rbbt-util 5.0.1 → 5.1.0
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- data/README.rdoc +17 -7
- data/lib/rbbt/annotations.rb +186 -484
- data/lib/rbbt/annotations/annotated_array.rb +174 -0
- data/lib/rbbt/annotations/util.rb +206 -0
- data/lib/rbbt/tsv/accessor.rb +53 -15
- data/lib/rbbt/tsv/manipulate.rb +2 -2
- data/lib/rbbt/tsv/parser.rb +1 -1
- data/lib/rbbt/util/misc.rb +4 -3
- data/lib/rbbt/util/named_array.rb +28 -2
- data/lib/rbbt/workflow/accessor.rb +1 -1
- data/lib/rbbt/workflow/step.rb +14 -3
- data/test/rbbt/test_annotations.rb +7 -3
- data/test/rbbt/tsv/test_index.rb +0 -1
- metadata +4 -2
data/README.rdoc
CHANGED
@@ -12,7 +12,7 @@
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12
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cp .bash_profile .bash_profile.save
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mv tmp.bash_profile .bash_profile
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. .bash_profile
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15
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-
rvm install 1.
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15
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+
rvm install 1.9.3
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16
16
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17
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2 - install tokyocabinet (Intructions for user install follow. For system level, make sure we have dev package)
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18
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1 - download source from http://fallabs.com/tokyocabinet/tokyocabinet-1.4.47.tar.gz
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@@ -43,7 +43,7 @@
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:script
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-
gem install specific_install
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46
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+
gem install specific_install hoe
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gem specific_install -l https://github.com/bensomers/png.git
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gem specific_install -l https://github.com/felipec/soap4r.git
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gem specific_install -l https://github.com/mikisvaz/tokyocabinet_19_fix.git
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@@ -53,18 +53,22 @@
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:script
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# RSRuby
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-
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56
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+
## Example in ubuntu
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gem install rsruby -- --with-R-dir=/usr/lib/R/lib/ --with-R-include=/usr/share/R/include
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+
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## Example in MAC
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gem install rsruby -- --with-R-dir=/Library/Frameworks/R.framework/Resources/
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# JRB
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export JAVA_HOME="full_path_to_jdk"
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gem install rjb
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63
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-
3 - install gems rbbt-util rbbt-sources rbbt-text rbbt-phgx
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3 - install gems rbbt-util rbbt-sources rbbt-text rbbt-phgx, ...
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:script
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67
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-
gem install rbbt-util rbbt-sources rbbt-text rbbt-phgx rbbt-entities rbbt-views
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+
gem install rbbt-util rbbt-sources rbbt-text rbbt-phgx rbbt-entities rbbt-views rbbt-dm rbbt-GE
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3.bis - Or install github repos and make ruby use them
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@@ -82,13 +86,19 @@
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82
86
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alias druby="env RBBT_LOG=0 ruby $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
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alias drake="env RBBT_LOG=0 rake $(for d in $HOME/git/rbbt-*;do echo -n "-I$d/lib ";done)"
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85
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-
4 -
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+
4 - Install other gems that you might need for some of my workflows
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+
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script
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+
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gem install redcarpet thin
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+
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5 - Set up R to find the helper lib
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:script
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echo "source(system('rbbt_Rutil.rb', intern =T));" >> $HOME/.Rprofile
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-
|
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+
6 - If you plan to run workflows you might want to redefine the default directory to place your workflows (~/.workflows)
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:script
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data/lib/rbbt/annotations.rb
CHANGED
@@ -1,598 +1,300 @@
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1
1
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require 'rbbt/util/misc'
|
2
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-
require 'rbbt/
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2
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+
require 'rbbt/annotations/annotated_array'
|
3
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+
require 'rbbt/annotations/util'
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3
4
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4
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-
|
5
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-
module Annotated
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6
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-
attr_accessor :annotation_types
|
7
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-
attr_accessor :context
|
8
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-
attr_accessor :container
|
9
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-
attr_accessor :container_index
|
10
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-
attr_accessor :id
|
11
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-
|
12
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-
def self.extended(base)
|
13
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-
base.annotation_types ||= []
|
14
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-
end
|
5
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+
#{{{ ANNOTATED
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15
6
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|
16
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-
|
17
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-
|
18
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annotation_types.collect do |mod|
|
19
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-
mod.annotations
|
20
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-
end.flatten.uniq
|
21
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-
end
|
7
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+
module Annotated
|
8
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+
attr_accessor :container, :container_index
|
22
9
|
|
23
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-
def
|
24
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-
|
25
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-
annotation_types.collect do |mod|
|
26
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-
mod.unmasked_annotations
|
27
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-
end.flatten.uniq
|
10
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+
def annotation_values
|
11
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@annotation_values ||= {}
|
28
12
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end
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29
13
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|
30
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-
def
|
31
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-
|
32
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(
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-
|
34
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-
hash[annotation] = value unless value.nil?
