madeline 0.1.1 → 0.1.2

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Files changed (13) hide show
  1. data/Manifest +4 -1
  2. data/README.md +12 -3
  3. data/Rakefile +1 -1
  4. data/ext/{madeline2-linux-x86_64 → madeline/madeline2-linux-x86_64} +0 -0
  5. data/lib/madeline.rb +4 -3
  6. data/lib/madeline/interface.rb +25 -9
  7. data/madeline.gemspec +5 -5
  8. data/test/fixtures/madeline.yml +5 -0
  9. data/test/labels.txt +11 -0
  10. data/test/madeline_test.rb +39 -16
  11. data/test/pedigree.txt +1 -1
  12. data/test/test_helper.rb +12 -0
  13. metadata +8 -4
data/Manifest CHANGED
@@ -1,8 +1,11 @@
1
1
  README.md
2
2
  Rakefile
3
- ext/madeline2-linux-x86_64
3
+ ext/madeline/madeline2-linux-x86_64
4
4
  lib/madeline.rb
5
5
  lib/madeline/interface.rb
6
+ test/fixtures/madeline.yml
7
+ test/labels.txt
6
8
  test/madeline_test.rb
7
9
  test/pedigree.txt
10
+ test/test_helper.rb
8
11
  Manifest
data/README.md CHANGED
@@ -13,19 +13,28 @@ sudo gem install madeline
13
13
  Usage
14
14
  -----
15
15
 
16
- The *Madeline::Interface* has a single method, `draw`, which can be passed a string or an open *IO* object, and returns the Madeline XML. The result is returned as a string, or, if a block is passed, yields as an *IO* object for streaming writes.
16
+ The *Madeline::Interface* has a single method, `draw`, which can be passed a string or an open *IO* object, and returns the Madeline XML. The draw method returns a filename and warnings, or, if a block is passed, yields the file contents and warnings.
17
17
 
18
18
  <pre>
19
19
  require 'rubygems'
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20
  require 'madeline'
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- Madeline::Interface.new.draw(File.open('pedigree.txt', 'r'))
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+ pedigree_filename, warnings = Madeline::Interface.new.draw(File.open('pedigree.txt', 'r'))
22
+ </pre>
23
+
24
+ <pre>
25
+ require 'rubygems'
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+ require 'madeline'
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+ pedigree, warnings = Madeline::Interface.new.draw(File.open('pedigree.txt','r')) { |filehandle, warnings|
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+ puts "warnings #{warnings}"
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+ pedigree = filehandle.read
30
+ }
22
31
  </pre>
23
32
 
24
33
  When creating a *Madeline::Interface*, you can pass [any options that the madeline2 program accepts](http://eyegene.ophthy.med.umich.edu/madeline/documentation.php) to the interface and they'll be forwarded. For example, to create an embedded result:
25
34
 
26
35
  <pre>
27
36
  artist = Madeline::Interface.new(:embedded => true)
28
- artist.draw(File.open('pedigree.txt', 'r'))
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+ pedigree_filename, warnings = artist.draw(File.open('pedigree.txt', 'r'))
29
38
  </pre>
30
39
 
31
40
  The default values of all the madeline2 flags are identical to the command-line version.
data/Rakefile CHANGED
@@ -4,7 +4,7 @@ require 'echoe'
4
4
  require 'rake/testtask'
5
5
  require 'rake/rdoctask'
6
6
 
7
- Echoe.new('madeline','0.1.1') do |p|
7
+ Echoe.new('madeline','0.1.2') do |p|
8
8
  p.description = "Interface to Madeline2"
9
9
  p.url = "http://github.com/dmauldin/madeline"
10
10
  p.author = "Denise Mauldin"
data/lib/madeline.rb CHANGED
@@ -1,13 +1,14 @@
1
1
  module Madeline
2
2
 
3
- VERSION = "0.1.0"
3
+ VERSION = "0.1.2"
4
4
 
5
5
  MADELINE_VERSION = "2.0"
6
6
 
7
- MADELINE_COMMAND = "ext/madeline2-linux-x86_64"
8
-
9
7
  MADELINE_ROOT = File.expand_path(File.dirname(__FILE__))
10
8
 
9
+ MADELINE_COMMAND = "#{MADELINE_ROOT}/../ext/madeline/madeline2-linux-x86_64"
10
+
11
+
11
12
  end
12
13
 
13
14
  require 'madeline/interface'
data/lib/madeline/interface.rb CHANGED
@@ -26,7 +26,8 @@ module Madeline
26
26
  tempfile.flush
27
27
  tempoutfile = Tempfile.new('madeline_output')
28
28
  begin
29
- log = `#{command} --outputprefix #{tempoutfile.path} --outputext .xml #{tempfile.path}`
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+ log = `#{command} --outputprefix #{tempoutfile.path} --outputext .xml #{tempfile.path} 2>&1`
30
+
30
31
  unless (log.match(/Pedigree output file is/)) then
31
32
  raise Error, "Madeline failed to run. Check Madeline path."
32
33
  end
@@ -34,19 +35,27 @@ module Madeline
34
35
  if (!File.exists?(filename)) then
35
36
  raise Error, "Output File doesn't exist."
36
37
  end
37
- f = File.new(filename,"r")
38
- return f.read
39
38
  rescue Exception
40
- raise Error, "Madeline failed to run. Tried #{@madeline}"
39
+ if log.nil? then
40
+ raise Error, "Madeline failed to run. Tried #{@madeline}"
41
+ else
42
+ raise Error, "Madeline had an error: #{log}"
43
+ end
41
44
  ensure
42
45
  tempfile.close!
43
46
  end
44
47
  unless $?.exitstatus.zero?
45
- raise Error, result
48
+ raise Error, log
46
49
  end
47
-
48
- yield(StringIO.new(result)) if block_given?
49
- result
50
+ warnings = Array.new
51
+ lines = log.split("\n")
52
+ lines.each do |line|
53
+ line.gsub!("\e[0m","") # remove the end color code from madeline2
54
+ warnings.push(line.match(/Warning:.*/)[0]) if line.match(/Warning:/)
55
+ end
56
+ warn = warnings.join("; ")
57
+ yield(File.new(filename), warn) if block_given?
58
+ return filename, warn
50
59
  end
51
60
 
52
61
  private
@@ -55,7 +64,14 @@ module Madeline
55
64
  options.map do |k, v|
56
65
  next if k == 'outputext'
57
66
  next if k == 'outputprefix'
58
- if (v == true || v == "true")
67
+ if (k.to_s == 'L')
68
+ if v.is_a?(Array)
69
+ vals = v.join(" ")
70
+ ["-L \"#{vals}\""]
71
+ else
72
+ ["-L \"#{v}\""]
73
+ end
74
+ elsif (v == true || v == "true")
59
75
  ["--#{k}"]
60
76
  elsif (v.is_a?(Array))
61
77
  v.map {|v2| ["--#{k}", v2.to_s]}
data/madeline.gemspec CHANGED
@@ -2,22 +2,22 @@
2
2
 
3
3
  Gem::Specification.new do |s|
4
4
  s.name = "madeline"
5
- s.version = "0.1.1"
5
+ s.version = "0.1.2"
6
6
 
7
7
  s.required_rubygems_version = Gem::Requirement.new(">= 1.2") if s.respond_to? :required_rubygems_version=
8
8
  s.authors = ["Denise Mauldin"]
9
- s.date = "2011-09-06"
9
+ s.date = "2011-09-08"
10
10
  s.description = "Interface to Madeline2"
11
11
  s.email = "denise.mauldin@gmail.com"
12
- s.extra_rdoc_files = ["README.md", "ext/madeline2-linux-x86_64", "lib/madeline.rb", "lib/madeline/interface.rb"]
13
- s.files = ["README.md", "Rakefile", "ext/madeline2-linux-x86_64", "lib/madeline.rb", "lib/madeline/interface.rb", "test/madeline_test.rb", "test/pedigree.txt", "Manifest", "madeline.gemspec"]
12
+ s.extra_rdoc_files = ["README.md", "ext/madeline/madeline2-linux-x86_64", "lib/madeline.rb", "lib/madeline/interface.rb"]
13
+ s.files = ["README.md", "Rakefile", "ext/madeline/madeline2-linux-x86_64", "lib/madeline.rb", "lib/madeline/interface.rb", "test/fixtures/madeline.yml", "test/labels.txt", "test/madeline_test.rb", "test/pedigree.txt", "test/test_helper.rb", "Manifest", "madeline.gemspec"]
14
14
  s.homepage = "http://github.com/dmauldin/madeline"
15
15
  s.rdoc_options = ["--line-numbers", "--inline-source", "--title", "Madeline", "--main", "README.md"]
16
16
  s.require_paths = ["lib", "ext"]
17
17
  s.rubyforge_project = "madeline"
18
18
  s.rubygems_version = "1.8.10"
19
19
  s.summary = "Interface to Madeline2"
20
- s.test_files = ["test/madeline_test.rb"]
20
+ s.test_files = ["test/test_helper.rb", "test/madeline_test.rb"]
21
21
 
22
22
  if s.respond_to? :specification_version then
23
23
  s.specification_version = 3
data/test/fixtures/madeline.yml ADDED
@@ -0,0 +1,5 @@
1
+ pedigree: "<?xml version=\"1.0\" standalone=\"no\"?>\n <svg version=\"1.1\" id=\"svgDC\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"370.44\" height=\"380.481\" onload=\"init()\" >\n <defs>\n <style type=\"text/css\"><![CDATA[\n\nline{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nrect{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nellipse{\n\tstroke: #000;\n fill: #fff;\n\tstroke-width:0.25mm;\n}\n\ntext{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:12px;\n}\n\n.smallText{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:9px;\n\tfill:#444;\n}\n\n.layer text{\n\tfill:#930;\n}\n\n.layer line{\n\tstroke:#000;\n}\n\n.birthOrder,.unknownTwins{\n\tfont-size: 8px;\n}\n\n.header{\n\tfont-size:18px;\n\tfont-weight:bold;\n}\n\n.keyBox{\n\tfill:#e5e5e5;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\n.mating:hover{\n\tstroke-width:1mm;\n\tstroke:#d56300;\n}\n\n.selectedIndividual{\n\tstroke-width:1mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#d00;\n fill:none;\n}\n\n.selectedIndividual:hover{\n\tstroke:#d00;\n\tfill:#ffbbbb;\n\tfill-opacity:0.70;\n}\n\n.solid{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:none;\n}\n\n.dashed{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.solid:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.dashed:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.filled{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#000;\n}\n\n.specialIcons{\n\tstroke-width:0.25mm;\n\tstroke-linecap:round;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#fff;\n}\n\n.specialLines{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tfill:none;\n}\n\n.thinLine{\n\tfill:none;\n\tstroke: #000;\n\tstroke-width:0.25mm;\n}\n\n.curvedConnector{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-width:0.5mm;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.curvedConnector:hover{\n\tstroke:#d56300;\n}\n\n.whiteInkLetter_1{\n\tfont-size: 12px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_2{\n\tfont-size: 10px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_3{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.whiteInkLetter{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.blackInkLetter_1{\n\tfont-size: 12px;\n}\n\n.blackInkLetter_2{\n\tfont-size: 10px;\n}\n\n.blackInkLetter_3{\n\tfont-size: 8px;\n}\n\n.blackInkLetter{\n\tfont-size: 8px;\n\tfill: #000;\n}\n\n]]></style>\n <script type=\"text/javascript\" xlink:href=\"javascript/madeline.js\"></script>\n <marker id=\"endArrow\" viewBox=\"0 0 10 10\" refX=\"1\" refY=\"5\" markerUnits=\"strokeWidth\" orient=\"auto\" markerWidth=\"5\" markerHeight=\"4\"> <polyline points=\"0,0 10,5 0,10 1,5\" fill=\"#000\" /> </marker>\n </defs>\n <g class=\"pedigree\" transform=\"translate(-462.86)\">\n\n <g id=\"bottomLayer\" class=\"layer\" >\n\n </g>\n <g id=\"layer0\" class=\"layer\" >\n </g>\n\n <g class=\"drawing\">\n <text x=\"557.36\" y=\"30\" text-anchor=\"middle\" class=\"header\" >madTest</text>\n <rect x=\"500.66\" y=\"38.66\" width=\"22.68\" height=\"22.68\" id=\"g43\" class=\"solid\"/>\n <text x=\"512\" y=\"92.5845\" text-anchor=\"middle\" >g43</text>\n <line x1=\"523.34\" y1=\"50\" x2=\"591.38\" y2=\"50\" />\n<circle cx=\"602.72\" cy=\"50\" r=\"11.34\" id=\"g44\" class=\"solid\"/>\n <text x=\"602.72\" y=\"92.5845\" text-anchor=\"middle\" >g44</text>\n <line class=\"mating\" id=\"g44:g43\" x1=\"557.36\" y1=\"50\" x2=\"557.36\" y2=\"123.907\" />\n <line class=\"solid\" x1=\"512\" y1=\"123.907\" x2=\"512\" y2=\"152.257\" />\n<circle cx=\"512\" cy=\"163.597\" r=\"11.34\" id=\"g47\" class=\"solid\"/>\n <text x=\"512\" y=\"206.181\" text-anchor=\"middle\" >g47</text>\n <line class=\"solid\" x1=\"648.08\" y1=\"123.907\" x2=\"648.08\" y2=\"152.257\" />\n<circle cx=\"648.08\" cy=\"163.597\" r=\"11.34\" id=\"g49\" class=\"solid\"/>\n <text x=\"648.08\" y=\"206.181\" text-anchor=\"middle\" >g49</text>\n <line x1=\"659.42\" y1=\"163.597\" x2=\"727.46\" y2=\"163.597\" />\n <rect x=\"727.46\" y=\"152.257\" width=\"22.68\" height=\"22.68\" id=\"g48\" class=\"solid\"/>\n <text x=\"738.8\" y=\"206.181\" text-anchor=\"middle\" >g48</text>\n <line class=\"mating\" id=\"g49:g48\" x1=\"693.44\" y1=\"163.597\" x2=\"693.44\" y2=\"237.504\" />\n <line class=\"solid\" x1=\"602.72\" y1=\"237.504\" x2=\"602.72\" y2=\"265.854\" />\n<circle cx=\"602.72\" cy=\"277.194\" r=\"11.34\" id=\"g50\" class=\"solid\"/>\n <text x=\"602.72\" y=\"319.778\" text-anchor=\"middle\" >g50</text>\n <line class=\"solid\" x1=\"693.44\" y1=\"237.504\" x2=\"693.44\" y2=\"265.854\" />\n<circle cx=\"693.44\" cy=\"277.194\" r=\"11.34\" id=\"g51\" class=\"solid\"/>\n <text x=\"693.44\" y=\"319.778\" text-anchor=\"middle\" >g51</text>\n <line class=\"solid\" x1=\"784.16\" y1=\"237.504\" x2=\"784.16\" y2=\"265.854\" />\n <rect x=\"772.82\" y=\"265.854\" width=\"22.68\" height=\"22.68\" id=\"g52\" class=\"solid\"/>\n <text x=\"784.16\" y=\"319.778\" text-anchor=\"middle\" >g52</text>\n <line x1=\"602.72\" y1=\"237.504\" x2=\"784.16\" y2=\"237.504\" />\n <line x1=\"512\" y1=\"123.907\" x2=\"648.08\" y2=\"123.907\" />\n </g>\n\n </g>\n </svg>\n\n"
2
