Merge pull request #27 from slr71/main

CORE-2006: dependency updates.
cyverse-de · Aug 6, 2024 · cfb5786 · cfb5786
2 parents 2844b25 + 54b5ce8
commit cfb5786
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diff --git a/.dockerignore b/.dockerignore
@@ -4,7 +4,6 @@
 pom.xml
 pom.xml.asc
 *.jar
-!opentelemetry-javaagent.jar
 *.class
 /.lein-*
 /.nrepl-port

diff --git a/.gitignore b/.gitignore
@@ -4,7 +4,6 @@
 pom.xml
 pom.xml.asc
 *.jar
-!opentelemetry-javaagent.jar
 *.class
 .eastwood
 /.lein-*
@@ -15,3 +14,5 @@ build.xml
 test2junit
 /.idea
 *.iml
+.clj-kondo
+.lsp
diff --git a/Dockerfile b/Dockerfile
@@ -1,12 +1,12 @@
-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/iplant-groups"
-
-ENV OTEL_TRACES_EXPORTER none
+RUN ln -s "/opt/java/openjdk/bin/java" "/bin/iplant-groups"
 
 COPY project.clj /usr/src/app/
 RUN lein deps
@@ -17,7 +17,7 @@ COPY . /usr/src/app
 RUN lein do clean, uberjar && \
     cp target/iplant-groups-standalone.jar .
 
-ENTRYPOINT ["iplant-groups", "-Dlogback.configurationFile=/etc/iplant/de/logging/iplant-groups-logging.xml", "-javaagent:/usr/src/app/opentelemetry-javaagent.jar", "-Dotel.resource.attributes=service.name=iplant-groups", "-cp", ".:iplant-groups-standalone.jar:/", "iplant_groups.core"]
+ENTRYPOINT ["iplant-groups", "-Dlogback.configurationFile=/etc/iplant/de/logging/iplant-groups-logging.xml", "-cp", ".:iplant-groups-standalone.jar:/", "iplant_groups.core"]
 CMD ["--help"]
 
 ARG git_commit=unknown

diff --git a/opentelemetry-javaagent.jar b/opentelemetry-javaagent.jar
diff --git a/project.clj b/project.clj
@@ -7,44 +7,40 @@
       (string/trim (:out (sh "git" "rev-parse" "HEAD")))
       ""))
 
-(defproject org.cyverse/iplant-groups "2.8.1-SNAPSHOT"
+(defproject org.cyverse/iplant-groups "3.0.1-SNAPSHOT"
   :description "A REST front-end for Grouper."
   :url "https://github.com/cyverse-de/iplant-groups"
   :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 "iplant-groups-standalone.jar"
-  :dependencies [[org.clojure/clojure "1.11.1"]
-                 [cheshire "5.12.0"]
-                 [clj-http "3.12.3"]
+  :dependencies [[org.clojure/clojure "1.11.3"]
+                 [cheshire "5.13.0"]
+                 [clj-http "3.13.0"]
                  [clj-time "0.15.2"]
                  [com.cemerick/url "0.1.1" :exclusions [com.cemerick/clojurescript.test]]
                  [medley "1.4.0"]
-                 [metosin/compojure-api "1.1.13"]
+                 [metosin/compojure-api "1.1.14"]
                  [me.raynes/fs "1.4.6"]
-                 [org.cyverse/clojure-commons "3.0.7"]
-                 [org.cyverse/common-cfg "2.8.2"]
-                 [org.cyverse/common-cli "2.8.1"]
-                 [org.cyverse/common-swagger-api "3.4.4"]
+                 [org.cyverse/clojure-commons "3.0.9"]
+                 [org.cyverse/common-cfg "2.8.3"]
+                 [org.cyverse/common-cli "2.8.2"]
+                 [org.cyverse/common-swagger-api "3.4.5"]
                  [org.cyverse/event-messages "0.0.1"]
-                 [org.cyverse/service-logging "2.8.3"]
-                 [com.novemberain/langohr "3.5.1"]
-                 [ring/ring-core "1.11.0"]
-                 [ring/ring-jetty-adapter "1.11.0"]]
-  :eastwood {:exclude-namespaces [:test-paths]
-             :linters [:wrong-arity :wrong-ns-form :wrong-pre-post :wrong-tag :misplaced-docstrings]}
-  :plugins [[jonase/eastwood "1.4.2"]
+                 [org.cyverse/service-logging "2.8.4"]
+                 [com.novemberain/langohr "5.4.0"]
+                 [ring/ring-core "1.12.2"]
+                 [ring/ring-jetty-adapter "1.12.2"]]
+  :eastwood {:exclude-linters [:unlimited-use]}
+  :plugins [[jonase/eastwood "1.4.3"]
             [lein-ancient "0.7.0"]
             [lein-ring "0.12.6"]
-            [test2junit "1.1.3"]]
-  :profiles {:dev {:resource-paths ["conf/test"]
-                   :jvm-opts ["-Dotel.javaagent.enabled=false"]}
+            [test2junit "1.4.4"]]
+  :profiles {:dev {:resource-paths ["conf/test"]}
              :uberjar {:aot :all}}
   :main ^:skip-aot iplant-groups.core
   :ring {:handler iplant-groups.routes/app
          :init    iplant-groups.core/init-service
          :port    31310}
   :uberjar-exclusions [#"(?i)META-INF/[^/]*[.](SF|DSA|RSA)"]
-  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/iplant-groups-logging.xml"
-             "-javaagent:./opentelemetry-javaagent.jar"
-             "-Dotel.resource.attributes=service.name=iplant-groups"])
+  :jvm-opts ["-Dlogback.configurationFile=/etc/iplant/de/logging/iplant-groups-logging.xml"])
diff --git a/src/iplant_groups/amqp.clj b/src/iplant_groups/amqp.clj
@@ -3,39 +3,11 @@
             [iplant-groups.util.config :as config]
             [langohr.core :as rmq]
             [langohr.channel :as lch]
-            [langohr.queue :as lq]
-            [langohr.consumers :as lc]
-            [langohr.exchange :as le]
             [langohr.basic :as lb]
             [service-logging.thread-context :as tc]
             [slingshot.slingshot :refer [try+]]
             [cheshire.core :as cheshire]))
 
-(defn- declare-queue
-  [channel {exchange-name :name} queue-cfg topics]
-  (lq/declare channel (:name queue-cfg) (assoc queue-cfg :exclusive false))
-  (doseq [key topics]
-    (lq/bind channel (:name queue-cfg) exchange-name {:routing-key key})))
-
-(defn- declare-exchange
-  [channel {exchange-name :name :as exchange-cfg}]
-  (le/topic channel exchange-name exchange-cfg))
-
-(defn- message-router
-  [handlers channel {:keys [delivery-tag routing-key] :as metadata} msg]
-  (let [handler (get handlers routing-key)]
-    (if-not (nil? handler)
-      (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/iplant_groups/clients/grouper.clj b/src/iplant_groups/clients/grouper.clj
@@ -99,7 +99,7 @@
   ([]
      (act-as-subject-lookup default-act-as-subject-id)))
 
-(defn- parse-boolean
+(defn- coerce-boolean
   [bool-str]
   (when bool-str (Boolean/parseBoolean bool-str)))
 
@@ -867,7 +867,7 @@
                       :roleLookups (format-role-lookup params)
                       :actions (format-action-names-lookup params)
                       :wsSubjectLookups (subject-lookups [subject_id])
-                      :immediateOnly (parse-boolean immediate_only)})})
+                      :immediateOnly (coerce-boolean immediate_only)})})
 
 (defn permission-assignment-search*
   [request-body]

diff --git a/src/iplant_groups/core.clj b/src/iplant_groups/core.clj
@@ -2,8 +2,6 @@
   (:gen-class)
   (:require [iplant-groups.routes :as routes]
             [iplant-groups.util.config :as config]
-            [iplant-groups.events :as events]
-            [iplant-groups.amqp :as amqp]
             [me.raynes.fs :as fs]
             [clj-http.client :as http]
             [clojure.tools.logging :as log]
@@ -25,12 +23,6 @@
    ["-v" "--version" "Print out the version number."]
    ["-h" "--help"]])
 
-(defn listen-for-events
-  []
-  (let [exchange-cfg (events/exchange-config)
-        queue-cfg    (events/queue-config)]
-    (amqp/connect exchange-cfg queue-cfg {"events.iplant-groups.ping" events/ping-handler})))
-
 (defn run-jetty
   []
   (require 'ring.adapter.jetty)
@@ -42,6 +34,5 @@
   (tc/with-logging-context config/svc-info
     (let [{:keys [options arguments errors summary]} (ccli/handle-args config/svc-info args cli-options)]
       (init-service (:config options))
-      (.start (Thread. listen-for-events))
       (http/with-connection-pool {:timeout 5 :threads 10 :insecure? false :default-per-route 10}
         (run-jetty)))))
diff --git a/src/iplant_groups/events.clj b/src/iplant_groups/events.clj
diff --git a/src/iplant_groups/routes.clj b/src/iplant_groups/routes.clj
@@ -17,40 +17,39 @@
 (defapi app
   {:exceptions cx/exception-handlers}
   (swagger-routes
-    {:ui      config/docs-uri
-     :options {:ui {:validatorUrl nil}}
-     :data    {:info {:title       "RESTful Service Facade for Grouper"
-                      :description "Documentation for the iplant-groups API"
-                      :version     "2.8.0"}
-               :tags [{:name "folders", :description "Folder Information"}
-                      {:name "groups", :description "Group Information"}
-                      {:name "service-info", :description "Service Status Information"}
-                      {:name "subjects", :description "Subject Information"}
-                      {:name "attributes", :description "Attribute/Permission Information"}]}})
-  (middleware
-   [clean-context
-    wrap-keyword-params
-    wrap-query-params
-    [wrap-routes wrap-logging]]
-   (context "/" []
+   {:ui      config/docs-uri
+    :options {:ui {:validatorUrl nil}}
+    :data    {:info {:title       "RESTful Service Facade for Grouper"
+                     :description "Documentation for the iplant-groups API"
+                     :version     "2.8.0"}
+              :tags [{:name "folders", :description "Folder Information"}
+                     {:name "groups", :description "Group Information"}
+                     {:name "service-info", :description "Service Status Information"}
+                     {:name "subjects", :description "Subject Information"}
+                     {:name "attributes", :description "Attribute/Permission Information"}]}})
+  (context "/" []
     :tags ["service-info"]
-    status-routes/status))
-  (middleware
-   [clean-context
-    wrap-keyword-params
-    wrap-query-params
-    add-user-to-context
-    wrap-logging]
-   (context "/folders" []
-    :tags ["folders"]
-    folder-routes/folders)
-   (context "/groups" []
-    :tags ["groups"]
-    group-routes/groups)
-   (context "/subjects" []
-    :tags ["subjects"]
-    subject-routes/subjects)
-   (context "/attributes" []
-    :tags ["attributes"]
-    attribute-routes/attributes)
-   (undocumented (route/not-found (json/encode {:success false :msg "unrecognized service path"})))))
+    :middleware [clean-context
+                 wrap-keyword-params
+                 wrap-query-params
+                 [wrap-routes wrap-logging]]
+    status-routes/status)
+  (context "/" []
+    :middleware [clean-context
+                 wrap-keyword-params
+                 wrap-query-params
+                 add-user-to-context
+                 wrap-logging]
+    (context "/folders" []
+      :tags ["folders"]
+      folder-routes/folders)
+    (context "/groups" []
+      :tags ["groups"]
+      group-routes/groups)
+    (context "/subjects" []
+      :tags ["subjects"]
+      subject-routes/subjects)
+    (context "/attributes" []
+      :tags ["attributes"]
+      attribute-routes/attributes)
+    (undocumented (route/not-found (json/encode {:success false :msg "unrecognized service path"})))))