Merge pull request #67 from slr71/main

CORE-2006: dependency updates.
cyverse-de · Aug 7, 2024 · 32de036 · 32de036
2 parents 12d7a10 + cc29658
commit 32de036
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diff --git a/.dockerignore b/.dockerignore
@@ -1,6 +1,5 @@
 /pom.xml
 *jar
-!opentelemetry-javaagent.jar
 /bin
 /lib
 /classes

diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,5 @@
 /pom.xml
 *jar
-!opentelemetry-javaagent.jar
 /bin
 /lib
 /classes

diff --git a/Dockerfile b/Dockerfile
@@ -1,23 +1,23 @@
-FROM clojure:openjdk-17-lein-alpine
+FROM clojure:temurin-22-lein-jammy
 
 WORKDIR /usr/src/app
 
-RUN apk add --no-cache git
+RUN apt-get update && \
+    apt-get install -y git && \
+    rm -rf /var/lib/apt/lists/*
 
-RUN ln -s "/opt/openjdk-17/bin/java" "/bin/data-info"
-
-ENV OTEL_TRACES_EXPORTER none
+RUN ln -s "/opt/java/openjdk/bin/java" "/bin/data-info"
 
 COPY project.clj /usr/src/app/
 RUN lein deps
 
 COPY conf/main/logback.xml /usr/src/app/
 COPY . /usr/src/app
 
-RUN lein uberjar && \
+RUN lein do clean, uberjar && \
     cp target/data-info-standalone.jar .
 
-ENTRYPOINT ["data-info", "-Dlogback.configurationFile=/etc/iplant/de/logging/data-info-logging.xml", "-javaagent:/usr/src/app/opentelemetry-javaagent.jar", "-Dotel.resource.attributes=service.name=data-info", "-cp", ".:data-info-standalone.jar", "data_info.core"]
+ENTRYPOINT ["data-info", "-Dlogback.configurationFile=/etc/iplant/de/logging/data-info-logging.xml", "-cp", ".:data-info-standalone.jar", "data_info.core"]
 CMD ["--help"]
 
