glycobook 0.1.0.alpha.12-java → 0.1.0.alpha.14-java

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 107dbcb98ac4fa90c819743960c2218b458e5919cf0a8a112567f5d88642ecef
+  metadata.gz: 9783edf50dd8884c859bd729245b8db2bfd1b460f9d492decb8b53b888aed05d
+  data.tar.gz: 763879fa7da8fd5d0d846eaa327970d426f689fe5426540616889742dc15f6fc
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-  data.tar.gz: e1b1fe8e756bda718aee3c965c51de801ba34f0a6b39cef5a1c246b026f839cfa403da344286c37bae32ca49e52969d2fede69ba3d8117fad34c10de275a2294
+  metadata.gz: 2226714ccd56a84dd8c5977140011983ffc9f5d27c934a78de632e72f2ffbd593e41d6117f0b73575aa88a69526e0d27219849917964f0370b3fac8714f0c379
+  data.tar.gz: d8cac73b68d01d07a22a1d90a5188fb987c24253f8d5dec048feee76260892dbd4879714677b8b9fd67d1288e05bde674f0e6ff92b8e9e25ed27010a53e621d8

data/jar.yml

@@ -10,8 +10,10 @@ list:
     file: "jar/wurcsframework-1.2.14.jar"
   - url: "https://gitlab.com/glycoinfo/wurcsframework/-/package_files/70458150/download"
     file: "jar/wurcsframework-1.0.1.jar"
-  - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.7/slf4j-api-2.0.7.jar"
+  - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-api/2.0.9/slf4j-api-2.0.9.jar"
     file: "jar/slf4j-api.jar"
+  - url: "https://repo1.maven.org/maven2/org/slf4j/slf4j-simple/2.0.9/slf4j-simple-2.0.9.jar"
+    file: "jar/slf4j-simple-2.0.9.jar"
   - url: "https://gitlab.glyco.info/glycosmos/subsumption/subsumption/-/package_files/567/download"
     file: "jar/subsumption.jar"
   - url: "https://gitlab.glyco.info/glycosmos/glytoucangroup/archetype/lib/-/package_files/489/download"

data/lib/glycobook/Loggerinit.rb

@@ -0,0 +1,33 @@
+require 'java'
+require 'logger'
+require_relative  '../jar/slf4j-api.jar'
+require_relative  '../jar/slf4j-simple.jar'
+
+java_import 'org.slf4j.LoggerFactory'
+
+module GlycoBook
+class JRubySLF4JLogger < Logger
+  def initialize(name)
+    super(STDOUT)  # STDOUT is dummy
+    @java_logger = LoggerFactory.getLogger(name)
+  end
+  def add(severity, message , progname , &block)
+
+  message = block.call if block
+  message = message.to_s
+
+  case severity
+    when 0  # Logger::DEBUG
+      @java_logger.debug(message)
+    when 1  # Logger::INFO
+      @java_logger.info(message)
+    when 2  # Logger::WARN
+      @java_logger.warn(message)
+    when 3, 4# Logger::ERROR, Logger::FATAL
+      @java_logger.error(message)
+    else
+      @java_logger.info(message)
+    end
+  end
+end
+end

data/lib/glycobook/gly_tou_can.rb

@@ -7,8 +7,6 @@ require_relative '../jar/slf4j-api.jar'
 java_import 'org.glytoucan.Archetype'
 java_import 'org.glycoinfo.WURCSFramework.wurcs.graph.WURCSGraph'
 java_import 'org.glycoinfo.WURCSFramework.util.WURCSException'
-java_import 'org.slf4j.Logger'
-java_import 'org.slf4j.LoggerFactory'
 
 module GlycoBook
 class GlyTouCan

data/lib/glycobook/glycan_builder.rb

@@ -2,7 +2,6 @@ require 'java'
 
 require_relative '../jar/glycanbuilder2.jar'
 require_relative '../jar/wurcsframework.jar'
-require_relative '../jar/slf4j-api.jar'
 require_relative "../jar/batik-all.jar"
 
 java_import 'java.io.ByteArrayOutputStream'

data/lib/glycobook/glycan_format_converter.rb

@@ -2,7 +2,6 @@ require 'java'
 
 require_relative '../jar/glycanformatconverter.jar'
 require_relative '../jar/wurcsframework.jar'
-require_relative '../jar/slf4j-api.jar'
 require_relative "../jar/MolecularFramework.jar"
 
 java_import 'org.glycoinfo.GlycanFormatconverter.io.GlycoCT.WURCSToGlycoCT'

data/lib/glycobook/subsumption.rb

@@ -2,7 +2,6 @@ require 'java'
 
 require_relative '../jar/subsumption.jar'
 require_relative '../jar/wurcsframework.jar'
-require_relative '../jar/slf4j-api.jar'
 
 java_import 'org.glycoinfo.subsumption.manipulation.GraphManager'
 java_import 'org.glycoinfo.WURCSFramework.wurcs.graph.WURCSGraph'
@@ -57,7 +56,7 @@ class Subsumption
     end
   end
 
-  java_import 'org.glycoinfo.subsumption.generator.BaseComposition'
+  java_import 'org.glycoinfo.subsumption.generator.BaseCompositionWithoutLinkage'
   def baseComposition(w)
     g = nil
     begin

data/lib/glycobook/wurcs_frame_work.rb

@@ -1,22 +1,23 @@
-# lib/my_gem.rb
 require 'java'
-require_relative  '../jar/slf4j-api.jar'
+
 module GlycoBook
-class WurcsFrameWork
+
+  class WurcsFrameWork
     require_relative  '../jar/wurcsframework.jar'
-  java_import 'org.glycoinfo.WURCSFramework.util.validation.WURCSValidator'
-  java_import 'org.slf4j.Logger'
-  def validator(w)
-    validator = WURCSValidator.new
-    validator.start(w)
-    reports = {}
-    reports["VALIDATOR"] = ["WURCSFramework-1.2.14"]
-    reports["WARNING"] = validator.getReport().hasWarning()
-    reports["ERROR"] = validator.getReport().hasError()
-    reports["UNVERIFIABLE"] = validator.getReport().hasUnverifiable()
-    return {"message" => reports,
+    java_import 'org.glycoinfo.WURCSFramework.util.validation.WURCSValidator'
+    java_import 'org.slf4j.Logger'
+    
+    def validator(w)
+      validator = WURCSValidator.new
+      validator.start(w)
+      reports = {}
+      reports["VALIDATOR"] = ["WURCSFramework-1.2.14"]
+      reports["WARNING"] = validator.getReport().hasWarning()
+      reports["ERROR"] = validator.getReport().hasError()
+      reports["UNVERIFIABLE"] = validator.getReport().hasUnverifiable()
+      return {"message" => reports,
             "StandardWURCS" => validator.getReport().standard_string(),
             "RESULTS" => validator.getReport().getResults() }
+    end
   end
 end
-end

data/lib/glycobook.rb

@@ -1,6 +1,7 @@
 module GlycoBook
 
 end
+require 'glycobook/Loggerinit'
 require 'glycobook/glycan_builder'
 require 'glycobook/glycan_format_converter'
 require 'glycobook/gly_tou_can'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: glycobook
 version: !ruby/object:Gem::Version
-  version: 0.1.0.alpha.12
+  version: 0.1.0.alpha.14
 platform: java
 authors:
 - Akihiro Fujita
@@ -34,6 +34,7 @@ files:
 - jar.yml
 - lib/bookinit.rb
 - lib/glycobook.rb
+- lib/glycobook/Loggerinit.rb
 - lib/glycobook/gly_tou_can.rb
 - lib/glycobook/glycan_builder.rb
 - lib/glycobook/glycan_format_converter.rb