Add dependencies.

project.clj

@@ -1,6 +1,6 @@
-(defproject tservice/quartet-rnaseq-report "v0.1.0"
-  :description "FIXME: write description"
-  :url "http://example.com/FIXME"
+(defproject tservice-plugins/quartet-rnaseq-report "v0.1.0"
+  :description "QC Report for Quartet RNA-Seq."
+  :url "https://github.com/tservice-plugins/quartet-rnaseq-report"
   :license {:name "Eclipse Public License"
             :url "http://www.eclipse.org/legal/epl-v10.html"}
   :min-lein-version "2.5.0"
@@ -17,7 +17,7 @@
   {:provided
    {:dependencies
     [[org.clojure/clojure "1.10.1"]
-     [tservice "0.3.1"]]}
+     [org.clojars.yjcyxky/tservice "0.5.6"]]}
 
    :uberjar
    {:auto-clean    true

resources/renv/.gitignore

@@ -0,0 +1,3 @@
+library/
+python/
+staging/

resources/renv/activate.R

@@ -0,0 +1,349 @@
+
+local({
+
+  # the requested version of renv
+  version <- "0.12.0"
+
+  # the project directory
+  project <- getwd()
+
+  # avoid recursion
+  if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
+    return(invisible(TRUE))
+
+  # signal that we're loading renv during R startup
+  Sys.setenv("RENV_R_INITIALIZING" = "true")
+  on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)
+
+  # signal that we've consented to use renv
+  options(renv.consent = TRUE)
+
+  # load the 'utils' package eagerly -- this ensures that renv shims, which
+  # mask 'utils' packages, will come first on the search path
+  library(utils, lib.loc = .Library)
+
+  # check to see if renv has already been loaded
+  if ("renv" %in% loadedNamespaces()) {
+
+    # if renv has already been loaded, and it's the requested version of renv,
+    # nothing to do
+    spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
+    if (identical(spec[["version"]], version))
+      return(invisible(TRUE))
+
+    # otherwise, unload and attempt to load the correct version of renv
+    unloadNamespace("renv")
+
+  }
+
+  # load bootstrap tools   
+  bootstrap <- function(version, library) {
+  
+    # read repos (respecting override if set)
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (is.na(repos))
+      repos <- getOption("repos")
+  
+    # fix up repos
+    on.exit(options(repos = repos), add = TRUE)
+    repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
+    options(repos = repos)
+  
+    # attempt to download renv
+    tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
+    if (inherits(tarball, "error"))
+      stop("failed to download renv ", version)
+  
+    # now attempt to install
+    status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
+    if (inherits(status, "error"))
+      stop("failed to install renv ", version)
+  
+  }
+  
+  renv_bootstrap_download_impl <- function(url, destfile) {
+  
+    mode <- "wb"
+  
+    # https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
+    fixup <-
+      Sys.info()[["sysname"]] == "Windows" &&
+      substring(url, 1L, 5L) == "file:"
+  
+    if (fixup)
+      mode <- "w+b"
+  
+    download.file(
+      url      = url,
+      destfile = destfile,
+      mode     = mode,
+      quiet    = TRUE
+    )
+  
+  }
+  
+  renv_bootstrap_download <- function(version) {
+  
+    methods <- list(
+      renv_bootstrap_download_cran_latest,
+      renv_bootstrap_download_cran_archive,
+      renv_bootstrap_download_github
+    )
+  
+    for (method in methods) {
+      path <- tryCatch(method(version), error = identity)
+      if (is.character(path) && file.exists(path))
+        return(path)
+    }
+  
+    stop("failed to download renv ", version)
+  
+  }
+  
+  renv_bootstrap_download_cran_latest <- function(version) {
+  
+    # check for renv on CRAN matching this version
+    db <- as.data.frame(available.packages(), stringsAsFactors = FALSE)
+  
+    entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+    if (nrow(entry) == 0) {
+      fmt <- "renv %s is not available from your declared package repositories"
+      stop(sprintf(fmt, version))
+    }
+  
+    message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
+  
+    info <- tryCatch(
+      download.packages("renv", destdir = tempdir()),
+      condition = identity
+    )
+  
+    if (inherits(info, "condition")) {
+      message("FAILED")
+      return(FALSE)
+    }
+  
+    message("OK")
+    info[1, 2]
+  
+  }
+  
+  renv_bootstrap_download_cran_archive <- function(version) {
+  
+    name <- sprintf("renv_%s.tar.gz", version)
+    repos <- getOption("repos")
+    urls <- file.path(repos, "src/contrib/Archive/renv", name)
+    destfile <- file.path(tempdir(), name)
+  
+    message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
+  
+    for (url in urls) {
+  
+      status <- tryCatch(
+        renv_bootstrap_download_impl(url, destfile),
+        condition = identity
+      )
+  
+      if (identical(status, 0L)) {
+        message("OK")
+        return(destfile)
+      }
+  
+    }
+  
+    message("FAILED")
+    return(FALSE)
+  
+  }
+  
+  renv_bootstrap_download_github <- function(version) {
+  
+    enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
+    if (!identical(enabled, "TRUE"))
+      return(FALSE)
+  
+    # prepare download options
+    pat <- Sys.getenv("GITHUB_PAT")
+    if (nzchar(Sys.which("curl")) && nzchar(pat)) {
+      fmt <- "--location --fail --header \"Authorization: token %s\""
+      extra <- sprintf(fmt, pat)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "curl", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    } else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
+      fmt <- "--header=\"Authorization: token %s\""
+      extra <- sprintf(fmt, pat)
+      saved <- options("download.file.method", "download.file.extra")
+      options(download.file.method = "wget", download.file.extra = extra)
+      on.exit(do.call(base::options, saved), add = TRUE)
+    }
+  
+    message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
+  
+    url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
+    name <- sprintf("renv_%s.tar.gz", version)
+    destfile <- file.path(tempdir(), name)
+  
+    status <- tryCatch(
+      renv_bootstrap_download_impl(url, destfile),
+      condition = identity
+    )
+  
+    if (!identical(status, 0L)) {
+      message("FAILED")
+      return(FALSE)
+    }
+  
+    message("Done!")
+    return(destfile)
+  
+  }
+  
+  renv_bootstrap_install <- function(version, tarball, library) {
+  
+    # attempt to install it into project library
+    message("* Installing renv ", version, " ... ", appendLF = FALSE)
+    dir.create(library, showWarnings = FALSE, recursive = TRUE)
+  
+    # invoke using system2 so we can capture and report output
+    bin <- R.home("bin")
+    exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
+    r <- file.path(bin, exe)
+    args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball))
+    output <- system2(r, args, stdout = TRUE, stderr = TRUE)
+    message("Done!")
+  
+    # check for successful install
+    status <- attr(output, "status")
+    if (is.numeric(status) && !identical(status, 0L)) {
+      header <- "Error installing renv:"
+      lines <- paste(rep.int("=", nchar(header)), collapse = "")
+      text <- c(header, lines, output)
+      writeLines(text, con = stderr())
+    }
+  
+    status
+  
+  }
+  
+  renv_bootstrap_prefix <- function() {
+  
+    # construct version prefix
+    version <- paste(R.version$major, R.version$minor, sep = ".")
+    prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
+  
+    # include SVN revision for development versions of R
+    # (to avoid sharing platform-specific artefacts with released versions of R)
+    devel <-
+      identical(R.version[["status"]],   "Under development (unstable)") ||
+      identical(R.version[["nickname"]], "Unsuffered Consequences")
+  
+    if (devel)
+      prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
+  
+    # build list of path components
+    components <- c(prefix, R.version$platform)
+  
+    # include prefix if provided by user
+    prefix <- Sys.getenv("RENV_PATHS_PREFIX")
+    if (nzchar(prefix))
+      components <- c(prefix, components)
+  
+    # build prefix
+    paste(components, collapse = "/")
+  
+  }
+  
+  renv_bootstrap_library_root <- function(project) {
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
+    if (!is.na(path))
+      return(path)
+  
+    path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
+    if (!is.na(path))
+      return(file.path(path, basename(project)))
+  
+    file.path(project, "renv/library")
+  
+  }
+  
+  renv_bootstrap_validate_version <- function(version) {
+  
+    loadedversion <- utils::packageDescription("renv", fields = "Version")
+    if (version == loadedversion)
+      return(TRUE)
+  
+    # assume four-component versions are from GitHub; three-component
+    # versions are from CRAN
+    components <- strsplit(loadedversion, "[.-]")[[1]]
+    remote <- if (length(components) == 4L)
+      paste("rstudio/renv", loadedversion, sep = "@")
+    else
+      paste("renv", loadedversion, sep = "@")
+  
+    fmt <- paste(
+      "renv %1$s was loaded from project library, but renv %2$s is recorded in lockfile.",
+      "Use `renv::record(\"%3$s\")` to record this version in the lockfile.",
+      "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
+      sep = "\n"
+    )
+  
+    msg <- sprintf(fmt, loadedversion, version, remote)
+    warning(msg, call. = FALSE)
+  
+    FALSE
+  
+  }
+  
+  renv_bootstrap_load <- function(project, libpath, version) {
+  
+    # try to load renv from the project library
+    if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
+      return(FALSE)
+  
+    # warn if the version of renv loaded does not match
+    renv_bootstrap_validate_version(version)
+  
+    # load the project
+    renv::load(project)
+  
+    TRUE
+  
+  }
+
+  # construct path to library root
+  root <- renv_bootstrap_library_root(project)
+
+  # construct library prefix for platform
+  prefix <- renv_bootstrap_prefix()
+
+  # construct full libpath
+  libpath <- file.path(root, prefix)
+
+  # attempt to load
+  if (renv_bootstrap_load(project, libpath, version))
+    return(TRUE)
+
+  # load failed; attempt to bootstrap
+  bootstrap(version, libpath)
+
+  # exit early if we're just testing bootstrap
+  if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+    return(TRUE)
+
+  # try again to load
+  if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
+    message("Successfully installed and loaded renv ", version, ".")
+    return(renv::load())
+  }
+
+  # failed to download or load renv; warn the user
+  msg <- c(
+    "Failed to find an renv installation: the project will not be loaded.",
+    "Use `renv::activate()` to re-initialize the project."
+  )
+
+  warning(paste(msg, collapse = "\n"), call. = FALSE)
+
+})

resources/renv/renv.lock

@@ -0,0 +1,20 @@
+{
+  "R": {
+    "Version": "3.6.3",
+    "Repositories": [
+      {
+        "Name": "CRAN",
+        "URL": "https://cloud.r-project.org"
+      }
+    ]
+  },
+  "Packages": {
+    "renv": {
+      "Package": "renv",
+      "Version": "0.13.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "9f10d9db5b50400c348920c5c603385e"
+    }
+  }
+}

resources/renv/settings.dcf

@@ -0,0 +1,6 @@
+external.libraries:
+ignored.packages:
+package.dependency.fields: Imports, Depends, LinkingTo
+snapshot.type: all
+use.cache: TRUE
+vcs.ignore.library: TRUE

resources/requirements.txt

@@ -0,0 +1 @@
+git+git://github.com/chinese-quartet/quartet-rnaseq-report#egg=quartet-rnaseq-report

resources/tservice-plugin.yaml

@@ -1,12 +1,25 @@
 info:
-  name: FIXME: write name
+  name: QC Report for Quartet RNA-Seq
   version: v0.1.0
-  description: FIXME: write description
+  description: Generate the QC Report for Quartet RNA-Seq data.
+  category: Report
+  home: https://github.com/clinico-omics/tservice-plugins
+  source: PGx
+  short_name: quartet-rnaseq-report
+  icons:
+    - src: ""
+      type: image/png
+      sizes: 192x192
+  author: PGx
 plugin:
   name: quartet-rnaseq-report
-  display-name: FIXME: write display name
+  display-name: QC Report for Quartet RNA-Seq
   lazy-load: false
 init:
+  # Unpack environment file to the directory, repository/envs/quartet-rnaseq-report
+  - step: unpack-env
+    envname: quartet-rnaseq-report
+    postunpack: clone-env /opt/local/quartet-rnaseq-report {{ ENV_DEST_DIR }}
   - step: load-namespace
     namespace: tservice.plugins.quartet-rnaseq-report
   - step: register-plugin

