sushi_fabric 1.1.3 → 1.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 03fa7b3efd213571886969d39e40cdb88e6af13e3b37a0ab195fafcc94a061da
+  metadata.gz: b34ce73bf64c4447679ec3fa06820fccf59857ea739a9b16e9a91907051c1894
+  data.tar.gz: 5d7f45f91531ecb9c7014b6b3694622694b6257845b607cec8819256cbff9a2f
 SHA512:
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+  metadata.gz: 190e59e9c16c3e1031fdc929e6c4a3627cd63d0e1b6ecaf95aeba88158a08af587a398c9903efbcaf3efdc2cafafd39f015a3714365e4b7ed45adcdb18b83a66
+  data.tar.gz: 5ee4d5c6a57b06fedb6cecdf0cc396376846e1fe1ed41d431f3104ab140e0bfd0dbb34cb4df144e0cd08390315355498e09228509ded24ab976466d155358c80

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20211104-160141'
+# Version = '20211207-151042'
 
 require 'csv'
 require 'fileutils'
@@ -384,14 +384,23 @@ class SushiApp
     @result_dir = File.join(@project, @result_dir_base)
     @scratch_result_dir = File.join(SCRATCH_DIR, @result_dir_base)
     @job_script_dir = File.join(@scratch_result_dir, 'scripts')
+    @uploaded_files_dir = File.join(@scratch_result_dir, 'uploaded')
     @gstore_result_dir = File.join(@gstore_dir, @result_dir)
     @gstore_script_dir = File.join(@gstore_result_dir, 'scripts')
     @gstore_project_dir = File.join(@gstore_dir, @project)
+    @gstore_uploaded_dir = File.join(@gstore_result_dir, 'uploaded')
     set_file_paths
   end
   def prepare_result_dir
     FileUtils.mkdir_p(@scratch_result_dir)
     FileUtils.mkdir_p(@job_script_dir)
+    @uploaded_files = []
+    @params.each do |key, value|
+      if @params[key, 'file_upload']
+        FileUtils.mkdir_p(@uploaded_files_dir)
+        @uploaded_files << value
+      end
+    end
   end
   def check_latest_modules_version(modules)
     command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{modules.join(" ")} 2>&1" | cut -f 1 -d " " | uniq ]
@@ -577,7 +586,12 @@ rm -rf #{@scratch_dir} || exit 1
     CSV.open(file_path, 'w', :col_sep=>"\t") do |out|
       out << ["sushi_app", self.class.name]
       @output_params.each do |key, value|
-        out << [key, value]
+        if @output_params[key, 'file_upload']
+          uploaded_file_path = File.join(@gstore_uploaded_dir, File.basename(value))
+          out << [key, uploaded_file_path]
+        else
+          out << [key, value]
+        end
       end
     end
     file_path
@@ -629,6 +643,18 @@ rm -rf #{@scratch_dir} || exit 1
     end
     com
   end
+  def copy_uploaded_files
+    if not @uploaded_files.empty?
+      @uploaded_files.each do |file|
+        FileUtils.cp(file, @uploaded_files_dir)
+        command = "cp #{file} #{@uploaded_files_dir}"
+        puts command
+        FileUtils.rm_r(File.dirname(file))
+        command = "rm -rf #{File.dirname(file)}"
+        puts command
+      end
+    end
+  end
   def copy_inputdataset_parameter_jobscripts
     org = @scratch_result_dir
     dest = @gstore_project_dir
@@ -841,6 +867,7 @@ rm -rf #{@scratch_dir} || exit 1
         end
       end
     end
+    copy_uploaded_files
     copy_inputdataset_parameter_jobscripts
 
     # job submittion

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.1.3"
+  VERSION = "1.1.4"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.3
+  version: 1.1.4
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-11-04 00:00:00.000000000 Z
+date: 2021-12-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler