Cleanup and upgrade clojure dependencies

deps.edn

@@ -6,32 +6,29 @@
              "clojars" {:url "https://repo.clojars.org/"}}
  :deps
  {org.clojure/clojure {:mvn/version "1.10.1"}
-  org.clojure/data.csv {:mvn/version "1.0.0"}
+  org.clojure/data.csv {:mvn/version "1.0.1"}
   org.clojure/tools.cli {:mvn/version "1.0.194"}
-  org.clojure/tools.logging {:mvn/version "1.1.0"}
-  clojure.java-time/clojure.java-time {:mvn/version "0.3.2"}
+  org.clojure/tools.logging {:mvn/version "1.2.4"}
+  clojure.java-time/clojure.java-time {:mvn/version "1.4.2"}
   aero/aero {:mvn/version "1.1.6"}
   bk/ring-gzip {:mvn/version "0.3.0"}
-  buddy/buddy-auth {:mvn/version "2.2.0"}
+  buddy/buddy-auth {:mvn/version "3.0.323"}
   buddy/buddy-hashers {:mvn/version "2.0.167"}
-  com.taoensso/nippy {:mvn/version "2.14.0"}
-  cheshire/cheshire {:mvn/version "5.10.0"}
   danlentz/clj-uuid {:mvn/version "0.1.9"}
   environ/environ {:mvn/version "1.2.0"}
-  expound/expound {:mvn/version "0.8.5"}
-  com.google.api-client/google-api-client {:mvn/version "1.35.2"}
+  expound/expound {:mvn/version "0.9.0"}
+  com.google.api-client/google-api-client {:mvn/version "2.2.0"}
   metosin/compojure-api {:mvn/version "2.0.0-alpha30"
                          :exclusions [frankiesardo/linked]}
-  metosin/muuntaja {:mvn/version "0.6.7"}
+  metosin/muuntaja {:mvn/version "0.6.8"}
   ikitommi/linked {:mvn/version "1.3.1-alpha1"}
-  mount/mount {:mvn/version "0.1.16"}
+  mount/mount {:mvn/version "0.1.17"}
   phrase/phrase {:mvn/version "0.3-alpha4"}
-  ring/ring-codec {:mvn/version "1.1.2"}
-  ring/ring-defaults {:mvn/version "0.3.2"}
-  ring/ring-jetty-adapter {:mvn/version "1.8.1"}
+  ring/ring-codec {:mvn/version "1.2.0"}
+  ring/ring-defaults {:mvn/version "0.4.0"}
+  ring/ring-jetty-adapter {:mvn/version "1.10.0"}
   semantic-csv/semantic-csv {:mvn/version "0.2.1-alpha1"}
   user-agent/user-agent {:mvn/version "0.1.1"}
-  com.taoensso/encore {:mvn/version "2.120.0"}
   magnetcoop/stork {:mvn/version "0.1.6"}}
  :aliases
  {:1.9 {:override-deps {org.clojure/clojure {:mvn/version "1.9.0"}}}

src/wormbase/names/batch/generic.clj

@@ -4,7 +4,7 @@
    [compojure.api.sweet :as sweet]
    [clj-uuid :as uuid]
    [datomic.api :as d]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [ring.util.http-response :refer [bad-request created not-found! not-modified ok]]
    [spec-tools.spec :as sts]
    [wormbase.db :as wdb]

src/wormbase/names/importers/processing.clj

@@ -7,7 +7,7 @@
    [clojure.string :as str]
    [datomic.api :as d]
    [environ.core :as environ]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [semantic-csv.core :as sc]
    [wormbase.names.auth :as wna]
    [wormbase.specs.entity :as wse]

src/wormbase/names/provenance.clj

@@ -3,7 +3,7 @@
             [clojure.spec.alpha :as s]
             [clojure.string :as str]
             [datomic.api :as d]
-            [java-time :as jt]
+            [java-time.api :as jt]
             [wormbase.db :as wdb]
             [wormbase.names.agent :as wna]
             [wormbase.names.util :as wnu]

src/wormbase/names/recent.clj

@@ -2,7 +2,7 @@
   (:require
    [compojure.api.sweet :as sweet]
    [datomic.api :as d]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [ring.util.http-response :refer [ok]]
    [wormbase.names.provenance :as wnp]
    [wormbase.names.util :as wnu]

src/wormbase/specs/provenance.clj

@@ -2,7 +2,7 @@
   (:require
    [clojure.spec.alpha :as s]
    [clojure.string :as str]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [spec-tools.core :as stc]
    [spec-tools.spec :as sts]
    [wormbase.specs.person] ;; side effecting: to bring in specs

src/wormbase/specs/recent.clj

@@ -2,7 +2,7 @@
   (:require
    [clojure.spec.alpha :as s]
    [clojure.string :as str]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [spec-tools.spec :as sts]
    [spec-tools.core :as stc]
    [wormbase.util :as wu]

src/wormbase/util.clj

@@ -5,7 +5,7 @@
    [clojure.string :as str]
    [clojure.walk :as w]
    [aero.core :as aero]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [wormbase.ids.core :as wic])
   (:import
    (java.io File PushbackReader)

test-system/deps.edn

@@ -2,7 +2,7 @@
  :deps {org.clojure/clojure {:mvn/version "1.10.1"}
         org.clojure/tools.cli {:mvn/version "1.0.194"}
         amazonica/amazonica {:mvn/version "0.3.152"}
-        clojure.java-time/clojure.java-time {:mvn/version "0.3.2"}}
+        clojure.java-time/clojure.java-time {:mvn/version "1.4.2"}}
  :aliases
  {:test {:extra-paths ["test"]
          :extra-deps {org.clojure/test.check {:mvn/version "1.0.0"}}}

test-system/src/wormbase/names/test_system.clj

@@ -6,7 +6,7 @@
    [amazonica.aws.dynamodbv2 :as ddb]
    [amazonica.aws.elasticbeanstalk :as eb]
    [amazonica.aws.securitytoken :as st]
-   [java-time :as jt]))
+   [java-time.api :as jt]))
 
 (def operator-iam-spec
   {:role-arn "arn:aws:iam::357210185381:role/wb-names-test-system-operator"

test/integration/merge_genes_test.clj

@@ -2,7 +2,7 @@
   (:require
    [clojure.test :as t]
    [datomic.api :as d]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [ring.util.http-predicates :as ru-hp]
    [wormbase.constdata :refer [elegans-ln]]
    [wormbase.db :as wdb]

test/wormbase/db_testing.clj

@@ -3,7 +3,7 @@
    [clojure.core.cache :as cache]
    [datomock.core :as dm]
    [datomic.api :as d]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [mount.core :as mount]
    [wormbase.db :as wdb]
    [wormbase.db.schema :as schema]))

test/wormbase/test_utils.clj

@@ -6,7 +6,7 @@
    [clojure.tools.logging :as log]
    [compojure.api.routes :as routes]
    [datomic.api :as d]
-   [java-time :as jt]
+   [java-time.api :as jt]
    [muuntaja.core :as muuntaja]
    [peridot.core :as p]
    [wormbase.constdata :refer [elegans-ln]]