glycobook 0.1.0.alpha.20-java → 0.1.0.alpha.21-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
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data/jar.yml CHANGED
@@ -1,24 +1,79 @@
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  ---
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- list:
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- - url: "https://repo1.maven.org/maven2/org/apache/xmlgraphics/batik-all/1.16/batik-all-1.16.jar"
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+ libraries:
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+ - name: batik-all
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+ info: "https://xmlgraphics.apache.org/batik/download.html"
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+ version: 1.16
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+ url: "https://repo1.maven.org/maven2/org/apache/xmlgraphics/batik-all/1.16/batik-all-1.16.jar"
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  file: "jar/batik-all.jar"
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- - url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/glycanbuilder/glycanbuilder2/1.23.1/glycanbuilder2-1.23.1.jar"
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+
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+ - name: glycanbuilder2
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+ info: "https://gitlab.com/glycoinfo/glycanbuilder2"
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+ version: 1.23.1
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+ url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/glycanbuilder/glycanbuilder2/1.23.1/glycanbuilder2-1.23.1.jar"
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  file: "jar/glycanbuilder2.jar"
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- - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
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+
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+ - name: wurcsframework
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+ info: "https://gitlab.com/glycoinfo/wurcsframework"
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+ version: 1.2.14
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+ url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
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  file: "jar/wurcsframework.jar"
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- - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
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+
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+ - name: wurcsframework-1.2.14
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+ info: "https://gitlab.com/glycoinfo/wurcsframework"
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+ version: 1.2.14
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+ url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/87428121/download"
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  file: "jar/wurcsframework-1.2.14.jar"
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- - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/70458150/download"
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+
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+ - name: wurcsframework-1.0.1
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+ info: "https://gitlab.com/glycoinfo/wurcsframework"
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+ version: 1.0.1
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+ url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/70458150/download"
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  file: "jar/wurcsframework-1.0.1.jar"
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- - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.9/slf4j-api-2.0.9.jar"
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+
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+ - name: slf4j-api
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+ info: "https://www.slf4j.org/index.html"
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+ version: 2.0.9
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+ url: https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.9/slf4j-api-2.0.9.jar
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  file: "jar/slf4j-api.jar"
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- - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/2.0.9/slf4j-simple-2.0.9.jar"
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+
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+ - name: slf4j-simple
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+ info: "https://www.slf4j.org/index.html"
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+ version: 2.0.9
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+ url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/2.0.9/slf4j-simple-2.0.9.jar"
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  file: "jar/slf4j-simple.jar"
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- - url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/590/download"
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+
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+ - name: subsumption
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+ info: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption"
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+ version: 0.9.6
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+ url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/590/download"
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  file: "jar/subsumption.jar"
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- - url: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib/-/package_files/489/download"
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+
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+ - name: archetype
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+ info: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib"
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+ version: 0.1.4
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+ url: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib/-/package_files/489/download"
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  file: "jar/archetype.jar"
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- - url: "https://gitlab.com/glycoinfo/glycanformatconverter/-/package_files/81149971/download"
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+
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+ - name: glycanformatconverter
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+ info: "https://gitlab.com/glycoinfo/glycanformatconverter"
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+ version: 2.10.0
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+ url: "https://gitlab.com/glycoinfo/glycanformatconverter/-/package_files/81149971/download"
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  file: "jar/glycanformatconverter.jar"
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- - url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/MolecularFramework/1.0.0/MolecularFramework-1.0.0.jar"
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+
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+ - name: MolecularFramework
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+ info: "https://github.com/glycoinfo/MolecularFramework"
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+ version: 1.0.0
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+ url: "https://raw.githubusercontent.com/glycoinfo/MavenRepository/master/org/eurocarbdb/MolecularFramework/1.0.0/MolecularFramework-1.0.0.jar"
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  file: "jar/MolecularFramework.jar"
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+
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+ - name: The Chemistry Development Kit
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+ info: https://github.com/cdk/cdk
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+ version: 2.9
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+ url: https://github.com/cdk/cdk/releases/download/cdk-2.9/cdk-2.9.jar
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+ file: jar/cdk.jar
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+
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+ - name: MolWURCS
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+ info: https://gitlab.com/glycoinfo/molwurcs
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+ version: 0.10.2
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+ url: https://gitlab.com/glycoinfo/molwurcs/-/package_files/89942780/download
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+ file: jar/MolWURCS.jar
data/lib/bookinit.rb CHANGED
@@ -36,35 +36,49 @@ Would you like to resolve Java dependencies?(No/yes)
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  end
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- # YAMLファイルからdownloads情報をロード
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- downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml")
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-
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- require 'open-uri'
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+ # YAMLファイルからdownloads情報をロード
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+ downloads = load_settings(ENV['HOME'] + "/.glycobook/jar.yml")
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- folder_path = File.dirname(__FILE__)+"/jar"
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- unless Dir.exist?(folder_path)
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- FileUtils.mkdir_p(folder_path)
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- puts "Folder created: #{folder_path}"
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- else
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- puts "Folder already exists: #{folder_path}"
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- end
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- # ダウンロードを実行する
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- downloads["list"].each do |download|
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+ require 'open-uri'
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- uri = URI(download["url"])
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- response = Net::HTTP.get_response(uri)
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- if response.is_a?(Net::HTTPSuccess)
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- begin
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- File.open(File.dirname(__FILE__)+"/"+download["file"], 'wb') do |file|
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- file.write(response.body)
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- puts "Installed " + download["file"]
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- end
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- rescue StandardError => e
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- puts "Failed to save file: #{download["file"]}. Error: #{e.message}"
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+ folder_path = File.dirname(__FILE__)+"/jar"
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+ unless Dir.exist?(folder_path)
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+ FileUtils.mkdir_p(folder_path)
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+ puts "Folder created: #{folder_path}"
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+ else
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+ puts "Folder already exists: #{folder_path}"
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+ end
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+ # ダウンロードを実行する
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+ downloads["libraries"].each do |download|
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+
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+ url = URI(download["url"])
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+ http = Net::HTTP.new(url.host, url.port)
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+ http.use_ssl = (url.scheme == 'https')
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+
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+ request = Net::HTTP::Get.new(url.request_uri)
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+ response = http.request(request)
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+
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+ if response.code.to_i == 302
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+ new_location = response['Location']
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+ url = URI.parse(new_location)
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+ http = Net::HTTP.new(url.host, url.port)
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+ http.use_ssl = (url.scheme == 'https')
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+ request = Net::HTTP::Get.new(url.request_uri)
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+ response = http.request(request)
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+ end
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+
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+ if response.code.to_i == 200
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+ begin
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+ File.open(File.dirname(__FILE__)+"/"+download["file"], 'wb') do |file|
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+ file.write(response.body)
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+ puts "Installed " + download["file"]
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  end
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- else
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- puts "Failed to download file: #{download["file"]}"
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+ rescue StandardError => e
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+ puts "Failed to save file: #{download["file"]}. Error: #{e.message}"
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  end
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+ else
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+ puts "Failed to download file: #{download["file"]}"
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+ end
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  end
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  end
@@ -0,0 +1,56 @@
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+ require "java"
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+
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+ require_relative '../jar/cdk.jar'
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+ require_relative '../jar/MolWURCS.jar'
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+
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+ java_import 'org.glycoinfo.MolWURCS.io.formats.ChemFormatType'
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+ java_import 'org.openscience.cdk.exception.CDKException'
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+ java_import 'org.openscience.cdk.interfaces.IAtomContainerSet'
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+ java_import 'org.openscience.cdk.io.IChemObjectWriter'
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+ java_import 'org.openscience.cdk.io.ISimpleChemObjectReader'
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+ java_import 'org.openscience.cdk.silent.AtomContainerSet'
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+ java_import 'java.io.StringReader'
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+ java_import 'java.nio.file.Files'
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+ java_import 'java.nio.file.Paths'
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+ java_import 'java.io.IOException'
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+ java_import 'java.lang.System'
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+ java_import 'java.util.ArrayList'
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+
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+ module GlycoBook
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+ class MolWURCS
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+
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+ def wurcs2mdlmol(w)
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+
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+ begin
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+ reader = ChemFormatType::WURCS.createReader
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+ reader.setReader(StringReader.new(w))
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+ return unless reader.accepts(AtomContainerSet.java_class)
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+ mols = AtomContainerSet.new
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+ mols = reader.read(mols)
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+ reader.close
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+ rescue CDKException, IOException => e
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+ e.printStackTrace()
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+ end
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+
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+ return if mols.nil?
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+
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+ # write mol
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+ string_writer = java.io.StringWriter.new
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+
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+ begin
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+ writer = org.openscience.cdk.io.SDFWriter.new(string_writer)
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+ if writer.accepts(mols.java_class)
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+ writer.write(mols)
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+ elsif writer.accepts(mols.get_atom_container(0).java_class)
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+ writer.write(mols.get_atom_container(0))
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+ end
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+ writer.close
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+ rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
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+ e.printStackTrace()
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+ end
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+
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+ return string_writer.to_s
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+ end
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+
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+ end
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+ end
data/lib/glycobook.rb CHANGED
@@ -7,6 +7,7 @@ require 'glycobook/glycan_format_converter'
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  require 'glycobook/gly_tou_can'
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  require 'glycobook/subsumption'
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  require 'glycobook/wurcs_frame_work'
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+ require 'glycobook/mol_wurcs'
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  require 'open-uri'
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  require 'net/http'
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  require 'fileutils'
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: glycobook
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  version: !ruby/object:Gem::Version
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- version: 0.1.0.alpha.20
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+ version: 0.1.0.alpha.21
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  platform: java
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  authors:
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  - Akihiro Fujita
@@ -38,6 +38,7 @@ files:
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  - lib/glycobook/gly_tou_can.rb
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  - lib/glycobook/glycan_builder.rb
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  - lib/glycobook/glycan_format_converter.rb
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+ - lib/glycobook/mol_wurcs.rb
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  - lib/glycobook/subsumption.rb
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  - lib/glycobook/wurcs_frame_work.rb
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  - lib/wurcsverify.rb
@@ -63,7 +64,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: 1.3.1
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  requirements: []
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- rubygems_version: 3.2.33
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+ rubygems_version: 3.3.26
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68
  signing_key:
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  specification_version: 4
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  summary: Glycobook is a JRuby library for glycaninformatics