sushi_fabric 0.9.5 → 1.0.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 9def7c5a0d2a5182b79d9ca135ce3e7f67cf16b9
-  data.tar.gz: 0af352dc611de0e1bef415b9be3f8b01839c0dcb
+SHA256:
+  metadata.gz: 795af5bedd1d25f2f6c41bcab16b699b015df28615ff1ef5a975f330ba8f7255
+  data.tar.gz: ebc667d556828450ae331a4e63ed07bde0b4871b97d18747bc71ff6e407f185a
 SHA512:
-  metadata.gz: 27ef36219db2c723c615e6039c6f6e9ec7dfec53d5ade06f4ae8b48cea03c529d34588c5eeea8c466bf37d7c21d197741debe69a043ed981ea208b3e43959530
-  data.tar.gz: c308e2f6654df1a0d246c6288e00adc811edfb2014aeff4f48c86d7459ee11f8d03dd2c01fa7e71ce80062a27be0114712ac64a3b25c641fec6d138ff2d528ce
+  metadata.gz: 6ae60c4d4acef1444c9b1bfdb11f2dc6455add3414cfc63412603051d992c402c67037c45ff136b905ac2166100e36fa3f1e3c8d313cea80bc24c31a3b7f2577
+  data.tar.gz: 8a046912e3b798e662b9e1131d5a0151f36cbb83e4eb986c9827dff6e410e1910c2965d383daba7a1dc9a5798f08c566feb72bb3c812cbdcbf1f7fe9d4cf575d

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20191219-104017'
+# Version = '20200724-120813'
 
 require 'csv'
 require 'fileutils'
@@ -237,6 +237,7 @@ class SushiApp
     @params['ram'] = nil
     @params['scratch'] = nil
     @params['node'] = ''
+    @params['queue'] = ''
     @params['process_mode'] = 'SAMPLE'
     @params['samples'] = ''
     @job_ids = []
@@ -391,8 +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
@@ -416,7 +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
@@ -443,6 +448,13 @@ cd $SCRATCH_DIR || exit 1
   end
   def job_footer
     @out.print "#### JOB IS DONE WE PUT THINGS IN PLACE AND CLEAN AUP\n"
+    if File.exist?("/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh")
+      @out.print <<-EOS
+. "/usr/local/ngseq/miniconda3/etc/profile.d/conda.sh"
+conda activate sushi
+      EOS
+    end
+
     if @output_files
       @output_files.map{|header| next_dataset[header]}.each do |file|
         # in actual case, to save under /srv/gstore/
@@ -755,28 +767,14 @@ 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 = []
@@ -801,20 +799,45 @@ 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 = "0.9.5"
+  VERSION = "1.0.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.5
+  version: 1.0.0
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-12-19 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.