+ arial_out: "<?xml version=\"1.0\" standalone=\"no\"?>\n <svg version=\"1.1\" id=\"svgDC\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"370.44\" height=\"380.481\" onload=\"init()\" >\n <defs>\n <style type=\"text/css\"><![CDATA[\n\nline{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nrect{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nellipse{\n\tstroke: #000;\n fill: #fff;\n\tstroke-width:0.25mm;\n}\n\ntext{\n\tfont-family:\"Arial\",sans-serif;\n\tfont-size:12px;\n}\n\n.smallText{\n\tfont-family:\"Arial\",sans-serif;\n\tfont-size:9px;\n\tfill:#444;\n}\n\n.layer text{\n\tfill:#930;\n}\n\n.layer line{\n\tstroke:#000;\n}\n\n.birthOrder,.unknownTwins{\n\tfont-size: 8px;\n}\n\n.header{\n\tfont-size:18px;\n\tfont-weight:bold;\n}\n\n.keyBox{\n\tfill:#e5e5e5;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\n.mating:hover{\n\tstroke-width:1mm;\n\tstroke:#d56300;\n}\n\n.selectedIndividual{\n\tstroke-width:1mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#d00;\n fill:none;\n}\n\n.selectedIndividual:hover{\n\tstroke:#d00;\n\tfill:#ffbbbb;\n\tfill-opacity:0.70;\n}\n\n.solid{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:none;\n}\n\n.dashed{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.solid:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.dashed:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.filled{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#000;\n}\n\n.specialIcons{\n\tstroke-width:0.25mm;\n\tstroke-linecap:round;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#fff;\n}\n\n.specialLines{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tfill:none;\n}\n\n.thinLine{\n\tfill:none;\n\tstroke: #000;\n\tstroke-width:0.25mm;\n}\n\n.curvedConnector{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-width:0.5mm;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.curvedConnector:hover{\n\tstroke:#d56300;\n}\n\n.whiteInkLetter_1{\n\tfont-size: 12px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_2{\n\tfont-size: 10px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_3{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.whiteInkLetter{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.blackInkLetter_1{\n\tfont-size: 12px;\n}\n\n.blackInkLetter_2{\n\tfont-size: 10px;\n}\n\n.blackInkLetter_3{\n\tfont-size: 8px;\n}\n\n.blackInkLetter{\n\tfont-size: 8px;\n\tfill: #000;\n}\n\n]]></style>\n <script type=\"text/javascript\" xlink:href=\"javascript/madeline.js\"></script>\n <marker id=\"endArrow\" viewBox=\"0 0 10 10\" refX=\"1\" refY=\"5\" markerUnits=\"strokeWidth\" orient=\"auto\" markerWidth=\"5\" markerHeight=\"4\"> <polyline points=\"0,0 10,5 0,10 1,5\" fill=\"#000\" /> </marker>\n </defs>\n <g class=\"pedigree\" transform=\"translate(-462.86)\">\n\n <g id=\"bottomLayer\" class=\"layer\" >\n\n </g>\n <g id=\"layer0\" class=\"layer\" >\n </g>\n\n <g class=\"drawing\">\n <text x=\"557.36\" y=\"30\" text-anchor=\"middle\" class=\"header\" >madTest</text>\n <rect x=\"500.66\" y=\"38.66\" width=\"22.68\" height=\"22.68\" id=\"g43\" class=\"solid\"/>\n <text x=\"512\" y=\"92.5845\" text-anchor=\"middle\" >g43</text>\n <line x1=\"523.34\" y1=\"50\" x2=\"591.38\" y2=\"50\" />\n<circle cx=\"602.72\" cy=\"50\" r=\"11.34\" id=\"g44\" class=\"solid\"/>\n <text x=\"602.72\" y=\"92.5845\" text-anchor=\"middle\" >g44</text>\n <line class=\"mating\" id=\"g44:g43\" x1=\"557.36\" y1=\"50\" x2=\"557.36\" y2=\"123.907\" />\n <line class=\"solid\" x1=\"512\" y1=\"123.907\" x2=\"512\" y2=\"152.257\" />\n<circle cx=\"512\" cy=\"163.597\" r=\"11.34\" id=\"g47\" class=\"solid\"/>\n <text x=\"512\" y=\"206.181\" text-anchor=\"middle\" >g47</text>\n <line class=\"solid\" 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x1=\"648.08\" y1=\"123.907\" x2=\"648.08\" y2=\"152.257\" />\n<circle cx=\"648.08\" cy=\"163.597\" r=\"11.34\" id=\"g49\" class=\"solid\"/>\n <text x=\"648.08\" y=\"206.181\" text-anchor=\"middle\" >g49</text>\n <line x1=\"659.42\" y1=\"163.597\" x2=\"727.46\" y2=\"163.597\" />\n <rect x=\"727.46\" y=\"152.257\" width=\"22.68\" height=\"22.68\" id=\"g48\" class=\"solid\"/>\n <text x=\"738.8\" y=\"206.181\" text-anchor=\"middle\" >g48</text>\n <line class=\"mating\" id=\"g49:g48\" x1=\"693.44\" y1=\"163.597\" x2=\"693.44\" y2=\"237.504\" />\n <line class=\"solid\" x1=\"602.72\" y1=\"237.504\" x2=\"602.72\" y2=\"265.854\" />\n<circle cx=\"602.72\" cy=\"277.194\" r=\"11.34\" id=\"g50\" class=\"solid\"/>\n <text x=\"602.72\" y=\"319.778\" text-anchor=\"middle\" >g50</text>\n <line class=\"solid\" x1=\"693.44\" y1=\"237.504\" x2=\"693.44\" y2=\"265.854\" />\n<circle cx=\"693.44\" cy=\"277.194\" r=\"11.34\" id=\"g51\" class=\"solid\"/>\n <text x=\"693.44\" y=\"319.778\" text-anchor=\"middle\" >g51</text>\n <line class=\"solid\" x1=\"784.16\" y1=\"237.504\" x2=\"784.16\" y2=\"265.854\" />\n <rect x=\"772.82\" y=\"265.854\" width=\"22.68\" height=\"22.68\" id=\"g52\" class=\"solid\"/>\n <text x=\"784.16\" y=\"319.778\" text-anchor=\"middle\" >g52</text>\n <line x1=\"602.72\" y1=\"237.504\" x2=\"784.16\" y2=\"237.504\" />\n <line x1=\"512\" y1=\"123.907\" x2=\"648.08\" y2=\"123.907\" />\n </g>\n\n </g>\n </svg>\n\n"
data/test/labels.txt ADDED
@@ -0,0 +1,11 @@
1
+ FamilyID IndividualID Gender Father Mother cond1 cond2 cond3 geneID:79083
2
+ family1 g44 F . . Y . . non,nfs
3
+ family1 g43 M . . . . . .
4
+ family1 g21 M . . Y Y Y non
5
+ family1 g50 F g48 g49 . . . .
6
+ family1 g47 F g43 g44 Y . . nfs,non
7
+ family1 g51 F g48 g49 Y . . non,nfs
8
+ family1 g48 M . . . . . .
9
+ family1 g56 M . . Y Y Y non,nfs
10
+ family1 g52 M g48 g49 Y Y Y non,nfs
11
+ family1 g49 F g43 g44 Y . . non,nfs
data/test/madeline_test.rb CHANGED
@@ -1,14 +1,10 @@
1
1
  require 'test/unit'
2
2
  require 'stringio'
3
+ require File.dirname(__FILE__) + '/test_helper'
4
+ require 'madeline'
3
5
 
