sushi_fabric 1.2.8 → 1.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 625777da16fc54a819726f5b5f82dcf309865c05c11f902a0065dd1d385d7307
-  data.tar.gz: 628bec7e0c32fa99832d35bd2016eaee2bcec4984f71089b23d4b9ebbe7b0c37
+  metadata.gz: 5fd326eaf8b9a5122f254584de8c7c05d17f787bc794d9f6c0ae6aece9d3c43a
+  data.tar.gz: e8974e60c798c7d530cde78b651bcfc0dddec8d1bd251211051c05fd891079bd
 SHA512:
-  metadata.gz: 928ddc2796c22bd809bbadc1b91c2a9aa4b15754b60a64a66d26c387b916386d5df39de3e5f8e42424e101256fe7ce55872521644ba96258b9381ea75cb3e59d
-  data.tar.gz: 2d669efcfc9afce6ffad2f07b18496744d0a4b7b52588c519fe791fb8ee2eb23a4c5c8e48855c037359fd6081ffae54c58e483835ddc0a384ffd1b0c9ce2383a
+  metadata.gz: b33a127381df9c20f85cb2f12a9b43e76676c53e9fc2aab9376ffae7a2892d056d96b87bf2b42e6e2f46682c778cf6908e413d4d7eee1dfaa7e8f9cf2db93bf9
+  data.tar.gz: 0dcb5d15ab77db9c9f3c081e75703dfc9978c97bc3e814471ad906e47a5c55f5f5997a74c5afdc1f860b342827f751c18c07eece1405919e5ea0b848aaf3b99d

data/lib/sushi_fabric/sushiApp.rb

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # encoding: utf-8
-# Version = '20240823-112404'
+# Version = '20241121-112242'
 
 require 'csv'
 require 'fileutils'
@@ -178,22 +178,24 @@ def save_data_set(data_set_arr, headers, rows, user=nil)
       end
       sample = Sample.new
       sample.key_value = sample_hash.to_s
-      sample.save unless sample.saved?
       data_set.samples << sample
     end
 
     data_set.md5 = data_set.md5hexdigest
-    unless data_set.saved?
-      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
-    else
-      headers[0] = DataSet.find_by_md5(data_set.md5)
-    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
@@ -794,7 +796,7 @@ rm -rf #{@scratch_dir} || exit 1
         end
         sample = Sample.new
         sample.key_value = sample_hash.to_s
-        sample.save unless sample.saved?
+        #sample.save # skip exact-match search
         data_set.samples << sample
       end
 
@@ -803,17 +805,20 @@ rm -rf #{@scratch_dir} || exit 1
       end
 
       data_set.md5 = data_set.md5hexdigest
-      unless data_set.saved?
-        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
-      else
-        headers[0] = DataSet.find_by_md5(data_set.md5)
-      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

data/lib/sushi_fabric/version.rb

@@ -1,3 +1,3 @@
 module SushiFabric
-  VERSION = "1.2.8"
+  VERSION = "1.3.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: sushi_fabric
 version: !ruby/object:Gem::Version
-  version: 1.2.8
+  version: 1.3.0
 platform: ruby
 authors:
 - Functional Genomics Center Zurich
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-08-23 00:00:00.000000000 Z
+date: 2024-11-21 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: