Merge pull request #11 from slr71/main

CORE-2006: dependency updates.

.dockerignore

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

.gitignore

@@ -1,6 +1,5 @@
 pom.xml
 *jar
-!opentelemetry-javaagent.jar
 lib
 classes
 *~
@@ -21,3 +20,5 @@ build/
 build.xml
 test2junit
 resources/
+.clj-kondo/
+.lsp/

Dockerfile

@@ -1,16 +1,14 @@
-FROM clojure:openjdk-17-lein
+FROM clojure:temurin-22-lein-jammy
 
 WORKDIR /usr/src/app
 
-#RUN apk add --no-cache --update git nodejs-lts npm && \
-#    rm -rf /var/cache/apk
-RUN apt update && apt install -y nodejs npm
+RUN apt-get update && \
+    apt-get install -y git nodejs npm && \
+    rm -rf /var/lib/apt/lists/*
 
 RUN npm install -g grunt-cli
 
-RUN ln -s "/usr/local/openjdk-17/bin/java" "/bin/kifshare"
-
-ENV OTEL_TRACES_EXPORTER none
+RUN ln -s "/opt/java/openjdk/bin/java" "/bin/kifshare"
 
 COPY project.clj /usr/src/app/
 RUN lein deps
@@ -26,7 +24,7 @@ COPY ui/ui.xml resources/
 RUN lein uberjar
 RUN cp target/kifshare-standalone.jar .
 
-ENTRYPOINT ["kifshare", "-Dlogback.configurationFile=/etc/iplant/de/logging/kifshare-logging.xml", "-javaagent:/usr/src/app/opentelemetry-javaagent.jar", "-Dotel.resource.attributes=service.name=kifshare", "-cp", ".:resources:kifshare-standalone.jar", "kifshare.core"]
+ENTRYPOINT ["kifshare", "-Dlogback.configurationFile=/etc/iplant/de/logging/kifshare-logging.xml", "-cp", ".:resources:kifshare-standalone.jar", "kifshare.core"]
 CMD ["--help"]
 
 ARG git_commit=unknown

project.clj

@@ -7,7 +7,7 @@
       (string/trim (:out (sh "git" "rev-parse" "HEAD")))
       ""))
 
-(defproject org.cyverse/kifshare "2.12.0-SNAPSHOT"
+(defproject org.cyverse/kifshare "3.0.1-SNAPSHOT"
   :description "CyVerse Quickshare for iRODS"
   :url "https://github.com/cyverse-de/kifshare"
 
@@ -17,49 +17,44 @@
   :manifest {"Git-Ref" ~(git-ref)}
   :uberjar-name "kifshare-standalone.jar"
 
-  :dependencies [[org.clojure/clojure "1.11.1"]
+  :dependencies [[org.clojure/clojure "1.11.4"]
                  [org.clojure/tools.logging "1.3.0"]
-                 [ch.qos.logback/logback-classic "1.5.3"]
-                 [net.logstash.logback/logstash-logback-encoder "7.4"]
+                 [ch.qos.logback/logback-classic "1.5.6"]
+                 [net.logstash.logback/logstash-logback-encoder "8.0"]
                  [hawk "0.2.11"]
+                 [hiccup "1.0.2"]
                  [medley "1.4.0"]
-                 [org.cyverse/clj-jargon "3.1.0"
+                 [org.cyverse/clj-jargon "3.1.1"
                    :exclusions [[org.slf4j/slf4j-log4j12]
                                 [log4j]]]
-                 [org.cyverse/debug-utils "2.8.1"]
-                 [org.cyverse/clojure-commons "2.8.0"]
-                 [org.cyverse/common-cli "2.8.1"]
-                 [org.cyverse/event-messages "0.0.1"]
-                 [com.novemberain/langohr "3.5.1"]
+                 [org.cyverse/debug-utils "2.9.0"]
+                 [org.cyverse/clojure-commons "3.0.9"]
+                 [org.cyverse/common-cli "2.8.2"]
                  [me.raynes/fs "1.4.6"]
-                 [cheshire "5.12.0"
+                 [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]]]
                  [slingshot "0.12.2"]
-                 [compojure "1.5.0"]
-                 [de.ubercode.clostache/clostache "1.4.0"]
+                 [compojure "1.7.1"]
                  [com.cemerick/url "0.1.1" :exclusions [com.cemerick/clojurescript.test]]
-                 [ring-logger "1.1.1"]]
+                 [ring/ring-core "1.12.2"]]
 
   :eastwood {:exclude-namespaces [:test-paths]
              :linters [:wrong-arity :wrong-ns-form :wrong-pre-post :wrong-tag :misplaced-docstrings]}
 
   :ring {:init kifshare.config/init
          :handler kifshare.core/app}
 
-  :profiles {:dev     {:resource-paths ["build" "conf" "dev-resources"]
-                       :jvm-opts ["-Dotel.javaagent.enabled=false"]}
+  :profiles {:dev     {:resource-paths ["build" "conf" "dev-resources"]}
              :uberjar {:aot :all}}
 
-  :plugins [[jonase/eastwood "1.4.2"]
+  :plugins [[jonase/eastwood "1.4.3"]
             [lein-ancient "0.7.0"]
-            [lein-ring "0.7.5"]
-            [test2junit "1.2.2"]]
+            [lein-ring "0.12.6"]
+            [test2junit "1.4.4"]]
 
   :main ^:skip-aot kifshare.core
-  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/kifshare-logging.xml"
-             "-javaagent:./opentelemetry-javaagent.jar"
-             "-Dotel.resource.attributes=service.name=kifshare"])
+  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/kifshare-logging.xml"])

src/kifshare/config.clj

@@ -145,42 +145,6 @@
   []
   (or (get @props "kifshare.irods.anon-user") "anonymous"))
 
-(defn amqp-uri
-  []
-  (or (get @props "kifshare.amqp.uri") "amqp://guest:guest@rabbit:5672/"))
-
-(defn exchange-name
-  []
-  (or (get @props "kifshare.amqp.exchange.name") "de"))
-
-(defn exchange-durable?
-  []
-  (if-let [val (get @props "kifshare.amqp.exchange.durable")]
-    (boolean (Boolean/valueOf val))
-    true))
-
-(defn exchange-auto-delete?
-  []
-  (if-let [val (get @props "kifshare.amqp.exchange.auto-delete")]
-    (boolean (Boolean/valueOf val))
-    false))
-
-(defn queue-name
-  []
-  (or (get @props "kifshare.amqp.queue.name") "events.kifshare.queue"))
-
-(defn queue-durable?
-  []
-  (if-let [val (get @props "kifshare.amqp.queue.durable")]
-    (boolean (Boolean/valueOf val))
-    true))
-
-(defn queue-auto-delete?
-  []
-  (if-let [val (get @props "kifshare.amqp.queue.auto-delete")]
-    (boolean (Boolean/valueOf val))
-    false))
-
 (def jgcfg (atom nil))
 
 (defn jargon-config [] @jgcfg)

src/kifshare/core.clj

@@ -5,19 +5,15 @@
          params
          keyword-params
          nested-params
-         multipart-params
-         stacktrace])
+         multipart-params])
   (:require [clojure-commons.file-utils :as ft]
             [clojure.tools.logging :as log]
             [compojure.route :as route]
-            [ring.logger :as logger]
             [ring.util.response :as resp]
             [ring.util.http-response :as http-resp]
             [kifshare.config :as cfg]
             [kifshare.tickets-controllers :as t-c]
             [kifshare.anon-controllers :as a-c]
-            [kifshare.amqp :as amqp]
-            [kifshare.events :as events]
             [kifshare.ui-template :as ui]
             [clojure.string :as string]
             [common-cli.core :as ccli]
@@ -153,8 +149,7 @@
       wrap-multipart-params
       wrap-keyword-params
       wrap-nested-params
-      wrap-params
-      wrap-stacktrace))
+      wrap-params))
 
 (def app
   (site-handler kifshare-routes))
@@ -171,32 +166,25 @@
   (or (:buffer-size opts)
       (* 1024 (Integer/parseInt (get @cfg/props "kifshare.app.download-buffer-size")))))
 
-(defn listen-for-events
-  []
-  (let [exchange-cfg (events/exchange-config)
-        queue-cfg    (events/queue-config)]
-    (amqp/connect exchange-cfg queue-cfg {"events.kifshare.ping" events/ping-handler})))
-
 (defn -main
   [& args]
-
-    (let [{:keys [options]} (ccli/handle-args svc-info args cli-options)]
-      (when-not (fs/exists? (:config options))
-        (ccli/exit 1 (str "The config file does not exist.")))
-      (when-not (fs/readable? (:config options))
-        (ccli/exit 1 "The config file is not readable."))
-      (cfg/local-init (:config options))
-      (cfg/jargon-init)
-      (cfg/log-config)
-      (.start (Thread. listen-for-events))
-      (with-redefs [clojure.java.io/buffer-size override-buffer-size]
-        (let [port (Integer/parseInt (string/trim (get @cfg/props "kifshare.app.port")))]
-          (ui/read-template)
-          (hawk/watch! {:watcher :polling}
-                       [{:paths ["resources/ui.xml"]
-                         :handler (fn [ctx e]
-                                    (when (= (:kind e) :modify)
-                                      (ui/read-template)))}])
-          (log/warn "Configured listen port is: " port)
-          (require 'ring.adapter.jetty)
-          ((eval 'ring.adapter.jetty/run-jetty) (logger/wrap-with-logger app) {:port port})))))
+
+  (let [{:keys [options]} (ccli/handle-args svc-info args cli-options)]
+    (when-not (fs/exists? (:config options))
+      (ccli/exit 1 (str "The config file does not exist.")))
+    (when-not (fs/readable? (:config options))
+      (ccli/exit 1 "The config file is not readable."))
+    (cfg/local-init (:config options))
+    (cfg/jargon-init)
+    (cfg/log-config)
+    (with-redefs [clojure.java.io/buffer-size override-buffer-size]
+      (let [port (Integer/parseInt (string/trim (get @cfg/props "kifshare.app.port")))]
+        (ui/read-template)
+        (hawk/watch! {:watcher :polling}
+                     [{:paths ["resources/ui.xml"]
+                       :handler (fn [ctx e]
+                                  (when (= (:kind e) :modify)
+                                    (ui/read-template)))}])
+        (log/warn "Configured listen port is: " port)
+        (require 'ring.adapter.jetty)
+        ((eval 'ring.adapter.jetty/run-jetty) app {:port port})))))

src/kifshare/ui_template.clj

@@ -1,7 +1,7 @@
 (ns kifshare.ui-template
   (:require [kifshare.config :as cfg]
-            [clostache.parser :as prs]
             [clojure.tools.logging :as log]
+            [clojure-commons.template :refer [render]]
             [cheshire.core :as json])
   (:import [org.apache.commons.io FileUtils]))
 
@@ -23,12 +23,12 @@
 (defn landing-page
   [ticket-id metadata-promise ticket-info]
   (log/debug "entered kifshare.ui-template/landing-page")
-  (prs/render @tmpl
-              (assoc ticket-info
-                     :metadata @metadata-promise
-                     :filesize (FileUtils/byteCountToDisplaySize
-                                (Long/parseLong (:filesize ticket-info)))
-                     :irods-url (cfg/irods-url)
-                     :de-url (cfg/de-url)
-                     :ticket-info-json (json/generate-string
-                                        (ui-ticket-info ticket-info)))))
+  (render @tmpl
+          (assoc ticket-info
+                 :metadata @metadata-promise
+                 :filesize (FileUtils/byteCountToDisplaySize
+                            (Long/parseLong (:filesize ticket-info)))
+                 :irods-url (cfg/irods-url)
+                 :de-url (cfg/de-url)
+                 :ticket-info-json (json/generate-string
+                                    (ui-ticket-info ticket-info)))))

test/kifshare/test/configs.clj

@@ -34,11 +34,4 @@
     (is (= (config/css-files)
            (string/split config/default-css-files #"\s*,\s*")))
     (is (= (config/javascript-files)
-           (string/split config/default-javascript-files #"\s*,\s*")))
-    (is (= (config/amqp-uri) "amqp://guest:guest@rabbit:5672/"))
-    (is (= (config/exchange-name) "de"))
-    (is (config/exchange-durable?))
-    (is (not (config/exchange-auto-delete?)))
-    (is (= (config/queue-name) "events.kifshare.queue"))
-    (is (config/queue-durable?))
-    (is (not (config/queue-auto-delete?)))))
+           (string/split config/default-javascript-files #"\s*,\s*")))))