|
35
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-
end
|
36
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-
hash
|
14
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+
def detach_annotations
|
15
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+
@annotation_values = @annotation_values.dup
|
16
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+
@annotation_values.instance_variable_set(:@annotation_md5, nil)
|
17
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+
@shared_annotations = false
|
37
18
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end
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38
19
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|
39
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-
def
|
40
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-
@
|
20
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+
def reset
|
21
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+
@info = nil
|
22
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+
@id = nil
|
23
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+
@self_md5 = nil
|
24
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+
@annotation_values.instance_variable_set(:@annotation_md5, nil)
|
41
25
|
end
|
42
26
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|
43
|
-
def
|
44
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-
annotation_types = info[:annotation_types] || []
|
45
|
-
annotation_types = annotation_types.split("|") if String === annotation_types
|
46
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-
|
47
|
-
return object if annotation_types.nil? or annotation_types.empty?
|
27
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+
def annotation_types
|
48
28
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|
49
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-
|
50
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-
|
51
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-
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52
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-
|
53
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-
|
54
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-
end
|
55
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-
|
56
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-
object.id = info[:entity_id] if info.include? :entity_id
|
57
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-
|
58
|
-
object.extend AnnotatedArray if annotated_array
|
59
|
-
|
60
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-
object
|
29
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+
@annotation_types ||= class << self; self; end.
|
30
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+
included_modules.
|
31
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+
select{|m|
|
32
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Annotation === m
|
33
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+
}
|
61
34
|
end
|
62
35
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|
63
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-
def
|
64
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-
if
|
65
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-
|
66
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-
else
|
67
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-
fields = fields.flatten
|
68
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-
info = self.info
|
69
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-
info[:annotated_array] = true if AnnotatedArray === self
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70
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-
values = []
|
71
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-
|
72
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fields.each do |field|
|
73
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values << case
|
74
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when Proc === field
|
75
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field.call(self)
|
76
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-
when field == "JSON"
|
77
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-
info.to_json
|
78
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-
when field == "annotation_types"
|
79
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-
annotation_types.collect{|t| t.to_s} * "|"
|
80
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-
when field == "literal"
|
81
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-
(Array === self ? "Array:" << self * "|" : self).gsub(/\n|\t/, ' ')
|
82
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-
when info.include?(field.to_sym)
|
83
|
-
res = info.delete(field.to_sym)
|
84
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-
Array === res ? "Array:" << res * "|" : res
|
85
|
-
when self.respond_to?(field)
|
86
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-
res = self.send(field)
|
87
|
-
Array === res ? "Array:"<< res * "|" : res
|
88
|
-
end
|
89
|
-
end
|
36
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+
def annotations
|
37
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+
if @annotations.nil?
|
38
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+
@annotations = []
|
90
39
|
|
91
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-
|
92
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-
|
93
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-
|
40
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+
annotation_types.each do |annotation_type|
|
41
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+
@annotations.concat annotation_type.annotations
|
42
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+
end
|
94
43
|
|
95
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-
|
96
|
-
if entry =~ /^Array:/
|
97
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-
entry["Array:".length..-1].split("|")
|
44
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+
@annotations
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98
45
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else
|
99
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-
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46
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+
@annotations
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100
47
|
end
|
101
48
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end
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102
49
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103
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-
def
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-
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105
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-
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106
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-
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107
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-
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108
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-
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109
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-
when literal_pos
|
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values[literal_pos]
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111
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-
else
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112
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id.dup
|
113
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-
end
|
114
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-
|
115
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-
object = resolve_array(object)
|
116
|
-
|
117
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-
if Array === values.first
|
118
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-
Misc.zip_fields(values).collect do |list|
|
119
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-
fields.each_with_index do |field,i|
|
120
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-
if field == "JSON"
|
121
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-
JSON.parse(list[i]).each do |key, value|
|
122
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info[key.to_sym] = value
|
123
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-
end
|
124
|
-
else
|
125
|
-
info[field.to_sym] = resolve_array(list[i])
|
126
|
-
end
|
127
|
-
end
|
50
|
+
def masked_annotations
|
51
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+
if @masked_annotations.nil?
|
52
|
+
@masked_annotations = []
|
53
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+
|
54
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+
annotation_types.each do |annotation_type|
|
55
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+
@masked_annotations.concat annotation_type.masked_annotations
|
128
56
|
end
|
57
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+
|
58
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+
@masked_annotations
|
129
59
|
else
|
130
|
-
|
131
|
-
if field == "JSON"
|
132
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-
JSON.parse(values[i]).each do |key, value|
|
133
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info[key.to_sym] = value
|
134
|
-
end
|
135
|
-
else
|
136
|
-
info[field.to_sym] = resolve_array(values[i])
|
137
|
-
end
|
138
|
-
end
|
60
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+
@masked_annotations
|
139
61
|
end
|
140
|
-
|
141
|
-
self.load(object, info)
|
142
62
|
end
|
143
63
|
|
144
|
-
def
|
145
|
-
|
146
|
-
hash = {}
|
147
|
-
annotations.each do |annotation|
|
148
|
-
if literal
|
149
|
-
hash[annotation.id] = annotation.info.merge(:literal => annotation)
|
150
|
-
else
|
151
|
-
hash[annotation.id] = annotation.info
|
152
|
-
end
|
153
|
-
end
|
154
|
-
hash.to_json
|
64
|
+
def unmasked_annotations
|
65
|
+
@unmasked_annotations ||= annotations - masked_annotations
|
155
66
|
end
|
156
67
|
|
157
|
-
def
|
158
|
-
return nil if annotations.nil?
|
159
|
-
fields = case
|
160
|
-
when ((fields.compact.empty?) and not annotations.empty?)
|
161
|
-
fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
|
162
|
-
fields << :annotation_types
|
163
|
-
when (fields == [:literal] and not annotations.empty?)
|
164
|
-
fields << :literal
|
165
|
-
when (fields == [:all] and Annotated === annotations)
|
166
|
-
fields = [:annotation_types] + annotations.annotations
|
167
|
-
fields << :literal
|
168
|
-
when (fields == [:all] and not annotations.empty?)
|
169
|
-
raise "Input array must be annotated or its elements must be" if not Annotated === annotations.compact.first and not Array === annotations.compact.first
|
170
|
-
raise "Input array must be annotated or its elements must be. No duble arrays of singly annotated entities." if not Annotated === annotations.compact.first and Array === annotations.compact.first
|
171
|
-
fields = [:annotation_types] + (Annotated === annotations ?
|
172
|
-
annotations.annotations :
|
173
|
-
annotations.compact.first.annotations)
|
174
|
-
fields << :literal
|
175
|
-
when annotations.empty?
|
176
|
-
[:annotation_types, :literal]
|
177
|
-
else
|
178
|
-
fields.flatten
|
179
|
-
end
|
180
|
-
|
181
|
-
fields = fields.collect{|f| f.to_s}
|
68
|
+
def info(masked = false)
|
182
69
|
|
183
|
-
|
184
|
-
|
185
|
-
|
186
|
-
|
187
|
-
|
188
|
-
when Array === annotations
|
189
|
-
tsv = TSV.setup({}, :key_field => "ID", :fields => fields, :type => :list, :unnamed => true)
|
190
|
-
annotations.compact.each_with_index do |annotation,i|
|
191
|
-
tsv[annotation.id + ":" << i.to_s] = annotation.tsv_values(*fields)
|
192
|
-
#tsv[annotation.id] = annotation.tsv_values(*fields)
|
193
|
-
end
|
194
|
-
else
|
195
|
-
raise "Annotations need to be an Array to create TSV"
|
70
|
+
if @info.nil?
|
71
|
+
info = annotation_values.dup
|
72
|
+
info[:annotation_types] = annotation_types
|
73
|
+
info[:annotated_array] = true if AnnotatedArray === self
|
74
|
+
@info = info
|
196
75
|
end
|
197
76
|
|
198
|
-
|
199
|
-
|
200
|
-
|
201
|
-
|
202
|
-
|
203
|
-
|
204
|
-
Annotated.load_tsv_values(id, values, tsv.fields)
|
205
|
-
end
|
206
|
-
|
207
|
-
case tsv.key_field
|
208
|
-
when "List"
|
209
|
-
annotated_entities.first
|
210
|
-
else
|
211
|
-
annotated_entities
|
77
|
+
if masked
|
78
|
+
if @masked_info.nil?
|
79
|
+
@masked_info = @info.dup
|
80
|
+
masked_annotations.each do |annotation|
|
81
|
+
@masked_info.delete annotation
|
82
|
+
end
|
212
83
|
end
|
84
|
+
@masked_info
|
85
|
+
else
|
86
|
+
@info
|
213
87
|
end
|
214
88
|
end
|
215
89
|
|
216
|
-
def
|
217
|
-
|
218
|
-
|
219
|
-
mod.setup(new, *info.values_at(*mod.all_annotations))
|
90
|
+
def annotation_md5
|
91
|
+
if annotation_values.instance_variable_get(:@annotation_md5).nil?
|
92
|
+
annotation_values.instance_variable_set(:@annotation_md5, Misc.hash2md5(annotation_values))
|
220
93
|
end
|
221
|
-
|
222
|
-
new
|
94
|
+
annotation_values.instance_variable_get(:@annotation_md5)
|
223
95
|
end
|
224
96
|
|
225
|
-
def
|
226
|
-
|
227
|
-
mod.setup(object, *info.values_at(*mod.annotations))
|
228
|
-
end
|
229
|
-
object.context = self.context
|
230
|
-
object.container = self.container
|
231
|
-
object
|
97
|
+
def self_md5
|
98
|
+
@self_md5 ||= Misc.digest(annotation_md5 + self.to_s)
|
232
99
|
end
|
233
|
-
end
|
234
|
-
|
235
|
-
|
236
|
-
module Annotation
|
237
|
-
def self.extended(base)
|
238
|
-
if not base.respond_to? :annotations
|
239
|
-
class << base
|
240
|
-
attr_accessor :annotations, :inheritance, :all_inheritance, :all_annotations, :masked_annotations
|
241
|
-
|
242
|
-
def unmasked_annotations
|
243
|
-
annotations - masked_annotations
|
244
|
-
end
|
245
|
-
self
|
246
|
-
end
|
247
|
-
|
248
|
-
base.annotations = []
|
249
|
-
base.masked_annotations = []
|
250
|
-
base.inheritance = []
|
251
|
-
base.all_annotations = []
|
252
|
-
base.all_inheritance = []
|
253
100
|
|
254
|
-
|
255
|
-
|
256
|
-
|
257
|
-
|
258
|
-
|
259
|
-
def self.extended(object)
|
260
|
-
self.send(:prev_annotation_extended, object)
|
261
|
-
object.extend Annotated unless Annotated === object
|
262
|
-
if not object.annotation_types.include? self
|
263
|
-
object.annotation_types.concat self.inheritance
|
264
|
-
object.annotation_types << self
|
265
|
-
object.annotation_types.uniq!
