sushi_fabric 0.9.4 → 0.9.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 8d9c4e224a34d7d928e2a656e07e41a943a8793c
-  data.tar.gz: b5f78a77a230d72f6ca9825d5d77b3a4a4df90b1
+SHA256:
+  metadata.gz: 379a56d5261eb7ed21137bd452583eb76e416cf774c987628b0d1c847bed6040
+  data.tar.gz: b68363a7da5c166ab7c38d8310b9d151ce490a1d3d4f6d48bdfa5a3484c0abf1
 SHA512:
-  metadata.gz: 926b9b3975f334ffe5203985cee62659e5d9280da0278e2c67c64e6beb96dfe3e8579ae4fc8665bc1276d2203cf3e36f8a46966710ef875756bbf91a1a9f8f05
-  data.tar.gz: 3f85a0c2ef2a2a63d0a87c4ecd09aa2c99952298cab670444a73111cfc0960ecbd08ce7ea0792e9d20d200f4e79b8acda05fccaeb71ce310da3eed2314742a54
+  metadata.gz: 15cbf3c8954c15999a91a5ab0e0f53dffc9a2ded3ecc5b0633e1d31c6480102cf44e245c94735c2d52251bdbc58c6262c7070b0b9853e7048659dbd5135130e9
+  data.tar.gz: b936c6a57a6683b1a19874627eb9bc4ba1719d0664f85794e4ee9d0face5eba3d424e06fd60158afbb53dc9b3b1c9b1330e94fdacdc17262f64ed1fdd1310eac

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20191115-103323'
+# Version = '20200724-111508'
 
 require 'csv'
 require 'fileutils'
@@ -227,6 +227,7 @@ class SushiApp
   attr_accessor :mango_run_name
   attr_accessor :input_dataset_bfabric_application_number
   attr_accessor :next_dataset_bfabric_application_number
+  attr_reader :inactivate_nodes
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -236,6 +237,7 @@ class SushiApp
     @params['ram'] = nil
     @params['scratch'] = nil
     @params['node'] = ''
+    @params['queue'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
     @job_ids = []
@@ -390,8 +392,13 @@ class SushiApp
   end
   def check_latest_module_version(mod)
     command_out =  %x[ bash -lc "source #{@module_source}; module whatis #{mod} 2>&1" ]
-    latest_mod = command_out.split.first
-    latest_mod = nil if latest_mod == "Failed"
+    latest_mod = nil
+    command_out.split("\n").each do |line|
+      if line =~ /#{mod}/
+        latest_mod = line.split.first
+        break
+      end
+    end
     latest_mod
   end
   def job_header
@@ -415,7 +422,6 @@ class SushiApp
                             modules_with_version = @modules.map{|mod| check_latest_module_version(mod)}
                             modules_with_version.compact!
                             "module add #{modules_with_version.join(' ')}"
-                            #"module add #{@modules.join(' ')}"
                           else
                             ""
                           end
@@ -754,28 +760,14 @@ 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 = []
@@ -800,20 +792,45 @@ 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 "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 = "0.9.4"
+  VERSION = "0.9.9"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.4
+  version: 0.9.9
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-11-15 00:00:00.000000000 Z
+date: 2020-07-24 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.