bivy 0.0.5

data/old_stuff/xml.tmp.xml

@@ -0,0 +1,115 @@
+<PubmedArticle>
+    <MedlineCitation Owner=\"NLM\" Status=\"MEDLINE\">
+        <PMID>17323448</PMID>
+        <DateCreated>
+            <Year>2007</Year>
+            <Month>02</Month>
+            <Day>23</Day>
+        </DateCreated>
+        <DateCompleted>
+            <Year>2007</Year>
+            <Month>03</Month>
+            <Day>27</Day>
+        </DateCompleted>
+        <Article PubModel=\"Print\">
+            <Journal>
+                <ISSN IssnType=\"Print\">0003-2700</ISSN>
+                <JournalIssue CitedMedium=\"Print\">
+                    <Volume>79</Volume>
+                    <Issue>3</Issue>
+                    <PubDate>
+                        <Year>2007</Year>
+                        <Month>Feb</Month>
+                        <Day>1</Day>
+                    </PubDate>
+                </JournalIssue>
+                <Title>Analytical chemistry</Title>
+                <ISOAbbreviation>Anal. Chem.</ISOAbbreviation>
+            </Journal>
+            <ArticleTitle>Separation media for microchips.</ArticleTitle>
+            <Pagination>
+                <MedlinePgn>800-8</MedlinePgn>
+            </Pagination>
+            <Affiliation>University of Arizona, USA. mwirth@email.arizona.edu</Affiliation>
+            <AuthorList CompleteYN=\"Y\">
+                <Author ValidYN=\"Y\">
+                    <LastName>Wirth</LastName>
+                    <ForeName>Mary J</ForeName>
+                    <Initials>MJ</Initials>
+                </Author>
+            </AuthorList>
+            <Language>eng</Language>
+            <GrantList CompleteYN=\"Y\">
+                <Grant>
+                    <GrantID>R01 GM65980</GrantID>
+                    <Acronym>GM</Acronym>
+                    <Agency>NIGMS</Agency>
+                </Grant>
+            </GrantList>
+            <PublicationTypeList>
+                <PublicationType>Journal Article</PublicationType>
+                <PublicationType>Research Support, N.I.H., Extramural</PublicationType>
+                <PublicationType>Review</PublicationType>
+            </PublicationTypeList>
+        </Article>
+        <MedlineJournalInfo>
+            <Country>United States</Country>
+            <MedlineTA>Anal Chem</MedlineTA>
+            <NlmUniqueID>0370536</NlmUniqueID>
+        </MedlineJournalInfo>
+        <ChemicalList>
+            <Chemical>
+                <RegistryNumber>9007-49-2</RegistryNumber>
+                <NameOfSubstance>DNA</NameOfSubstance>
+            </Chemical>
+        </ChemicalList>
+        <CitationSubset>IM</CitationSubset>
+        <MeshHeadingList>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"Y\">Chemical Fractionation</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"N\">DNA</DescriptorName>
+                <QualifierName MajorTopicYN=\"N\">analysis</QualifierName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"Y\">Microchip Analytical Procedures</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"N\">Oligonucleotide Array Sequence Analysis</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"N\">Protein Array Analysis</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"N\">Proteomics</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName MajorTopicYN=\"N\">Research</DescriptorName>
+            </MeshHeading>
+        </MeshHeadingList>
+        <NumberOfReferences>54</NumberOfReferences>
+    </MedlineCitation>
+    <PubmedData>
+        <History>
+            <PubMedPubDate PubStatus=\"pubmed\">
+                <Year>2007</Year>
+                <Month>2</Month>
+                <Day>27</Day>
+                <Hour>9</Hour>
+                <Minute>0</Minute>
+            </PubMedPubDate>
+            <PubMedPubDate PubStatus=\"medline\">
+                <Year>2007</Year>
+                <Month>3</Month>
+                <Day>28</Day>
+                <Hour>9</Hour>
+                <Minute>0</Minute>
+            </PubMedPubDate>
+        </History>
+        <PublicationStatus>ppublish</PublicationStatus>
+        <ArticleIdList>
+            <ArticleId IdType=\"pubmed\">17323448</ArticleId>
+        </ArticleIdList>
+    </PubmedData>
+</PubmedArticle>

data/scripts/merge_bibs.rb

@@ -0,0 +1,70 @@
+#!/usr/bin/ruby -w
+
+require 'yaml'
+
+require 'optparse'
+
+$force = false
+opts = OptionParser.new do |op|
+  op.banner = "usage: #{File.basename(__FILE__)} bib.yml ..."
+  op.separator "on matching key or pmid aborts with informative warning"
+  op.separator "otherwise, outputs file 'merged.yml'"
+  op.on("-f", "--force", "gives warnings but still prints merged.yml") { $force = true }
+end
+
+opts.parse!
+
+if ARGV.size < 2
+  puts opts.to_s
+  exit
+end
+
+all_pmids = {}
+all_refs = {}
+overlapping_refs = Hash.new {|h,k| h[k] = [] }
+overlapping_pmids = Hash.new {|h,k| h[k] = [] }
+one_bad = false
+ARGV.each do |file|
+  yml = YAML.load_file(file)
+  yml.each do |k,v|
+    if all_refs.key?(k) 
+      unless all_refs[k] == v
+        overlapping_refs[k].push(v)
+      end
+    elsif all_pmids.key?(k)
+      overlapping_pmids[k].push(v)
+    end
+    all_refs[k] = v
+  end
+end
+
+bad_keys = overlapping_refs.size > 0 || overlapping_pmids.size > 0
+
+if bad_keys
+  if overlapping_refs.size > 0
+    puts "Overlapping KEYS (but different entries): "
+    overlapping_refs.each do |k,v|
+      puts "#{k}:" 
+      v.each do |val|
+        puts "<<<<<<<<<<<<<"
+        puts "#{val.to_yaml}"
+        puts ">>>>>>>>>>>>>"
+      end
+    end
+  end
+  if overlapping_pmids.size > 0
+    puts "Overlapping PMIDs: "
+    overlapping_pmids.each do |k,v|
+      puts "#{k}:" 
+      v.each do |val|
+        puts "<<<<<<<<<<<<<"
+        puts "#{val.to_yaml}"
+        puts ">>>>>>>>>>>>>"
+      end
+    end
+  end
+end
+if !bad_keys || $force
+  puts "printing to file: \"merged.yml\""
+  File.open('merged.yml', 'w') {|out| out.print(all_refs.to_yaml) }
+end

data/spec/bibliography_spec.rb

@@ -0,0 +1,127 @@
+require 'spec_helper'
+
+require 'bibliography'
+require 'citation'
+#require 'format/html'
+
+
+describe 'basic bibliography test' do
+  before do
+    authors = %w(HQ BY JT).zip(%w(Dork Man Prince)).map do |init, last|
+      Citation::Author.new(last, init)
+    end
+    hash = {
+      :authors => authors, :title => "Silly Title", :journal_medline => 'Jail Cell', :journal_full => 'Jail Cell', :journal_iso => 'Jail Cell', :year => '1996', :month => 'Aug', :vol => 32, :pages => '32-8', :ident => 'Prince1996', :quotes => []
+    }
+    @cit1 = Citation::Article.new(hash)
+    authors2 = %w(BM).zip(%w(Smith)).map do |init, last|
+      Citation::Author.new(last, init)
+    end
+    hash2 = {
+      :authors => authors2, :title => "Wacky Backy", :publisher => 'Rocky Mountain Publishing', :year => '2003', :ident => 'Smelly2003'
+    }
+    @cit2 = Citation::Book.new(hash2)
+    @cits = [@cit1, @cit2]
+  end
+
+  it 'makes a YAML round trip' do
+    yaml = <<END
+--- 
+month: Aug
+journal_full: Jail Cell
+journal_iso: Jail Cell
+journal_medline: Jail Cell
+title: Silly Title
+ident: Prince1996
+year: "1996"
+authors: 
+- Dork, HQ
+- Man, BY
+- Prince, JT
+pages: 32-8
+quotes: []
+bibtype: article
+vol: 32
+END
+
+    YAML.load(@cit1.to_yaml).is YAML.load(yaml) # just frozen really
+
+    bibyaml = <<END2
+Prince1996:
+  month: Aug
+  journal_full: Jail Cell
+  journal_iso: Jail Cell
+  journal_medline: Jail Cell
+  title: Silly Title
+  year: "1996"
+  authors: 
+  - Dork, HQ
+  - Man, BY
+  - Prince, JT
+  pages: 32-8
+  quotes: []
+  bibtype: article
+  vol: 32
+END2
+
+    bib = Bibliography.new
+    bib.citations = [@cit1]
+    created_yaml = bib.to_yaml
+
+    # frozen
+    YAML.load(created_yaml).is YAML.load(bibyaml)
+
+    bib_from_yaml = Bibliography.from_yaml(bibyaml)
+    #assert_equal(bibbib_from_yaml, "bibs are the same from objects and from yaml")
+    #assert_equal(bib.citations.first, bib_from_yaml.citations.first, "cits are the same from objects and from yaml")
+    bc1 = bib.citations.first
+    bc2 = bib_from_yaml.citations.first
+    %w(bibtype ident journal_full journal_medline journal_iso month pages title vol year).map {|v| v.to_sym}.each do |x|
+      bc2.send(x).is bc1.send(x)
+    end
+    bc2.send(:authors).is bc1.send(:authors)
+  end
+
+  xit 'writes a bibliography' do  # better description??
+    frozen = <<END
+<html>
+<body>
+<ol>
+  <li>Dork H.Q., Man B.Y., Prince J.T. <span style="font-style:italic;">Jail Cell.</span> <span style="font-weight:bold;">1996</span>, <span style="font-style:italic;">32</span>, 32-8.</li>
+  <li>Smith B.M. <span style="font-style:italic;">Wacky Backy.</span> <span style="font-weight:bold;">2003</span>.</li>
+</ol>
+</body>
+</html>
+END
+    bib = Bibliography.new(@cits)
+    bib.write(Format::HTML.new).is frozen
+  end
+
+  it 'adds citations to the bibliography' do
+    authors = %w(JT).zip(%w(Prince)).map do |init, last|
+      Citation::Author.new(last, init)
+    end
+    hash = {
+      :authors => authors, :title => "Theory of Everything", :journal_medline => 'OmiOmics', :journal_full => 'OmiOmics', :journal_iso => 'OmiOmics', :year => '2010', :month => 'Jan', :vol => 1010, :pages => '35-9', :ident => 'Prince2010', :quotes => []
+    }
+    diff_cit = Citation::Article.new(hash)
+
+    # single
+    bib = Bibliography.new([@cit1, @cit2])
+    cits_before = bib.citations.dup
+    ans = bib.add(@cit1)
+    ans.size.is 1
+    # rejects identical id
+    ans.first.is @cit1
+    # cits unchanged
+    bib.citations.is cits_before
+
+    ans = bib.add(@cit1, diff_cit)
+    ans.size.is 1
+    # rejects identical id
+    ans.first.is @cit1
+    # added a guy
+    bib.citations.is cits_before.push(diff_cit)  
+  end
+
+end

data/spec/formatter_spec.rb

@@ -0,0 +1,14 @@
+
+require 'spec_helper'
+require 'formatter'
+
+describe 'replacing citations' do
+  it 'does basic citation replacement' do
+    string = "This is the#[billy211], document#[mark2006, john2007, simon2010].  Why do you think it is like it is? #[mark2006, billy211].  How are you doing? [#[sally32, mark2006]]. And you #[billy211, mark2006, simon2010, markus32]."
+    (new_string, ordered_cits) = Formatter.new.replace_citations_numerically(string, '#[', ']', ', ')
+    # returns ordered citations
+    ordered_cits.is %w(billy211 mark2006 john2007 simon2010 sally32 markus32)
+    # returns a new string properly formatted
+    new_string.is "This is the1, document2-4.  Why do you think it is like it is? 1-2.  How are you doing? [2,5]. And you 1-2,4,6."
+  end
+end

data/spec/formatter_spec/cits_after.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<office:document-content xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" office:version="1.0"><office:scripts/><office:font-face-decls><style:font-face style:name="Helvetica" svg:font-family="Helvetica"/><style:font-face style:name="Tahoma1" svg:font-family="Tahoma"/><style:font-face style:name="Times" svg:font-family="Times"/><style:font-face style:name="AR PL ShanHeiSun Uni" svg:font-family="&apos;AR PL ShanHeiSun Uni&apos;" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="DejaVuSans" svg:font-family="DejaVuSans" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="Tahoma" svg:font-family="Tahoma" style:font-family-generic="system" style:font-pitch="variable"/></office:font-face-decls><office:automatic-styles><style:style style:name="T1" style:family="text"><style:text-properties style:text-position="super 58%"/></style:style></office:automatic-styles><office:body><office:text><office:forms form:automatic-focus="false" form:apply-design-mode="false"/><text:sequence-decls><text:sequence-decl text:display-outline-level="0" text:name="Illustration"/><text:sequence-decl text:display-outline-level="0" text:name="Table"/><text:sequence-decl text:display-outline-level="0" text:name="Text"/><text:sequence-decl text:display-outline-level="0" text:name="Drawing"/></text:sequence-decls><text:p text:style-name="Standard">line 1: ruby is great.#[Mycit2008] <text:s/>It is also great,#[Hello2004] and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 2: ruby is great.<text:span text:style-name="T1">#[Mycit2008]</text:span> <text:s/>It is also great,<text:span text:style-name="T1">#[Hello2004]</text:span> and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 3: ruby is great.#[Mycit2008] <text:s/>It is also great,#[Hello2004] and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 4: ruby is great.<text:span text:style-name="T1">#[Mycit2008]</text:span> <text:s/>It is also great,<text:span text:style-name="T1">#[Hello2004]</text:span> and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard"/></office:text></office:body></office:document-content>

data/spec/formatter_spec/cits_before.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<office:document-content xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" office:version="1.0"><office:scripts/><office:font-face-decls><style:font-face style:name="Helvetica" svg:font-family="Helvetica"/><style:font-face style:name="Tahoma1" svg:font-family="Tahoma"/><style:font-face style:name="Times" svg:font-family="Times"/><style:font-face style:name="AR PL ShanHeiSun Uni" svg:font-family="&apos;AR PL ShanHeiSun Uni&apos;" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="DejaVuSans" svg:font-family="DejaVuSans" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="Tahoma" svg:font-family="Tahoma" style:font-family-generic="system" style:font-pitch="variable"/></office:font-face-decls><office:automatic-styles><style:style style:name="T1" style:family="text"><style:text-properties style:text-position="super 58%"/></style:style></office:automatic-styles><office:body><office:text><office:forms form:automatic-focus="false" form:apply-design-mode="false"/><text:sequence-decls><text:sequence-decl text:display-outline-level="0" text:name="Illustration"/><text:sequence-decl text:display-outline-level="0" text:name="Table"/><text:sequence-decl text:display-outline-level="0" text:name="Text"/><text:sequence-decl text:display-outline-level="0" text:name="Drawing"/></text:sequence-decls><text:p text:style-name="Standard">line 1: ruby is great#[Mycit2008]. <text:s/>It is also great#[Hello2004], and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 2: ruby is great<text:span text:style-name="T1">#[Mycit2008]</text:span>. <text:s/>It is also great<text:span text:style-name="T1">#[Hello2004]</text:span>, and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 3: ruby is great#[Mycit2008]. <text:s/>It is also great#[Hello2004], and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 4: ruby is great<text:span text:style-name="T1">#[Mycit2008]</text:span>. <text:s/>It is also great<text:span text:style-name="T1">#[Hello2004]</text:span>, and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard"/></office:text></office:body></office:document-content>