src/tservice/plugins/quartet_rnaseq_report.clj

@@ -1,23 +1,19 @@
 (ns tservice.plugins.quartet-rnaseq-report
-  (:require [clojure.core.async :as async]
-            [clojure.data.json :as json]
+  (:require [clojure.data.json :as json]
             [clojure.spec.alpha :as s]
             [clojure.tools.logging :as log]
-            [tservice.lib.commons :as comm :refer [get-path-variable]]
-            [tservice.plugins.quartet-rnaseq-report.exp2qcdt :as exp2qcdt]
-            [tservice.plugins.quartet-rnaseq-report.merge-exp :as me]
             [spec-tools.core :as st]
-            [spec-tools.json-schema :as json-schema]
-            [tservice.config :refer [get-workdir env]]
-            [tservice.events :as events]
-            [tservice.lib.filter-files :as ff]
-            [tservice.lib.fs :as fs-lib]
-            [tservice.util :as u]
-            [tservice.util.files :as files]
-            [clojure.java.io :as io]
-            [tservice.db.handler :as db-handler]
             [clojure.java.shell :as shell :refer [sh]]
-            [tservice.vendor.multiqc :as mq]))
+            [tservice.lib.files :as ff]
+            [tservice.lib.fs :as fs-lib]
+            [tservice.vendor.multiqc :as mq]
+            [tservice.api.config :refer [add-env-to-path]]
+            [tservice.api.storage.fs :as fs-api]
+            [tservice.api.data.csv :refer [write-csv!]]
+            [tservice.api.task :refer [publish-event! make-plugin-metadata make-events-init create-task! update-process!]]
+            [tservice.plugins.quartet-rnaseq-report.exp2qcdt :as exp2qcdt]
+            [tservice.plugins.quartet-rnaseq-report.merge-exp :as me]
+            [tservice.plugins.quartet-rnaseq-report.util :refer [gen-multiqc-config]]))
 
 ;;; ------------------------------------------------ Event Specs ------------------------------------------------
 (s/def ::name
@@ -36,17 +32,9 @@
     :swagger/default     ""
     :reason              "Not a valid description."}))
 
-(s/def ::project_id
-  (st/spec
-   {:spec                #(some? (re-matches #"[a-f0-9]{8}(-[a-f0-9]{4}){4}[a-f0-9]{8}" %))
-    :type                :string
-    :description         "project-id"
-    :swagger/default     "40644dec-1abd-489f-a7a8-1011a86f40b0"
-    :reason              "Not valid a project-id."}))
-
 (s/def ::filepath
   (st/spec
-   {:spec                (s/and string? #(re-matches #"^[a-zA-Z0-9]+:\/\/(\/|\.\/)?[a-zA-Z0-9_\/]+.*" %))
+   {:spec                (s/and string? #(re-matches #"^oss:\/\/[a-zA-Z0-9_\/]+.*" %))
     :type                :string
     :description         "File path for covertor."
     :swagger/default     nil
@@ -152,78 +140,46 @@
 (def quartet-rna-report-params-body
   "A spec for the body parameters."
   (s/keys :req-un [::name ::description ::filepath ::metadata ::parameters]
-          :opt-un [::project_id]))
+          :opt-un [::description]))
 
 ;;; ------------------------------------------------ Event Metadata ------------------------------------------------
 (def metadata
-  {:route    ["/report/quartet-rnaseq-report"
-              {:tags ["Report"]
-               :post {:summary "Parse the results of the quartet-rnaseq-qc app and generate the report."
-                      :parameters {:body quartet-rna-report-params-body}
-                      :responses {201 {:body {:results string? :log string? :report string? :id string?}}}
-                      :handler (fn [{{{:keys [name description project_id filepath metadata parameters]} :body} :parameters}]
-                                 (let [workdir (get-workdir)
-                                       from-path (u/replace-path filepath workdir)
-                                       uuid (u/uuid)
-                                       relative-dir (fs-lib/join-paths "download" uuid)
-                                       to-dir (fs-lib/join-paths workdir relative-dir)
-                                       log-path (fs-lib/join-paths to-dir "log")]
-                                   (fs-lib/create-directories! to-dir)
-                                   (spit log-path (json/write-str {:status "Running" :msg ""}))
-                                   (events/publish-event! :quartet_rnaseq_report-convert
-                                                          {:datadir from-path
-                                                           :parameters parameters
-                                                           :metadata metadata
-                                                           :dest-dir to-dir})
-                                   (db-handler/create-report! {:id (u/uuid)
-                                                               :report_name name
-                                                               :project_id project_id
-                                                               :app_name "quartet_rnaseq_report"
-                                                               :description description
-                                                               :report_path (fs-lib/join-paths relative-dir "multiqc.html")
-                                                               :started_time (u/time->int (u/now))
-                                                               :finished_time nil
-                                                               :archived_time nil
-                                                               :report_type "multireport"
-                                                               :status "Started"
-                                                               :log (fs-lib/join-paths relative-dir "log")})
-                                   {:status 201
-                                    :body {:results (fs-lib/join-paths relative-dir)
-                                           :report (fs-lib/join-paths relative-dir "multiqc_report.html")
-                                           :log (fs-lib/join-paths relative-dir "log")
-                                           :id uuid}}))}
-               :get {:summary "A json shema for quartet-rnaseq-report."
-                     :parameters {}
-                     :responses {200 {:body map?}}
-                     :handler (fn [_]
-                                {:status 200
-                                 :body (json-schema/transform quartet-rna-report-params-body)})}}]
-   :manifest {:description "Parse the results of the quartet-rna-qc app and generate the report."
-              :category "Report"
-              :home "https://github.com/clinico-omics/quartet-rnaseq-report"
-              :name "Quartet RNA-Seq Report"
-              :source "PGx"
-              :short_name "quartet-rnaseq-report"
-              :icons [{:src "", :type "image/png", :sizes "192x192"}
-                      {:src "", :type "image/png", :sizes "192x192"}]
-              :author "Jun Shang"
-              :hidden false
-              :id "f65d87fd3dd2213d91bb15900ba57c11"
-              :app_name "shangjun/quartet-rnaseq-report"}})
-
-(def ^:const quartet-rnaseq-report-topics
-  "The `Set` of event topics which are subscribed to for use in quartet-rnaseq-report tracking."
-  #{:quartet_rnaseq_report-convert})
-
-(def ^:private quartet-rnaseq-report-channel
-  "Channel for receiving event quartet-rnaseq-report we want to subscribe to for quartet-rnaseq-report events."
-  (async/chan))
+  (make-plugin-metadata
+   {: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}]
+               (let [workdir (ff/get-workdir)
+                     report-file (fs-lib/join-paths workdir "multireport.html")
+                     log-path (fs-lib/join-paths workdir "log")
+                     response {:report report-file
+                               :log log-path
+                               :response-type :data2report}
+                     task-id (create-task! {:name name
+                                            :description (or description "Generate the QC Report for Quartet RNA-Seq data.")
+                                            :payload payload
+                                            :plugin-name "quartet-rnaseq-report"
+                                            :plugin-type "ReportPlugin"
+                                            :plugin-version "v0.1.0"
+                                            :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
+                                  :metadata metadata
+                                  :dest-dir workdir
+                                  :task-id task-id})
+                 response))
+    :plugin-type :ReportPlugin
+    :response-type :data2report}))
 
 ;;; ------------------------------------------------ Event Processing ------------------------------------------------
 
 (defn- decompression-tar
   [filepath]
-  (shell/with-sh-env {:PATH   (get-path-variable)
+  (shell/with-sh-env {:PATH   (add-env-to-path "quartet-rnaseq-report")
                       :LC_ALL "en_US.utf-8"
                       :LANG   "en_US.utf-8"}
     (let [command ["bash" "-c"
@@ -236,20 +192,14 @@
 
 (defn- filter-mkdir-copy
   [fmc-datadir fmc-patterns fmc-destdir fmc-newdir]
-  (let [files-keep (ff/batch-filter-files fmc-datadir fmc-patterns)
+  (let [files-keep (fs-api/batch-filter-files fmc-datadir fmc-patterns)
         files-keep-dir (fs-lib/join-paths fmc-destdir fmc-newdir)]
     (fs-lib/create-directories! files-keep-dir)
-    (ff/copy-files! files-keep files-keep-dir {:replace-existing true})))
-
-(defn- extract-config-file
-  [filename dest-path]
-  (when (io/resource filename)
-    (files/with-open-path-to-resource [filepath filename]
-      (files/copy-files! filepath dest-path))))
+    (fs-api/copy-files! files-keep files-keep-dir {:replace-existing true})))
 
 (defn- quartet-rnaseq-report!
   "Chaining Pipeline: filter-files -> copy-files -> merge_exp_file -> exp2qcdt -> multiqc."
-  [datadir parameters metadata dest-dir]
+  [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"
@@ -276,17 +226,19 @@
       (filter-mkdir-copy datadir [".*call-qualimapRNAseq/.*tar.gz"] dest-dir "results/post_alignment_qc/rnaseq_qc")
       (filter-mkdir-copy datadir [".*call-fastqc/.*.zip"] dest-dir "results/rawqc/fastqc")
       (filter-mkdir-copy datadir [".*call-fastqscreen/.*.txt"] dest-dir "results/rawqc/fastq_screen")
-      (me/merge-exp-files! (ff/list-files ballgown-dir {:mode "file"}) exp-fpkm-filepath)
-      (me/merge-exp-files! (ff/list-files count-dir {:mode "file"}) exp-count-filepath)
+      (update-process! task-id 10)
+      (me/merge-exp-files! (fs-api/list-files ballgown-dir {:mode "file"}) exp-fpkm-filepath)
+      (me/merge-exp-files! (fs-api/list-files count-dir {:mode "file"}) exp-count-filepath)
       (spit parameters-file (json/write-str parameters))
-      (comm/write-csv! metadata-file metadata)
+      (write-csv! metadata-file metadata)
       ;;(decompression-tar files-qualimap-bam)
       ;;(decompression-tar files-qualimap-RNA)
-      (doseq [files-qualimap-bam-tar (ff/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/bam_qc") [".*tar.gz"])]
+      (doseq [files-qualimap-bam-tar (fs-api/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/bam_qc") [".*tar.gz"])]
         (decompression-tar files-qualimap-bam-tar))
-      (doseq [files-qualimap-RNA-tar (ff/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/rnaseq_qc") [".*tar.gz"])]
+      (doseq [files-qualimap-RNA-tar (fs-api/batch-filter-files (fs-lib/join-paths dest-dir "results/post_alignment_qc/rnaseq_qc") [".*tar.gz"])]
         (decompression-tar files-qualimap-RNA-tar))
-      (extract-config-file "quartet_rnaseq_report.yaml" config-path)
+      (update-process! task-id 50)
+      (gen-multiqc-config config-path)
       (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"})
@@ -297,26 +249,14 @@
             log (json/write-str result)]
         (log/info "Status: " result)
         (spit log-path log))
+      (update-process! task-id 100)
       (catch Exception e
+        (update-process! task-id -1)
         (let [log (json/write-str {:status "Error" :msg (.toString e)})]
           (log/info "Status: " log)
           (spit log-path log))))))
 
