joerivandervelde-molgenis-gem 0.0.2
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- data/LICENCE +165 -0
- data/README.rdoc +17 -0
- data/lib/molgenis_dot.rb +167 -0
- data/lib/molgenis_model.rb +55 -0
- data/lib/molgenis_parser.rb +98 -0
- metadata +90 -0
data/LICENCE
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GNU LESSER GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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This version of the GNU Lesser General Public License incorporates
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the terms and conditions of version 3 of the GNU General Public
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License, supplemented by the additional permissions listed below.
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0. Additional Definitions.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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data/README.rdoc
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= MOLGENIS[http://molgenis.sourceforge.net] Metamodel Interaction gem
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Author:: Morris Swertz, Joeri van der Velde
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Version:: 0.0.1
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Contact:: m.a.swertz@rug.nl
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URL:: http://molgenis.sourceforge.net/
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Licence:: LGPL 3 (See LICENCE or http://www.gnu.org/licenses/lgpl.html)
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Copyright:: (c) 2004-2009 University of Groningen, University Medical Center Groningen, Inventory.nl
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== Synopsis
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This is a Ruby library to support the interaction with and visualization of MOLGENIS meta models [http://molgenis.sourceforge.net].
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- GraphViz[http://www.graphviz.org/Download.php] (a graph visualization package)
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- Rdoc gem
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- LibXml gem
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data/lib/molgenis_dot.rb
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require "erb"
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module MOLGENIS
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class Dot
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def write_dot(stream, model)
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b = binding
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template = %q{
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digraph G {
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compound = true
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fontname = "Bitstream Vera Sans"
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fontsize = 8
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page = "12f,12f"
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pagedir="TB"
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rankdir="BT"
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clusterrank = "local"
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bgcolor = "white"
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overlap = "false"
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splines = "false"
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layers = "1:2"
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outputorder="edgesfirst"
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node [
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fontname = "Arial"
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fontsize = 8
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shape = "record"
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color = "#808080"
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style="filled"
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fillcolor = "white"
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layer = "2"
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]
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edge [
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fontname = "Bitstream Vera Sans"
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fontsize = 8
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layer = "1"
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]
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<% if model.modules.size > 0 %>
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subgraph cluster_legend {
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rankdir ="LR";
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label = "module legend"
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color = "white"
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fillcolor = "white"
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rankType = "same"
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<% model.modules.each { |m| %>
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"<%= m.name %>"
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[
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style = "filled"
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colorscheme= "pastel19"
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fillcolor = "<%= m.color %>"
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fontname = "Arial"
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fontcolor = "black"
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color = "black"
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label = "{<%= m.name %>}"
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]
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<% } %>
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node [
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style = "invis"
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width = 0
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]
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"spook_legend"
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}
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<% end %>
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subgraph cluster_main {
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rankdir ="TB";
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pagedir="TB"
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fillcolor = "white"
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<% model.all_entities.each { |entity| %>
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"<%= entity.name %>"
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[
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style = "filled"
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<% if entity.color == 0 %>
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fillcolor="lemonchiffon1"
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<% else %>
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colorscheme=pastel19
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fillcolor = "<%=entity.color%>"
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<% end %>
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<%if entity.abstract %>
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fontname = "Arial-Italic"
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fontcolor = "dimgrey"
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color = "dimgrey"
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<% else %>
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fontname = "Arial"
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fontcolor = "black"
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color = "black"
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<% end %>
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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%>}"
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]
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<% } %>
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/*interface relationships*/
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edge [
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arrowhead = "empty"
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color = "grey"
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]
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<% model.all_entities.each do |entity| %>
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<% if entity.implements %>
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<% entity.implements.each do |interface| %>
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"<%= entity.name %>" -> "<%= interface %>"
