simple_bioc 0.0.4 → 0.0.5
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- checksums.yaml +4 -4
- data/lib/simple_bioc/bioc_reader.rb +17 -9
- data/lib/simple_bioc/bioc_writer.rb +2 -0
- data/lib/simple_bioc/version.rb +1 -1
- data/lib/simple_bioc.rb +41 -0
- data/simple_bioc.gemspec +1 -0
- data/spec/simple_bioc_spec.rb +17 -0
- metadata +16 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 7f41d51c5fdefb00b99d4fc0dfcd79e3f2f7738b
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4
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+
data.tar.gz: 6ca95848028aa0b04b2b44fb3563111218cd5c26
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: fb18148c22f361d66ca12413e1f0c34cbfcc1d03cc65ede1e6f08a44978e0406455ddbadf727b8802b4bde9d6360f1dce2a42d45e7cedae44db5818ea847b939
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7
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+
data.tar.gz: cb892612b41da3f73e9edc58836f290ff04a348e86869a487e92af577274e058f51b6b1eedcddab194926e7fcf3bc3f10634a01510baa33a7d3da62b83e926af
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@@ -7,20 +7,28 @@ module BioCReader
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7
7
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def read(path, options)
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8
8
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collection = nil
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9
9
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File.open(path) do |file|
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10
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-
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11
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-
config.noent.strict.noblanks
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12
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-
end
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13
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-
xml = xml_doc.at_xpath("//collection")
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14
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-
if xml.nil?
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15
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-
fail 'Wrong format'
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16
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-
end
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17
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-
collection = SimpleBioC::Collection.new
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18
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-
read_collection(xml, collection, options)
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10
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+
collection = read_from_file_or_string(file, options)
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19
11
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end
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20
12
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21
13
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collection
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22
14
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end
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23
15
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16
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+
def read_from_file_or_string(file_or_string, options)
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17
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collection = nil
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18
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+
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19
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xml_doc = Nokogiri::XML(file_or_string) do |config|
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20
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config.noent.strict.noblanks
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21
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+
end
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22
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+
xml = xml_doc.at_xpath("//collection")
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23
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+
if xml.nil?
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24
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fail 'Wrong format'
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25
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+
end
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26
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+
collection = SimpleBioC::Collection.new
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27
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+
read_collection(xml, collection, options)
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28
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+
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29
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collection
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30
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+
end
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31
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+
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24
32
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def read_text(xml, name)
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25
33
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node = xml.at_xpath(name)
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26
34
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node && node.content
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data/lib/simple_bioc/version.rb
CHANGED
data/lib/simple_bioc.rb
CHANGED
@@ -24,6 +24,47 @@ module SimpleBioC
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24
24
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BioCReader.read(file_path, options)
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25
25
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end
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26
26
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|
27
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+
# parse a BioC XML file and convert it into a collection instance
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28
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#
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29
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+
# ==== Arguments
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30
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+
# * +file_path+ - file object for parse
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31
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+
# * +options+ - (optional) additional options
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32
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#
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33
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+
# ==== Options
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34
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# * +documents+ - specify IDs of documents to parse. The result will include only the specified documents
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35
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#
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36
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# ==== Examples
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37
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+
# file = File.open(path)
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38
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+
# collection = SimpleBioC.from_xml(file)
|
39
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+
# collection = SimpleBioC.from_xml(file, {documents:[21785578, 21488974]})
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40
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+
def from_xml_file(file, options = {})
|
41
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+
options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array)
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42
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+
BioCReader.read_from_file_or_string(file, options)
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43
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+
end
|
44
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+
|
45
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+
# parse a BioC XML string and convert it into a collection instance
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46
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+
#
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47
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+
# ==== Arguments
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48
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+
# * +string+ - xml string (text) for parse
|
49
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+
# * +options+ - (optional) additional options
|
50
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+
#
|
51
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+
# ==== Options
|
52
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+
# * +documents+ - specify IDs of documents to parse. The result will include only the specified documents
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53
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#
|
54
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+
# ==== Examples
|
55
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+
# content = "<?xml version=\"1.0\" encoding=\"UTF-8\"?> ..."
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56
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# collection = SimpleBioC.from_xml(content)
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57
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+
# collection = SimpleBioC.from_xml(content, {documents:[21785578, 21488974]})
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58
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+
def from_xml_string(string, options = {})
|
59
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options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array)
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60
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BioCReader.read_from_file_or_string(string, options)
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61
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end
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62
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+
|
63
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def from_json(json, options = {})
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64
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options[:documents] = options[:documents].map{|e| e.to_s} if options[:documents].kind_of?(Array)
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65
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BioCReader.read_from_json(json, options)
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66
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end
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67
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+
|
27
68
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# convert a collection instance to a BioC XML text. Output will return as string
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28
69
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#
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29
70
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# ==== Arguments
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data/simple_bioc.gemspec
CHANGED
@@ -19,6 +19,7 @@ Gem::Specification.new do |spec|
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19
19
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spec.require_paths = ["lib"]
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20
20
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21
21
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spec.add_dependency "nokogiri", "~> 1.6"
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22
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+
spec.add_dependency "json_builder", "~> 3.1"
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22
23
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23
24
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spec.add_development_dependency "bundler", "~> 1.3"
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24
25
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spec.add_development_dependency "rake", "~> 10.3"
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data/spec/simple_bioc_spec.rb
CHANGED
@@ -28,4 +28,21 @@ describe "Simple function" do
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28
28
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output = SimpleBioC.to_xml(collection, {save_with: 0})
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29
29
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expect(output).to include('<location offset="1" length="2"/><text>annotation text</text>')
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30
30
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end
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31
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+
|
32
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+
it "should read bioc from file" do
|
33
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f = File.open("./xml/everything.xml")
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34
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collection = SimpleBioC.from_xml_file(f)
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35
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f.close
|
36
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output = SimpleBioC.to_xml(collection)
|
37
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expect(output).to include('<!DOCTYPE collection SYSTEM "BioC.dtd">')
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38
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end
|
39
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+
|
40
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+
it "should read bioc from string" do
|
41
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f = File.open("./xml/everything.xml")
|
42
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contents = f.read
|
43
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collection = SimpleBioC.from_xml_file(contents)
|
44
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f.close
|
45
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output = SimpleBioC.to_xml(collection)
|
46
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expect(output).to include('<!DOCTYPE collection SYSTEM "BioC.dtd">')
|
47
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+
end
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31
48
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end
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
|
2
2
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name: simple_bioc
|
3
3
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version: !ruby/object:Gem::Version
|
4
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-
version: 0.0.
|
4
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+
version: 0.0.5
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5
5
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platform: ruby
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6
6
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authors:
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7
7
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- Dongseop Kwon
|
8
8
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autorequire:
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9
9
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bindir: bin
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10
10
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cert_chain: []
|
11
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-
date: 2015-
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11
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+
date: 2015-06-22 00:00:00.000000000 Z
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12
12
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dependencies:
|
13
13
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- !ruby/object:Gem::Dependency
|
14
14
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name: nokogiri
|
@@ -24,6 +24,20 @@ dependencies:
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24
24
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- - "~>"
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25
25
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- !ruby/object:Gem::Version
|
26
26
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version: '1.6'
|
27
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+
- !ruby/object:Gem::Dependency
|
28
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+
name: json_builder
|
29
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+
requirement: !ruby/object:Gem::Requirement
|
30
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+
requirements:
|
31
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+
- - "~>"
|
32
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+
- !ruby/object:Gem::Version
|
33
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+
version: '3.1'
|
34
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+
type: :runtime
|
35
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+
prerelease: false
|
36
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+
version_requirements: !ruby/object:Gem::Requirement
|
37
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+
requirements:
|
38
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+
- - "~>"
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39
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+
- !ruby/object:Gem::Version
|
40
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+
version: '3.1'
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27
41
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- !ruby/object:Gem::Dependency
|
28
42
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name: bundler
|
29
43
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requirement: !ruby/object:Gem::Requirement
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