sushi_fabric 0.9.6 → 0.9.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 326d811109da5893c3ac6ea35f946f18849e1bb4
-  data.tar.gz: adce9f2299a8b16217cfd715f82ad0f894f3b0d9
+SHA256:
+  metadata.gz: 8ca5afb9de9e23912a2d514c547ff22d2edaf0a6c440e3663a0ac3fce59933f9
+  data.tar.gz: 7a906efa08a1bd3ee1b33dd02ff9a4350f241042626120278b720b3b3294d013
 SHA512:
-  metadata.gz: 9369616e25ddabc40f335f5490bb925591cb52f642e6326cccfbe2205bc807be81983e1f530993ae0256488f3903fc3b3c47e09a2a6f0d261e93e475f712921e
-  data.tar.gz: fedae1c8626fb161831a5e2989c9aeab0cccf54459d09996339f1005322908a4a368326804fec7cee52639fd43272f71d3703de4180640ad3aebe52514ea04a8
+  metadata.gz: 482274611996c4e8c2d483088d1bcd8966d6136f849f7b77782d5ac0834556a56682fc2049f8c70da3aa48131bfa71ae13322a8e001252d4744d76787d9c2a23
+  data.tar.gz: 561434d611bc97fe9e30a035db0f3e3b71cbec89dc767f2531e2bf1b03905030364cf1bd833a0c432cad0d184a87a6552ae90430fe03c47f272611799d35cdea

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20200409-110502'
+# Version = '20200703-164839'
 
 require 'csv'
 require 'fileutils'
@@ -759,28 +759,14 @@ rm -rf #{@scratch_dir} || exit 1
     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, 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
-
-    puts
-    print 'job scripts: '
-    p @job_scripts
     print 'result dataset: '
     p @result_dataset
 
     # copy application data to gstore 
     @next_dataset_tsv_path = save_next_dataset_as_tsv
 
-    if !@job_ids.empty? and @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
+    if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
       data_set_arr = []
       headers = []
       rows = []
@@ -805,20 +791,46 @@ rm -rf #{@scratch_dir} || exit 1
         unless @off_bfabric_registration
           if next_dataset = DataSet.find_by_id(@next_dataset_id)
             next_dataset.register_bfabric(bfabric_application_number: @next_dataset_bfabric_application_number)
+            if next_dataset.workunit_id
+              @job_scripts.each do |job_script|
+                open(job_script, "a") do |out|
+                  out.puts "module load Dev/Python"
+                  out.puts "WORKUNIT_ID=#{next_dataset.workunit_id}"
+                  out.puts "update_resource_size -w $WORKUNIT_ID"
+                end
+              end
+            end
           end
         end
+      end
+    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, 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
+
+    puts
+    print 'job scripts: '
+    p @job_scripts
 
-        # save job and dataset relation in Sushi DB
-        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
-          new_job.data_set.save
-        end
 
+    unless @job_ids.empty? or NO_ROR
+      # save job and dataset relation in Sushi DB
+      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
+        new_job.data_set.save
       end
     end
     copy_nextdataset

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.9.6"
+  VERSION = "0.9.7"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.6
+  version: 0.9.7
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-09 00:00:00.000000000 Z
+date: 2020-07-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -84,8 +84,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 3.0.3
 signing_key: 
 specification_version: 4
 summary: workflow manager client.