sushi_fabric 0.9.0 → 0.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 427128c3c395e175874c00dd5cdc0bd3a17a062c
-  data.tar.gz: c1adc24e9c0c02cb980bb772905e661673008a19
+  metadata.gz: 59143df589de70270b5fc2456f1b96b56995ca9b
+  data.tar.gz: 05affa8d9d4782a1cf96ef7efa291232a4247b6a
 SHA512:
-  metadata.gz: 3a0bd9e974f7a85905b94e7fe537a766b13986f92d5d760753715522b2c9278f9d03c038832e568ad57eb61362e026544291d3410c57eccae84f9109bf5dcf0c
-  data.tar.gz: 41cbb1a4c7708d984b754b2fe6bd3e5d7c40f63e4126161f76b8f2050382cbd95f1d8379ba97edd1e4dbf90ddfddcd318f788fc4e43d661cbe0c8c08435886ce
+  metadata.gz: d2881e2a987d99718892498fe463f570ea4c53c27fb8bf1960de37802d1c43122d0d9b902b6e7d48c2b7f348bda6cb01c54afd2667b5d0f41217ad76b27de97d
+  data.tar.gz: 3ca221e5d42416287c15f5b8065adf7254d0848d8548b10afcac8a034d393f613440d5d48e47d6653a83157254a75c9db48c75cdc2f722e1569260b26c5c3ec5

data/bin/sushi_fabric

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20170908-105900'
+# Version = '20190425-141759'
 
 require 'sushi_fabric'
 
@@ -22,8 +22,11 @@ Usage:
   o.on(:next_dataset_name, '-n next_dataset_name', '--next_dataset_name', 'Next DataSet Name (default: Analysis_Category+ID+Date )')
   o.on(:off_bfab, '-f', '--off_bfab', 'Do NOT register the dataset in BFabric (default: false, namely register in BFabric)')
   o.on(:mango_run_name, '-g mango_run_name', '--mango_run_name', 'ManGO RunName_oBFabricID')
+  o.on(:input_dataset_application, '-a bfabric_application_number', '--input_dataset_application', 'BFabric Application Number for input DataSet')
+  o.on(:next_dataset_application, '-A bfabric_application_number', '--next_dataset_application', 'BFabric Application Number for next DataSet')
   o.parse!(ARGV)
 end
+
 opt.project = 'p' + opt.project
 if File.exist?('lib')
   $: << 'lib'
@@ -78,6 +81,12 @@ end
 if opt.mango_run_name
   usecase.mango_run_name = opt.mango_run_name
 end
+if opt.input_dataset_application
+  usecase.input_dataset_bfabric_application_number = opt.input_dataset_application
+end
+if opt.next_dataset_application
+  usecase.next_dataset_bfabric_application_number = opt.next_dataset_application
+end
 if opt.run_mode
   usecase.run
 else

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20190104-191156'
+# Version = '20190425-142129'
 
 require 'csv'
 require 'fileutils'
@@ -225,6 +225,8 @@ class SushiApp
   attr_accessor :logger
   attr_accessor :off_bfabric_registration
   attr_accessor :mango_run_name
+  attr_accessor :input_dataset_bfabric_application_number
+  attr_accessor :next_dataset_bfabric_application_number
   def initialize
     @gstore_dir = GSTORE_DIR
     @project = nil
@@ -275,7 +277,7 @@ class SushiApp
         if @dataset_sushi_id = save_data_set(data_set_arr.to_a.flatten, headers, rows, @current_user)
           unless @off_bfabric_registration
             if dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
-              dataset.register_bfabric
+              dataset.register_bfabric(bfabric_application_number: @input_dataset_bfabric_application_number)
             end
           end
         elsif data_set = headers[0] and data_set.instance_of?(DataSet)
@@ -586,6 +588,7 @@ rm -rf #{@scratch_dir} || exit 1
     org = @scratch_result_dir
     dest = @gstore_project_dir
     copy_commands(org, dest, 'now').each do |command|
+      puts `which python`
       puts command
       unless system command
         raise "fails in copying input_dataset, parameters and jobscript files from /scratch to /gstore"
@@ -597,6 +600,7 @@ rm -rf #{@scratch_dir} || exit 1
     org = @next_dataset_tsv_path
     dest = File.join(@gstore_project_dir, @result_dir_base)
     copy_commands(org, dest, 'now').each do |command|
+      puts `which python`
       puts command
       unless system command
         raise "fails in copying next_dataset files from /scratch to /gstore"
@@ -786,7 +790,7 @@ rm -rf #{@scratch_dir} || exit 1
 
         unless @off_bfabric_registration
           if next_dataset = DataSet.find_by_id(@next_dataset_id)
-            next_dataset.register_bfabric
+            next_dataset.register_bfabric(bfabric_application_number: @next_dataset_bfabric_application_number)
           end
         end
 

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "0.9.0"
+  VERSION = "0.9.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-04 00:00:00.000000000 Z
+date: 2019-04-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler