Fix some bugs.

resources/corrplot/bin/corrplot.sh

@@ -66,9 +66,6 @@ fi
 if [ -z "$OUTPUT_FILE" ]; then
 	echo "-o argument is not specified."
 	exit 1
-elif [ ! -f "$OUTPUT_FILE" ]; then
-	echo "$OUTPUT_FILE is not a valid file."
-	exit 1
 else
 	OUTPUT_FILE=$(realpath $OUTPUT_FILE)
 fi

resources/templates/args.json.template

@@ -1,10 +1,10 @@
 {
   "datafile": "{{ datafile }}",
-  "corr_vars": {{ corr_vars }},
-  "method": "{{ method | default: "square" }}",
-  "corr_type": "{{ corr_type | default: "full" }}",
-  "hc_method": "{{ hc_method | default: "complete" }}",
+  "corr_vars": {{ corr_vars|json|safe }},
+  "method": "{{ method|default:"square" }}",
+  "corr_type": "{{ corr_type|default:"full" }}",
+  "hc_method": "{{ hc_method|default:"complete" }}",
   "hc_order": {{ hc_order }},
-  "sig_level": {{ sig_level | default: 0.05 }},
-  "title": "{{ title | default: "This is a correlation plot" }}"
+  "sig_level": {{ sig_level|default:0.05 }},
+  "title": "{{ title|default:"This is a correlation plot" }}"
 }

resources/tservice-plugin.yaml

@@ -19,6 +19,7 @@ init:
   - step: unpack-env
     envname: corrplot
     envtype: environment
+    post-unpack-cmd: chmod a+x {{ ENV_DEST_DIR }}/bin/corrplot.sh
   - step: unpack-env
     envname: templates
     envtype: configuration

src/tservice/plugins/corrplot.clj

@@ -20,10 +20,10 @@
 
 (s/def ::corr_vars
   (st/spec
-   {:spec                vector?
-    :type                :vector
+   {:spec                (s/coll-of string?)
+    :type                :array
     :description         "Variables."
-    :swagger/default     []
+    :swagger/default     nil
     :reason              "The corr_vars must be a vector."}))
 
 (s/def ::method
@@ -54,7 +54,7 @@
 (s/def ::hc_order
   (st/spec
    {:spec                #{true false}
-    :type                :boolean
+    :type                :bool
     :description         "Logical value. If TRUE, correlation matrix will be hc.ordered using hclust function."
     :swagger/default     true
     :reason              "The hc_order must be one of true, false."}))
@@ -63,9 +63,9 @@
   (st/spec
    {:spec                #(and (>= % 0) (<= % 1))
     :type                :float
-    :description         "Logical value. If TRUE, correlation matrix will be hc.ordered using hclust function."
+    :description         "Significant level, greater than 0 and less than 1."
     :swagger/default     0.05
-    :reason              "The hc_order must be one of true, false."}))
+    :reason              "The sig_level must be a float."}))
 
 (def corrplot-params-body
   "A spec for the body parameters."
@@ -128,13 +128,16 @@
         args-template (fs-lib/join-paths template-dir "args.json.template")
         output-file (fs-lib/join-paths dest-dir "plotly.json")]
     (corrplot/make-args-json! args-template context args-json)
-    (log/info "Make an argument json file: %s" args-json)
+    (log/info "Make an argument json file: " args-json)
     (update-process! task-id 30)
     (let [result (corrplot/call-corrplot! args-json output-file env-dir)
-          status (:status result)]
+          status (:status result)
+          process (if (= status "Success") 100 -1)]
       (spit log-path (json/write-str result))
-      (log/info "The task is finished, result file is %s" output-file)
-      (update-process! task-id (if (= status "Success") 100 -1)))))
+      (update-process! task-id process)
+      (if (= status "Success")
+        (log/info "The task is finished, result file is " output-file)
+        (log/error "The task is failed, error msg is located in " log-path)))))
 
 ;;; --------------------------------------------------- Lifecycle ----------------------------------------------------
 (def events-init

src/tservice/plugins/corrplot/common.clj

@@ -18,7 +18,7 @@
   (log/info (format "Render Template (%s) with Environment Context: %s" template-file context))
   (let [template (slurp template-file)
         args-json (parser/render template context)]
-    (spit output-file (json/write-str args-json))))
+    (spit output-file args-json)))
 
 (defn call-corrplot!
   [input-file output-file plugin-env-dir]