glydevkit 0.2.0.pre.beta.3-java → 0.2.0.pre.beta.5-java

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 10216bee959df9fcfa6bf6fc7739ec44b4df0044cb4af79c1c05656fc119f871
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+  data.tar.gz: 2028230f807361373c1bbb0d89eca163a3f929e80ff795e38093dfbe49957ef2f01720a1f50c2487ebb9fd4335c976e4e57ea97bc8b426a097f682a6d8d1c252

data/jar.yml

@@ -92,6 +92,6 @@ libraries:
 
   - name: MolWURCS
     info: https://gitlab.com/glycoinfo/molwurcs
-    version: 0.10.2
-    url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/89942780/download
+    version: 0.11.0
+    url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/106726568/download
     file: jar/MolWURCS.jar

data/lib/glydevkit/glytoucan_data_handler.rb

@@ -0,0 +1,110 @@
+require 'json'
+require 'uri'
+require 'net/http'
+require 'zlib'
+java_import 'java.util.Base64'
+
+module GlyDevKit
+    class GlytoucanDataHandler
+    attr_reader :all_data
+
+    def initialize
+        @gtcfilepath = File.join(Dir.home, '.glycobook', 'gtcdata.json')
+        if File.exist?(@gtcfilepath)
+        creation_time = File.ctime(@gtcfilepath)
+        one_hours_ago = Time.now - (1 * 60 * 60) # 1時間前の時刻
+        if creation_time > one_hours_ago
+            @all_data = JSON.parse(File.read(@gtcfilepath))
+            return
+        end
+        end
+        @all_data = save_glytoucan_data
+    end
+
+    def get_wurcs_by_gtcid(id)
+        return "not found" if @all_data["wurcs"][id].nil?
+        decode_lambda = ->(encoded_str) { decode(encoded_str) }
+        @all_data["wurcs"][id]&.map(&decode_lambda)
+    end
+
+    def get_gtcid_by_wurcs(w)
+        return "not found" if @all_data["encode-wurcs-key"][encode(w)].nil?
+        @all_data["encode-wurcs-key"][encode(w)]
+    end
+
+    private
+
+    require 'zlib'
+    java_import 'java.util.Base64'
+    
+    def encode(input_string)
+      compressed_data = Zlib::Deflate.deflate(input_string)
+      encoder = Base64.getUrlEncoder()
+      encoder.encodeToString(compressed_data.to_java_bytes)
+    end
+    
+    def decode(encoded_string)
+      decoder = Base64.getUrlDecoder()
+      compressed_data = decoder.decode(encoded_string)
+      Zlib::Inflate.inflate(String.from_java_bytes(compressed_data))
+    end
+    
+
+    def sparql_query
+        <<-EOS
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX glycan: <http://purl.jp/bio/12/glyco/glycan#>
+
+SELECT DISTINCT ?Saccharide ?WurcsSeq
+WHERE {
+GRAPH <http://rdf.glytoucan.org/core> {
+    ?Saccharide glycan:has_resource_entry ?ResEntry .
+    ?s glycan:has_resource_entry ?ResEntry .
+}
+
+?Saccharide glycan:has_glycosequence ?GSeq .
+
+GRAPH <http://rdf.glytoucan.org/sequence/wurcs> {
+    OPTIONAL {
+    ?GSeq glycan:has_sequence ?WurcsSeq .
+    }
+}
+
+FILTER NOT EXISTS {
+    GRAPH <http://rdf.glytoucan.org/archive> {
+    ?Saccharide rdf:type ?ArchiveSaccharide .
+    }
+}
+}
+EOS
+    end
+
+    def fetch_glytoucan_data
+        hash1 = {}
+        hash2 = {}
+        api = 'https://ts.glytoucan.org/sparql?default-graph-uri=&query=' + URI.encode_www_form_component(sparql_query) + '&format=application%2Fsparql-results%2Bjson&timeout=0&signal_void=on'
+        response = JSON.parse(Net::HTTP.get(URI(api)))
+        response['results']['bindings'].map do |item|
+        id = URI(item['Saccharide']['value']).path.split('/').last
+        encode_wurcs = encode(item['WurcsSeq']['value'])
+        if hash1[id].nil?
+            hash1[id] = [encode_wurcs]
+        else
+            hash1[id].push(encode_wurcs)
+        end
+        if hash2[encode_wurcs].nil?
+            hash2[encode_wurcs] = [id]
+        else
+            hash2[encode_wurcs].push(id)
+        end
+        end
+        return {"wurcs" => hash1, "encode-wurcs-key" => hash2}
+    end
+
+    def save_glytoucan_data
+        data = fetch_glytoucan_data
+        File.write(@gtcfilepath, data.to_json)
+        data
+    end
+    end
+end

data/lib/glydevkit.rb

@@ -5,6 +5,8 @@ require 'glydevkit/Loggerinit'
 require 'glydevkit/glycan_builder'
 require 'glydevkit/glycan_format_converter'
 require 'glydevkit/gly_tou_can'
+require 'glydevkit/cdk'
+require 'glydevkit/glytoucan_data_handler'
 require 'glydevkit/subsumption'
 require 'glydevkit/wurcs_frame_work'
 require 'glydevkit/mol_wurcs'

