ms-ident 0.0.2 → 0.0.3
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- data/VERSION +1 -1
- data/lib/ms/ident/pepxml.rb +2 -1
- data/spec/ms/ident/pepxml_spec.rb +8 -2
- metadata +4 -4
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.0.
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1
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+
0.0.3
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data/lib/ms/ident/pepxml.rb
CHANGED
@@ -18,6 +18,7 @@ end
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|
18
18
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class Ms::Ident::Pepxml
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19
19
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XML_STYLESHEET_LOCATION = '/tools/bin/TPP/tpp/schema/pepXML_std.xsl'
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20
20
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DEFAULT_PEPXML_VERSION = MsmsPipelineAnalysis::PEPXML_VERSION
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21
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+
XML_ENCODING = 'UTF-8'
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21
22
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23
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attr_accessor :msms_pipeline_analysis
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23
24
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@@ -50,7 +51,7 @@ class Ms::Ident::Pepxml
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50
51
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# if no outfile is given, an xml string is returned. summary_xml should
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51
52
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# have already been set and is not influenced by the outfile given here.
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52
53
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def to_xml(outfile=nil)
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53
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-
builder = Nokogiri::XML::Builder.new
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54
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+
builder = Nokogiri::XML::Builder.new(:encoding => XML_ENCODING)
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54
55
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msms_pipeline_analysis.to_xml(builder)
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55
56
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add_stylesheet(builder.doc, Ms::Ident::Pepxml::XML_STYLESHEET_LOCATION)
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56
57
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string = builder.doc.to_xml
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@@ -13,6 +13,8 @@ describe "creating an Ms::Ident::Pepxml" do
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13
13
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extend Ms::Ident
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14
14
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|
15
15
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it "can be creating in a nested fashion reflecting internal structure" do
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16
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+
tags_that_should_be_present = %w(msms_pipeline_analysis msms_run_summary sample_enzyme search_summary spectrum_query search_result search_hit modification_info mod_aminoacid_mass search_score)
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17
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+
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16
18
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pepxml = Pepxml.new do |msms_pipeline_analysis|
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17
19
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msms_pipeline_analysis.merge!(:summary_xml => "020.xml") do |msms_run_summary|
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18
20
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# prep the sample enzyme and search_summary
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@@ -84,8 +86,12 @@ describe "creating an Ms::Ident::Pepxml" do
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|
84
86
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end
|
85
87
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end
|
86
88
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end
|
87
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-
|
88
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-
|
89
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+
xml = pepxml.to_xml
|
90
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+
tags_that_should_be_present.each do |tag|
|
91
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+
xml.matches /<#{tag} ?/
|
92
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+
end
|
93
|
+
xml.matches /<\?xml version="1.0" encoding="UTF-8"\?>/
|
94
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+
xml.matches %r{<\?xml-stylesheet type="text/xsl" href="/tools/bin/TPP/tpp/schema/pepXML_std.xsl"\?>}
|
89
95
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end
|
90
96
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end
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91
97
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metadata
CHANGED
@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
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5
5
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segments:
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- 0
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7
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- 0
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8
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-
-
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9
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-
version: 0.0.
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8
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+
- 3
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9
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+
version: 0.0.3
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10
10
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platform: ruby
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11
11
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authors:
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12
12
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- John T. Prince
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@@ -14,7 +14,7 @@ autorequire:
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|
14
14
|
bindir: bin
|
15
15
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cert_chain: []
|
16
16
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|
17
|
-
date: 2011-02-
|
17
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+
date: 2011-02-28 00:00:00 -07:00
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18
18
|
default_executable:
|
19
19
|
dependencies:
|
20
20
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- !ruby/object:Gem::Dependency
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@@ -169,7 +169,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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|
169
169
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requirements:
|
170
170
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- - ">="
|
171
171
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- !ruby/object:Gem::Version
|
172
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-
hash:
|
172
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+
hash: 3918611084548908133
|
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segments:
|
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- 0
|
175
175
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version: "0"
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