oasis-etm 0.1.0

data/spec/fixtures/niso-jats/niso-jats-table-wrap.xml

@@ -0,0 +1,78 @@
+
+<oasis:table frame="all" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table">
+<oasis:tgroup cols="7">
+<oasis:colspec colnum="1" colname="col1" align="center" colsep="1"/>
+<oasis:colspec colnum="2" colname="col2" align="center" colsep="1"/>
+<oasis:colspec colnum="3" colname="col3" align="center" colsep="1"/>
+<oasis:colspec colnum="4" colname="col4" align="center" colsep="1"/>
+<oasis:colspec colnum="5" colname="col5" align="center" colsep="1" colwidth="2"/>
+<oasis:colspec colnum="6" colname="col6" align="center" colsep="1"/>
+<oasis:colspec colnum="7" colname="col7" align="char" charoff="30" char="."/>
+<oasis:thead valign="middle">
+<oasis:row>
+<oasis:entry morerows="1"></oasis:entry>
+<oasis:entry namest="col2" nameend="col4" align="center"
+morerows="1">Institutional care</oasis:entry>
+<oasis:entry morerows="1"></oasis:entry>
+<oasis:entry namest="col6" nameend="col7" align="center"
+morerows="1">&#x2003;Bed use (days)</oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry namest="col2" nameend="col4" rowsep="1"></oasis:entry>
+<oasis:entry namest="col6" nameend="col7" rowsep="1"></oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry>Control group</oasis:entry>
+<oasis:entry align="center">Day hospital</oasis:entry>
+<oasis:entry align="center">Control</oasis:entry>
+<oasis:entry align="center">Odds ratio (95&#x0025; CI)</oasis:entry>
+<oasis:entry></oasis:entry>
+<oasis:entry align="center">Day hospital</oasis:entry>
+<oasis:entry align="center">Control</oasis:entry>
+</oasis:row>
+</oasis:thead>
+<oasis:tbody valign="middle">
+<oasis:row>
+<oasis:entry namest="col1" nameend="col7" rowsep="1"></oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry>Comprehensive care (5 trials)</oasis:entry>
+<oasis:entry align="center">151/597<xref ref-type="table-fn"
+rid="TF1-150"></xref></oasis:entry>
+<oasis:entry align="center">159/584</oasis:entry>
+<oasis:entry align="center">0.91 (0.70 to 1.19)</oasis:entry>
+<oasis:entry></oasis:entry>
+<oasis:entry align="center">20.5</oasis:entry>
+<oasis:entry align="char" char="." charoff="30">21.4</oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry>Domiciliary care (4 trials)</oasis:entry>
+<oasis:entry align="center">20/216</oasis:entry>
+<oasis:entry align="center">&#x2002;19/227</oasis:entry>
+<oasis:entry align="center">1.61 (0.30 to 8.55)</oasis:entry>
+<oasis:entry></oasis:entry>
+<oasis:entry align="center">&#x2002;7.7</oasis:entry>
+<oasis:entry align="char" char="." charoff="30">11.1</oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry>No comprehensive care (3 trials)</oasis:entry>
+<oasis:entry align="center">37/411</oasis:entry>
+<oasis:entry align="center">&#x2002;66/403</oasis:entry>
+<oasis:entry align="center">0.50<xref ref-type="table-fn"
+rid="TF1-151"></xref> (0.26 to 0.96)</oasis:entry>
+<oasis:entry></oasis:entry>
+<oasis:entry align="center">11.2</oasis:entry>
+<oasis:entry align="char" char="." charoff="30">11.7</oasis:entry>
+</oasis:row>
+<oasis:row>
+<oasis:entry>Total</oasis:entry>
+<oasis:entry align="center">208/1224</oasis:entry>
+<oasis:entry align="center">244/1214</oasis:entry>
+<oasis:entry align="center">0.77 (0.52 to 1.13)</oasis:entry>
+<oasis:entry></oasis:entry>
+<oasis:entry align="center">15.0</oasis:entry>
+<oasis:entry align="char" char="." charoff="30">16.4</oasis:entry>
+</oasis:row>
+</oasis:tbody>
+</oasis:tgroup>
+</oasis:table>

data/spec/oasis/etm/colspec_spec.rb

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+RSpec.describe Oasis::Etm::Colspec do
+  let(:xml) do
+    <<~XML
+      <colspec
+        colnum="1"
+        colname="col1"
+        colwidth="1*"
+        colsep="1"
+        rowsep="1"
+        align="center"
+        char="."
+        charoff="50"/>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:colspec) { described_class.from_xml(xml) }
+
+    it "parses all attributes" do
+      expect(colspec.colnum).to eq(1)
+      expect(colspec.colname).to eq("col1")
+      expect(colspec.colwidth).to eq("1*")
+      expect(colspec.colsep).to eq(1)
+      expect(colspec.rowsep).to eq(1)
+      expect(colspec.align).to eq("center")
+      expect(colspec.char).to eq(".")
+      expect(colspec.charoff).to eq("50")
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:colspec) do
+      described_class.new(
+        colnum: 1,
+        colname: "col1",
+        colwidth: "1*",
+        colsep: 1,
+        rowsep: 1,
+        align: "center",
+        char: ".",
+        charoff: "50",
+      )
+    end
+
+    it "generates valid XML" do
+      expect(colspec.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm/entry_spec.rb

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+# spec/oasis/etm/entry_spec.rb
+RSpec.describe Oasis::Etm::Entry do
+  let(:xml) do
+    <<~XML
+      <entry
+        colname="col1"
+        namest="col1"
+        nameend="col2"
+        morerows="1"
+        colsep="1"
+        rowsep="1"
+        align="center"
+        char="."
+        charoff="50"
+        valign="middle">Cell content</entry>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:entry) { described_class.from_xml(xml) }
+
+    it "parses attributes" do
+      expect(entry.colname).to eq("col1")
+      expect(entry.namest).to eq("col1")
+      expect(entry.nameend).to eq("col2")
+      expect(entry.morerows).to eq(1)
+      expect(entry.colsep).to eq(1)
+      expect(entry.rowsep).to eq(1)
+      expect(entry.align).to eq("center")
+      expect(entry.char).to eq(".")
+      expect(entry.charoff).to eq("50")
+      expect(entry.valign).to eq("middle")
+    end
+
+    it "parses content" do
+      expect(entry.content).to eq("Cell content")
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:entry) do
+      described_class.new(
+        colname: "col1",
+        namest: "col1",
+        nameend: "col2",
+        morerows: 1,
+        colsep: 1,
+        rowsep: 1,
+        align: "center",
+        char: ".",
+        charoff: "50",
+        valign: "middle",
+        content: "Cell content",
+      )
+    end
+
+    it "generates valid XML" do
+      expect(entry.to_xml).to be_analogous_with(xml)
+    end
+  end
+
+  context "with validation" do
+    it "validates align values" do
+      entry = described_class.new(align: "invalid")
+      errors = entry.validate
+      expect(errors).to match_array(
+        have_attributes(
+          message: /align is `invalid`, must be one of the following \[left, right, center, justify, char\]/,
+        ),
+      )
+    end
+
+    it "validates valign values" do
+      entry = described_class.new(valign: "invalid")
+      errors = entry.validate
+      expect(errors).to match_array(
+        have_attributes(
+          message: /valign is `invalid`, must be one of the following \[top, middle, bottom\]/,
+        ),
+      )
+    end
+
+    it "validates colsep values" do
+      entry = described_class.new(colsep: 2)
+      errors = entry.validate
+      expect(errors).to match_array(
+        have_attributes(
+          message: /colsep is `2`, must be one of the following \[0, 1\]/,
+        ),
+      )
+    end
+
+    it "validates rowsep values" do
+      entry = described_class.new(rowsep: 2)
+      errors = entry.validate
+      expect(errors).to match_array(
+        have_attributes(
+          message: /rowsep is `2`, must be one of the following \[0, 1\]/,
+        ),
+      )
+    end
+  end
+end

data/spec/oasis/etm/row_spec.rb

@@ -0,0 +1,43 @@
+RSpec.describe Oasis::Etm::Row do
+  let(:xml) do
+    <<~XML
+      <row rowsep="1" valign="middle">
+        <entry>Cell 1</entry>
+        <entry>Cell 2</entry>
+        <entry>Cell 3</entry>
+      </row>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:row) { described_class.from_xml(xml) }
+
+    it "parses attributes" do
+      expect(row.rowsep).to eq(1)
+      expect(row.valign).to eq("middle")
+    end
+
+    it "parses entries" do
+      expect(row.entries.size).to eq(3)
+      expect(row.entries.map(&:content)).to eq(["Cell 1", "Cell 2", "Cell 3"])
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:row) do
+      described_class.new(
+        rowsep: 1,
+        valign: "middle",
+        entries: [
+          Oasis::Etm::Entry.new(content: "Cell 1"),
+          Oasis::Etm::Entry.new(content: "Cell 2"),
+          Oasis::Etm::Entry.new(content: "Cell 3"),
+        ],
+      )
+    end
+
+    it "generates valid XML" do
+      expect(row.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm/table_spec.rb

