- [REF] Make session count names clearer in query response [#282](https://github.com/neurobagel/api/pull/282) ([@alyssadai](https://github.com/alyssadai))
+- [ENH] Support queries of session-level phenotypic attributes [#264](https://github.com/neurobagel/api/pull/264) ([@alyssadai](https://github.com/alyssadai))
+
+#### 🚀 Enhancements
+
+- [ENH] Added root endpoint with welcome message and API docs link [#286](https://github.com/neurobagel/api/pull/286) ([@samadpls](https://github.com/samadpls))
+- [MNT] Release new data model [#300](https://github.com/neurobagel/api/pull/300) ([@surchs](https://github.com/surchs))
+- Delete .github/workflows/add_pr2project.yml [#244](https://github.com/neurobagel/api/pull/244) ([@surchs](https://github.com/surchs))
+
+#### 📝 Documentation
+
+- [DOC] Added warning about quoting in `.env` file for Docker commands [#284](https://github.com/neurobagel/api/pull/284) ([@samadpls](https://github.com/samadpls))
+- [DOC] Add sample default SPARQL query to repo [#277](https://github.com/neurobagel/api/pull/277) ([@alyssadai](https://github.com/alyssadai))
+
+####  🧪 Tests
+
+- [TST] Refactor tests [#269](https://github.com/neurobagel/api/pull/269) ([@alyssadai](https://github.com/alyssadai))
+
+#### 🔩 Dependency Updates
+
+- Bumped fastapi, starlette, and typing_extensions [#295](https://github.com/neurobagel/api/pull/295) ([@rmanaem](https://github.com/rmanaem))
+
+#### Authors: 4
+
+- Abdul Samad Siddiqui ([@samadpls](https://github.com/samadpls))
+- Alyssa Dai ([@alyssadai](https://github.com/alyssadai))
+- Arman Jahanpour ([@rmanaem](https://github.com/rmanaem))
+- Sebastian Urchs ([@surchs](https://github.com/surchs))

README.md

@@ -51,7 +51,7 @@ git clone https://github.com/neurobagel/api.git
 
 ### Set the environment variables
 Create a file called `.env` in the root of the repository to store the environment variables used by the app. 
-This repository contains a [template `.env` file](/.template-env) that you can copy and edit.
+See the Neurobagel recipes repo for a [template `.env` file](https://github.com/neurobagel/recipes/blob/main/dev/template.env) you can copy and edit.
 
 To run API requests against a graph, at least two environment variables must be set: `NB_GRAPH_USERNAME` and `NB_GRAPH_PASSWORD`.
 
@@ -65,31 +65,22 @@ To run API requests against a graph, at least two environment variables must be
 The below instructions for Docker and Python assume that you have at least set `NB_GRAPH_USERNAME` and `NB_GRAPH_PASSWORD` in your `.env`.
 
 ### Docker
-First, [install docker](https://docs.docker.com/get-docker/).
+First, [install Docker](https://docs.docker.com/get-docker/).
 
 You can then run a Docker container for the API in one of three ways:
 #### Option 1 (RECOMMENDED): Use the `docker-compose.yaml` file
 
-First, [install docker compose](https://docs.docker.com/compose/install/).
+First, [install Docker Compose](https://docs.docker.com/compose/install/).
 
-If needed, update your `.env` file with optional environment variables for the docker compose configuration.
+Refer to our [official documentation](https://neurobagel.org/infrastructure/#launch-the-neurobagel-node-api-and-graph-stack) for instructions on using the template configuration files from our [recipes](https://github.com/neurobagel/recipes) repository to spin up a local Neurobagel API and graph backend with Docker Compose.
 
 **TIP:** Double check that the environment variables are resolved with your expected values using the command `docker compose config`.
 
-> :information_source: **Note: Deploying the Neurobagel query tool**
->
-> When you deploy the API locally with `docker compose`, 
-> you will only spin up the graph backend and the API service. 
-> If you want to use the graphical browser query tool
-> as a standalone service for your local API, 
-> you will have to deploy it manually.
-> Please refer to our [documentation for details](https://neurobagel.org/infrastructure/#as-a-standalone-service).
-
-Use Docker Compose to spin up the containers by running the following in the repository root (where the `docker-compose.yml` file is):
+Use Docker Compose to spin up your API and graph containers by running the following in the directory where the `docker-compose.yml` file is):
 ```bash
 docker compose up -d
 ```
-If you want to ensure you have the latest images use the command below:
+Or, to ensure you have the latest images:
 
 ```bash
 docker compose pull && docker compose up -d

app/api/crud.py

@@ -19,7 +19,7 @@
 ]
 
 
-def post_query_to_graph(query: str, timeout: float = 30.0) -> dict:
+def post_query_to_graph(query: str, timeout: float = None) -> dict:
     """
     Makes a post request to the graph API to perform a query, using parameters from the environment.
 
@@ -30,7 +30,7 @@ def post_query_to_graph(query: str, timeout: float = 30.0) -> dict:
     query : str
         The full SPARQL query string.
     timeout : float, optional
-        The maximum duration for the request, by default 5.0 seconds.
+        The maximum duration for the request in seconds, by default None.
 
     Returns
     -------

app/api/utility.py

@@ -206,50 +206,27 @@ def create_query(
                      nb:hasLabel ?session_id.
             OPTIONAL {{
                 ?session nb:hasAcquisition/nb:hasContrastType ?image_modal.
-                OPTIONAL {{
-                    ?session nb:hasFilePath ?session_file_path.
-                }}
-            }}
-            OPTIONAL {{
-                ?dataset_uuid nb:hasPortalURI ?dataset_portal_uri.
-            }}
-            OPTIONAL {{
-                ?session nb:hasAge ?age.
-            }}
-            OPTIONAL {{
-                ?session nb:hasSex ?sex.
-            }}
-            OPTIONAL {{
-                ?session nb:hasDiagnosis ?diagnosis.
-            }}
-            OPTIONAL {{
-                ?session nb:isSubjectGroup ?subject_group.
-            }}
-            OPTIONAL {{
-                ?session nb:hasAssessment ?assessment.
+                OPTIONAL {{?session nb:hasFilePath ?session_file_path.}}
             }}
+            OPTIONAL {{?dataset_uuid nb:hasPortalURI ?dataset_portal_uri.}}
+            OPTIONAL {{?session nb:hasAge ?age.}}
+            OPTIONAL {{?session nb:hasSex ?sex.}}
+            OPTIONAL {{?session nb:hasDiagnosis ?diagnosis.}}
+            OPTIONAL {{?session nb:isSubjectGroup ?subject_group.}}
+            OPTIONAL {{?session nb:hasAssessment ?assessment.}}
             {{
                 SELECT ?subject (count(distinct ?phenotypic_session) as ?num_matching_phenotypic_sessions)
                 WHERE {{
                     ?subject a nb:Subject.
                     OPTIONAL {{
                         ?subject nb:hasSession ?phenotypic_session.
                         ?phenotypic_session a nb:PhenotypicSession.
-                        OPTIONAL {{
-                            ?phenotypic_session nb:hasAge ?age.
-                        }}
-                        OPTIONAL {{
-                            ?phenotypic_session nb:hasSex ?sex.
-                        }}
-                        OPTIONAL {{
-                            ?phenoypic_session nb:hasDiagnosis ?diagnosis.
-                        }}
-                        OPTIONAL {{
-                            ?phenotypic_session nb:isSubjectGroup ?subject_group.
-                        }}
-                        OPTIONAL {{
-                            ?phenotypic_session nb:hasAssessment ?assessment.
-                        }}
+
+                        OPTIONAL {{?phenotypic_session nb:hasAge ?age.}}
+                        OPTIONAL {{?phenotypic_session nb:hasSex ?sex.}}
+                        OPTIONAL {{?phenotypic_session nb:hasDiagnosis ?diagnosis.}}
+                        OPTIONAL {{?phenotypic_session nb:isSubjectGroup ?subject_group.}}
+                        OPTIONAL {{?phenotypic_session nb:hasAssessment ?assessment.}}
                     }}
                     {phenotypic_session_level_filters}
                 }} GROUP BY ?subject
@@ -260,7 +237,8 @@ def create_query(
                     ?subject a nb:Subject.
                     OPTIONAL {{
                         ?subject nb:hasSession ?imaging_session.
-                        ?imaging_session nb:hasAcquisition/nb:hasContrastType ?image_modal.
+                        ?imaging_session a nb:ImagingSession;
+                            nb:hasAcquisition/nb:hasContrastType ?image_modal.
                     }}
                     {imaging_session_level_filters}
                 }} GROUP BY ?subject

docs/default_neurobagel_query.rq

@@ -18,50 +18,27 @@ WHERE {
              nb:hasLabel ?session_id.
     OPTIONAL {
         ?session nb:hasAcquisition/nb:hasContrastType ?image_modal.
-        OPTIONAL {
-            ?session nb:hasFilePath ?session_file_path.
-        }
-    }
-    OPTIONAL {
-        ?dataset_uuid nb:hasPortalURI ?dataset_portal_uri.
-    }
-    OPTIONAL {
-        ?session nb:hasAge ?age.
-    }
-    OPTIONAL {
-        ?session nb:hasSex ?sex.
-    }
-    OPTIONAL {
-        ?session nb:hasDiagnosis ?diagnosis.
-    }
-    OPTIONAL {
-        ?session nb:isSubjectGroup ?subject_group.
-    }
-    OPTIONAL {
-        ?session nb:hasAssessment ?assessment.
-    }
+        OPTIONAL {?session nb:hasFilePath ?session_file_path.}
+    }
+    OPTIONAL {?dataset_uuid nb:hasPortalURI ?dataset_portal_uri.}
+    OPTIONAL {?session nb:hasAge ?age.}
+    OPTIONAL {?session nb:hasSex ?sex.}
+    OPTIONAL {?session nb:hasDiagnosis ?diagnosis.}
+    OPTIONAL {?session nb:isSubjectGroup ?subject_group.}
+    OPTIONAL {?session nb:hasAssessment ?assessment.}
     {
         SELECT ?subject (count(distinct ?phenotypic_session) as ?num_matching_phenotypic_sessions)
         WHERE {
             ?subject a nb:Subject.
             OPTIONAL {
                 ?subject nb:hasSession ?phenotypic_session.
                 ?phenotypic_session a nb:PhenotypicSession.
-                OPTIONAL {
-                    ?phenotypic_session nb:hasAge ?age.
-                }
-                OPTIONAL {
-                    ?phenotypic_session nb:hasSex ?sex.
-                }
-                OPTIONAL {
-                    ?phenoypic_session nb:hasDiagnosis ?diagnosis.
-                }
-                OPTIONAL {
-                    ?phenotypic_session nb:isSubjectGroup ?subject_group.
-                }
-                OPTIONAL {
-                    ?phenotypic_session nb:hasAssessment ?assessment.
-                }
+
+                OPTIONAL {?phenotypic_session nb:hasAge ?age.}
+                OPTIONAL {?phenotypic_session nb:hasSex ?sex.}
+                OPTIONAL {?phenotypic_session nb:hasDiagnosis ?diagnosis.}
+                OPTIONAL {?phenotypic_session nb:isSubjectGroup ?subject_group.}
+                OPTIONAL {?phenotypic_session nb:hasAssessment ?assessment.}
             }
 
         } GROUP BY ?subject
@@ -72,7 +49,8 @@ WHERE {
             ?subject a nb:Subject.
             OPTIONAL {
                 ?subject nb:hasSession ?imaging_session.
-                ?imaging_session nb:hasAcquisition/nb:hasContrastType ?image_modal.
+                ?imaging_session a nb:ImagingSession;
+                    nb:hasAcquisition/nb:hasContrastType ?image_modal.
             }
 
         } GROUP BY ?subject

requirements.txt

@@ -6,16 +6,16 @@ coverage==7.0.0
 click==8.1.3
 distlib==0.3.6
 exceptiongroup==1.0.4
-fastapi==0.95.2
+fastapi==0.110.1
 filelock==3.8.0
 h11==0.14.0
 httpcore==0.16.2
 httpx==0.23.1
 identify==2.5.9
-idna==3.4
+idna==3.7
 iniconfig==1.1.1
 nodeenv==1.7.0
-orjson==3.8.6
+orjson==3.9.15
 packaging==21.3
 pandas==1.5.2
 platformdirs==2.5.4
@@ -27,9 +27,9 @@ pytest==7.2.0
 PyYAML==6.0
 rfc3986==1.5.0
 sniffio==1.3.0
-starlette==0.27.0
+starlette==0.37.2
 toml==0.10.2
 tomli==2.0.1
-typing_extensions==4.4.0
+typing_extensions==4.11.0
 uvicorn==0.20.0
 virtualenv==20.16.7