[FIX] Address performance issues in SPARQL query (#308)

* Print out the response durations * [FIX] Correct typo in query template Fixes #306 * [REF] SPARQL OPTIONAL inline For improved readability * [ENH] Explicit imaging session type Removes need to traverse entire graph Improves query performance by a lot * Revert "Print out the response durations" it served its purpose This reverts commit ffc36ae. * [MNT] Ran black also addressed flake8 complaints * [DOC] Add updated query template
neurobagel · Apr 16, 2024 · d276155 · d276155
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Showing 2 changed files with 31 additions and 75 deletions.
diff --git a/app/api/utility.py b/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

diff --git a/docs/default_neurobagel_query.rq b/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