|
266
|
-
end
|
267
|
-
end
|
101
|
+
# ToDo This does not make much sense, why not change :id directly
|
102
|
+
def id
|
103
|
+
@id ||= self.respond_to?(:annotation_id) ?
|
104
|
+
annotation_id : self_md5
|
105
|
+
end
|
268
106
|
|
269
|
-
|
270
|
-
base.inheritance << self
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base.all_inheritance.concat self.all_inheritance if self.respond_to? :all_inheritance
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base.all_inheritance << self
|
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base.all_inheritance.uniq!
|
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base.update_annotations
|
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|
-
end
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|
-
end
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+
def annotate(object)
|
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108
|
|
109
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+
annotation_types.each do |annotation|
|
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+
object.extend annotation
|
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111
|
end
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-
end
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112
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-
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@all_annotations = all_inheritance.inject([]){|acc,mod| acc.concat mod.all_annotations}.concat(@annotations)
|
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|
-
end
|
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object.instance_variable_set(:@annotation_types, nil)
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114
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285
|
-
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286
|
-
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287
|
-
|
115
|
+
if object.instance_variables.include?(:@annotation_values)
|
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|
+
hash = {}
|
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|
+
object.instance_variable_get(:@annotation_values).each{|k,v| hash[k] = v}
|
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|
+
self.annotation_values.each{|k,v| hash[k] = v}
|
288
119
|
|
289
|
-
|
290
|
-
|
120
|
+
object.instance_variable_set(:@annotation_values, hash)
|
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|
+
object.instance_variable_set(:@shared_annotations, false)
|
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|
+
else
|
123
|
+
object.instance_variable_set(:@annotation_values, self.annotation_values)
|
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+
object.instance_variable_set(:@shared_annotations, true)
|
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+
@shared_annotations = true
|
291
126
|
end
|
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-
end
|
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127
|
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|
-
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|
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object.extend self unless self === object
|
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|
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all_annotations.each do |annotation|
|
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|
-
object.send(annotation.to_s + '=', info[annotation])
|
298
|
-
end
|
128
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+
object
|
299
129
|
end
|
300
130
|
|
301
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-
def
|
302
|
-
|
303
|
-
|
304
|
-
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305
|
-
|
306
|
-
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307
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-
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308
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-
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309
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-
|
310
|
-
value = value.split("|") if String === value and value.index "|"
|
311
|
-
object.send("#{name}=", value)
|
131
|
+
def clean_annotations(recursive = false)
|
132
|
+
case
|
133
|
+
when self.nil?
|
134
|
+
nil
|
135
|
+
when Array === self
|
136
|
+
if recursive
|
137
|
+
[].concat self.collect{|e| e.respond_to?(:clean_annotations)? e.clean_annotations : e}
|
138
|
+
else
|
139
|
+
[].concat self
|
312
140
|
end
|
141
|
+
when String === self
|
142
|
+
"" << self
|
313
143
|
else
|
314
|
-
|
315
|
-
value = value.split("|") if String === value and value.index "|"
|
316
|
-
object.send("#{name}=", value)
|
317
|
-
end
|
144
|
+
self.dup
|
318
145
|
end
|
146
|
+
end
|
319
147
|
|
320
|
-
|
148
|
+
def make_list
|
149
|
+
new = [self]
|
150
|
+
self.annotate(new)
|
151
|
+
new.extend AnnotatedArray
|
152
|
+
new
|
321
153
|
end
|
322
154
|
end
|
323
155
|
|
324
|
-
module AnnotatedArray
|
325
|
-
extend ChainMethods
|
326
156
|
|
327
|
-
|
157
|
+
#{{{ ANNOTATION
|
328
158
|
|
329
|
-
|
330
|
-
|
331
|
-
end
|
159
|
+
module Annotation
|
160
|
+
attr_accessor :annotations, :masked_annotations
|
332
161
|
|
333
|
-
def
|
334
|
-
|
162
|
+
def annotations
|
163
|
+
@annotations ||= []
|
335
164
|
end
|
336
165
|
|
337
|
-
def
|
338
|
-
|
166
|
+
def masked_annotations
|
167
|
+
@masked_annotations ||= []
|
339
168
|
end
|
340
169
|
|
341
|
-
def
|
342
|
-
|
343
|
-
return nil if value.nil?
|
344
|
-
return value if clean
|
345
|
-
return value unless String === value or Array === value
|
346
|
-
|
347
|
-
value = value.dup if value.frozen?
|
348
|
-
|
349
|
-
annotation_types.each do |mod|
|
350
|
-
value.extend mod unless mod === value
|
351
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s << "=", self.send(annotation)) end
|
352
|
-
end
|
353
|
-
|
354
|
-
value.context = self.context
|
355
|
-
value.container = self
|
356
|
-
value.container_index = pos
|
357
|
-
|
358
|
-
value.extend AnnotatedArray if Array === value and AnnotatedArray === self
|
359
|
-
|
360
|
-
value
|
170
|
+
def unmasked_annotations
|
171
|
+
annotations - masked_annotations
|
361
172
|
end
|
362
173
|
|
363
|
-
def
|
364
|
-
i = 0
|
365
|
-
info = info
|
366
|
-
super do |value|
|
367
|
-
if String === value or Array === value
|
368
|
-
value = value.dup if value.frozen? and not value.nil?
|
174
|
+
def annotation(*list)
|
369
175
|
|
370
|
-
|
371
|
-
|
372
|
-
|
373
|
-
end
|
374
|
-
|
375
|
-
value.extend AnnotatedArray if Array === value and AnnotatedArray === self
|
376
|
-
|
377
|
-
value.context = self.context
|
378
|
-
value.container = self
|
379
|
-
value.container_index = i
|
176
|
+
list.each do |annot|
|
177
|
+
next if annotations.include? annot.to_sym
|
178
|
+
annotations << annot.to_sym
|
380
179
|
|
180
|
+
# Getter
|
181
|
+
self.send(:define_method, annot.to_s) do
|
182
|
+
annotation_values[annot]
|
381
183
|
end
|
382
184
|
|
383
|
-
|
384
|
-
|
385
|
-
|
386
|
-
|
387
|
-
|
185
|
+
# Setter
|
186
|
+
self.send(:define_method, "#{ annot}=") do |value|
|
187
|
+
if @shared_annotations
|
188
|
+
detach_annotations # avoid side effects
|
189
|
+
end
|
388
190
|
|
389
|
-
|
390
|
-
res = []
|
191
|
+
reset
|
391
192
|
|
392
|
-
|
393
|
-
each do |value|
|
394
|
-
res << yield(value)
|
395
|
-
end
|
396
|
-
else
|
397
|
-
each do |value|
|
398
|
-
res << value
|
193
|
+
annotation_values[annot] = value
|
399
194
|
end
|
400
195
|
end
|
401
|
-
|
402
|
-
res
|
403
196
|
end
|
404
197
|
|
405
|
-
def
|
406
|
-
|
407
|
-
|
408
|
-
|
409
|
-
|
410
|
-
each do |value|
|
411
|
-
res << value if yield(value)
|
412
|
-
end
|
413
|
-
end
|
414
|
-
|
415
|
-
annotation_types.each do |mod|
|
416
|
-
res.extend mod unless mod === res
|
417
|
-
mod.annotations.each do |annotation| res.send(annotation.to_s + "=", self.send(annotation)) end
|
418
|
-
end
|
419
|
-
|
420
|
-
res.context = self.context
|
421
|
-
res.container = self.container
|
422
|
-
|
423
|
-
res.extend AnnotatedArray if AnnotatedArray === self
|
424
|
-
|
425
|
-
res
|
198
|
+
def setup_hash(object, values)
|
199
|
+
object.instance_variable_set(:@annotation_values, values)
|
200
|
+
object.instance_variable_set(:@shared_annotations, true)
|
201
|
+
object.reset
|
202
|
+
object
|
426
203
|
end
|
427
204
|
|
428
|
-
def
|
429
|
-
|
430
|
-
|
431
|
-
|
432
|
-
end
|
205
|
+
