sushi_fabric 1.2.9 → 1.3.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: f4d98401899172185098c8f8d78f782acb032d5e1849ca7142d713e36ae250b6
+  metadata.gz: 1cad308291efa3003ad82f9145250b8ab3a1b58c540a390e76b34b5f5f4aa486
+  data.tar.gz: 6bb026994c95dc5a98e04fe880baed61ae6226bd2a4c9a76e46f4774cb4525bd
 SHA512:
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-  data.tar.gz: dcf130309a2d75527972c1c3a78d265f1a9b161654f2798940074cc0b6c193b261bcd950d40c709888746ea24d310008bda24a37166ae9ad2c90b8755b6f57a2
+  metadata.gz: 91b181a841ecf30d19308d9287419d4384d7167ab48ea7b0642a5e33d65160cb89f631fed808c372d9f12af52b73c11ce2769f93a02fc396154999426961a44b
+  data.tar.gz: 197f0d52d86b044f5aa4284724b601f2598ad6903f99b970fd1a8d9f6d0236033046902cd0b3fe29fa607db46fc16237f97b12554a65aecaf803f1f76a6d312e

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20241108-111516'
+# Version = '20241122-134036'
 
 require 'csv'
 require 'fileutils'
@@ -81,6 +81,8 @@ end
     require "#{SUSHI_APP_DIR}/app/models/data_set"
     require "#{SUSHI_APP_DIR}/app/models/sample"
     require "#{SUSHI_APP_DIR}/app/models/job"
+    require "#{SUSHI_APP_DIR}/app/jobs/application_job"
+    require "#{SUSHI_APP_DIR}/app/jobs/make_whole_tree_job"
   else
     NO_ROR = true
   end
@@ -178,18 +180,24 @@ def save_data_set(data_set_arr, headers, rows, user=nil)
       end
       sample = Sample.new
       sample.key_value = sample_hash.to_s
-      sample.save # skip exact-match search
       data_set.samples << sample
     end
 
     data_set.md5 = data_set.md5hexdigest
-    project.data_sets << data_set
-    parent_data_set.data_sets << data_set if parent_data_set
-    data_set.save
-    if user
-      user.data_sets << data_set
-      user.save
-    end
+		if data_set_ = DataSet.find_by_md5(data_set.md5) and data_set_.project_id == data_set.project_id
+			data_set = data_set_
+		else
+			data_set.samples.each do |sample|
+				sample.save
+			end
+			project.data_sets << data_set
+			parent_data_set.data_sets << data_set if parent_data_set
+			data_set.save
+			if user
+				user.data_sets << data_set
+				user.save
+			end
+		end
     data_set.id
   end
 end
@@ -790,7 +798,7 @@ rm -rf #{@scratch_dir} || exit 1
         end
         sample = Sample.new
         sample.key_value = sample_hash.to_s
-        sample.save # skip exact-match search
+        #sample.save # skip exact-match search
         data_set.samples << sample
       end
 
@@ -799,13 +807,20 @@ rm -rf #{@scratch_dir} || exit 1
       end
 
       data_set.md5 = data_set.md5hexdigest
-      project.data_sets << data_set
-      parent_data_set.data_sets << data_set if parent_data_set
-      data_set.save
-      if user
-        user.data_sets << data_set
-        user.save
-      end
+			if data_set_ = DataSet.find_by_md5(data_set.md5) and data_set_.project_id == data_set.project_id
+				data_set = data_set_
+			else
+				data_set.samples.each do |sample|
+					sample.save
+				end
+				project.data_sets << data_set
+				parent_data_set.data_sets << data_set if parent_data_set
+				data_set.save
+				if user
+					user.data_sets << data_set
+					user.save
+				end
+			end
       data_set.id
     end
   end
@@ -841,6 +856,7 @@ rm -rf #{@scratch_dir} || exit 1
     @next_dataset_tsv_path = save_next_dataset_as_tsv
 
     if @dataset_sushi_id and dataset = DataSet.find_by_id(@dataset_sushi_id.to_i)
+      @project_id = dataset.project.id
       data_set_arr = []
       headers = []
       rows = []
@@ -899,6 +915,12 @@ rm -rf #{@scratch_dir} || exit 1
         new_job.data_set.save
       end
     end
+
+    # Update dataset tree
+    if @project_id
+      puts "# Update dataset tree by ActiveJob"
+      MakeWholeTreeJob.perform_later(@project_id)
+    end
     copy_nextdataset
   end
   def run

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.2.9"
+  VERSION = "1.3.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.2.9
+  version: 1.3.1
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-11-08 00:00:00.000000000 Z
+date: 2024-11-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -69,7 +69,7 @@ homepage: ''
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -84,8 +84,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.5
-signing_key: 
+rubygems_version: 3.4.19
+signing_key:
 specification_version: 4
 summary: workflow manager client.
 test_files: