Updated Zuko/Asami, and needed to include Cheshire directly as a result

cli/project.clj

@@ -1,17 +1,17 @@
-(defproject org.clojars.quoll/naga-cli "0.3.14"
+(defproject org.clojars.quoll/naga-cli "0.3.15-SNAPSHOT"
   :description "Forward Chaining Rule Engine CLI"
   :url "http://github.com/threatgrid/naga"
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
-  :dependencies [[org.clojars.quoll/naga "0.3.14"]
-                 [org.clojure/clojure "1.10.2"]
+  :dependencies [[org.clojars.quoll/naga "0.3.15-SNAPSHOT"]
+                 [org.clojure/clojure "1.10.3"]
                  [prismatic/schema "1.1.12"]
                  [org.clojure/tools.cli "0.3.5"]
                  [org.clojure/core.cache "1.0.207"]
                  [org.clojars.quoll/parsatron "0.0.10"]
                  [cheshire "5.10.0"]
                  [org.clojars.quoll/naga-store "0.5.2"]
-                 [org.clojars.quoll/asami "1.2.15"]
+                 [org.clojars.quoll/asami "2.0.0-alpha6"]
                  ; [com.datomic/datomic-pro "0.9.5697" :exclusions [com.google.guava/guava] ; uncomment for Datomic Pro
                  [com.datomic/datomic-free "0.9.5697"]
                  [org.postgresql/postgresql "9.3-1102-jdbc41"]]

cli/src/naga/cli.clj

@@ -13,7 +13,8 @@
             [zuko.entity.writer :as data-writer]
             [asami.core]
             [naga.storage.datomic.core]
-            [naga.storage.asami.core])
+            [naga.storage.asami.core]
+            [cheshire.core :as j])
   (:import [clojure.lang ExceptionInfo]
            [java.net URI]
            [java.io File]))
@@ -138,7 +139,10 @@
         {:keys [rules axioms]} (pabu/read-stream in-stream)
 
         basic-store (store/assert-data fresh-store axioms)
-        json-data (data-writer/stream->triples (:graph basic-store) json-file)
+        json-data (with-open [r (io/reader json-file)]
+                    (data-writer/entities->triples
+                      (:graph basic-store)
+                      (j/parse-stream r true)))
         loaded-store (store/assert-data basic-store json-data)
 
         config (assoc store-config :store loaded-store)
@@ -147,7 +151,7 @@
 
         ;; run the program
         [store stats] (e/run config program)
-        output (data-reader/graph->str (:graph store))]
+        output (j/generate-string (data-reader/graph->entities (:graph store) false))]
     (spit out-file output)))
 
 (defn -main [& args]

cli/test/tmp/out.json

@@ -1 +1 @@
-[{"id":"fred","sibling":"barney","parent":"mary","uncle":"george"},{"id":"barney","parent":"mary","uncle":"george","sibling":"fred"},{"id":"george","type":"male","sibling":"mary"},{"id":"mary","sibling":"george","brother":"george"}]
+[{"id":"fred","sibling":"barney","parent":"mary","uncle":"george"},{"id":"barney","parent":"mary","uncle":"george","sibling":"fred"},{"id":"mary","sibling":"george","brother":"george"},{"id":"george","type":"male","sibling":"mary"}]

project.clj

@@ -3,17 +3,19 @@
   :url "http://github.com/threatgrid/naga"
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
-  :dependencies [[org.clojure/clojure "1.10.2"]
+  :dependencies [[org.clojure/clojure "1.10.3"]
                  [prismatic/schema "1.1.12"]
                  [org.clojure/core.cache "1.0.207"]
                  [org.clojars.quoll/parsatron "0.0.10"]
                  [org.clojars.quoll/naga-store "0.5.2"]
-                 [org.clojars.quoll/asami "1.2.15"]]
+                 [org.clojars.quoll/asami "2.0.0-alpha6"]
+                 [cheshire "5.10.0"]]
   :plugins [[lein-cljsbuild "1.1.8"]]
   :deploy-repositories {"releases" {:url "https://repo.clojars.org" :creds :gpg}}
   :profiles {
     :dev {
       :dependencies [[org.clojure/clojurescript "1.10.773"]
+                     [tailrecursion/cljs-priority-map "1.2.1"]
                      [org.clojars.quoll/qtest "0.1.1"]
                      ; [com.datomic/datomic-pro "0.9.5697" :exclusions [com.google.guava/guava] ; uncomment for Datomic Pro
                      [com.datomic/datomic-free "0.9.5697" :exclusions [com.google.guava/guava]]