It's a new version and not compatible with previous version.

.gitignore

 /.nrepl-port
 .hgignore
 .hg/
+.clj-kondo

project.clj

-(defproject tservice-plugins/quartet-metqc-report "v0.1.3"
+(defproject quartet-metqc-report "0.1.3"
   :description "Visualizes Quality Control(QC) results for Quartet Project."
-  :url "https://github.com/tservice-plugins/quartet-metqc-report"
+  :url "https://github.com/chinese-quartet/quartet-metqc-report"
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
   :min-lein-version "2.5.0"
 
   :dependencies
   [[org.clojure/data.csv "1.0.0"]
-   [me.raynes/fs "1.4.6"]
+   [com.github.yjcyxky/local-fs "0.1.5"]
    [org.clojure/tools.logging "1.1.0"]
-   [org.clojure/core.async "0.4.500"
-    :exclusions [org.clojure/tools.reader]]]
+   [metosin/spec-tools "0.10.5"]]
+
+  :test-paths ["test"]
+  :plugins [[lein-cloverage "1.0.13"]
+            [lein-shell "0.5.0"]
+            [lein-changelog "0.3.2"]]
+
+  :aliases {"update-version" ["shell" "sed" "-i" "" "s/version \"[0-9.]*\"/version \"${:version}\"/" "src/quartet_metqc_report/version.clj"]}
+  :deploy-repositories [["releases" :clojars]]
+  :release-tasks [["change" "version" "leiningen.release/bump-version"]
+                  ["change" "version" "leiningen.release/bump-version" "release"]
+                  ["changelog" "release"]
+                  ["update-version"]
+                  ["deploy"]]
 
   :profiles
   {:provided
    {:dependencies
     [[org.clojure/clojure "1.10.1"]
-     [org.clojars.yjcyxky/tservice "0.6.0"]]}
+     [com.github.yjcyxky/tservice-core "0.2.0"]]}
 
    :uberjar
    {:auto-clean    true
     :omit-source   true
     :javac-options ["-target" "1.8", "-source" "1.8"]
     :target-path   "target/%s"
-    :resource-paths ["resources"]
-    :uberjar-name  "quartet-metqc-report.tservice-plugin.jar"}})
+    :resource-paths ["resources"]}})

resources/tservice-plugin.yaml

   version: v0.1.3
   description: Generate the QC Report for Quartet Metabolomics data.
   category: Report
-  home: https://github.com/tservice-plugins/quartet-metqc-report
-  source: PGx
+  home: https://github.com/chinese-quartet/quartet-metqc-report
+  source: Chinese Quartet
   short_name: quartet-metqc-report
   icons:
     - src: ""
       type: image/png
       sizes: 192x192
-  author: PGx
+  author: Jingcheng Yang
+  maintainers:
+    - Jingcheng Yang
+  tags:
+    - R
+    - Chart
+  readme: https://github.com/chinese-quartet/quartet-metqc-report/blob/master/README.md
 plugin:
   name: quartet-metqc-report
   display-name: QC Report for Quartet Metabolomics
 init:
   # Unpack environment file to the directory, repository/envs/quartet-metqc-report
   - step: unpack-env
-    envname: quartet-metqc-report
-    postunpack: chmod a+x {{ENV_DEST_DIR}}/bin/metqc.sh
+    envtype: environment
+    envname: bin
+    postunpack: chmod a+x {{ENV_DIR}}/bin/metqc.sh
+  - step: unpack-env
+    envtype: environment
+    envname: renv
+  - step: unpack-env
+    envtype: environment
+    envname: requirements.txt
+  - step: unpack-env
+    envtype: environment
+    envname: renv.lock
   - step: load-namespace
-    namespace: tservice.plugins.quartet-metqc-report
+    namespace: quartet-metqc-report.core
   - step: register-plugin
-    entrypoint: tservice.plugins.quartet-metqc-report/metadata
+    entrypoint: quartet-metqc-report.core/metadata
   - step: init-event
-    entrypoint: tservice.plugins.quartet-metqc-report/events-init
+    entrypoint: quartet-metqc-report.core/events-init

src/quartet_metqc_report/core.clj

+(ns quartet-metqc-report.core
+  (:require [tservice-core.tasks.http :as http-task]
+            [quartet-metqc-report.spec :as spec]
+            [quartet-metqc-report.task :as task]))
+
+(def metadata
+  (http-task/make-routes "quartet-metqc-report" :ReportPlugin
+                         {:method-type :post
+                          :endpoint "quartet-metqc-report"
+                          :summary "Generate the QC Report for Quartet Metabolomics data."
+                          :body-schema spec/quartet-metqc-report-params-body
+                          :response-schema any?
+                          :handler task/post-handler}))
+
+(def events-init task/events-init)

src/quartet_metqc_report/metqc.clj

+(ns quartet-metqc-report.metqc
+  "A wrapper for metqc tool."
+  (:require [clojure.string :as clj-str]
+            [local-fs.core :as fs-lib]
+            [clojure.java.shell :as shell :refer [sh]]
+            [tservice-core.plugins.util :refer [call-command!]]
+            [tservice-core.plugins.env :refer [get-context-path add-env-to-path]]
+            [clojure.tools.logging :as log]
+            [quartet-metqc-report.version :as v]))
+
+(defn call-metqc!
+  "Call metqc bash script. more details on https://github.com/chinese-quartet/MetQC
+   exp-file: Proteomics profiled data. 
+   meta-file: proteomics metadata.
+   result-dir: A directory for result files."
+  [exp-file meta-file result-dir]
+  (let [command ["bash" "-c"
+                 (format "metqc.sh -d %s -m %s -o %s" exp-file meta-file result-dir)]
+        path-var (add-env-to-path v/plugin-name)
+        rprofile (fs-lib/join-paths (get-context-path :env v/plugin-name) "Rprofile")]
+    (log/info "PATH variable: " path-var)
+    (log/info "Rprofile file is in " rprofile)
+    (shell/with-sh-env {:PATH   path-var
+                        :R_PROFILE_USER rprofile
+                        :LC_ALL "en_US.utf-8"
+                        :LANG   "en_US.utf-8"}
+      (let [result (apply sh command)]
+        {:status (if (= (:exit result) 0) "Success" "Error")
+         :msg (str (:out result) "\n" (:err result))}))))
+
+(defn multiqc
+  "A multiqc wrapper for generating multiqc report:
+   TODO: set the absolute path of multiqc binary instead of environment variable
+
+  Required:
+  analysis-dir: Analysis directory, e.g. data directory from project
+  outdir: Create report in the specified output directory.
+
+  Options:
+  | key                | description |
+  | -------------------|-------------|
+  | :dry-run?          | Dry run mode |
+  | :filename          | Report filename. Use 'stdout' to print to standard out. |
+  | :comment           | Custom comment, will be printed at the top of the report. |
+  | :title             | Report title. Printed as page header, used for filename if not otherwise specified. |
+  | :force?            | Overwrite any existing reports |
+  | :prepend-dirs?     | Prepend directory to sample names |
+  | :template          | default, other custom template    |
+  | :config            | Where is the config file          |
+  | :env               | An environemnt map for running multiqc, such as {:PATH (get-path-variable)} |
+
+  Example:
+  (multiqc 'XXX' 'YYY' {:filename       'ZZZ'
+                        :comment        ''
+                        :title          ''
+                        :force?         true
+                        :prepend-dirs?  true})"
+  [analysis-dir outdir {:keys [dry-run? filename comment title force? prepend-dirs? template config env]
+                        :or   {dry-run?      false
+                               force?        true
+                               prepend-dirs? false
+                               filename      "multiqc_report.html"
+                               comment       ""
+                               template      "default"
+                               title         "iSEQ Analyzer Report"}}]
+  (let [force-arg   (if force? "--force" "")
+        dirs-arg    (if prepend-dirs? "--dirs" "")
+        config-arg  (if config (str "-c " config) "")
+        multiqc-command (filter #(> (count %) 0) ["multiqc"
+                                                  force-arg dirs-arg config-arg
+                                                  "--title" (format "'%s'" title)
+                                                  "--comment" (format "'%s'" comment)
+                                                  "--filename" filename
+                                                  "--outdir" outdir
+                                                  "-t" template
+                                                  analysis-dir])
+        command (clj-str/join " " multiqc-command)]
+    (if dry-run?
+      (log/info command)
+      (if env
+        (call-command! command env)
+        (call-command! command)))))
+
+(defn is-localpath?
+  [filepath]
+  (re-matches #"^file:\/\/.*" filepath))
+
+(defn correct-filepath
+  [filepath]
+  (if (is-localpath? filepath)
+    (clj-str/replace filepath #"^file:\/\/" "")
+    filepath))

src/quartet_metqc_report/spec.clj

+(ns quartet-metqc-report.spec
+  (:require [clojure.spec.alpha :as s]
+            [spec-tools.core :as st]))
+
+;;; ------------------------------------------------ Event Specs ------------------------------------------------
+(s/def ::metadata_file
+  (st/spec
+   {:spec                (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
+    :type                :string
+    :description         "File path for metadata file, such as file:///xxx/xxx/metadata.csv"
+    :swagger/default     nil
+    :reason              "The filepath must be string."}))
+
+(s/def ::data_file
+  (st/spec
+   {:spec                (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
+    :type                :string
+    :description         "File path for metabolomics profiled data, such as file:///xxx/xxx/data.csv"
+    :swagger/default     nil
+    :reason              "The filepath must be string."}))
+
+(s/def ::name
+  (st/spec
+   {:spec                string?
+    :type                :string
+    :description         "The name of the report"
+    :swagger/default     ""
+    :reason              "Not a valid name"}))
+
+(s/def ::description
+  (st/spec
+   {:spec                string?
+    :type                :string
+    :description         "Description of the report"
+    :swagger/default     ""
+    :reason              "Not a valid description."}))
+
+(def quartet-metqc-report-params-body
+  "A spec for the body parameters."
+  (s/keys :req-un [::name ::data_file ::metadata_file]
+          :opt-un [::description]))

src/quartet_metqc_report/task.clj

+(ns quartet-metqc-report.task
+  (:require [quartet-metqc-report.metqc :as metqc]
+            [local-fs.core :as fs-lib]
+            [tservice-core.plugins.env :refer [add-env-to-path create-task! update-task!]]
+            [tservice-core.plugins.util :as util]
+            [clojure.data.json :as json]
+            [clojure.tools.logging :as log]
+            [tservice-core.tasks.async :refer [publish-event! make-events-init]]))
+
+(defn date
+  []
+  (.format (java.text.SimpleDateFormat. "yyyy-MM-dd")
+           (new java.util.Date)))
+
+(defn update-process!
+  [^String task-id ^Integer percentage]
+  (let [record (cond
+                 (= percentage 100) {:status "Finished"
+                                     :percentage 100
+                                     :finished_time (util/time->int (util/now))}
+                 (= percentage -1) {:status "Failed"
+                                    :finished_time (util/time->int (util/now))}
+                 :else {:percentage percentage})
+        record (merge {:id task-id} record)]
+    (update-task! record)))
+
+(defn update-log-process!
+  "Update message into log file and process into database."
+  [log-path coll task-id process]
+  (spit log-path (json/write-str coll))
+  (update-process! task-id process))
+
+(defn post-handler
+  [{{:keys [name data_file metadata_file description owner plugin-context]
+     :or {description (format "Quality control report for %s" name)}
+     :as payload} :body}]
+  (log/info (format "Create a report %s with %s" name payload))
+  (let [payload (merge {:description description} payload)
+        data-file (metqc/correct-filepath data_file)
+        metadata-file (metqc/correct-filepath metadata_file)
+        workdir (fs-lib/dirname data-file)
+        log-path (fs-lib/join-paths workdir "log")
+        response {:report (format "%s/multiqc_report.html" workdir)
+                  :log log-path}
+        task-id (create-task! {:name           name
+                               :description    description
+                               :payload        payload
+                               :owner          owner
+                               :plugin-name    "quartet-metqc-report"
+                               :plugin-type    "ReportPlugin"
+                               :plugin-version (:plugin-version plugin-context)
+                               :response       response})
+        result-dir (fs-lib/join-paths workdir "results")]
+    (fs-lib/create-directories! result-dir)
+    (spit log-path (json/write-str {:status "Running"
+                                    :msg ""}))
+    (update-process! task-id 0)
+    (publish-event! "quartet_metqc_report"
+                    {:data-file data-file
+                     :metadata-file metadata-file
+                     :dest-dir workdir
+                     :task-id task-id
+                     :metadata {:name name
+                                :description description
+                                :plugin-name "quartet-metqc-report"
+                                :plutin-type "ReportPlugin"
+                                :plugin-version (:plugin-version plugin-context)}})
+    response))
+
+(defn- make-report!
+  [{:keys [data-file metadata-file dest-dir metadata task-id]}]
+  (let [log-path (fs-lib/join-paths dest-dir "log")
+        result-dir (fs-lib/join-paths dest-dir "results")
+        parameters-file (fs-lib/join-paths result-dir "general_information.json")
+        results (util/chain-fn-coll [(fn []
+                                       (update-process! task-id 20)
+                                       (metqc/call-metqc! data-file metadata-file result-dir))
+                                     (fn []
+                                       (update-process! task-id 50)
+                                       (spit parameters-file (json/write-str {"Report Name" (:name metadata)
+                                                                              "Description" (:description metadata)
+                                                                              "Report Tool" (format "%s-%s"
+                                                                                                    (:plugin-name metadata)
+                                                                                                    (:plugin-version metadata))
+                                                                              "Team" "Quartet Team"
+                                                                              "Date" (date)}))
+                                       {:status "Success" :msg ""})
+                                     (fn []
+                                       (update-process! task-id 80)
+                                       (metqc/multiqc result-dir dest-dir
+                                                      {:template "quartet_metabolite_report"
+                                                       :title "Quartet Report for Metabolomics"
+                                                       :env {:PATH (add-env-to-path "quartet-metqc-report")}}))]
+                                    (fn [result] (= (:status result) "Success")))
+        status (:status (last results))
+        msg (apply str (map :msg results))
+        process (if (= status "Success") 100 -1)]
+    (log/info (format "Running batch command: %s" (pr-str results)))
+    (update-log-process! log-path {:status status
+                                   :msg msg}
+                         task-id process)))
+
+(def events-init
+  "Automatically called during startup; start event listener for quartet_metqc_report events."
+  (make-events-init "quartet_metqc_report" make-report!))

src/quartet_metqc_report/version.clj

+(ns quartet-metqc-report.version)
+
+(def plugin-name "quartet-metqc-report")
+(def version "0.1.3")

