Updated deps, remove jdbc, RocksDB updates

clingen-data-model · Jul 23, 2024 · 5111709 · 5111709
1 parent 5f72f54
commit 5111709
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diff --git a/deps.edn b/deps.edn
@@ -2,9 +2,7 @@
  {"central"
   {:url "https://repo1.maven.org/maven2/"}
   "clojars"
-  {:url "https://repo.clojars.org/"}
-  "cognitect-dev-tools"
-  {:url "https://dev-tools.cognitect.com/maven/releases/"}}
+  {:url "https://repo.clojars.org/"}}
 
  :paths ["src"]
 
@@ -17,53 +15,45 @@
                       {:git/tag "v0.5.1" :git/sha "dfb30dd"}}
          :main-opts ["-m" "cognitect.test-runner"]
          :exec-fn cognitect.test-runner.api/test}
-  :dev {:extra-deps {io.github.nubank/morse {:git/tag "v2023.04.30.01"
-                                             :git/sha "d99b09c"}
-                     djblue/portal {:mvn/version "0.51.1"}
-                     io.github.nextjournal/clerk {:mvn/version "0.15.957"}
+  :dev {:extra-deps {djblue/portal {:mvn/version "0.57.0"}
                      org.slf4j/slf4j-simple {:mvn/version "2.0.7"}}}}
 
  :deps
- {org.clojure/clojure                               {:mvn/version "1.11.2"}
+ {org.clojure/clojure                               {:mvn/version "1.11.3"}
 
   ;; Interceptors and HTTP server
-  io.pedestal/pedestal.jetty                        {:mvn/version "0.6.3"}
-  io.pedestal/pedestal.route                        {:mvn/version "0.6.3"}
-  io.pedestal/pedestal.service                      {:mvn/version "0.6.3"}
+  io.pedestal/pedestal.jetty                        {:mvn/version "0.7.0"}
+  io.pedestal/pedestal.route                        {:mvn/version "0.7.0"}
+  io.pedestal/pedestal.service                      {:mvn/version "0.7.0"}
 
   ;; Serialization
-  com.taoensso/nippy                                {:mvn/version "3.2.0"}
-  digest/digest                                     {:mvn/version "1.4.10"}
-  org.clojure/data.json                             {:mvn/version "2.4.0"}
+  com.taoensso/nippy                                {:mvn/version "3.4.2"}
+  net.openhft/zero-allocation-hashing               {:mvn/version "0.26ea0"}
+  org.clojure/data.json                             {:mvn/version "2.5.0"}
 
   ;; Kafka
-  org.apache.kafka/kafka-clients                    {:mvn/version "3.6.1"}
+  org.apache.kafka/kafka-clients                    {:mvn/version "3.7.1"}
 
   ;; Compression for storage artifacts
   org.apache.commons/commons-compress               {:mvn/version "1.26.1"}
   org.lz4/lz4-java                                  {:mvn/version "1.8.0"}
 
   ;; Datastores
-
-  ;; JDBC
-  com.github.seancorfield/next.jdbc                 {:mvn/version "1.3.909"}
-  com.zaxxer/HikariCP                               {:mvn/version "5.1.0"}
-  org.postgresql/postgresql                         {:mvn/version "42.7.1"}
 
   ;; Rocks 
-  org.rocksdb/rocksdbjni                            {:mvn/version "8.8.1"}
+  org.rocksdb/rocksdbjni                            {:mvn/version "9.4.0"}
 
   ;; Jena 
-  org.apache.jena/jena-arq                          {:mvn/version "5.0.0"}
-  org.apache.jena/jena-core                         {:mvn/version "5.0.0"}
-  org.apache.jena/jena-iri                          {:mvn/version "5.0.0"}
-  org.apache.jena/jena-tdb2                         {:mvn/version "5.0.0"}
-  org.apache.jena/jena-text                         {:mvn/version "5.0.0"}
-  org.apache.jena/jena-shacl                        {:mvn/version "5.0.0"}
+  org.apache.jena/jena-arq                          {:mvn/version "5.1.0"}
+  org.apache.jena/jena-core                         {:mvn/version "5.1.0"}
+  org.apache.jena/jena-iri                          {:mvn/version "5.1.0"}
+  org.apache.jena/jena-tdb2                         {:mvn/version "5.1.0"}
+  org.apache.jena/jena-text                         {:mvn/version "5.1.0"}
+  org.apache.jena/jena-shacl                        {:mvn/version "5.1.0"}
 
   ;; Google Cloud Storage
-  com.google.cloud/google-cloud-storage             {:mvn/version "2.22.0"}
-  com.google.cloud/google-cloud-secretmanager       {:mvn/version "2.32.0"}
+  com.google.cloud/google-cloud-storage             {:mvn/version "2.40.1"}
+  com.google.cloud/google-cloud-secretmanager       {:mvn/version "2.46.0"}
 
 }}
 
diff --git a/src/genegraph/framework/app.clj b/src/genegraph/framework/app.clj
@@ -5,7 +5,6 @@
             [genegraph.framework.protocol :as p]
             [genegraph.framework.storage :as s]
             [genegraph.framework.storage.rocksdb]
-            [genegraph.framework.storage.jdbc]
             [genegraph.framework.storage.rdf :as rdf]
             [genegraph.framework.storage.gcs]
             [genegraph.framework.storage.atom]

diff --git a/src/genegraph/framework/event.clj b/src/genegraph/framework/event.clj
@@ -3,8 +3,7 @@
   on events"
   (:require [clojure.data.json :as json]
             [clojure.edn :as edn]
-            [genegraph.framework.storage :as storage]
-            [next.jdbc :as jdbc]))
+            [genegraph.framework.storage :as storage]))
 
 (defmulti add-model ::format)
 
@@ -70,14 +69,3 @@
           ::publish
           conj
           publish-event))
-
-(defn execute [event instance command]
-  "add deferred execute effect to event"
-  (let [commit-promise (promise)]
-    (update event
-            ::effects
-            conj
-            {:command jdbc/execute!
-             :args [(get-in event [::storage/storage instance])
-                    command]
-             :commit-promise commit-promise})))
diff --git a/src/genegraph/framework/storage/jdbc.clj b/src/genegraph/framework/storage/jdbc.clj
diff --git a/src/genegraph/framework/storage/rdf.clj b/src/genegraph/framework/storage/rdf.clj
@@ -74,7 +74,10 @@
               (.begin db ReadWrite/WRITE)
               (RDFDataMgr/read db is Lang/NQUADS)
               (.commit db)
-              (finally (.end db)))))
+              (catch Exception e
+                (.abort db))
+              (finally
+                (.end db)))))
         (p/system-update this {:state :failed-restoring-snapshot
                                :msg "Snapshot does not exist"}))))