sushi_fabric 1.1.3 → 1.1.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 03fa7b3efd213571886969d39e40cdb88e6af13e3b37a0ab195fafcc94a061da
+  metadata.gz: 59e67c9d4fe0a5833a2f5cee1cea4bed7961a88ee86e1d393c009855458a5940
+  data.tar.gz: a109369c8f10c36f910587e9185ba71e66f56ad1985671cf1a13084b84e9162b
 SHA512:
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-  data.tar.gz: 23ceb3abf7b4928ccdc92b1fc04fe745d9924374a7767d583f5a64e8947464463aa4577ba548ef1648cf4ce13c0a5f39aae93ba5468bce0d8d809c4aada436e2
+  metadata.gz: 61b7d5dbd9570f10935795ec7db46adf4f030f379f699617085c533f52e4c1978f69d9f0190ae6bb5968e09d820aec02c1181ece79eb9463c89ac689a08bcdc6
+  data.tar.gz: 7e96d353ec8b808060117dc88e0c762469d0eaae15ab52ee0dc96fcc9c52438864a81dcbfed11713f03c9c613adcf960b61c28b536ed03c2275e3e9aa500d41b

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20211104-160141'
+# Version = '20220207-142315'
 
 require 'csv'
 require 'fileutils'
@@ -116,7 +116,11 @@ class ::Hash
     if v
       @defaults[k] = v
     else
-      @defaults[k]
+      if @defaults
+        @defaults[k]
+      else
+        ""
+      end
     end
   end
   def data_type(k)
@@ -252,7 +256,7 @@ class SushiApp
   end
   def set_input_dataset
     if @dataset_tsv_file
-      dataset_tsv = CSV.readlines(@dataset_tsv_file, {:headers=>true, :col_sep=>"\t"})
+      dataset_tsv = CSV.readlines(@dataset_tsv_file, :headers=>true, :col_sep=>"\t")
       @dataset_hash = []
       @dataset = []
       dataset_tsv.each do |row|
@@ -384,14 +388,23 @@ 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 +590,14 @@ 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(@result_dir, "uploaded", File.basename(value))
+          out << [key, uploaded_file_path]
+          @params[key] = uploaded_file_path
+          @output_params[key] = uploaded_file_path
+        else
+          out << [key, value]
+        end
       end
     end
     file_path
@@ -629,6 +649,18 @@ 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
@@ -779,6 +811,12 @@ rm -rf #{@scratch_dir} || exit 1
       data_set.id
     end
   end
+  def save_parameters_in_sushi_db
+    if @next_dataset_id and next_dataset = DataSet.find_by_id(@next_dataset_id)
+      next_dataset.job_parameters = @output_params
+      next_dataset.save
+    end
+  end
   def main(mock=false)
     ## sushi writes creates the job scripts and builds the result data set that is to be generated
     @result_dataset = []
@@ -825,6 +863,7 @@ rm -rf #{@scratch_dir} || exit 1
       unless NO_ROR
         @current_user ||= nil
         @next_dataset_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user, @child)
+        save_parameters_in_sushi_db
 
         unless @off_bfabric_registration
           if next_dataset = DataSet.find_by_id(@next_dataset_id)
@@ -841,6 +880,7 @@ 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 = "1.1.7"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.1.3
+  version: 1.1.7
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-11-04 00:00:00.000000000 Z
+date: 2022-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -69,7 +69,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3.1
-signing_key: 
+rubygems_version: 3.2.32
+signing_key:
 specification_version: 4
 summary: workflow manager client.
 test_files: