joerivandervelde-molgenis-gem 0.0.2

data/LICENCE

@@ -0,0 +1,165 @@
+		   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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+
+
+  This version of the GNU Lesser General Public License incorporates
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data/README.rdoc

@@ -0,0 +1,17 @@
+= MOLGENIS[http://molgenis.sourceforge.net] Metamodel Interaction gem
+
+Author::        Morris Swertz, Joeri van der Velde
+Version::       0.0.1
+Contact::       m.a.swertz@rug.nl
+URL::           http://molgenis.sourceforge.net/
+Licence::       LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
+Copyright::     (c) 2004-2009 University of Groningen, University Medical Center Groningen, Inventory.nl
+
+
+
+== Synopsis
+
+This is a Ruby library to support the interaction with and visualization of MOLGENIS meta models [http://molgenis.sourceforge.net].  
+- GraphViz[http://www.graphviz.org/Download.php] (a graph visualization package)
+- Rdoc gem
+- LibXml gem

data/lib/molgenis_dot.rb

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+require "erb"
+
+
+module MOLGENIS
+  class Dot
+    def write_dot(stream, model)
+    b = binding 
+    template = %q{
+    digraph G {
+    compound = true
+    fontname = "Bitstream Vera Sans"
+    fontsize = 8
+    page = "12f,12f"
+    pagedir="TB"
+    rankdir="BT"
+    clusterrank = "local"
+    bgcolor = "white"  
+    overlap = "false"
+    splines = "false"
+    layers = "1:2"
+    outputorder="edgesfirst"
+    
+
+        node [
+            fontname = "Arial"
+            fontsize = 8
+            shape = "record"
+            color = "#808080"
+            style="filled"
+            fillcolor = "white"
+            layer = "2" 
+        ]
+
+        edge [
+                fontname = "Bitstream Vera Sans"
+                fontsize = 8
+                layer = "1"
+        ]
+    <% if model.modules.size > 0 %>    
+    subgraph cluster_legend {
+        rankdir ="LR";
+        label = "module legend"
+        color = "white"
+        fillcolor = "white"
+        rankType = "same"
+        <% model.modules.each { |m| %>
+        "<%= m.name %>"
+        [
+                  style = "filled"
+                  colorscheme= "pastel19"
+                  fillcolor = "<%= m.color %>"
+                  fontname = "Arial"
+                  fontcolor = "black"
+                  color = "black"
+                  label = "{<%= m.name %>}" 
+        ]
+        <% } %>
+        
+        node [
+              style = "invis"
+              width = 0
+        ]
+        "spook_legend"
+    }       
+    <% end %>
+    
+    subgraph cluster_main {  
+        rankdir ="TB";
+        pagedir="TB" 
+        fillcolor = "white"
+        
+      <% model.all_entities.each { |entity| %>
+      "<%= entity.name %>"
+           [      
+                style = "filled"
+                <% if entity.color == 0 %>
+                fillcolor="lemonchiffon1"
+                <% else %>
+                colorscheme=pastel19
+                fillcolor = "<%=entity.color%>"
+                <% end %>
+                <%if entity.abstract %>
+                fontname = "Arial-Italic"
+                fontcolor = "dimgrey"
+                color = "dimgrey"
+                <% else %>
+                fontname = "Arial"
+                fontcolor = "black"
+                color = "black"
+                <% end %>
+                label = "{<% if entity.abstract %>Interface:<% end %><%= entity.name %><% entity.implements.each do |interface| %>\nimplements <%=interface%><% end %>|<% entity.fields.each do |f| %><% if !f.system %><%=f.name%> : <%=f.type %><% if (f.type=="xref" || f.type=="mref") %>(<%= f.xref_entity %>.<%=f.xref_field %>)<%end%>\l<%end%><%end%>}"
+            ]    
+      <% } %>
+      
+   /*interface relationships*/
+          edge [
+                  arrowhead = "empty"
+                  color = "grey"
+          ]
+  <% model.all_entities.each do |entity|  %>
+        <% if entity.implements %>
+           <% entity.implements.each do |interface| %>
+             "<%= entity.name %>" -> "<%= interface %>"
+            <%end%>
+        <%end %>
+  <% end %> 
+      
+  /*extends relationships*/
+          edge [
+                  arrowhead = "empty"
+                  color = "black"
+          ]
+  <% model.all_entities.each do |entity|  %>
+        <% if entity.extends %>
+         "<%= entity.name %>" -> "<%= entity.extends %>"
+        <%end %>
+  <% end %>    
+      
+  /*one to many 'xref' foreign key relationships*/
+          edge [
+                  arrowhead = "open"
+                  taillabel = "*"
+          ]
+          
+  <% model.all_entities.each do |entity|  %>
+        <% entity.fields.each do |f| %>
+           <% if f.type == "xref" %>
+          "<%= entity.name %>" -> "<%= f.xref_entity%>"
+       <% end %>
+    <% end %>
+  <% end %>
+  
+  /*one to many 'mref' foreign key relationships*/
+          edge [
+               arrowhead = "open"
+               arrowtail = "open"
+               color = "black"
+               taillabel = "*"
+               arrowsize = 0.6
+               rank = "same"
+          ]
+          
+  <% model.all_entities.each do |entity|  %>
+        <% entity.fields.each do |f| %>
+           <% if f.type == "mref" %>
+          "<%= entity.name %>" -> "<%= f.xref_entity%>"
+       <% end %>
+    <% end %>
+  <% end %>
+  
+          node [
+              style = "invis"
+              width = 0
+          ]
+          "spook_main" 
+      }
+      
+      edge [style = "invis"]
+      <% if model.modules.size > 0%>"spook_legend" -> "spook_main"<% end %>
+    }
+    }.gsub(/^  /, '')
+    imagedot = ERB.new(template, 0, "%<>")
+    stream.puts imagedot.result(b)
+    stream.flush
+    end
+  end
+end

data/lib/molgenis_model.rb

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+
+module MOLGENIS # :nodoc:
+  
+  # The model for a given MOLGENIS model
+  class MolgenisModel
+    # The list of all the entities that make up the model
+    attr_accessor :version,:name,:label,:entities, :modules, :description
+    
+    # Creates an empty model a
+    def initialize
+      @entities = []
+      @modules = []
+    end
+    
+    def all_entities
+      all_entities = []
+      @entities.each{|entity|
+        all_entities << entity
+      }
+      @modules.each { |module_obj|
+        module_obj.entities.each {|entity|
+          all_entities << entity
+        }
+        
+      }
+      puts all_entities.size
+      puts @modules.size
+      all_entities
+    end
+  end  
+  
+  class ModuleModel
+    attr_accessor :name,:label,:entities, :description, :color
+    
+    def initialize
+      @entities = []
+    end
+  end
+  
+  #Definition of an Entity in MOLGENIS model
+  class EntityModel
+    attr_accessor :name, :label, :fields, :abstract,:implements,:extends,:module_name,:color
+    
+    # Creates an empty entity 
+    def initialize
+      @fields = []
+      @implements = []
+    end
+    
+  end
+  
+  class FieldModel
+    attr_accessor :name,:type,:system,:xref_entity,:xref_field      
+  end
+end

data/lib/molgenis_parser.rb

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+require "libxml"
+
+module MOLGENIS
+  
+  class Parser
+    # Returns the model for the given molgenis_model.
+    # The method accepts objects of classes File, StringIO and String only.
+    # ===Usage
+    # foo = ... # stuff to initialize foo here
+    # bar = MOLGENIS_MODEL:Parser.new.parse(foo)
+    def parse(molgenis_src)
+      case molgenis_src.class.to_s
+        when /^string$/i
+        document = LibXML::XML::Parser.string(molgenis_src).parse
+        when /^stringio|file$/i
+        molgenis_src.rewind
+        document = LibXML::XML::Parser.string(molgenis_src.read).parse
+      else
+        raise "Error parsing file."
+      end
+      
+      root = document.root
+      return nil if(root.name != "molgenis")
+      
+      raise "Doesn't appear to be a MOLGENIS model" if root.name != "molgenis"
+      version = root["version"]
+      
+      create_model(root, version)
+    end
+    
+    def create_model(element, version) # :nodoc:
+      model = MolgenisModel.new
+      model.name = element.attributes['name']
+      puts element.attributes['name'] + model.name
+      model.version = version
+      model.description = ""
+      element.find("description").each { |desc| 
+        desc.children.each { |el| 
+          model.description = model.description + el.to_s
+        }
+      }     
+      
+      color = 0
+      parse_entities(element.find("entity"),model, color)
+      
+      element.find("module").each { |module_xml|
+      
+        module_obj = ModuleModel.new
+        module_attributes = module_xml.attributes
+        module_obj.name = module_attributes["name"]
+        entities = module_xml.find("entity")
+        
+        color += 1
+        module_obj.color = color
+        parse_entities(entities,module_obj,color)
+        
+        model.modules << module_obj
+      }
+     
+      return model
+    end
+    
+    def parse_entities(entities,module_obj,colorno)
+       if entities
+        entities.each do |entity_xml|
+          entity = EntityModel.new
+          entity.module_name = module_obj.name
+          entity_attributes = entity_xml.attributes
+          entity.name = entity_attributes["name"]
+          entity.color = colorno
+          entity_attributes["implements"].split(",").each { |interface|
+            entity.implements << interface
+          } if !entity_attributes["implements"].nil?
+          entity.extends = entity_attributes["extends"]
+
+          entity_xml.find("field").each do |field_xml|
+            field = FieldModel.new
+            field_attributes = field_xml.attributes
+            field.name = field_attributes["name"]
+            field.type = field_attributes["type"]
+            if(field_attributes["xref_field"])
+              split = field_attributes["xref_field"].split(".")
+              if(split.size == 2)
+                field.xref_entity = split[0]
+                field.xref_field = split[1]
+              else
+                field.xref_field = split[0]
+                field.xref_entity = field_attributes["xref_entity"]
+              end
+            end
+            entity.fields << field
+          end
+          module_obj.entities << entity
+        end
+      end
+    end
+  end  
+end

metadata

@@ -0,0 +1,90 @@
+--- !ruby/object:Gem::Specification 
+name: joerivandervelde-molgenis-gem
+version: !ruby/object:Gem::Version 
+  version: 0.0.2
+platform: ruby
+authors: 
+- Morris Swertz
+- Joeri van der Velde
+autorequire: ""
+bindir: bin
+cert_chain: 
+date: 2009-08-27 00:00:00 -07:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: libxml-ruby
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.1.3
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: rdoc
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 2.4.3
+    version: 
+- !ruby/object:Gem::Dependency 
+  name: darkfish-rdoc
+  type: :runtime
+  version_requirement: 
+  version_requirements: !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 1.1.5
+    version: 
+description: This gem has simple classes to allow parsing and visualization of MOLGENIS datamodels.
+email: m.a.swertz@rug.nl
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- README.rdoc
+- LICENCE
+files: 
+- lib/molgenis_dot.rb
+- lib/molgenis_model.rb
+- lib/molgenis_parser.rb
+- README.rdoc
+- LICENCE
+has_rdoc: true
+homepage: http://gbic.target.rug.nl/trac/molgenis
+licenses: 
+post_install_message: 
+rdoc_options: 
+- -N
+- --tab-width=2
+- --main=README.rdoc
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: 1.0.1
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.5
+signing_key: 
+specification_version: 1
+summary: A Ruby implementation of the interaction of MOLGENIS datamodels (XML).
+test_files: []
+