 ARG git_commit=unknown

diff --git a/conf/test/logback.xml → conf/test/logback-test.xml b/conf/test/logback.xml → conf/test/logback-test.xml
diff --git a/opentelemetry-javaagent.jar b/opentelemetry-javaagent.jar
diff --git a/project.clj b/project.clj
@@ -14,57 +14,54 @@
             :url "http://iplantcollaborative.org/sites/default/files/iPLANT-LICENSE.txt"}
   :manifest {"Git-Ref" ~(git-ref)}
   :uberjar-name "data-info-standalone.jar"
-  :dependencies [[org.clojure/clojure "1.11.1"]
-                 [cheshire "5.12.0"
+  :dependencies [[org.clojure/clojure "1.11.3"]
+                 [cheshire "5.13.0"
                    :exclusions [[com.fasterxml.jackson.dataformat/jackson-dataformat-cbor]
                                 [com.fasterxml.jackson.dataformat/jackson-dataformat-smile]
                                 [com.fasterxml.jackson.core/jackson-annotations]
                                 [com.fasterxml.jackson.core/jackson-databind]
                                 [com.fasterxml.jackson.core/jackson-core]]]
                  [com.cemerick/url "0.1.1" :exclusions [com.cemerick/clojurescript.test]]
-                 [dire "0.5.4"]
+                 [org.cyverse/dire "0.5.5-SNAPSHOT"]
                  [me.raynes/fs "1.4.6"]
-                 [org.apache.tika/tika-core "2.9.1"]
+                 [org.apache.tika/tika-core "2.9.2" :exclusions [org.slf4j/slf4j-api]]
                  [net.sf.opencsv/opencsv "2.3"]
-                 [de.ubercode.clostache/clostache "1.4.0" :exclusions [org.clojure/core.incubator]]
-                 [org.cyverse/clj-irods "0.3.5"]
-                 [org.cyverse/clj-icat-direct "2.9.5"
-                   :exclusions [[org.slf4j/slf4j-log4j12]
+                 [org.cyverse/clj-irods "0.3.6"]
+                 [org.cyverse/clj-icat-direct "2.9.6"
+                   :exclusions [[org.slf4j/slf4j-api]
+                                [org.slf4j/slf4j-log4j12]
                                 [log4j]]]
-                 [org.cyverse/clj-jargon "3.1.0"
-                   :exclusions [[org.slf4j/slf4j-log4j12]
+                 [org.cyverse/clj-jargon "3.1.1"
+                   :exclusions [[org.slf4j/slf4j-api]
+                                [org.slf4j/slf4j-log4j12]
                                 [log4j]]]
                  [javax.servlet/servlet-api "2.5"]
-                 [metosin/compojure-api "1.1.13"]
-                 [ring/ring-jetty-adapter "1.11.0"] ;; update this when underlying ring version changes, probably
-                 [org.slf4j/slf4j-api "1.7.31"]
-                 [org.cyverse/otel "0.2.5"]
-                 [org.cyverse/clojure-commons "3.0.7"]
-                 [org.cyverse/common-cli "2.8.1"]
-                 [org.cyverse/common-cfg "2.8.2"]
-                 [org.cyverse/common-swagger-api "3.4.4"]
-                 [org.cyverse/heuristomancer "2.8.6"]
-                 [org.cyverse/kameleon "3.0.8"]
-                 [org.cyverse/metadata-client "3.1.1"]
-                 [org.cyverse/async-tasks-client "0.0.4"]
-                 [org.cyverse/metadata-files "2.1.0"]
-                 [org.cyverse/oai-ore "1.0.3"]
-                 [org.cyverse/service-logging "2.8.3"]
-                 [org.cyverse/event-messages "0.0.1"]
-                 [com.novemberain/langohr "3.5.1"]
+                 [metosin/compojure-api "1.1.14"]
+                 [ring/ring-jetty-adapter "1.12.2" :exclusions [org.slf4j/slf4j-api]]
+                 [org.cyverse/clojure-commons "3.0.9-SNAPSHOT"]
+                 [org.cyverse/common-cli "2.8.2"]
+                 [org.cyverse/common-cfg "2.8.3"]
+                 [org.cyverse/common-swagger-api "3.4.5"]
+                 [org.cyverse/heuristomancer "2.8.7"]
+                 [org.cyverse/kameleon "3.0.10"]
+                 [org.cyverse/metadata-client "3.1.2"]
+                 [org.cyverse/async-tasks-client "0.0.5"]
+                 [org.cyverse/metadata-files "2.1.1"]
+                 [org.cyverse/oai-ore "1.0.4"]
+                 [org.cyverse/service-logging "2.8.4"]
+                 [com.novemberain/langohr "5.4.0"]
                  [slingshot "0.12.2"]]
   :eastwood {:exclude-namespaces [data-info.routes.schemas.tickets
                                   data-info.routes.schemas.stats
                                   data-info.routes.schemas.sharing
                                   data-info.routes.schemas.trash
                                   :test-paths]
              :linters [:wrong-arity :wrong-ns-form :wrong-pre-post :wrong-tag :misplaced-docstrings]}
-  :plugins [[jonase/eastwood "1.4.2"]
+  :plugins [[jonase/eastwood "1.4.3"]
             [lein-ancient "0.7.0"]
-            [test2junit "1.1.3"]]
+            [test2junit "1.4.4"]]
   :profiles {:dev     {:plugins        [[lein-ring "0.12.5"]]
-                       :resource-paths ["conf/test"]
-                       :jvm-opts       ["-Dotel.javaagent.enabled=false"]}
+                       :resource-paths ["conf/test"]}
              :repl    {:source-paths ["repl"]}
              :uberjar {:aot :all}}
   :main ^:skip-aot data-info.core
@@ -73,4 +70,4 @@
          :port 31360
          :auto-reload? false}
   :uberjar-exclusions [#".*[.]SF" #"LICENSE" #"NOTICE"]
-  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/data-info-logging.xml" "-javaagent:./opentelemetry-javaagent.jar" "-Dotel.resource.attributes=service.name=data-info"])
+  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/data-info-logging.xml"])
diff --git a/src/data_info/amqp.clj b/src/data_info/amqp.clj
@@ -28,14 +28,6 @@
       (handler channel metadata msg)
       (log/error (format "[amqp/message-router] [%s] [%s] unroutable" routing-key (String. msg))))))
 
-(defn connect
-  [exchange-cfg queue-cfg handlers]
-  (let [channel (lch/open (rmq/connect {:uri (config/amqp-uri)}))]
-    (log/info (format "[amqp/connect] [%s]" (config/amqp-uri)))
-    (declare-exchange channel exchange-cfg)
-    (declare-queue channel exchange-cfg queue-cfg (keys handlers))
-    (lc/blocking-subscribe channel (:name queue-cfg) (partial message-router handlers))))
-
 (defn publish-msg
   [routing-key msg]
   (try+

diff --git a/src/data_info/clients/async_tasks.clj b/src/data_info/clients/async_tasks.clj
@@ -6,7 +6,6 @@
             [clojure.string :as string]
             [clj-irods.core :refer [make-threadpool]]
             [clj-irods.cache-tools :as c]
-            [otel.otel :as otel]
             [async-tasks-client.core :as async-tasks-client]))
 
 ;; https://stackoverflow.com/questions/12068640/retrying-something-3-times-before-throwing-an-exception-in-clojure
@@ -27,16 +26,14 @@
 
 (defn- retry-via-threadpool
   [pool retries handler f & args]
-  (let [ag (agent nil)
-        s (otel/current-span)]
-    (send-via pool ag (fn [_nil] (c/otel-with-subspan [s]
-                                   (try+
-                                     (apply retry-with-handler retries handler f args)
-                                     (catch Object o
-                                       {::error o})))))
+  (let [ag (agent nil)]
+    (send-via pool ag (fn [_nil] (try+
+                                  (apply retry-with-handler retries handler f args)
+                                  (catch Object o
+                                    {::error o}))))
     (delay (if-let [err (::error @ag)]
-      (throw+ err)
-      @ag))))
+             (throw+ err)
+             @ag))))
 
 (defn get-by-id
   [id]
@@ -68,49 +65,50 @@
 
 (defn run-async-thread
   [async-task-id thread-function prefix]
-  (otel/with-span [outer-span ["run-async-thread" {:kind :producer :attributes {"async-task-id" (str async-task-id)}}]]
-    (let [^Runnable task-thread (fn []
-                                  (with-open [_ (otel/span-scope outer-span)]
-                                    (otel/with-span [s ["async thread" {:kind :consumer :attributes {"async-task-id" (str async-task-id)}}]]
-                                      (thread-function async-task-id))))]
-      (.start (Thread. task-thread (str prefix "-" (string/replace async-task-id #".*/tasks/" "")))))
-    async-task-id))
+  (let [^Runnable task-thread (fn [] (thread-function async-task-id))]
+    (.start (Thread. task-thread (str prefix "-" (string/replace async-task-id #".*/tasks/" "")))))
+  async-task-id)
+
+(defn create-update-fn [async-task-id pool]
+  (fn [path action]
+    (log/info "Updating async task:" async-task-id ":" path action)
+    ;; we use the thread pool version here to be non-blocking, but elsewhere we use it so things happen in order (but
+    ;; deref the result to wait for the result before continuing)
+    (retry-via-threadpool
+     pool 3
+     (fn [e t] (log/error (:throwable t) "failed updating async task"))
+     add-status async-task-id {:status "running"
+                               :detail (format "[%s] %s: %s" (config/service-identifier) path (name action))})))
 
 (defn paths-async-thread
   ([async-task-id jargon-fn end-fn]
    (paths-async-thread async-task-id jargon-fn end-fn true))
   ([async-task-id jargon-fn end-fn use-client-user?]
-   (otel/with-span [s ["paths-async-thread" {:attributes {"async-task-id" (str async-task-id)}}]]
-     (let [pool (make-threadpool (str async-task-id "-async-tasks-update") 1)
-           {:keys [username] :as async-task} (get-by-id async-task-id)
-           update-fn (fn [path action]
-                       (otel/with-span [s ["update-fn"]]
-                         (log/info "Updating async task:" async-task-id ":" path action)
-                         ;; we use the thread pool version here to be non-blocking, but elsewhere we use it so things happen in order (but deref the result to wait for the result before continuing)
-                         (retry-via-threadpool pool 3
-                           (fn [e t] (log/error (:throwable t) "failed updating async task"))
-                           add-status async-task-id {:status "running" :detail (format "[%s] %s: %s" (config/service-identifier) path (name action))})))]
-       (try+
-         (deref (retry-via-threadpool pool 3
-           (fn [e t] (log/error (:throwable t) "failed updating async task with started status"))
-           add-status async-task-id {:status "started"}))
-         (if use-client-user?
-           (irods/with-jargon-exceptions :client-user username [cm]
-             (otel/with-span [s ["jargon-fn" {:attributes {"client-user" username}}]]
-               (jargon-fn cm async-task update-fn)))
-           (irods/with-jargon-exceptions [cm]
-             (otel/with-span [s ["jargon-fn"]]
-               (jargon-fn cm async-task update-fn))))
-           ;; For the completed statuses we want a lot of retries because the presence or absence of an end date controls locking behavior
-           (deref (retry-via-threadpool pool 100
-             (fn [e t] (log/error (:throwable t) "failed updating async task with completed status"))
-             add-completed-status async-task-id {:status "completed" :detail (str "[" (config/service-identifier) "]")}))
-         (otel/with-span [s ["end-fn"]]
-           (end-fn async-task false))
-         (catch Object _
-           (log/error (:throwable &throw-context) "failed processing async task" async-task-id)
-           (deref (retry-via-threadpool pool 100
-             (fn [e t] (log/error (:throwable t) "failed updating async task with completed status"))
-             add-completed-status async-task-id {:status "failed" :detail (format "[%s] %s" (config/service-identifier) (pr-str (:throwable &throw-context)))}))
-           (end-fn async-task true))))
-     (log/info "Finished processing async task " async-task-id))))
+   (let [pool                              (make-threadpool (str async-task-id "-async-tasks-update") 1)
+         {:keys [username] :as async-task} (get-by-id async-task-id)
+         update-fn                         (create-update-fn async-task-id pool)]
+     (try+
+      (deref (retry-via-threadpool pool 3
+                                   (fn [e t] (log/error (:throwable t) "failed updating async task with started status"))
+                                   add-status async-task-id {:status "started"}))
+      (if use-client-user?
+        (irods/with-jargon-exceptions :client-user username [cm]
+          (jargon-fn cm async-task update-fn))
+        (irods/with-jargon-exceptions [cm] (jargon-fn cm async-task update-fn)))
+      ;; For the completed statuses we want a lot of retries because the presence or absence of an end date controls
+      ;; locking behavior
+      (deref (retry-via-threadpool
+              pool 100
+              (fn [e t] (log/error (:throwable t) "failed updating async task with completed status"))
+              add-completed-status async-task-id {:status "completed" :detail (str "[" (config/service-identifier) "]")}))
+      (end-fn async-task false)
+      (catch Object _
+        (log/error (:throwable &throw-context) "failed processing async task" async-task-id)
+        (deref (retry-via-threadpool
+                pool 100
+                (fn [e t] (log/error (:throwable t) "failed updating async task with completed status"))
+                add-completed-status async-task-id
+                {:status "failed"
+                 :detail (format "[%s] %s" (config/service-identifier) (pr-str (:throwable &throw-context)))}))
+        (end-fn async-task true))))
+   (log/info "Finished processing async task " async-task-id)))
diff --git a/src/data_info/core.clj b/src/data_info/core.clj
@@ -5,7 +5,6 @@
             [data-info.routes :as routes]
             [data-info.util.config :as config]
             [data-info.amqp :as amqp]
-            [data-info.events :as events]
             [me.raynes.fs :as fs]
             [common-cli.core :as ccli]
             [service-logging.thread-context :as tc]
@@ -69,13 +68,6 @@
   (icat/configure-icat))
 