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<%end%>
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<%end %>
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<% end %>
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/*extends relationships*/
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edge [
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arrowhead = "empty"
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color = "black"
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]
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<% model.all_entities.each do |entity| %>
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<% if entity.extends %>
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"<%= entity.name %>" -> "<%= entity.extends %>"
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<%end %>
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<% end %>
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/*one to many 'xref' foreign key relationships*/
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edge [
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arrowhead = "open"
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taillabel = "*"
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]
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<% model.all_entities.each do |entity| %>
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<% entity.fields.each do |f| %>
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<% if f.type == "xref" %>
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"<%= entity.name %>" -> "<%= f.xref_entity%>"
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<% end %>
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<% end %>
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<% end %>
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/*one to many 'mref' foreign key relationships*/
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edge [
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arrowhead = "open"
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arrowtail = "open"
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color = "black"
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taillabel = "*"
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arrowsize = 0.6
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rank = "same"
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]
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<% model.all_entities.each do |entity| %>
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<% entity.fields.each do |f| %>
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<% if f.type == "mref" %>
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"<%= entity.name %>" -> "<%= f.xref_entity%>"
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<% end %>
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<% end %>
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<% end %>
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node [
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style = "invis"
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width = 0
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]
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"spook_main"
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}
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edge [style = "invis"]
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<% if model.modules.size > 0%>"spook_legend" -> "spook_main"<% end %>
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}
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}.gsub(/^ /, '')
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imagedot = ERB.new(template, 0, "%<>")
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stream.puts imagedot.result(b)
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stream.flush
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end
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end
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end
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module MOLGENIS # :nodoc:
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# The model for a given MOLGENIS model
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class MolgenisModel
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# The list of all the entities that make up the model
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attr_accessor :version,:name,:label,:entities, :modules, :description
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# Creates an empty model a
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def initialize
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@entities = []
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@modules = []
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end
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def all_entities
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all_entities = []
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@entities.each{|entity|
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all_entities << entity
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}
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@modules.each { |module_obj|
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module_obj.entities.each {|entity|
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all_entities << entity
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}
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}
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puts all_entities.size
|
27
|
+
puts @modules.size
|
28
|
+
all_entities
|
29
|
+
end
|
30
|
+
end
|
31
|
+
|
32
|
+
class ModuleModel
|
33
|
+
attr_accessor :name,:label,:entities, :description, :color
|
34
|
+
|
35
|
+
def initialize
|
36
|
+
@entities = []
|
37
|
+
end
|
38
|
+
end
|
39
|
+
|
40
|
+
#Definition of an Entity in MOLGENIS model
|
41
|
+
class EntityModel
|
42
|
+
attr_accessor :name, :label, :fields, :abstract,:implements,:extends,:module_name,:color
|
43
|
+
|
44
|
+
# Creates an empty entity
|
45
|
+
def initialize
|
46
|
+
@fields = []
|
47
|
+
@implements = []
|
48
|
+
end
|
49
|
+
|
50
|
+
end
|
51
|
+
|
52
|
+
class FieldModel
|
53
|
+
attr_accessor :name,:type,:system,:xref_entity,:xref_field
|
54
|
+
end
|
55
|
+
end
|
@@ -0,0 +1,98 @@
|
|
1
|
+
require "libxml"
|
2
|
+
|
3
|
+
module MOLGENIS
|
4
|
+
|
5
|
+
class Parser
|
6
|
+
# Returns the model for the given molgenis_model.
|
7
|
+
# The method accepts objects of classes File, StringIO and String only.
|
8
|
+
# ===Usage
|
9
|
+
# foo = ... # stuff to initialize foo here
|
10
|
+
# bar = MOLGENIS_MODEL:Parser.new.parse(foo)
|
11
|
+
def parse(molgenis_src)
|
12
|
+
case molgenis_src.class.to_s
|
13
|
+
when /^string$/i
|
14
|
+
document = LibXML::XML::Parser.string(molgenis_src).parse
|
15
|
+
when /^stringio|file$/i
|
16
|
+
molgenis_src.rewind
|
17
|
+
document = LibXML::XML::Parser.string(molgenis_src.read).parse
|
18
|
+
else
|
19
|
+
raise "Error parsing file."
|
20
|
+
end
|
21
|
+
|
22
|
+
root = document.root
|
23
|
+
return nil if(root.name != "molgenis")
|
24
|
+
|
25
|
+
raise "Doesn't appear to be a MOLGENIS model" if root.name != "molgenis"
|
26
|
+
version = root["version"]
|
27
|
+
|
28
|
+
create_model(root, version)
|
29
|
+
end
|
30
|
+
|
31
|
+
def create_model(element, version) # :nodoc:
|
32
|
+
model = MolgenisModel.new
|
33
|
+
model.name = element.attributes['name']
|
34
|
+
puts element.attributes['name'] + model.name
|
35
|
+
model.version = version
|
36
|
+
model.description = ""
|
37
|
+
element.find("description").each { |desc|
|
38
|
+
desc.children.each { |el|
|
39
|
+
model.description = model.description + el.to_s
|
40
|
+
}
|
41
|
+
}
|
42
|
+
|
43
|
+
color = 0
|
44
|
+
parse_entities(element.find("entity"),model, color)
|
45
|
+
|
46
|
+
element.find("module").each { |module_xml|
|
47
|
+
|
48
|
+
module_obj = ModuleModel.new
|
49
|
+
module_attributes = module_xml.attributes
|
50
|
+
module_obj.name = module_attributes["name"]
|
51
|
+
entities = module_xml.find("entity")
|
52
|
+
|
53
|
+
color += 1
|
54
|
+
module_obj.color = color
|
55
|
+
parse_entities(entities,module_obj,color)
|
56
|
+
|
57
|
+
model.modules << module_obj
|
58
|
+
}
|
59
|
+
|
60
|
+
return model
|
61
|
+
end
|
62
|
+
|
63
|
+
def parse_entities(entities,module_obj,colorno)
|
64
|
+
if entities
|
65
|
+
entities.each do |entity_xml|
|
66
|
+
entity = EntityModel.new
|
67
|
+
entity.module_name = module_obj.name
|
68
|
+
entity_attributes = entity_xml.attributes
|
69
|
+
entity.name = entity_attributes["name"]
|
70
|
+
entity.color = colorno
|
71
|
+
entity_attributes["implements"].split(",").each { |interface|
|
72
|
+
entity.implements << interface
|
73
|
+
} if !entity_attributes["implements"].nil?
|
74
|
+
entity.extends = entity_attributes["extends"]
|
75
|
+
|
76
|
+
entity_xml.find("field").each do |field_xml|
|
77
|
+
field = FieldModel.new
|
78
|
+
field_attributes = field_xml.attributes
|
79
|
+
field.name = field_attributes["name"]
|
80
|
+
field.type = field_attributes["type"]
|
81
|
+
if(field_attributes["xref_field"])
|
82
|
+
split = field_attributes["xref_field"].split(".")
|
83
|
+
if(split.size == 2)
|
84
|
+
field.xref_entity = split[0]
|
85
|
+
field.xref_field = split[1]
|
86
|
+
else
|
87
|
+
field.xref_field = split[0]
|
88
|
+
field.xref_entity = field_attributes["xref_entity"]
|
89
|
+
end
|
90
|
+
end
|
91
|
+
entity.fields << field
|
92
|
+
end
|
93
|
+
module_obj.entities << entity
|
94
|
+
end
|
95
|
+
end
|
96
|
+
end
|
97
|
+
end
|
98
|
+
end
|
metadata
ADDED
@@ -0,0 +1,90 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: joerivandervelde-molgenis-gem
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.2
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Morris Swertz
|
8
|
+
- Joeri van der Velde
|
9
|
+
autorequire: ""
|
10
|
+
bindir: bin
|
11
|
+
cert_chain:
|
12
|
+
date: 2009-08-27 00:00:00 -07:00
|
13
|
+
default_executable:
|
14
|
+
dependencies:
|
15
|
+
- !ruby/object:Gem::Dependency
|
16
|
+
name: libxml-ruby
|
17
|
+
type: :runtime
|
18
|
+
version_requirement:
|
19
|
+
version_requirements: !ruby/object:Gem::Requirement
|
20
|
+
requirements:
|
21
|
+
- - ">="
|
22
|
+
- !ruby/object:Gem::Version
|
23
|
+
version: 1.1.3
|
24
|
+
version:
|
25
|
+
- !ruby/object:Gem::Dependency
|
26
|
+
name: rdoc
|
27
|
+
type: :runtime
|
28
|
+
version_requirement:
|
29
|
+
version_requirements: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ">="
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 2.4.3
|
34
|
+
version:
|
35
|
+
- !ruby/object:Gem::Dependency
|
36
|
+
name: darkfish-rdoc
|
37
|
+
type: :runtime
|
38
|
+
version_requirement:
|
39
|
+
version_requirements: !ruby/object:Gem::Requirement
|
40
|
+
requirements:
|
41
|
+
- - ">="
|
42
|
+
- !ruby/object:Gem::Version
|
43
|
+
version: 1.1.5
|
44
|
+
version:
|
45
|
+
description: This gem has simple classes to allow parsing and visualization of MOLGENIS datamodels.
|
46
|
+
email: m.a.swertz@rug.nl
|
47
|
+
executables: []
|
48
|
+
|
49
|
+
extensions: []
|
50
|
+
|
51
|
+
extra_rdoc_files:
|
52
|
+
- README.rdoc
|
53
|
+
- LICENCE
|
54
|
+
files:
|
55
|
+
- lib/molgenis_dot.rb
|
56
|
+
- lib/molgenis_model.rb
|
57
|
+
- lib/molgenis_parser.rb
|
58
|
+
- README.rdoc
|
59
|
+
- LICENCE
|
60
|
+
has_rdoc: true
|
61
|
+
homepage: http://gbic.target.rug.nl/trac/molgenis
|
62
|
+
licenses:
|
63
|
+
post_install_message:
|
64
|
+
rdoc_options:
|
65
|
+
- -N
|
66
|
+
- --tab-width=2
|
67
|
+
- --main=README.rdoc
|
68
|
+
require_paths:
|
69
|
+
- lib
|
70
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
71
|
+
requirements:
|
72
|
+
- - ">="
|
73
|
+
- !ruby/object:Gem::Version
|
74
|
+
version: 1.0.1
|
75
|
+
version:
|
76
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
77
|
+
requirements:
|
78
|
+
- - ">="
|
79
|
+
- !ruby/object:Gem::Version
|
80
|
+
version: "0"
|
81
|
+
version:
|
82
|
+
requirements: []
|
83
|
+
|
84
|
+
rubyforge_project:
|
85
|
+
rubygems_version: 1.3.5
|
86
|
+
signing_key:
|
87
|
+
specification_version: 1
|
88
|
+
summary: A Ruby implementation of the interaction of MOLGENIS datamodels (XML).
|
89
|
+
test_files: []
|
90
|
+
|