4
6
  class MadelineTest < Test::Unit::TestCase
5
- require 'madeline'
6
-
7
- def setup
8
- @pedigree_out = "<?xml version=\"1.0\" standalone=\"no\"?>\n <svg version=\"1.1\" id=\"svgDC\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"370.44\" height=\"380.481\" onload=\"init()\" >\n <defs>\n <style type=\"text/css\"><![CDATA[\n\nline{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nrect{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nellipse{\n\tstroke: #000;\n fill: #fff;\n\tstroke-width:0.25mm;\n}\n\ntext{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:12px;\n}\n\n.smallText{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:9px;\n\tfill:#444;\n}\n\n.layer text{\n\tfill:#930;\n}\n\n.layer line{\n\tstroke:#000;\n}\n\n.birthOrder,.unknownTwins{\n\tfont-size: 8px;\n}\n\n.header{\n\tfont-size:18px;\n\tfont-weight:bold;\n}\n\n.keyBox{\n\tfill:#e5e5e5;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\n.mating:hover{\n\tstroke-width:1mm;\n\tstroke:#d56300;\n}\n\n.selectedIndividual{\n\tstroke-width:1mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#d00;\n fill:none;\n}\n\n.selectedIndividual:hover{\n\tstroke:#d00;\n\tfill:#ffbbbb;\n\tfill-opacity:0.70;\n}\n\n.solid{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:none;\n}\n\n.dashed{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.solid:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.dashed:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.filled{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#000;\n}\n\n.specialIcons{\n\tstroke-width:0.25mm;\n\tstroke-linecap:round;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#fff;\n}\n\n.specialLines{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tfill:none;\n}\n\n.thinLine{\n\tfill:none;\n\tstroke: #000;\n\tstroke-width:0.25mm;\n}\n\n.curvedConnector{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-width:0.5mm;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.curvedConnector:hover{\n\tstroke:#d56300;\n}\n\n.whiteInkLetter_1{\n\tfont-size: 12px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_2{\n\tfont-size: 10px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_3{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.whiteInkLetter{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.blackInkLetter_1{\n\tfont-size: 12px;\n}\n\n.blackInkLetter_2{\n\tfont-size: 10px;\n}\n\n.blackInkLetter_3{\n\tfont-size: 8px;\n}\n\n.blackInkLetter{\n\tfont-size: 8px;\n\tfill: #000;\n}\n\n]]></style>\n <script type=\"text/javascript\" xlink:href=\"javascript/madeline.js\"></script>\n <marker id=\"endArrow\" viewBox=\"0 0 10 10\" refX=\"1\" refY=\"5\" markerUnits=\"strokeWidth\" orient=\"auto\" markerWidth=\"5\" markerHeight=\"4\"> <polyline points=\"0,0 10,5 0,10 1,5\" fill=\"#000\" /> </marker>\n </defs>\n <g class=\"pedigree\" transform=\"translate(-462.86)\">\n\n <g id=\"bottomLayer\" class=\"layer\" >\n\n </g>\n <g id=\"layer0\" class=\"layer\" >\n </g>\n\n <g class=\"drawing\">\n <text x=\"557.36\" y=\"30\" text-anchor=\"middle\" class=\"header\" >madTest</text>\n <rect x=\"500.66\" y=\"38.66\" width=\"22.68\" height=\"22.68\" id=\"g43\" class=\"solid\"/>\n <text x=\"512\" y=\"92.5845\" text-anchor=\"middle\" >g43</text>\n <line x1=\"523.34\" y1=\"50\" x2=\"591.38\" y2=\"50\" />\n<circle cx=\"602.72\" cy=\"50\" r=\"11.34\" id=\"g44\" class=\"solid\"/>\n <text x=\"602.72\" y=\"92.5845\" text-anchor=\"middle\" >g44</text>\n <line class=\"mating\" id=\"g44:g43\" x1=\"557.36\" y1=\"50\" x2=\"557.36\" y2=\"123.907\" />\n <line class=\"solid\" x1=\"512\" y1=\"123.907\" x2=\"512\" y2=\"152.257\" />\n<circle cx=\"512\" cy=\"163.597\" r=\"11.34\" id=\"g47\" class=\"solid\"/>\n <text x=\"512\" y=\"206.181\" text-anchor=\"middle\" >g47</text>\n <line class=\"solid\" x1=\"648.08\" y1=\"123.907\" x2=\"648.08\" y2=\"152.257\" />\n<circle cx=\"648.08\" cy=\"163.597\" r=\"11.34\" id=\"g49\" class=\"solid\"/>\n <text x=\"648.08\" y=\"206.181\" text-anchor=\"middle\" >g49</text>\n <line x1=\"659.42\" y1=\"163.597\" x2=\"727.46\" y2=\"163.597\" />\n <rect x=\"727.46\" y=\"152.257\" width=\"22.68\" height=\"22.68\" id=\"g48\" class=\"solid\"/>\n <text x=\"738.8\" y=\"206.181\" text-anchor=\"middle\" >g48</text>\n <line class=\"mating\" id=\"g49:g48\" x1=\"693.44\" y1=\"163.597\" x2=\"693.44\" y2=\"237.504\" />\n <line class=\"solid\" x1=\"602.72\" y1=\"237.504\" x2=\"602.72\" y2=\"265.854\" />\n<circle cx=\"602.72\" cy=\"277.194\" r=\"11.34\" id=\"g50\" class=\"solid\"/>\n <text x=\"602.72\" y=\"319.778\" text-anchor=\"middle\" >g50</text>\n <line class=\"solid\" x1=\"693.44\" y1=\"237.504\" x2=\"693.44\" y2=\"265.854\" />\n<circle cx=\"693.44\" cy=\"277.194\" r=\"11.34\" id=\"g51\" class=\"solid\"/>\n <text x=\"693.44\" y=\"319.778\" text-anchor=\"middle\" >g51</text>\n <line class=\"solid\" x1=\"784.16\" y1=\"237.504\" x2=\"784.16\" y2=\"265.854\" />\n <rect x=\"772.82\" y=\"265.854\" width=\"22.68\" height=\"22.68\" id=\"g52\" class=\"solid\"/>\n <text x=\"784.16\" y=\"319.778\" text-anchor=\"middle\" >g52</text>\n <line x1=\"602.72\" y1=\"237.504\" x2=\"784.16\" y2=\"237.504\" />\n <line x1=\"512\" y1=\"123.907\" x2=\"648.08\" y2=\"123.907\" />\n </g>\n\n </g>\n </svg>\n\n"
9
- @arial_out = "<?xml version=\"1.0\" standalone=\"no\"?>\n <svg version=\"1.1\" id=\"svgDC\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"370.44\" height=\"380.481\" onload=\"init()\" >\n <defs>\n <style type=\"text/css\"><![CDATA[\n\nline{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nrect{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nellipse{\n\tstroke: #000;\n fill: #fff;\n\tstroke-width:0.25mm;\n}\n\ntext{\n\tfont-family:\"Arial\",sans-serif;\n\tfont-size:12px;\n}\n\n.smallText{\n\tfont-family:\"Arial\",sans-serif;\n\tfont-size:9px;\n\tfill:#444;\n}\n\n.layer text{\n\tfill:#930;\n}\n\n.layer line{\n\tstroke:#000;\n}\n\n.birthOrder,.unknownTwins{\n\tfont-size: 8px;\n}\n\n.header{\n\tfont-size:18px;\n\tfont-weight:bold;\n}\n\n.keyBox{\n\tfill:#e5e5e5;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\n.mating:hover{\n\tstroke-width:1mm;\n\tstroke:#d56300;\n}\n\n.selectedIndividual{\n\tstroke-width:1mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#d00;\n fill:none;\n}\n\n.selectedIndividual:hover{\n\tstroke:#d00;\n\tfill:#ffbbbb;\n\tfill-opacity:0.70;\n}\n\n.solid{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:none;\n}\n\n.dashed{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.solid:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.dashed:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.filled{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#000;\n}\n\n.specialIcons{\n\tstroke-width:0.25mm;\n\tstroke-linecap:round;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#fff;\n}\n\n.specialLines{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tfill:none;\n}\n\n.thinLine{\n\tfill:none;\n\tstroke: #000;\n\tstroke-width:0.25mm;\n}\n\n.curvedConnector{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-width:0.5mm;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.curvedConnector:hover{\n\tstroke:#d56300;\n}\n\n.whiteInkLetter_1{\n\tfont-size: 12px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_2{\n\tfont-size: 10px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_3{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.whiteInkLetter{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.blackInkLetter_1{\n\tfont-size: 12px;\n}\n\n.blackInkLetter_2{\n\tfont-size: 10px;\n}\n\n.blackInkLetter_3{\n\tfont-size: 8px;\n}\n\n.blackInkLetter{\n\tfont-size: 8px;\n\tfill: #000;\n}\n\n]]></style>\n <script type=\"text/javascript\" xlink:href=\"javascript/madeline.js\"></script>\n <marker id=\"endArrow\" viewBox=\"0 0 10 10\" refX=\"1\" refY=\"5\" markerUnits=\"strokeWidth\" orient=\"auto\" markerWidth=\"5\" markerHeight=\"4\"> <polyline points=\"0,0 10,5 0,10 1,5\" fill=\"#000\" /> </marker>\n </defs>\n <g class=\"pedigree\" transform=\"translate(-462.86)\">\n\n <g id=\"bottomLayer\" class=\"layer\" >\n\n </g>\n <g id=\"layer0\" class=\"layer\" >\n </g>\n\n <g class=\"drawing\">\n <text x=\"557.36\" y=\"30\" text-anchor=\"middle\" class=\"header\" >madTest</text>\n <rect x=\"500.66\" y=\"38.66\" width=\"22.68\" height=\"22.68\" id=\"g43\" class=\"solid\"/>\n <text x=\"512\" y=\"92.5845\" text-anchor=\"middle\" >g43</text>\n <line x1=\"523.34\" y1=\"50\" x2=\"591.38\" y2=\"50\" />\n<circle cx=\"602.72\" cy=\"50\" r=\"11.34\" id=\"g44\" class=\"solid\"/>\n <text x=\"602.72\" y=\"92.5845\" text-anchor=\"middle\" >g44</text>\n <line class=\"mating\" id=\"g44:g43\" x1=\"557.36\" y1=\"50\" x2=\"557.36\" y2=\"123.907\" />\n <line class=\"solid\" x1=\"512\" y1=\"123.907\" x2=\"512\" y2=\"152.257\" />\n<circle cx=\"512\" cy=\"163.597\" r=\"11.34\" id=\"g47\" class=\"solid\"/>\n <text x=\"512\" y=\"206.181\" text-anchor=\"middle\" >g47</text>\n <line class=\"solid\" x1=\"648.08\" y1=\"123.907\" x2=\"648.08\" y2=\"152.257\" />\n<circle cx=\"648.08\" cy=\"163.597\" r=\"11.34\" id=\"g49\" class=\"solid\"/>\n <text x=\"648.08\" y=\"206.181\" text-anchor=\"middle\" >g49</text>\n <line x1=\"659.42\" y1=\"163.597\" x2=\"727.46\" y2=\"163.597\" />\n <rect x=\"727.46\" y=\"152.257\" width=\"22.68\" height=\"22.68\" id=\"g48\" class=\"solid\"/>\n <text x=\"738.8\" y=\"206.181\" text-anchor=\"middle\" >g48</text>\n <line class=\"mating\" id=\"g49:g48\" x1=\"693.44\" y1=\"163.597\" x2=\"693.44\" y2=\"237.504\" />\n <line class=\"solid\" x1=\"602.72\" y1=\"237.504\" x2=\"602.72\" y2=\"265.854\" />\n<circle cx=\"602.72\" cy=\"277.194\" r=\"11.34\" id=\"g50\" class=\"solid\"/>\n <text x=\"602.72\" y=\"319.778\" text-anchor=\"middle\" >g50</text>\n <line class=\"solid\" x1=\"693.44\" y1=\"237.504\" x2=\"693.44\" y2=\"265.854\" />\n<circle cx=\"693.44\" cy=\"277.194\" r=\"11.34\" id=\"g51\" class=\"solid\"/>\n <text x=\"693.44\" y=\"319.778\" text-anchor=\"middle\" >g51</text>\n <line class=\"solid\" x1=\"784.16\" y1=\"237.504\" x2=\"784.16\" y2=\"265.854\" />\n <rect x=\"772.82\" y=\"265.854\" width=\"22.68\" height=\"22.68\" id=\"g52\" class=\"solid\"/>\n <text x=\"784.16\" y=\"319.778\" text-anchor=\"middle\" >g52</text>\n <line x1=\"602.72\" y1=\"237.504\" x2=\"784.16\" y2=\"237.504\" />\n <line x1=\"512\" y1=\"123.907\" x2=\"648.08\" y2=\"123.907\" />\n </g>\n\n </g>\n </svg>\n\n"
10
- @embedded_out = " <svg version=\"1.1\" id=\"svgDC\" xmlns=\"http://www.w3.org/2000/svg\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" width=\"370.44\" height=\"380.481\" onload=\"init()\" >\n <defs>\n <style type=\"text/css\"><![CDATA[\n\nline{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nrect{\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\nellipse{\n\tstroke: #000;\n fill: #fff;\n\tstroke-width:0.25mm;\n}\n\ntext{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:12px;\n}\n\n.smallText{\n\tfont-family:\"DejaVu Sans\",sans-serif;\n\tfont-size:9px;\n\tfill:#444;\n}\n\n.layer text{\n\tfill:#930;\n}\n\n.layer line{\n\tstroke:#000;\n}\n\n.birthOrder,.unknownTwins{\n\tfont-size: 8px;\n}\n\n.header{\n\tfont-size:18px;\n\tfont-weight:bold;\n}\n\n.keyBox{\n\tfill:#e5e5e5;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tstroke-linejoin:miter;\n\tstroke-linecap:square;\n}\n\n.mating:hover{\n\tstroke-width:1mm;\n\tstroke:#d56300;\n}\n\n.selectedIndividual{\n\tstroke-width:1mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#d00;\n fill:none;\n}\n\n.selectedIndividual:hover{\n\tstroke:#d00;\n\tfill:#ffbbbb;\n\tfill-opacity:0.70;\n}\n\n.solid{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:none;\n}\n\n.dashed{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.solid:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.dashed:hover{\n\tfill:#ffb787;\n\tfill-opacity:0.70;\n\tstroke:#d56300;\n\tstroke-width:1mm;\n}\n\n.filled{\n\tstroke-width:0.5mm;\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#000;\n}\n\n.specialIcons{\n\tstroke-width:0.25mm;\n\tstroke-linecap:round;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tfill:#fff;\n}\n\n.specialLines{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#000;\n\tstroke-width:0.5mm;\n\tfill:none;\n}\n\n.thinLine{\n\tfill:none;\n\tstroke: #000;\n\tstroke-width:0.25mm;\n}\n\n.curvedConnector{\n\tstroke-linecap:square;\n\tstroke-linejoin:miter;\n\tstroke:#98afc7;\n\tstroke-width:0.5mm;\n\tstroke-dasharray:2mm,1mm;\n\tstroke-dashoffset:1.0mm;\n\tfill:none;\n}\n\n.curvedConnector:hover{\n\tstroke:#d56300;\n}\n\n.whiteInkLetter_1{\n\tfont-size: 12px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_2{\n\tfont-size: 10px;\n\tfill: #fff;\n}\n\n.whiteInkLetter_3{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.whiteInkLetter{\n\tfont-size: 8px;\n\tfill: #fff;\n}\n\n.blackInkLetter_1{\n\tfont-size: 12px;\n}\n\n.blackInkLetter_2{\n\tfont-size: 10px;\n}\n\n.blackInkLetter_3{\n\tfont-size: 8px;\n}\n\n.blackInkLetter{\n\tfont-size: 8px;\n\tfill: #000;\n}\n\n]]></style>\n <script type=\"text/javascript\" xlink:href=\"javascript/madeline.js\"></script>\n <marker id=\"endArrow\" viewBox=\"0 0 10 10\" refX=\"1\" refY=\"5\" markerUnits=\"strokeWidth\" orient=\"auto\" markerWidth=\"5\" markerHeight=\"4\"> <polyline points=\"0,0 10,5 0,10 1,5\" fill=\"#000\" /> </marker>\n </defs>\n <g class=\"pedigree\" transform=\"translate(-462.86)\">\n\n <g id=\"bottomLayer\" class=\"layer\" >\n\n </g>\n <g id=\"layer0\" class=\"layer\" >\n </g>\n\n <g class=\"drawing\">\n <text x=\"557.36\" y=\"30\" text-anchor=\"middle\" class=\"header\" >madTest</text>\n <rect x=\"500.66\" y=\"38.66\" width=\"22.68\" height=\"22.68\" id=\"g43\" class=\"solid\"/>\n <text x=\"512\" y=\"92.5845\" text-anchor=\"middle\" >g43</text>\n <line x1=\"523.34\" y1=\"50\" x2=\"591.38\" y2=\"50\" />\n<circle cx=\"602.72\" cy=\"50\" r=\"11.34\" id=\"g44\" class=\"solid\"/>\n <text x=\"602.72\" y=\"92.5845\" text-anchor=\"middle\" >g44</text>\n <line class=\"mating\" id=\"g44:g43\" x1=\"557.36\" y1=\"50\" x2=\"557.36\" y2=\"123.907\" />\n <line class=\"solid\" x1=\"512\" y1=\"123.907\" x2=\"512\" y2=\"152.257\" />\n<circle cx=\"512\" cy=\"163.597\" r=\"11.34\" id=\"g47\" class=\"solid\"/>\n <text x=\"512\" y=\"206.181\" text-anchor=\"middle\" >g47</text>\n <line class=\"solid\" x1=\"648.08\" y1=\"123.907\" x2=\"648.08\" y2=\"152.257\" />\n<circle cx=\"648.08\" cy=\"163.597\" r=\"11.34\" id=\"g49\" class=\"solid\"/>\n <text x=\"648.08\" y=\"206.181\" text-anchor=\"middle\" >g49</text>\n <line x1=\"659.42\" y1=\"163.597\" x2=\"727.46\" y2=\"163.597\" />\n <rect x=\"727.46\" y=\"152.257\" width=\"22.68\" height=\"22.68\" id=\"g48\" class=\"solid\"/>\n <text x=\"738.8\" y=\"206.181\" text-anchor=\"middle\" >g48</text>\n <line class=\"mating\" id=\"g49:g48\" x1=\"693.44\" y1=\"163.597\" x2=\"693.44\" y2=\"237.504\" />\n <line class=\"solid\" x1=\"602.72\" y1=\"237.504\" x2=\"602.72\" y2=\"265.854\" />\n<circle cx=\"602.72\" cy=\"277.194\" r=\"11.34\" id=\"g50\" class=\"solid\"/>\n <text x=\"602.72\" y=\"319.778\" text-anchor=\"middle\" >g50</text>\n <line class=\"solid\" x1=\"693.44\" y1=\"237.504\" x2=\"693.44\" y2=\"265.854\" />\n<circle cx=\"693.44\" cy=\"277.194\" r=\"11.34\" id=\"g51\" class=\"solid\"/>\n <text x=\"693.44\" y=\"319.778\" text-anchor=\"middle\" >g51</text>\n <line class=\"solid\" x1=\"784.16\" y1=\"237.504\" x2=\"784.16\" y2=\"265.854\" />\n <rect x=\"772.82\" y=\"265.854\" width=\"22.68\" height=\"22.68\" id=\"g52\" class=\"solid\"/>\n <text x=\"784.16\" y=\"319.778\" text-anchor=\"middle\" >g52</text>\n <line x1=\"602.72\" y1=\"237.504\" x2=\"784.16\" y2=\"237.504\" />\n <line x1=\"512\" y1=\"123.907\" x2=\"648.08\" y2=\"123.907\" />\n </g>\n\n </g>\n </svg>\n\n"
11
- end
7
+ fixtures :madeline
12
8
 
13
9
  def test_init
14
10
  assert_nothing_raised do
@@ -18,14 +14,16 @@ class MadelineTest < Test::Unit::TestCase
18
14
 
19
15
  def test_construction
20
16
  artist = Madeline::Interface.new()
21
- pedigree = artist.draw(File.open('test/pedigree.txt','r'))
22
- assert_equal(@pedigree_out, pedigree)
17
+ pedigree_file, warnings = artist.draw(File.open('test/pedigree.txt','r'))
18
+ pedigree = File.read(pedigree_file)
19
+ assert_equal(@@fixtures["pedigree"], pedigree)
23
20
  end
24
21
 
25
22
  def test_madeline_location
26
23
  artist = Madeline::Interface.new(:madeline => '/u5/tools/bin/madeline2')
27
- pedigree = artist.draw(File.open('test/pedigree.txt','r'))
28
- assert_equal(@pedigree_out, pedigree)
24
+ pedigree_file, warnings = artist.draw(File.open('test/pedigree.txt','r'))
25
+ pedigree = File.read(pedigree_file)
26
+ assert_equal(@@fixtures["pedigree"], pedigree)
29
27
  end
30
28
 
31
29
  def test_bad_madeline_location
@@ -37,20 +35,45 @@ class MadelineTest < Test::Unit::TestCase
37
35
 
38
36
  def test_arial
39
37
  artist = Madeline::Interface.new(:font => "Arial")
40
- pedigree = artist.draw(File.open('test/pedigree.txt','r'))
41
- assert_equal(@arial_out, pedigree)
38
+ pedigree_file, warnings = artist.draw(File.open('test/pedigree.txt','r'))
39
+ pedigree = File.read(pedigree_file)
40
+ assert_equal(@@fixtures["arial_out"], pedigree)
42
41
  end
43
42
 
44
43
  def test_embedded
45
44
  artist = Madeline::Interface.new(:embedded => true)
46
- pedigree = artist.draw(File.open('test/pedigree.txt','r'))
47
- assert_equal(@embedded_out, pedigree)
45
+ pedigree_file, warnings = artist.draw(File.open('test/pedigree.txt','r'))
46
+ pedigree = File.read(pedigree_file)
47
+ assert_equal(@@fixtures["embedded_out"], pedigree)
48
48
  end
49
49
 
50
50
  def test_bad_file_location
51
51
  artist = Madeline::Interface.new()
52
52
  assert_raises(Errno::ENOENT,"No such file or directory") do
53
- pedigree = artist.draw(File.open('test/blah.txt','r'))
53
+ pedigree, warnings = artist.draw(File.open('test/blah.txt','r'))
54
54
  end
55
55
  end
56
+
57
+ def test_labels
58
+ artist = Madeline::Interface.new(:L => 'CM')
59
+ pedigree_file, warnings = artist.draw(File.open('test/labels.txt','r'))
60
+ pedigree = File.read(pedigree_file)
61
+ assert_equal(@@fixtures["single_label_out"], pedigree)
62
+ end
63
+
64
+ def test_multiple_labels
65
+ artist = Madeline::Interface.new(:L => ["CM","TTLD"])
66
+ pedigree_file, warnings = artist.draw(File.open('test/labels.txt','r'))
67
+ pedigree = File.read(pedigree_file)
68
+ assert_equal(@@fixtures["label_out"], pedigree)
69
+ end
70
+
71
+ def test_block
72
+ artist = Madeline::Interface.new(:L => ["CM","TTLD"])
73
+ file = File.open('test/labels.txt','r')
74
+ artist.draw(file) { |filehandle, warnings|
75
+ pedigree = filehandle.read
76
+ assert_equal(@@fixtures["label_out"], pedigree)
77
+ }
78
+ end
56
79
  end
data/test/pedigree.txt CHANGED
@@ -1,4 +1,4 @@
1
- FamilyID IndividualID Gender Father Mother C1 C2 C3 1739
1
+ FamilyID IndividualID Gender Father Mother C1 C2 C3 GeneID:1739
2
2
  madTest g44 F . . Y . . non
3
3
  madTest g43 M . . . . . .
4
4
  madTest g50 F g48 g49 . . . .
data/test/test_helper.rb ADDED
@@ -0,0 +1,12 @@
1
+ require 'test/unit'
2
+ require 'yaml'
3
+ class Test::Unit::TestCase
4
+ @@fixtures = {}
5
+ def self.fixtures fixture
6
+ # load and cache the YAML
7
+ item = YAML.load_file("test/fixtures/#{fixture.to_s}.yml")
8
+ item.each do |name, value|
9
+ @@fixtures[name] = value
10
+ end
11
+ end
12
+ end
metadata CHANGED
@@ -2,7 +2,7 @@
2
2
  name: madeline
3
3
  version: !ruby/object:Gem::Version
4
4
  prerelease:
5
- version: 0.1.1
5
+ version: 0.1.2
6
6
  platform: ruby
7
7
  authors:
8
8
  - Denise Mauldin
@@ -10,7 +10,7 @@ autorequire:
10
10
  bindir: bin
11
11
  cert_chain: []
12
12
 
13
- date: 2011-09-06 00:00:00 Z
13
+ date: 2011-09-08 00:00:00 Z
14
14
  dependencies: []
15
15
 
16
16
  description: Interface to Madeline2
@@ -21,17 +21,20 @@ extensions: []
21
21
 
22
22
  extra_rdoc_files:
23
23
  - README.md
24
- - ext/madeline2-linux-x86_64
24
+ - ext/madeline/madeline2-linux-x86_64
25
25
  - lib/madeline.rb
26
26
  - lib/madeline/interface.rb
27
27
  files:
28
28
  - README.md
29
29
  - Rakefile
30
- - ext/madeline2-linux-x86_64
30
+ - ext/madeline/madeline2-linux-x86_64
31
31
  - lib/madeline.rb
32
32
  - lib/madeline/interface.rb
33
+ - test/fixtures/madeline.yml
34
+ - test/labels.txt
33
35
  - test/madeline_test.rb
34
36
  - test/pedigree.txt
37
+ - test/test_helper.rb
35
38
  - Manifest
36
39
  - madeline.gemspec
37
40
  homepage: http://github.com/dmauldin/madeline
@@ -68,4 +71,5 @@ signing_key:
68
71
  specification_version: 3
69
72
  summary: Interface to Madeline2
70
73
  test_files:
74
+ - test/test_helper.rb
71
75
  - test/madeline_test.rb