Merge pull request #271 from slr71/main

CORE-2006: update dependencies.

.dockerignore

@@ -4,7 +4,6 @@
 pom.xml
 pom.xml.asc
 *.jar
-!opentelemetry-javaagent.jar
 *.class
 /.lein-*
 /.nrepl-port

.gitignore

@@ -1,6 +1,5 @@
 pom.xml
 *.jar
-!opentelemetry-javaagent.jar
 /lib/
 /classes/
 /bin

Dockerfile

@@ -1,10 +1,10 @@
-FROM clojure:openjdk-17-lein-alpine
+FROM clojure:temurin-22-lein-jammy
 
 WORKDIR /usr/src/app
 
-RUN apk upgrade apk-tools && \
-    apk upgrade && \
-    apk add --no-cache git
+RUN apt-get update && \
+    apt-get install -y git && \
+    rm -rf /var/lib/apt/lists/*
 
 CMD ["--help"]
 
@@ -14,7 +14,7 @@ RUN mkdir -p /etc/iplant/de/crypto && \
     touch /etc/iplant/de/crypto/secring.gpg && \
     touch /etc/iplant/de/crypto/trustdb.gpg
 
-RUN ln -s "/opt/openjdk-17/bin/java" "/bin/apps"
+RUN ln -s "/opt/java/openjdk/bin/java" "/bin/apps"
 
 ENV OTEL_TRACES_EXPORTER none
 
@@ -29,7 +29,7 @@ RUN lein do clean, uberjar && \
     lein clean && \
     rm -r ~/.m2/repository
 
-ENTRYPOINT ["apps", "-Dlogback.configurationFile=/etc/iplant/de/logging/apps-logging.xml", "-javaagent:/usr/src/app/opentelemetry-javaagent.jar", "-Dotel.resource.attributes=service.name=apps", "-cp", ".:apps-standalone.jar:/", "apps.core"]
+ENTRYPOINT ["apps", "-Dlogback.configurationFile=/etc/iplant/de/logging/apps-logging.xml", "-cp", ".:apps-standalone.jar:/", "apps.core"]
 
 ARG git_commit=unknown
 ARG version=unknown

project.clj

@@ -7,52 +7,46 @@
       (string/trim (:out (sh "git" "rev-parse" "HEAD")))
       ""))
 
-(defproject org.cyverse/apps "2.15.0-SNAPSHOT"
+(defproject org.cyverse/apps "3.0.3-SNAPSHOT"
   :description "Framework for hosting DiscoveryEnvironment metadata services."
   :url "https://github.com/cyverse-de/apps"
   :license {:name "BSD"
-            :url "http://iplantcollaborative.org/sites/default/files/iPLANT-LICENSE.txt"}
+            :url "https://cyverse.org/license"}
   :manifest {"Git-Ref" ~(git-ref)}
   :uberjar-name "apps-standalone.jar"
-  :dependencies [[org.clojure/clojure "1.11.1"]
-                 [clj-http "3.12.3"]
+  :dependencies [[org.clojure/clojure "1.11.3"]
+                 [clj-http "3.13.0"]
                  [com.cemerick/url "0.1.1" :exclusions [com.cemerick/clojurescript.test]]
                  [com.google.guava/guava "23.0"]
-                 [de.ubercode.clostache/clostache "1.4.0"]
-                 [com.github.seancorfield/honeysql "2.4.972"]
+                 [com.github.seancorfield/honeysql "2.6.1147"]
                  [medley "1.4.0"]
-                 [metosin/compojure-api "1.1.13"]
-                 [org.cyverse/async-tasks-client "0.0.4"]
-                 [org.cyverse/authy "2.8.0"]
-                 [org.cyverse/clojure-commons "3.0.7"]
-                 [org.cyverse/debug-utils "2.8.1"]
-                 [org.cyverse/kameleon "3.0.6"]
-                 [org.cyverse/mescal "3.1.11"]
-                 [org.cyverse/metadata-client "3.1.1"]
-                 [org.cyverse/common-cli "2.8.1"]
-                 [org.cyverse/common-cfg "2.8.2"]
-                 [org.cyverse/common-swagger-api "3.4.4"]
-                 [org.cyverse/cyverse-groups-client "0.1.8"]
-                 [org.cyverse/otel "0.2.5"]
-                 [org.cyverse/permissions-client "2.8.3"]
-                 [org.cyverse/service-logging "2.8.3"]
-                 [org.cyverse/event-messages "0.0.1"]
-                 [org.flatland/ordered "1.15.10"]
-                 [com.novemberain/langohr "3.7.0"]
+                 [metosin/compojure-api "1.1.14"]
+                 [org.cyverse/async-tasks-client "0.0.5"]
+                 [org.cyverse/authy "3.0.1"]
+                 [org.cyverse/clojure-commons "3.0.8"]
+                 [org.cyverse/debug-utils "2.9.0"]
+                 [org.cyverse/kameleon "3.0.10"]
+                 [org.cyverse/mescal "3.1.12"]
+                 [org.cyverse/metadata-client "3.1.2"]
+                 [org.cyverse/common-cli "2.8.2"]
+                 [org.cyverse/common-cfg "2.8.3"]
+                 [org.cyverse/common-swagger-api "3.4.5"]
+                 [org.cyverse/cyverse-groups-client "0.1.9"]
+                 [org.cyverse/permissions-client "2.8.4"]
+                 [org.cyverse/service-logging "2.8.4"]
+                 [org.flatland/ordered "1.15.12"]
                  [me.raynes/fs "1.4.6"]
-                 [mvxcvi/clj-pgp "1.1.0"]
+                 [mvxcvi/clj-pgp "1.1.1"]
                  [pandect "1.0.2"]
-                 [ring/ring-jetty-adapter "1.9.6"]]
+                 [ring/ring-jetty-adapter "1.12.2"]]
   :eastwood {:exclude-namespaces [apps.protocols :test-paths]
              :linters [:wrong-arity :wrong-ns-form :wrong-pre-post :wrong-tag :misplaced-docstrings]}
   :plugins [[lein-ancient "0.7.0"]
             [lein-cljfmt "0.9.2"]
-            [lein-swank "1.4.5"]
             [test2junit "1.4.4"]
-            [jonase/eastwood "1.3.0"]]
-  :profiles {:dev {:plugins        [[lein-ring "0.12.5"]]
-                   :resource-paths ["conf/test"]
-                   :jvm-opts       ["-Dotel.javaagent.enabled=false"]}
+            [jonase/eastwood "1.4.3"]]
+  :profiles {:dev {:plugins        [[lein-ring "0.12.6"]]
+                   :resource-paths ["conf/test"]}
              :repl {:source-paths ["repl"]}
              :uberjar {:aot :all}}
   :repl-options {:timeout 120000}
@@ -61,4 +55,4 @@
          :init apps.core/load-config-from-file
          :port 31323}
   :uberjar-exclusions [#"(?i)META-INF/[^/]*[.](SF|DSA|RSA)"]
-  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/apps-logging.xml"  "-javaagent:./opentelemetry-javaagent.jar" "-Dotel.resource.attributes=service.name=apps"])
+  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/apps-logging.xml"])

src/apps/clients/async_tasks.clj

@@ -2,7 +2,6 @@
   (:require [apps.util.config :as config]
             [clojure.string :as string]
             [clojure.tools.logging :as log]
-            [otel.otel :as otel]
             [async-tasks-client.core :as async-tasks-client]))
 
 (defn get-by-id
@@ -35,12 +34,8 @@
 
 (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/" "")))))
+  (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 new-task

src/apps/clients/notifications.clj

@@ -14,7 +14,7 @@
             [apps.persistence.jobs :as jp]
             [apps.persistence.tool-requests :as tp]
             [apps.util.config :as config])
-  (:use [apps.service.util :only [uuid?]]
+  (:use [apps.service.util :only [valid-uuid?]]
         [cemerick.url :only [url]]
         [pandect.algo.sha256 :only [sha256]]))
 
@@ -72,7 +72,7 @@
    same app, so this function arbitrarily takes the first notification type associated with the app for now.
    Also, apps that do not run in the DE will always have a notification type of `analysis`."
   [app-id app-version-id]
-  (or (when (uuid? app-id) (first (amp/get-app-notification-types app-version-id)))
+  (or (when (valid-uuid? app-id) (first (amp/get-app-notification-types app-version-id)))
       "analysis"))
 
 (defn- format-job-status-update

src/apps/clients/notifications/common_sharing.clj

@@ -1,6 +1,6 @@
 (ns apps.clients.notifications.common-sharing
-  (:use [clostache.parser :only [render]])
-  (:require [apps.clients.iplant-groups :as ipg]))
+  (:require [apps.clients.iplant-groups :as ipg]
+            [apps.util.string :refer [render]]))
 
 (def grouping-threshold 10)