sushi_fabric 0.7.1 → 0.7.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 5356f95d5e80384882e30f434ca9e81cb7af0078
+  metadata.gz: 5979375fed31ca635c84b55e996d5fc40254c3de
+  data.tar.gz: 9814016fb3137614502cc9a34fc2e041d6e6e85a
 SHA512:
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+  metadata.gz: 42a57301a53a0bd6ea81c66302d38658e4516095853740c279e6abca13c774270f2ab3935e02be1e7aa8f25abfafc62e1f5128953383c18ff7cbf7275637bf89
+  data.tar.gz: 6f152feb2f8466f42c8914591059d406a4873c5030572d6dd4216168f5aa3fa192a8cf907786a3fa9f33cecdb947841fb6450ace952974d64e0e3df9785dc0c0

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20170303-160743'
+# Version = '20170324-161522'
 
 require 'csv'
 require 'fileutils'
@@ -442,10 +442,15 @@ rm -rf #{@scratch_dir} || exit 1
     end
     job_id
   end
-  def submit(job_script)
+  def submit(job_script, mock=false)
     begin
-      job_id = submit_command(job_script)
-      job_id = job_id.to_i
+      job_id = unless mock
+                 i = submit_command(job_script)
+                 i.to_i
+               else
+                 #Time.now.to_f.to_s.gsub('.', '')
+                 1234
+               end
       unless job_id.to_i > 1
         @logger.error("#"*50)
         time = Time.now.strftime("[%Y.%m.%d %H:%M:%S]")
@@ -658,7 +663,7 @@ rm -rf #{@scratch_dir} || exit 1
       data_set.id
     end
   end
-  def main
+  def main(mock=false)
     ## sushi writes creates the job scripts and builds the result data set that is to be generated
     @result_dataset = []
     @job_scripts = []
@@ -673,13 +678,18 @@ rm -rf #{@scratch_dir} || exit 1
       warn "the process mode (#{@params['process_mode']}) is not defined"
       raise "stop job submitting"
     end
+    if mock
+      make_dummy_files
+    end
     copy_inputdataset_parameter_jobscripts
 
     # job submittion
+    gstore_job_script_paths = []
     @job_scripts.each_with_index do |job_script, i|
-      if job_id = submit(job_script)
+      if job_id = submit(job_script, mock)
         @job_ids << job_id
         print "Submit job #{File.basename(job_script)} job_id=#{job_id}"
+        gstore_job_script_paths << File.join(@gstore_script_dir, File.basename(job_script))
       end
     end
 
@@ -721,9 +731,10 @@ rm -rf #{@scratch_dir} || exit 1
         end
 
         # save job and dataset relation in Sushi DB
-        job_ids.each do |job_id|
+        job_ids.each_with_index do |job_id, i|
           new_job = Job.new
           new_job.submit_job_id = job_id.to_i
+          new_job.script_path = gstore_job_script_paths[i]
           new_job.next_dataset_id = @next_dataset_id
           new_job.save
           new_job.data_set.jobs << new_job
@@ -756,6 +767,53 @@ rm -rf #{@scratch_dir} || exit 1
       main
     end
   end
+  def make_dummy_files
+    dummy_files_header = []
+    headers = @result_dataset.map{|row| row.keys}.flatten.uniq
+    headers.select{|header| header.tag?('File')||header.tag?('Link')}.each do |header|
+      dummy_files_header << header
+    end
+    dummy_files_ = []
+    @result_dataset.each do |row|
+      dummy_files_.concat(dummy_files_header.map{|header| row[header]})
+    end
+    dummy_files = []
+    dummy_files_.each do |file|
+      dummy_files << file.gsub(@result_dir, '')
+    end
+    dummy_files.uniq!
+
+    dirs = []
+    dummy_files.permutation(2).each do |a,b|
+      if a.include?(b) and b !~ /\./
+        dirs << b
+      end
+    end
+    dirs.each do |dir|
+      dummy_files.delete(dir)
+    end
+    dirs.each do |dir|
+      command = "mkdir -p #{File.join(@scratch_result_dir, dir)}"
+      puts command
+      `#{command}`
+    end
+    dummy_files.each do |file|
+      command = if file =~ /.html/
+                  "echo 'Hello, SUSHI world!' > #{File.join(@scratch_result_dir, file)}"
+                else
+                  "touch #{File.join(@scratch_result_dir, file)}"
+                end
+      puts command
+      `#{command}`
+    end
+  end
+  def mock_run
+    test_run
+    prepare_result_dir
+    save_parameters_as_tsv
+    save_input_dataset_as_tsv
+    main(true)
+  end
   def test_run
     set_input_dataset
     set_dir_paths

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.7.1"
+  VERSION = "0.7.2"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.7.1
+  version: 0.7.2
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-03-03 00:00:00.000000000 Z
+date: 2017-03-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler