Remove parameters.

.gitignore

@@ -9,3 +9,4 @@ pom.xml.asc
 /.nrepl-port
 .hgignore
 .hg/
+.lsp

project.clj

@@ -1,4 +1,4 @@
-(defproject tservice-plugins/quartet-rnaseq-report "v0.1.2"
+(defproject tservice-plugins/quartet-rnaseq-report "v0.1.3"
   :description "QC Report for Quartet RNA-Seq."
   :url "https://github.com/tservice-plugins/quartet-rnaseq-report"
   :license {:name "Eclipse Public License"

resources/tservice-plugin.yaml

@@ -3,7 +3,7 @@ info:
   version: v0.1.0
   description: Generate the QC Report for Quartet RNA-Seq data.
   category: Report
-  home: https://github.com/clinico-omics/tservice-plugins
+  home: https://github.com/tservice-plugins/quartet-rnaseq-report
   source: PGx
   short_name: quartet-rnaseq-report
   icons:
@@ -19,6 +19,7 @@ init:
   # Unpack environment file to the directory, repository/envs/quartet-rnaseq-report
   - step: unpack-env
     envname: quartet-rnaseq-report
+    postunpack: chmod a+x {{ENV_DEST_DIR}}/bin/exp2qcdt.sh
   - step: load-namespace
     namespace: tservice.plugins.quartet-rnaseq-report
   - step: register-plugin

src/tservice/plugins/quartet_rnaseq_report.clj

@@ -72,74 +72,9 @@
 (s/def ::metadata
   (s/coll-of ::metadat-item))
 
-(s/def ::lab
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Lab name."
-    :swagger/default     []
-    :reason              "The lab_name must be string."}))
-
-(s/def ::sequencing_platform
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Sequencing Platform."
-    :swagger/default     []
-    :reason              "The sequencing_platform must be string."}))
-
-(s/def ::sequencing_method
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Sequencing Method"
-    :swagger/default     []
-    :reason              "The sequencing_method must be string."}))
-
-(s/def ::library_protocol
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Library protocol."
-    :swagger/default     []
-    :reason              "The library_protocol must be string."}))
-
-(s/def ::library_kit
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Library kit."
-    :swagger/default     []
-    :reason              "The library_kit must be string."}))
-
-(s/def ::read_length
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Read length"
-    :swagger/default     []
-    :reason              "The read_length must be string."}))
-
-(s/def ::date
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Date"
-    :swagger/default     []
-    :reason              "The date must be string."}))
-
-(s/def ::parameters
-  (s/keys :req-un [::lab
-                   ::sequencing_platform
-                   ::sequencing_method
-                   ::library_protocol
-                   ::library_kit
-                   ::read_length
-                   ::date]))
-
 (def quartet-rna-report-params-body
   "A spec for the body parameters."
-  (s/keys :req-un [::name ::description ::filepath ::metadata ::parameters]
+  (s/keys :req-un [::name ::description ::filepath ::metadata]
           :opt-un [::description]))
 
 ;;; ------------------------------------------------ Event Metadata ------------------------------------------------
@@ -148,7 +83,7 @@
    {:name "quartet-rnaseq-report"
     :summary "Generate the QC Report for Quartet RNA-Seq data."
     :params-schema quartet-rna-report-params-body
-    :handler (fn [{:keys [name description filepath metadata parameters] :as payload}]
+    :handler (fn [{:keys [name description filepath metadata] :as payload}]
                (let [workdir (ff/get-workdir)
                      report-file (fs-lib/join-paths workdir "multireport.html")
                      log-path (fs-lib/join-paths workdir "log")
@@ -160,14 +95,17 @@
                                             :payload payload
                                             :plugin-name "quartet-rnaseq-report"
                                             :plugin-type "ReportPlugin"
-                                            :plugin-version "v0.1.1"
+                                            :plugin-version "v0.1.3"
                                             :response response})]
                  (fs-lib/create-directories! workdir)
                  (spit log-path (json/write-str {:status "Running" :msg ""}))
                  (update-process! task-id 0)
                  (publish-event! "quartet_rnaseq_report"
                                  {:data-dir filepath
-                                  :parameters parameters
+                                  :parameters {:name name
+                                               :description description
+                                               :plugin-name "quartet-rnaseq-report"
+                                               :plugin-version "v0.1.3"}
                                   :metadata metadata
                                   :dest-dir workdir
                                   :task-id task-id})
@@ -197,9 +135,14 @@
     (fs-lib/create-directories! files-keep-dir)
     (fs-api/copy-files! files-keep files-keep-dir {:replace-existing true})))
 
+(defn date
+  []
+  (.format (java.text.SimpleDateFormat. "yyyy-MM-dd")
+           (new java.util.Date)))
+
 (defn- quartet-rnaseq-report!
   "Chaining Pipeline: filter-files -> copy-files -> merge_exp_file -> exp2qcdt -> multiqc."
-  [datadir parameters metadata dest-dir task-id]
+  [{:keys [datadir parameters metadata dest-dir task-id]}]
   (log/info "Generate quartet rnaseq report: " datadir parameters metadata dest-dir)
   (let [metadata-file (fs-lib/join-paths dest-dir
                                          "results"
@@ -239,6 +182,13 @@
         (decompression-tar files-qualimap-RNA-tar))
       (update-process! task-id 50)
       (gen-multiqc-config config-path)
+      (spit parameters-file (json/write-str {"Report Name" (:name parameters)
+                                             "Description" (:description parameters)
+                                             "Report Tool" (format "%s-%s"
+                                                                   (:plugin-name parameters)
+                                                                   (:plugin-version parameters))
+                                             "Team" "Quartet Team"
+                                             "Date" (date)}))
       (let [exp2qcdt-result (exp2qcdt/call-exp2qcdt! exp-fpkm-filepath exp-count-filepath metadata-file result-dir)
             multiqc-result (if (= (:status exp2qcdt-result) "Success")
                              (mq/multiqc result-dir dest-dir {:config config-path :template "default" :title "Quartet RNA report"})