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+RSpec.describe Oasis::Etm::Table do
+  let(:xml) do
+    <<~XML
+      <table frame="all" colsep="1" rowsep="1">
+        <title>Sample Table</title>
+        <tgroup cols="3">
+          <colspec colnum="1" colwidth="1*"/>
+          <colspec colnum="2" colwidth="2*"/>
+          <colspec colnum="3" colwidth="1*"/>
+          <thead>
+            <row>
+              <entry>Header 1</entry>
+              <entry>Header 2</entry>
+              <entry>Header 3</entry>
+            </row>
+          </thead>
+          <tbody>
+            <row>
+              <entry>Cell 1</entry>
+              <entry>Cell 2</entry>
+              <entry>Cell 3</entry>
+            </row>
+          </tbody>
+        </tgroup>
+      </table>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:table) { described_class.from_xml(xml) }
+
+    it "parses table attributes" do
+      expect(table.frame).to eq("all")
+      expect(table.colsep).to eq(1)
+      expect(table.rowsep).to eq(1)
+    end
+
+    it "parses title" do
+      expect(table.title).to eq("Sample Table")
+    end
+
+    it "parses tgroup" do
+      expect(table.tgroups.size).to eq(1)
+      expect(table.tgroups.first.cols).to eq(3)
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:table) do
+      described_class.new(
+        frame: "all",
+        colsep: 1,
+        rowsep: 1,
+        title: "Sample Table",
+        tgroups: [
+          Oasis::Etm::Tgroup.new(
+            cols: 3,
+            colspecs: [
+              Oasis::Etm::Colspec.new(colnum: 1, colwidth: "1*"),
+              Oasis::Etm::Colspec.new(colnum: 2, colwidth: "2*"),
+              Oasis::Etm::Colspec.new(colnum: 3, colwidth: "1*"),
+            ],
+            thead: Oasis::Etm::Thead.new(
+              rows: [
+                Oasis::Etm::Row.new(
+                  entries: [
+                    Oasis::Etm::Entry.new(content: "Header 1"),
+                    Oasis::Etm::Entry.new(content: "Header 2"),
+                    Oasis::Etm::Entry.new(content: "Header 3"),
+                  ],
+                ),
+              ],
+            ),
+            tbody: Oasis::Etm::Tbody.new(
+              rows: [
+                Oasis::Etm::Row.new(
+                  entries: [
+                    Oasis::Etm::Entry.new(content: "Cell 1"),
+                    Oasis::Etm::Entry.new(content: "Cell 2"),
+                    Oasis::Etm::Entry.new(content: "Cell 3"),
+                  ],
+                ),
+              ],
+            ),
+          ),
+        ],
+      )
+    end
+
+    it "generates valid XML" do
+      expect(table.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm/tbody_spec.rb

@@ -0,0 +1,48 @@
+RSpec.describe Oasis::Etm::Tbody do
+  let(:xml) do
+    <<~XML
+      <tbody valign="top">
+        <row>
+          <entry>Cell 1</entry>
+          <entry>Cell 2</entry>
+          <entry>Cell 3</entry>
+        </row>
+      </tbody>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:tbody) { described_class.from_xml(xml) }
+
+    it "parses valign attribute" do
+      expect(tbody.valign).to eq("top")
+    end
+
+    it "parses rows" do
+      expect(tbody.rows.size).to eq(1)
+      expect(tbody.rows.first.entries.size).to eq(3)
+      expect(tbody.rows.first.entries.first.content).to eq("Cell 1")
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:tbody) do
+      described_class.new(
+        valign: "top",
+        rows: [
+          Oasis::Etm::Row.new(
+            entries: [
+              Oasis::Etm::Entry.new(content: "Cell 1"),
+              Oasis::Etm::Entry.new(content: "Cell 2"),
+              Oasis::Etm::Entry.new(content: "Cell 3"),
+            ],
+          ),
+        ],
+      )
+    end
+
+    it "generates valid XML" do
+      expect(tbody.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm/tgroup_spec.rb