 
-(defn listen-for-events
-  []
-  (let [exchange-cfg (events/exchange-config)
-        queue-cfg    (events/queue-config)]
-    (amqp/connect exchange-cfg queue-cfg {"events.data-info.ping" events/ping-handler})))
-
-
 (defn- cli-options
   []
   [["-c" "--config PATH" "Path to the config file"
@@ -101,5 +93,4 @@
         (ccli/exit 1 "The config file is not readable."))
       (load-configuration-from-file (:config options))
       (icat/configure-icat)
-      (.start (Thread. listen-for-events))
       (run-jetty))))
diff --git a/src/data_info/events.clj b/src/data_info/events.clj
diff --git a/src/data_info/routes.clj b/src/data_info/routes.clj
@@ -29,29 +29,29 @@
 
 (defapi app
   (swagger-routes
-    {:ui config/docs-uri
-     :options {:ui {:supported-submit-methods ["get", "post", "put", "delete", "patch", "head"]
-                    :validator-url            nil}}
-     :data {:info {:title "Discovery Environment Data Info API"
-                   :description "Documentation for the Discovery Environment Data Info REST API"
-                   :version "2.8.0"}
-            :tags [{:name "service-info", :description "Service Information"}
-                   {:name "data-by-id", :description "Data Operations (by ID)"}
-                   {:name "data", :description "Data Operations"}
-                   {:name "tickets", :description "Ticket Operations"}
-                   {:name "bulk", :description "Bulk Operations"}
-                   {:name "navigation", :description "Navigation"}
-                   {:name "users", :description "User Operations"}
-                   {:name "filetypes", :description "File Type Metadata"}
-                   {:name "groups", :description "Group Operations"}]}})
-  (middleware
-    [add-user-to-context
-     wrap-query-params
-     wrap-lcase-params
-     params/wrap-keyword-params
-     [wrap-exceptions cx/exception-handlers]
-     util/req-logger
-     log-validation-errors]
+   {:ui      config/docs-uri
+    :options {:ui {:supported-submit-methods ["get", "post", "put", "delete", "patch", "head"]
+                   :validator-url            nil}}
+    :data    {:info {:title       "Discovery Environment Data Info API"
+                     :description "Documentation for the Discovery Environment Data Info REST API"
+                     :version     "2.8.0"}
+              :tags [{:name "service-info", :description "Service Information"}
+                     {:name "data-by-id", :description "Data Operations (by ID)"}
+                     {:name "data", :description "Data Operations"}
+                     {:name "tickets", :description "Ticket Operations"}
+                     {:name "bulk", :description "Bulk Operations"}
+                     {:name "navigation", :description "Navigation"}
+                     {:name "users", :description "User Operations"}
+                     {:name "filetypes", :description "File Type Metadata"}
+                     {:name "groups", :description "Group Operations"}]}})
+  (context "/" []
+    :middleware [add-user-to-context
+                 wrap-query-params
+                 wrap-lcase-params
+                 params/wrap-keyword-params
+                 [wrap-exceptions cx/exception-handlers]
+                 util/req-logger
+                 log-validation-errors]
     status-routes/status
     data-routes/data-operations
     rename-routes/rename-routes