data/spec/formatter_spec/content.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<office:document-content xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" office:version="1.0"><office:scripts/><office:font-face-decls><style:font-face style:name="Helvetica" svg:font-family="Helvetica"/><style:font-face style:name="Tahoma1" svg:font-family="Tahoma"/><style:font-face style:name="Times" svg:font-family="Times"/><style:font-face style:name="AR PL ShanHeiSun Uni" svg:font-family="&apos;AR PL ShanHeiSun Uni&apos;" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="DejaVuSans" svg:font-family="DejaVuSans" style:font-family-generic="system" style:font-pitch="variable"/><style:font-face style:name="Tahoma" svg:font-family="Tahoma" style:font-family-generic="system" style:font-pitch="variable"/></office:font-face-decls><office:automatic-styles><style:style style:name="T1" style:family="text"><style:text-properties style:text-position="super 58%"/></style:style></office:automatic-styles><office:body><office:text><office:forms form:automatic-focus="false" form:apply-design-mode="false"/><text:sequence-decls><text:sequence-decl text:display-outline-level="0" text:name="Illustration"/><text:sequence-decl text:display-outline-level="0" text:name="Table"/><text:sequence-decl text:display-outline-level="0" text:name="Text"/><text:sequence-decl text:display-outline-level="0" text:name="Drawing"/></text:sequence-decls><text:p text:style-name="Standard">line 1: ruby is great#[Mycit2008]. <text:s/>It is also great#[Hello2004], and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 2: ruby is great<text:span text:style-name="T1">#[Mycit2008]</text:span>. <text:s/>It is also great<text:span text:style-name="T1">#[Hello2004]</text:span>, and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 3: ruby is great.#[Mycit2008] <text:s/>It is also great,#[Hello2004] and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard">line 4: ruby is great.<text:span text:style-name="T1">#[Mycit2008]</text:span> <text:s/>It is also great,<text:span text:style-name="T1">#[Hello2004]</text:span> and cool.</text:p><text:p text:style-name="Standard"/><text:p text:style-name="Standard"/></office:text></office:body></office:document-content>

data/spec/ooffice_spec.rb

@@ -0,0 +1,27 @@
+require 'spec_helper'
+
+require 'fileutils'
+require 'ooffice'
+
+describe 'basic test' do
+  before do
+    @doc_permanent = TESTFILES + '/doc1.odt' 
+    @doc = TESTFILES + '/doc1.tmp.odt'
+    @newdoc = 'doc1.tmp.new.odt'
+    @newdoc_with_path = TESTFILES + '/doc1.tmp.new.odt'
+    FileUtils.cp @doc_permanent, @doc 
+  end
+
+  after do
+    FileUtils.rm @doc
+  end
+
+  it 'can change the document' do
+    start_read = 300
+    OpenOffice.new.modify_content(@doc, @newdoc) {|string| string.sub(/john/,'peter')} 
+    ok File.exist?(@newdoc_with_path)
+    # can mess up the file end
+    IO.read(@newdoc_with_path, 3000, start_read).isnt IO.read(@doc, 3000, start_read)
+    File.unlink @newdoc_with_path
+  end
+end

data/spec/pubmed_spec.rb

@@ -0,0 +1,26 @@
+
+require 'spec_helper'
+require 'pubmed'
+
+
+describe 'basic pubmed testing' do
+  before do
+    @pmid = 17323448
+  end
+  it 'adds a journal given a pubmed id' do
+    begin
+      pm = PubMed.new(@pmid)
+      hash = {:title=>"Separation media for microchips.", :journal_medline =>"Anal Chem", :journal_iso=> 'Anal. Chem.', :journal_full => 'Analytical chemistry', :year=>"2007", :month=>"Feb", :vol=>"79", :issue=>"3", :pages=>"800-8", :ident=>"Wirth2007", :pmid=>17323448, :quotes => []}
+      hash.each do |k,v|
+        # "#{k}: attributes on pubmed retrieval"
+        pm.send(k).is v
+      end
+      pm.authors.first.last.is 'Wirth'
+      pm.authors.first.initials.is 'MJ'
+
+    rescue SocketError
+      ok !puts("No Internet Connection, skipping test")
+    end
+  end
+end
+

data/spec/spec_helper.rb

@@ -0,0 +1,7 @@
+require 'rubygems'
+require 'spec/more'
+
+
+TESTFILES = File.dirname(__FILE__) + '/testfiles'
+
+Bacon.summary_on_exit

metadata

@@ -0,0 +1,136 @@
+--- !ruby/object:Gem::Specification 
+name: bivy
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 5
+  version: 0.0.5
+platform: ruby
+authors: 
+- John Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-11-01 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: spec-more
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+description: uses a simple YAML format to store bibliographies.  Then modifies citations in openoffice and outputs a bibliography (in different forms) for inclusion in the document
+email: jtprince@gmail.com
+executables: 
+- pubmed_to_bivy.rb
+- bivy.rb
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+- TODO
+files: 
+- .gitignore
+- History
+- LICENSE
+- README.rdoc
+- Rakefile
+- TODO
+- VERSION
+- bin/bivy.rb
+- bin/pubmed_to_bivy.rb
+- doc/config.yaml
+- doc/src/default.css
+- doc/src/default.template
+- doc/src/tutorial/basic_flow.page
+- doc/src/tutorial/index.page
+- doc/src/tutorial/new_formats_and_media.page
+- jrn_abbrev/abbr_html.tgz
+- jrn_abbrev/abbr_to_journal.yaml
+- jrn_abbrev/download_abbrevs.rb
+- jrn_abbrev/for_ruby_class.rb
+- jrn_abbrev/html_to_yaml.rb
+- lib/bibliography.rb
+- lib/bivy.rb
+- lib/citation.rb
+- lib/format.rb
+- lib/format/acs.rb
+- lib/format/bioinformatics.rb
+- lib/format/bmc.rb
+- lib/format/jtp.rb
+- lib/format/mla.rb
+- lib/formatter.rb
+- lib/journal.rb
+- lib/journal/iso_to_full.yaml
+- lib/journal/medline_to_full.yaml
+- lib/journal/medline_to_iso.yaml
+- lib/media.rb
+- lib/media/html.rb
+- lib/ooffice.rb
+- lib/pubmed.rb
+- lib/rtf.rb
+- old_stuff/old_list2refs.rb
+- old_stuff/pubmed2html.rb
+- old_stuff/pubmed_bib_write.rb
+- old_stuff/xml.tmp.xml
+- scripts/merge_bibs.rb
+- spec/bibliography_spec.rb
+- spec/citation_positions.odt
+- spec/formatter_spec.rb
+- spec/formatter_spec/cits_after.xml
+- spec/formatter_spec/cits_before.xml
+- spec/formatter_spec/content.xml
+- spec/ooffice_spec.rb
+- spec/pubmed_spec.rb
+- spec/spec_helper.rb
+- spec/testfiles/doc1.odt
+has_rdoc: true
+homepage: http://github.com/jtprince/bivy
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: roll your own citation manager (if you like that sort of thing)
+test_files: 
+- spec/pubmed_spec.rb
+- spec/bibliography_spec.rb
+- spec/ooffice_spec.rb
+- spec/formatter_spec.rb
+- spec/spec_helper.rb