@@ -0,0 +1,97 @@
+RSpec.describe Oasis::Etm::Tgroup do
+  let(:xml) do
+    <<~XML
+      <tgroup cols="3" colsep="1" rowsep="1" align="center">
+        <colspec colnum="1" colwidth="1*"/>
+        <colspec colnum="2" colwidth="2*"/>
+        <colspec colnum="3" colwidth="1*"/>
+        <thead>
+          <row>
+            <entry>Header 1</entry>
+            <entry>Header 2</entry>
+            <entry>Header 3</entry>
+          </row>
+        </thead>
+        <tbody>
+          <row>
+            <entry>Cell 1</entry>
+            <entry>Cell 2</entry>
+            <entry>Cell 3</entry>
+          </row>
+        </tbody>
+      </tgroup>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:tgroup) { described_class.from_xml(xml) }
+
+    it "parses required attributes" do
+      expect(tgroup.cols).to eq(3)
+    end
+
+    it "parses optional attributes" do
+      expect(tgroup.colsep).to eq(1)
+      expect(tgroup.rowsep).to eq(1)
+      expect(tgroup.align).to eq("center")
+    end
+
+    it "parses colspecs" do
+      expect(tgroup.colspecs.size).to eq(3)
+      expect(tgroup.colspecs.first.colnum).to eq(1)
+      expect(tgroup.colspecs.first.colwidth).to eq("1*")
+    end
+
+    it "parses thead" do
+      expect(tgroup.thead).to be_a(Oasis::Etm::Thead)
+      expect(tgroup.thead.rows.size).to eq(1)
+    end
+
+    it "parses tbody" do
+      expect(tgroup.tbody).to be_a(Oasis::Etm::Tbody)
+      expect(tgroup.tbody.rows.size).to eq(1)
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:tgroup) do
+      described_class.new(
+        cols: 3,
+        colsep: 1,
+        rowsep: 1,
+        align: "center",
+        colspecs: [
+          Oasis::Etm::Colspec.new(colnum: 1, colwidth: "1*"),
+          Oasis::Etm::Colspec.new(colnum: 2, colwidth: "2*"),
+          Oasis::Etm::Colspec.new(colnum: 3, colwidth: "1*"),
+        ],
+        thead: Oasis::Etm::Thead.new(
+          rows: [
+            Oasis::Etm::Row.new(
+              entries: [
+                Oasis::Etm::Entry.new(content: "Header 1"),
+                Oasis::Etm::Entry.new(content: "Header 2"),
+                Oasis::Etm::Entry.new(content: "Header 3"),
+              ],
+            ),
+          ],
+        ),
+        tbody: Oasis::Etm::Tbody.new(
+          rows: [
+            Oasis::Etm::Row.new(
+              entries: [
+                Oasis::Etm::Entry.new(content: "Cell 1"),
+                Oasis::Etm::Entry.new(content: "Cell 2"),
+                Oasis::Etm::Entry.new(content: "Cell 3"),
+              ],
+            ),
+          ],
+        ),
+      )
+    end
+
+    it "generates valid XML" do
+      expect(tgroup.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm/thead_spec.rb

@@ -0,0 +1,48 @@
+RSpec.describe Oasis::Etm::Thead do
+  let(:xml) do
+    <<~XML
+      <thead valign="middle">
+        <row>
+          <entry>Header 1</entry>
+          <entry>Header 2</entry>
+          <entry>Header 3</entry>
+        </row>
+      </thead>
+    XML
+  end
+
+  describe ".from_xml" do
+    subject(:thead) { described_class.from_xml(xml) }
+
+    it "parses valign attribute" do
+      expect(thead.valign).to eq("middle")
+    end
+
+    it "parses rows" do
+      expect(thead.rows.size).to eq(1)
+      expect(thead.rows.first.entries.size).to eq(3)
+      expect(thead.rows.first.entries.first.content).to eq("Header 1")
+    end
+  end
+
+  describe "#to_xml" do
+    subject(:thead) do
+      described_class.new(
+        valign: "middle",
+        rows: [
+          Oasis::Etm::Row.new(
+            entries: [
+              Oasis::Etm::Entry.new(content: "Header 1"),
+              Oasis::Etm::Entry.new(content: "Header 2"),
+              Oasis::Etm::Entry.new(content: "Header 3"),
+            ],
+          ),
+        ],
+      )
+    end
+
+    it "generates valid XML" do
+      expect(thead.to_xml).to be_analogous_with(xml)
+    end
+  end
+end