data/lib/init.rb

@@ -2,6 +2,10 @@ require 'open-uri'
 require 'net/http'
 require 'fileutils'
 require 'yaml'
+require 'digest'
+require 'fileutils'
+require 'terminal-table'
+
 
 module Init
 
@@ -67,7 +71,55 @@ Set recommended Java library version? (No/yes)
       end
     end
   end
+  
+  def self.switch_WFW_version(version)
+    base = File.dirname(__FILE__) + "/jar/"
+    
+    source_file = File.join(base, "wurcsframework-#{version}.jar")
+    destination_file = File.join(base, "wurcsframework.jar")
+  
+    if File.exist?(source_file)
+      begin
+        FileUtils.cp(source_file, destination_file)
+        puts "Switched to version #{version} successfully!"
+      rescue StandardError => e
+        puts "Failed to switch versions: #{e.message}"
+      end
+    else
+      puts "Source file #{source_file} does not exist."
+    end
+  end
+
+  def self.show_WFW_version()
+    target_file_path = File.dirname(__FILE__) + '/jar/wurcsframework.jar'  
+    folder_path = File.dirname(__FILE__) + '/jar' 
+  
+    matching_files = find_matching_files(target_file_path, folder_path)
+  
+    unless matching_files.empty?
+      matching_files.each do |file|
+        version = extract_version_from_filename(file)
+        if version
+          puts "version number: #{version}"
+        else
+          puts ""
+        end
+      end
+    end
+  end
 
+  def self.show_dependencies
+    yaml_data = File.read(Dir.home+'/.glycobook/jar.yml')
+    parsed_data = YAML.load(yaml_data)
+    rows = []
+    rows.push(["name","version","Link"])
+    parsed_data["libraries"].each{|item|
+      rows.push([item["name"].to_s , item["version"].to_s , item["info"].to_s ])
+    }
+    puts Terminal::Table.new rows: rows
+end
+
+  private
   # Loads the settings from a YAML file and prepares the environment.
   #
   # @param file_path [String] The path to the settings file.
@@ -98,4 +150,40 @@ Set recommended Java library version? (No/yes)
 
     downloads
   end
-end
+
+  def self.calculate_file_hash(file_path)
+    hash_func = Digest::SHA256.new
+    begin
+      File.open(file_path, 'rb') do |file|
+        while chunk = file.read(8192)
+          hash_func.update(chunk)
+        end
+      end
+    rescue IOError => e
+      puts "ファイルの読み込み中にエラーが発生しました: #{file_path}, エラー: #{e}"
+      return nil
+    end
+    hash_func.hexdigest
+  end
+  
+  def self.find_matching_files(target_file_path, folder_path)
+    target_file_hash = calculate_file_hash(target_file_path)
+    return unless target_file_hash
+  
+    matching_files = Dir.glob("#{folder_path}/**/*").select do |file_path|
+      next unless File.file?(file_path)
+      next if File.identical?(target_file_path, file_path) 
+  
+      file_hash = calculate_file_hash(file_path)
+      file_hash == target_file_hash unless file_hash.nil?
+    end
+  
+    matching_files
+  end
+  
+  def self.extract_version_from_filename(filename)
+    match_data = filename.match(/-(\d+\.\d+\.\d+)\.jar$/)
+    match_data ? match_data[1] : nil
+  end
+
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: glydevkit
 version: !ruby/object:Gem::Version
-  version: 0.2.0.pre.beta.3
+  version: 0.2.0.pre.beta.5
 platform: java
 authors:
 - Akihiro Fujita
@@ -11,20 +11,48 @@ cert_chain: []
 date: 2024-10-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: java
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.0.2
-  type: :runtime
+  name: java
   prerelease: false
+  type: :runtime
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.0.2
-description: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glycaninformatics
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  name: yaml
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  name: terminal-table
+  prerelease: false
+  type: :runtime
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glyco-informatics
 email:
 - akihirof0005@gmail.com
 executables: []
@@ -37,6 +65,7 @@ files:
 - lib/glydevkit/gly_tou_can.rb
 - lib/glydevkit/glycan_builder.rb
 - lib/glydevkit/glycan_format_converter.rb
+- lib/glydevkit/glytoucan_data_handler.rb
 - lib/glydevkit/mol_wurcs.rb
 - lib/glydevkit/subsumption.rb
 - lib/glydevkit/wurcs_frame_work.rb
@@ -61,12 +90,12 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ">="
+  - - ">"
     - !ruby/object:Gem::Version
-      version: '0'
+      version: 1.3.1
 requirements: []
-rubygems_version: 3.5.18
+rubygems_version: 3.3.26
 signing_key:
 specification_version: 4
-summary: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glycaninformatics
+summary: The Glycoscience Development Kit (GlyDevKit) is a JRuby library for glyco-informatics
 test_files: []