From c879960a9849ef73638ba60dfe016f056aeb2c69 Mon Sep 17 00:00:00 2001
From: Tristan Nelson <thnelson@geisinger.edu>
Date: Thu, 15 Aug 2024 10:51:40 -0400
Subject: [PATCH] Apply fix for Jena bug

https://github.com/apache/jena/issues/2584
---
 src/genegraph/gene_validity.clj | 11 ++++++---
 src/genegraph/notebooks.clj     |  2 +-
 src/genegraph/user.clj          | 44 ++++++++++++++++++++++++++++++++-
 3 files changed, 52 insertions(+), 5 deletions(-)

diff --git a/src/genegraph/gene_validity.clj b/src/genegraph/gene_validity.clj
index 22d488d..45c10e9 100644
--- a/src/genegraph/gene_validity.clj
+++ b/src/genegraph/gene_validity.clj
@@ -521,13 +521,18 @@
 (defn gv-ready-fn [e]
   (let [tdb (get-in e [::storage/storage :gv-tdb])
         type-count (fn [t]
-                     (count (type-query tdb {:type t})))]
-    (rdf/tx tdb
+                     (count (type-query tdb {:type t})))
+        in-tx (.isInTransaction tdb)]
+    (try
+      (when-not in-tx
+        (.begin tdb ReadWrite/READ))
       (let [gv-count (type-count
                       :sepio/GeneValidityEvidenceLevelAssertion)
             ac-count (type-count :sepio/ActionabilityReport)
             gd-count (type-count :sepio/GeneDosageReport)]
-        (log/info :fn ::gv-ready-fn
+        (.commit tdb) ; https://github.com/apache/jena/issues/2584
+        (.end tdb)
+        #_(log/info :fn ::gv-ready-fn
                   :gv-count gv-count
                   :ac-count ac-count
                   :gd-count gd-count)
diff --git a/src/genegraph/notebooks.clj b/src/genegraph/notebooks.clj
index c482544..adae4e7 100644
--- a/src/genegraph/notebooks.clj
+++ b/src/genegraph/notebooks.clj
@@ -13,7 +13,7 @@
              (assoc gv/gv-tdb
                     :snapshot-handle {:type :file
                                       :base "/Users/tristan/code/genegraph-gene-validity/data/"
-                                      :path "gv-tdb-v11.nq.gz"})}})
+                                      :path "gv-tdb-v12.nq.gz"})}})
 
 
 (comment
diff --git a/src/genegraph/user.clj b/src/genegraph/user.clj
index 51f3466..9aa4d80 100644
--- a/src/genegraph/user.clj
+++ b/src/genegraph/user.clj
@@ -118,7 +118,32 @@
   (def gv-test-app (p/init gv-test-app-def))
   (p/start gv-test-app)
   (p/stop gv-test-app)
+  
+  (time
+   (let [c (hc/build-http-client {})
+         lock (Semaphore. 10)]
+     (dotimes [n 10000]
+       (.acquire lock)
+       (Thread/startVirtualThread
+        (fn []
+          (hc/get "http://localhost:8888/ready")
+          (.release lock))))))
 
+  (time
+   (let [c (hc/build-http-client {})
+         lock (Semaphore. 10)
+         db @(get-in gv-test-app [:storage :gv-tdb :instance])]
+     (dotimes [n 100000]
+       (.acquire lock)
+       (Thread/startVirtualThread
+        (fn []
+          (try
+            (let [db @(get-in gv-test-app [:storage :gv-tdb :instance])]
+              (gv/gv-ready-fn {::storage/storage {:gv-tdb db}}))
+            (finally (.release lock))))))))
+
+  (let [db @(get-in gv-test-app [:storage :gv-tdb :instance])]
+    (gv/gv-ready-fn {::storage/storage {:gv-tdb db}}))
   )
 
 ;; Downloading events
@@ -1299,10 +1324,27 @@ select ?x where {
                       ::event/skip-local-effects true
                       ::event/skip-publish-effects true)))
 
+
+    (let [tdb @(get-in gv-test-app [:storage :gv-tdb :instance])]
+    (rdf/tx tdb
+      (let [r (rdf/resource "CGGV:fe942eb4-ba59-43bf-89e0-243522ba7cbf"
+                        tdb)]
+        (rdf/pp-model (storage/read tdb (str r))))))
+
   
   (-> dnase1
       last
-      process-gv-event
+      process-gv-event 
       :gene-validity/model
       rdf/pp-model)
   )
+
+
+(comment
+  (time
+   (let [tdb @(get-in gv-test-app [:storage :gv-tdb :instance])]
+     (dotimes [n 100000]
+       (rdf/tx tdb
+         (+ 1 1)))))
+
+ )