def clean_and_setup_hash(object, hash)
|
206
|
+
annotation_values = object.instance_variable_get(:@annotation_values)
|
207
|
+
annotation_values = annotation_values.nil? ? {} : annotation_values.dup
|
208
|
+
annotation_values.instance_variable_set(:@annotation_md5, nil)
|
433
209
|
|
434
|
-
|
435
|
-
|
436
|
-
|
437
|
-
|
438
|
-
|
439
|
-
|
440
|
-
res.container = self.container
|
441
|
-
|
442
|
-
res.extend AnnotatedArray if AnnotatedArray === self
|
443
|
-
|
444
|
-
res
|
445
|
-
end
|
210
|
+
hash.each do |key, value|
|
211
|
+
begin
|
212
|
+
next unless @annotations.include? (key = key.to_sym)
|
213
|
+
rescue
|
214
|
+
next
|
215
|
+
end
|
446
216
|
|
447
|
-
|
448
|
-
value = (self & list)
|
217
|
+
value = value.split("|") if String === value and value.index "|"
|
449
218
|
|
450
|
-
|
451
|
-
value.extend mod unless mod === value
|
452
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
219
|
+
annotation_values[key] = value
|
453
220
|
end
|
454
221
|
|
455
|
-
|
456
|
-
|
222
|
+
object.instance_variable_set(:@annotation_values, annotation_values)
|
223
|
+
object.instance_variable_set(:@shared_annotations, false)
|
457
224
|
|
458
|
-
|
225
|
+
object.reset
|
459
226
|
|
460
|
-
|
227
|
+
object
|
461
228
|
end
|
462
229
|
|
463
|
-
def
|
464
|
-
|
465
|
-
|
466
|
-
|
467
|
-
value.extend mod unless mod === value
|
468
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
469
|
-
end
|
470
|
-
|
471
|
-
value.context = self.context
|
472
|
-
value.container = self.container
|
230
|
+
def setup_positional(object, *values)
|
231
|
+
annotation_values = object.instance_variable_get(:@annotation_values)
|
232
|
+
annotation_values = annotation_values.nil? ? {} : annotation_values.dup
|
233
|
+
annotation_values.instance_variable_set(:@annotation_md5, nil)
|
473
234
|
|
474
|
-
|
235
|
+
annotations.zip(values).each do |name, value|
|
475
236
|
|
476
|
-
|
477
|
-
end
|
478
|
-
|
479
|
-
def compact
|
480
|
-
value = super
|
237
|
+
value = value.split("|") if String === value and value.index "|"
|
481
238
|
|
482
|
-
|
483
|
-
value.extend mod unless mod === value
|
484
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
239
|
+
annotation_values[name] = value
|
485
240
|
end
|
486
241
|
|
487
|
-
|
488
|
-
value.container = self.container
|
242
|
+
object.instance_variable_set(:@annotation_values, annotation_values)
|
489
243
|
|
490
|
-
|
244
|
+
object.reset
|
491
245
|
|
492
|
-
|
246
|
+
object
|
493
247
|
end
|
494
|
-
|
495
|
-
def uniq
|
496
|
-
value = super
|
497
|
-
|
498
|
-
annotation_types.each do |mod|
|
499
|
-
value.extend mod unless mod === value
|
500
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
501
|
-
end
|
502
248
|
|
503
|
-
|
504
|
-
|
505
|
-
|
506
|
-
value.extend AnnotatedArray if AnnotatedArray === self
|
507
|
-
|
508
|
-
value
|
509
|
-
end
|
249
|
+
def setup(object, *values)
|
250
|
+
return object if object.nil?
|
510
251
|
|
511
|
-
|
512
|
-
|
252
|
+
object.extend self
|
253
|
+
object.extend AnnotatedArray if Array === object
|
254
|
+
object.instance_variable_set(:@annotation_types, nil)
|
513
255
|
|
514
|
-
|
515
|
-
|
516
|
-
|
256
|
+
if Hash === (hash = values.last)
|
257
|
+
clean_and_setup_hash(object, hash)
|
258
|
+
else
|
259
|
+
setup_positional(object, *values)
|
517
260
|
end
|
518
261
|
|
519
|
-
|
520
|
-
value.container = self.container
|
521
|
-
|
522
|
-
value.extend AnnotatedArray if AnnotatedArray === self
|
523
|
-
|
524
|
-
value
|
262
|
+
object
|
525
263
|
end
|
526
264
|
|
527
|
-
def
|
528
|
-
|
529
|
-
|
530
|
-
|
531
|
-
|
532
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
533
|
-
end
|
534
|
-
|
535
|
-
value.context = self.context
|
536
|
-
value.container = self.container
|
537
|
-
|
538
|
-
value.extend AnnotatedArray if AnnotatedArray === self
|
539
|
-
|
540
|
-
value
|
265
|
+
def fast_setup(object, hash, shared = false)
|
266
|
+
object.extend self
|
267
|
+
object.extend AnnotatedArray if Array === object
|
268
|
+
object.instance_variable_set(:@annotation_values, hash)
|
269
|
+
object.instance_variable_set(:@shared_annotations, true) if shared
|
541
270
|
end
|
542
271
|
|
543
|
-
def
|
544
|
-
|
545
|
-
|
546
|
-
annotation_types.each do |mod|
|
547
|
-
value.extend mod unless mod === value
|
548
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
272
|
+
def self.extended(object)
|
273
|
+
object.module_eval do
|
274
|
+
include Annotated
|
549
275
|
end
|
550
|
-
|
551
|
-
value.context = self.context
|
552
|
-
value.container = self.container
|
553
|
-
|
554
|
-
value.extend AnnotatedArray if AnnotatedArray === self
|
555
|
-
|
556
|
-
value
|
557
276
|
end
|
558
277
|
|
559
|
-
def
|
560
|
-
|
278
|
+
def included(mod)
|
279
|
+
mod.instance_variable_set(:@annotations, self.annotations.dup)
|
280
|
+
mod.instance_variable_set(:@masked_annotations, self.masked_annotations.dup)
|
281
|
+
end
|
282
|
+
end
|
561
283
|
|
562
|
-
annotation_types.each do |mod|
|
563
|
-
value.extend mod unless mod === value
|
564
|
-
mod.annotations.each do |annotation| value.send(annotation.to_s + "=", self.send(annotation)) end
|
565
|
-
end
|
566
284
|
|
567
|
-
|
285
|
+
if __FILE__ == $0
|
568
286
|
|
569
|
-
|
287
|
+
module Gene
|
288
|
+
extend Annotation
|
289
|
+
annotation :format, :organism
|
570
290
|
end
|
571
291
|
|
572
|
-
|
573
|
-
|
574
|
-
when (Symbol === method or String === method)
|
575
|
-
method = self.send(method)
|
576
|
-
when Array === method
|
577
|
-
method = method.dup
|
578
|
-
else
|
579
|
-
raise "Unknown format of method: of class #{method.class}"
|
580
|
-
end
|
292
|
+
a = %w(1 2 3 4 5 6 6)
|
293
|
+
Gene.setup a, "Ensembl Gene ID", "Hsa"
|
581
294
|
|
582
|
-
|
583
|
-
|
584
|
-
super do |e|
|
585
|
-
value << e if method.shift
|
586
|
-
end
|
295
|
+
puts a.reject{|a| a.to_i < 6}.collect{|e| e.format}
|
587
296
|
|
588
|
-
|
589
|
-
|
590
|
-
value
|
591
|
-
end
|
592
|
-
|
593
|
-
def self.annotate(list)
|
594
|
-
list[0].annotate list unless AnnotatedArray === list or list[0].nil? or (not list[0].respond_to? :annotate)
|
595
|
-
end
|
297
|
+
puts
|
596
298
|
|
299
|
+
puts a.reject{|a| a.to_i < 6}.uniq.collect{|e| e.format}
|
597
300
|
end
|
598
|
-
|