src/tservice/plugins/quartet_metqc_report.clj

-(ns tservice.plugins.quartet-metqc-report
-  (:require [clojure.data.json :as json]
-            [clojure.spec.alpha :as s]
-            [spec-tools.core :as st]
-            [clojure.tools.logging :as log]
-            [tservice.lib.files :as ff]
-            [tservice.api.config :refer [add-env-to-path]]
-            [tservice.lib.fs :as fs-lib]
-            [tservice.vendor.multiqc :as mq]
-            [tservice.plugins.quartet-metqc-report.metqc :as metqc]
-            [tservice.api.task :refer [make-events-init publish-event! make-plugin-metadata create-task! update-process!]]))
-
-;;; ------------------------------------------------ Event Specs ------------------------------------------------
-(s/def ::metadata_file
-  (st/spec
-   {:spec                (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
-    :type                :string
-    :description         "File path for metadata file, such as file:///xxx/xxx/metadata.csv"
-    :swagger/default     nil
-    :reason              "The filepath must be string."}))
-
-(s/def ::data_file
-  (st/spec
-   {:spec                (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)[a-zA-Z0-9_]+.*" %))
-    :type                :string
-    :description         "File path for metabolomics profiled data, such as file:///xxx/xxx/data.csv"
-    :swagger/default     nil
-    :reason              "The filepath must be string."}))
-
-(s/def ::name
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "The name of the report"
-    :swagger/default     ""
-    :reason              "Not a valid name"}))
-
-(s/def ::description
-  (st/spec
-   {:spec                string?
-    :type                :string
-    :description         "Description of the report"
-    :swagger/default     ""
-    :reason              "Not a valid description."}))
-
-(def quartet-metqc-report-params-body
-  "A spec for the body parameters."
-  (s/keys :req-un [::name ::data_file ::metadata_file]
-          :opt-un [::description]))
-
-;;; ------------------------------------------------ Event Metadata ------------------------------------------------
-(def metadata
-  (make-plugin-metadata
-   {:name "quartet-metqc-report"
-    :summary "Visualizes Quality Control(QC) results from metabolomics data for Quartet Project."
-    :params-schema quartet-metqc-report-params-body
-    :handler (fn [{:keys [name data_file metadata_file description owner plugin-context]
-                   :or {description (format "Quality control report for %s" name)}
-                   :as payload}]
-               (let [payload (merge {:description description} payload)
-                     data-file (metqc/correct-filepath data_file)
-                     metadata-file (metqc/correct-filepath metadata_file)
-                     workdir (metqc/dirname data-file)
-                     log-path (fs-lib/join-paths workdir "log")
-                     response {:report (format "%s/multiqc_report.html" workdir)
-                               :log log-path
-                               :response-type :data2report}
-                     task-id (create-task! {:name           name
-                                            :description    description
-                                            :payload        payload
-                                            :owner          owner
-                                            :plugin-name    "quartet-metqc-report"
-                                            :plugin-type    "ReportPlugin"
-                                            :plugin-version (:plugin-version plugin-context)
-                                            :response       response})
-                     result-dir (fs-lib/join-paths workdir "results")]
-                 (fs-lib/create-directories! result-dir)
-                 (log/info (format "Create a report %s with %s in %s" name payload workdir))
-                 (spit log-path (json/write-str {:status "Running"
-                                                 :msg ""}))
-                 (update-process! task-id 0)
-                 (publish-event! "quartet_metqc_report"
-                                 {:data-file data-file
-                                  :metadata-file metadata-file
-                                  :dest-dir workdir
-                                  :task-id task-id
-                                  :metadata {:name name
-                                             :description description
-                                             :plugin-name "quartet-metqc-report"
-                                             :plutin-type "ReportPlugin"
-                                             :plugin-version (:plugin-version plugin-context)}})
-                 response))
-    :plugin-type :ReportPlugin
-    :response-type :data2report}))
-
-(defn update-log-process!
-  "Update message into log file and process into database."
-  [log-path coll task-id process]
-  (spit log-path (json/write-str coll))
-  (update-process! task-id process))
-
-(defn date
-  []
-  (.format (java.text.SimpleDateFormat. "yyyy-MM-dd")
-           (new java.util.Date)))
-
-(defn- make-report!
-  [{:keys [data-file metadata-file dest-dir metadata task-id]}]
-  (let [log-path (fs-lib/join-paths dest-dir "log")
-        result-dir (fs-lib/join-paths dest-dir "results")
-        parameters-file (fs-lib/join-paths result-dir "general_information.json")
-        results (ff/chain-fn-coll [(fn []
-                                     (update-process! task-id 20)
-                                     (metqc/call-metqc! data-file metadata-file result-dir))
-                                   (fn []
-                                     (update-process! task-id 50)
-                                     (spit parameters-file (json/write-str {"Report Name" (:name metadata)
-                                                                            "Description" (:description metadata)
-                                                                            "Report Tool" (format "%s-%s"
-                                                                                                  (:plugin-name metadata)
-                                                                                                  (:plugin-version metadata))
-                                                                            "Team" "Quartet Team"
-                                                                            "Date" (date)}))
-                                     {:status "Success" :msg ""})
-                                   (fn []
-                                     (update-process! task-id 80)
-                                     (mq/multiqc result-dir dest-dir
-                                                 {:template "quartet_metabolite_report"
-                                                  :title "Quartet Report for Metabolomics"
-                                                  :env {:PATH (add-env-to-path "quartet-metqc-report")}}))]
-                                  (fn [result] (= (:status result) "Success")))
-        status (:status (last results))
-        msg (apply str (map :msg results))
-        process (if (= status "Success") 100 -1)]
-    (log/info (format "Running batch command: %s" (pr-str results)))
-    (update-log-process! log-path {:status status
-                                   :msg msg}
-                         task-id process)))
-
-;;; --------------------------------------------------- Lifecycle ----------------------------------------------------
-
-(def events-init
-  "Automatically called during startup; start event listener for quartet_metqc_report events."
-  (make-events-init "quartet_metqc_report" make-report!))

src/tservice/plugins/quartet_metqc_report/metqc.clj

-(ns tservice.plugins.quartet-metqc-report.metqc
-  "A wrapper for metqc tool."
-  (:require [tservice.api.config :refer [add-env-to-path]]
-            [tservice.lib.files :refer [is-localpath? get-plugin-jar-env-dir]]
-            [clojure.string :as clj-str]
-            [tservice.lib.fs :as fs-lib]
-            [clojure.java.shell :as shell :refer [sh]]
-            [clojure.java.io :refer [file]]))
-
-(defn call-metqc!
-  "Call metqc bash script. more details on https://github.com/chinese-quartet/MetQC
-   exp-file: Proteomics profiled data. 
-   meta-file: proteomics metadata.
-   result-dir: A directory for result files.
-  "
-  [exp-file meta-file result-dir]
-  (shell/with-sh-env {:PATH   (add-env-to-path "quartet-metqc-report")
-                      :R_PROFILE_USER (fs-lib/join-paths (get-plugin-jar-env-dir "quartet-metqc-report") "Rprofile")
-                      :LC_ALL "en_US.utf-8"
-                      :LANG   "en_US.utf-8"}
-    (let [command ["bash" "-c"
-                   (format "metqc.sh -d %s -m %s -o %s" exp-file meta-file result-dir)]
-          result  (apply sh command)
-          status (if (= (:exit result) 0) "Success" "Error")
-          msg (str (:out result) "\n" (:err result))]
-      {:status status
-       :msg msg})))
-
-(defn correct-filepath
-  [filepath]
-  (if (is-localpath? filepath)
-    (clj-str/replace filepath #"^file:\/\/" "")
-    filepath))
-
-(defn ^String basename
-  "Returns the basename of 'path'.
-   This works by calling getName() on a java.io.File instance. It's prefered
-   over last-dir-in-path for that reason.
-   Parameters:
-     path - String containing the path for an item in iRODS.
-   Returns:
-     String containing the basename of path."
-  [^String path]
-  (.getName (file path)))
-
-(defn ^String dirname
-  "Returns the dirname of 'path'.
-   This works by calling getParent() on a java.io.File instance.
-   Parameters:
-     path - String containing the path for an item in iRODS.
-   Returns:
-     String containing the dirname of path."
-  [^String path]
-  (when path (.getParent (file path))))