-(defn- process-quartet-rnaseq-report-event!
-  "Handle processing for a single event notification received on the quartet-rnaseq-report-channel"
-  [quartet-rnaseq-report-event]
-  ;; try/catch here to prevent individual topic processing exceptions from bubbling up.  better to handle them here.
-  (try
-    (when-let [{topic :topic object :item} quartet-rnaseq-report-event]
-      ;; TODO: only if the definition changed??
-      (case (events/topic->model topic)
-        "quartet_rnaseq_report" (quartet-rnaseq-report! (:datadir object) (:parameters object) (:metadata object) (:dest-dir object))))
-    (catch Throwable e
-      (log/warn (format "Failed to process quartet-rnaseq-report event. %s" (:topic quartet-rnaseq-report-event)) e))))
-
 ;;; --------------------------------------------------- Lifecycle ----------------------------------------------------
-
-(defn events-init
-  "Automatically called during startup; start event listener for quartet-rnaseq-report events."
-  []
-  (events/start-event-listener! quartet-rnaseq-report-topics quartet-rnaseq-report-channel process-quartet-rnaseq-report-event!))
+(def events-init
+  "Automatically called during startup; start event listener for quartet_rnaseq_report events."
+  (make-events-init "quartet_rnaseq_report" quartet-rnaseq-report!))

src/tservice/plugins/quartet_rnaseq_report/exp2qcdt.clj

@@ -1,17 +1,8 @@
 (ns tservice.plugins.quartet-rnaseq-report.exp2qcdt
   "A wrapper for exp2qcdt tool."
-  (:require [tservice.lib.commons :refer [get-path-variable]]
-            [tservice.config :refer [get-plugin-dir]]
-            [tservice.lib.fs :as fs]
+  (:require [tservice.api.config :refer [add-env-to-path]]
             [clojure.java.shell :as shell :refer [sh]]))
 
-(defn add-env-to-path
-  "Add the path of the plugin's environment into the PATH and return the PATH"
-  []
-  (let [env-bin-path (fs/join-paths (get-plugin-dir) "plugins" "repository" "quartet-rnaseq-report" "bin")
-        path (get-path-variable)]
-    (str env-bin-path ":" path)))
-
 (defn call-exp2qcdt!
   "Call exp2qcdt bash script.
    exp-file: FPKM file , each row is the expression values of a gene and each column is a library.
@@ -20,7 +11,7 @@
    result-dir: A directory for result files.
   "
   [exp-file cnt-file meta-file result-dir]
-  (shell/with-sh-env {:PATH   (add-env-to-path)
+  (shell/with-sh-env {:PATH   (add-env-to-path "quartet-rnaseq-report")
                       :LC_ALL "en_US.utf-8"
                       :LANG   "en_US.utf-8"}
     (let [command ["bash" "-c"

src/tservice/plugins/quartet_rnaseq_report/merge_exp.clj

@@ -1,6 +1,6 @@
 (ns tservice.plugins.quartet-rnaseq-report.merge-exp
   "Merge expression files."
-  (:require [tservice.lib.commons :refer [read-csv write-csv! vec-remove write-csv-by-cols!]]))
+  (:require [tservice.api.data.csv :refer [read-csv vec-remove write-csv-by-cols!]]))
 
 (set! *warn-on-reflection* true)
 

src/tservice/plugins/quartet_rnaseq_report/util.clj

@@ -0,0 +1,15 @@
+(ns tservice.plugins.quartet-rnaseq-report.util
+  (:require [clj-yaml.core :as yaml]))
+
+(defn gen-multiqc-config
+  [config-file]
+  (let [config (yaml/generate-string
+                {:run_modules ["rnaseq_data_generation_information"
+                               "rnaseq_performance_assessment"
+                               "rnaseq_raw_qc"
+                               "rnaseq_post_alignment_qc"
+                               "rnaseq_quantification_qc"
+                               "rnaseq_supplementary"]
+                 :skip_generalstats true}
+                :dumper-options {:flow-style :block})]
+    (spit config-file config)))