data/spec/oasis/etm_spec.rb

@@ -0,0 +1,81 @@
+# frozen_string_literal: true
+
+require "pathname"
+
+RSpec.describe Oasis::Etm do
+  fixtures_dir = Pathname.new(__dir__).join("../fixtures")
+
+  describe "XML round-trip conversion" do
+    describe "native XML" do
+      xml_files = Dir[fixtures_dir.join("native", "*.xml")]
+
+      xml_files.each do |file_path|
+        context "with file #{Pathname.new(file_path).relative_path_from(fixtures_dir)}" do
+          let(:xml_string) { File.read(file_path) }
+
+          it "performs lossless round-trip conversion" do
+            parsed = Oasis::Etm::Table.from_xml(xml_string)
+            generated = parsed.to_xml(
+              pretty: true,
+              declaration: true,
+              encoding: "utf-8",
+            )
+
+            cleaned_xml_string = xml_string
+              .gsub(/^<\?xml.*\n/, "")
+
+            expect(generated).to be_analogous_with(cleaned_xml_string)
+          end
+        end
+      end
+    end
+
+    describe "namespaced XML (ISOSTS)" do
+      xml_files = Dir[fixtures_dir.join("isosts", "*.xml")]
+
+      xml_files.each do |file_path|
+        context "with file #{Pathname.new(file_path).relative_path_from(fixtures_dir)}" do
+          let(:xml_string) { File.read(file_path) }
+
+          it "performs lossless round-trip conversion" do
+            parsed = Oasis::Etm::Table.from_xml(xml_string)
+            generated = parsed.to_xml(
+              pretty: true,
+              declaration: true,
+              encoding: "utf-8",
+            )
+
+            cleaned_xml_string = xml_string
+              .gsub(/^<\?xml.*\n/, "")
+
+            expect(generated).to be_analogous_with(cleaned_xml_string)
+          end
+        end
+      end
+    end
+
+    describe "namespaced XML (NISO JATS)" do
+      xml_files = Dir[fixtures_dir.join("niso-jats", "*.xml")]
+
+      xml_files.each do |file_path|
+        context "with file #{Pathname.new(file_path).relative_path_from(fixtures_dir)}" do
+          let(:xml_string) { File.read(file_path) }
+
+          it "performs lossless round-trip conversion" do
+            parsed = Oasis::Etm::Table.from_xml(xml_string)
+            generated = parsed.to_xml(
+              pretty: true,
+              declaration: true,
+              encoding: "utf-8",
+            )
+
+            cleaned_xml_string = xml_string
+              .gsub(/^<\?xml.*\n/, "")
+
+            expect(generated).to be_analogous_with(cleaned_xml_string)
+          end
+        end
+      end
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,31 @@
+# frozen_string_literal: true
+
+require "oasis-etm"
+require "nokogiri"
+require "xml-c14n"
+
+# Require all support files
+Dir[File.join(__dir__, "support", "**", "*.rb")].each { |f| require f }
+
+RSpec.configure do |config|
+  # Enable flags like --only-failures and --next-failure
+  config.example_status_persistence_file_path = ".rspec_status"
+
+  # Disable RSpec exposing methods globally on `Module` and `main`
+  config.disable_monkey_patching!
+
+  config.expect_with :rspec do |c|
+    c.syntax = :expect
+  end
+end
+
+require "lutaml/model"
+require "lutaml/model/xml_adapter/nokogiri_adapter"
+require "lutaml/model/json_adapter/standard_json_adapter"
+require "lutaml/model/yaml_adapter/standard_yaml_adapter"
+
+Lutaml::Model::Config.configure do |config|
+  config.xml_adapter = Lutaml::Model::XmlAdapter::NokogiriAdapter
+  config.json_adapter = Lutaml::Model::JsonAdapter::StandardJsonAdapter
+  config.yaml_adapter = Lutaml::Model::YamlAdapter::StandardYamlAdapter
+end