version 3.0

Author: komstat

JGA_metadata.xlsx

@@ -3,8 +3,8 @@
 ## 日本語
 
 * 生命情報・DDBJ センター
-* 公開日: 2024-07-04
-* version: v2.9.1
+* 公開日: 2024-07-05
+* version: v3.0
 
 [Bioinformation and DDBJ Center](https://www.ddbj.nig.ac.jp/index-e.html) のデータベースに登録するためのメタデータ XML を生成、チェックするツール。
 * [DDBJ Sequence Read Archive (DRA)](https://www.ddbj.nig.ac.jp/dra/submission.html): Submission、Experiment、Run と Analysis (任意) XML を生成・チェックするためのエクセルとスクリプト
@@ -13,6 +13,7 @@
 
 ## 履歴
 
+* 2024-07-05: v3.0 シート名に DB prefix を付加
 * 2024-07-04: v2.9.1 Sample 属性を全て ATTRIBUTE に格納
 * 2024-06-14: v2.9 Sample 属性追加、及び、公開指定の削除
 * 2024-05-28: v2.8.1 file bug fix
@@ -336,6 +337,7 @@ These files are Excel, container images and tools for generation and validation
 
 ## History
 
+* 2024-07-05: v3.0 DB prefix added to sheet name
 * 2024-07-04: v2.9.1 Store all sample attributes in SAMPLE_ATTRIBUTE
 * 2024-06-14: v2.9 Sample attributes added and hold/release removed
 * 2024-05-28: v2.8.1 file bug fix

README.md

@@ -18,13 +18,15 @@ require 'date'
 # 2023-09-04 version 2.0 Analysis support
 # 2023-11-21 version 2.1 Analysis reference to Run
 # 2023-12-21 version 2.2 center name changes
+# 2024-07-05 version 3.0 new sheet names with DB prefixes
 #
 
 # Options
 account = ""
 submission_no = ""
 bioproject_accession = ""
 center_name = ""
+sheet_without_prefix = false
 OptionParser.new{|opt|
 
   opt.on('-a [VALUE]', 'D-way account ID'){|v|
@@ -51,6 +53,11 @@ OptionParser.new{|opt|
     puts "Center name: #{v}"
   }
 
+  opt.on('-r', 'sheet name without prefix'){|v|
+		sheet_without_prefix = true
+    puts "Previous sheet name without prefix"
+  }
+
   begin
     opt.parse!
   rescue
@@ -91,7 +98,11 @@ rescue
 end
 
 # metadata sheets
-meta_object = ['Submission', 'Experiment', 'Run', 'Run-file', 'Analysis']
+if sheet_without_prefix
+	meta_object = ['Submission', 'Experiment', 'Run', 'Run-file', 'Analysis']
+else
+	meta_object = ['DRA_Submission', 'DRA_Experiment', 'DRA_Run', 'DRA_Run-file', 'DRA_Analysis']
+end
 
 # array for metadata objects
 submission_a = Array.new
@@ -109,15 +120,15 @@ for meta in meta_object
 
     case meta
 
-    when "Submission" then
+    when /Submission$/ then
       submission_a.push([i, line])
-    when "Experiment" then
+    when /Experiment$/ then
       experiment_a.push([i, line])
-    when "Run" then
+    when /Run$/ then
       run_a.push([i, line])
-    when "Run-file" then
+    when /Run-file$/ then
       run_file_a.push([i, line])
-    when "Analysis" then
+    when /Analysis$/ then
       analysis_a.push([i, line])
     end
 

example/JSUB999999_jga_metadata.xlsx

@@ -11,6 +11,7 @@ require 'optparse'
 #
 
 # Update history
+# 2024-07-05 DB prefix added to sheet name
 # 2024-07-04 Record all sample attributes in the sample attribute elements
 # 2024-05-17 Change the way of describing Sample attributes
 # 2022-12-23 Change handling of submission date
@@ -23,6 +24,7 @@ submission_no = ""
 submission_id = ""
 study_accession = ""
 previous_sample_attrs_flag = false
+sheet_without_prefix = false
 OptionParser.new{|opt|
 
   opt.on('-j [JSUB ID]', 'JSUB/ASUB submission ID'){|v|
@@ -42,6 +44,11 @@ OptionParser.new{|opt|
 		puts "Previous added Sample attributes format: #{previous_sample_attrs_flag}"
   }
 
+  opt.on('-p', 'sheet without prefix'){
+  	sheet_without_prefix = true
+		puts "Previous sheet name without DB prefix"
+  }
+	
   begin
     opt.parse!
   rescue
@@ -75,7 +82,11 @@ rescue
 end
 
 # sheets
-meta_object = ['Submission', 'Study', 'Sample', 'Experiment', 'Data', 'Analysis', 'Dataset', 'File']
+if sheet_without_prefix
+	meta_object = ['Submission', 'Study', 'Sample', 'Experiment', 'Data', 'Analysis', 'Dataset', 'File']
+else
+	meta_object = ['JGA_Submission', 'JGA_Study', 'JGA_Sample', 'JGA_Experiment', 'JGA_Data', 'JGA_Analysis', 'JGA_Dataset', 'JGA_File']
+end
 
 # array for metadata objects
 submission_a = Array.new
@@ -97,21 +108,21 @@ for meta in meta_object
 
     case meta
 
-    when "Submission" then
+    when /Submission$/ then
       submission_a.push([i, line])
-    when "Study" then
+    when /Study$/ then
       study_a.push([i, line])
-    when "Sample" then
+    when /Sample$/ then
       sample_a.push([i, line.map(&:to_s)])
-    when "Experiment" then
+    when /Experiment$/ then
       experiment_a.push([i, line])
-    when "Data" then
+    when /Data$/ then
       data_a.push([i, line])
-    when "Analysis" then
+    when /Analysis$/ then
       analysis_a.push([i, line])
-    when "Dataset" then
+    when /Dataset$/ then
       dataset_a.push([i, line])
-    when "File" then
+    when /File$/ then
       file_a.push([i, line])
     end