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Diffstat (limited to 'lib/qmrf-report.rb')
| -rw-r--r-- | lib/qmrf-report.rb | 140 |
1 files changed, 140 insertions, 0 deletions
diff --git a/lib/qmrf-report.rb b/lib/qmrf-report.rb new file mode 100644 index 0000000..fdce433 --- /dev/null +++ b/lib/qmrf-report.rb @@ -0,0 +1,140 @@ +require "nokogiri" + +# OpenTox module +module OpenTox + + #Class for QMRF reporting. + # + #Provides a ruby OpenTox class to prepare an initial version of a QMRF report. + #The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 (https://sourceforge.net/projects/qmrf/) + #@example Report + # require "" + # report = OpenTox::QMRFReport.new + # report.change_qmrf_tag "QSAR_title", "My QSAR Title" + # report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"} + # report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1 + # puts report.to_xml + + class QMRFReport + # QMRF XML Schema file + SCHEMA_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xsd") + # QMRF XML Template file + TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml") + + attr_accessor :xml, :report + + # Open an existing QMRF xml report + # @param [String] file Name of the file + def open file + xml = File.read("#{file}") + @report = Nokogiri.XML(xml) + end + + # Initialize a new report instance from qmrf template + def initialize + xml = File.read(TEMPLATE_FILE) + @report = Nokogiri.XML(xml) + end + + # returns XML representation (QMRF XML report) of report instance + # @return [String] returns XML + def to_xml + @report.to_xml + end + + # Change a value + # e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title> + # @param [String] key Name of the node + # @param [String] value Value to change + # @return [Error] returns Error message if fails + def change_qmrf_tag key, value + raise "Can not edit attribute #{key} directly. Edit the catalog with 'report.change_catalog(catalog, key, value)'." if ["QSAR_software","QSAR_Algorithm", ""].include? key + t = @report.at_css key + t.content = value + end + + # Change a catalog + # @param [String] catalog Name of the catalog - One of "software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog" in QMRF v1.3 + # @param [String] id Single entry node in the catalog e.G.: "<software contact='mycontact@mydomain.dom' description="My QSAR Software " id="software_catalog_2" name="MySoftware" number="" url="https://mydomain.dom"/> + # @param [Hash] valuehash Key-Value Hash with attributes for a single catalog node + # @return [Error] returns Error message if fails + def change_catalog catalog, id, valuehash + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + valuehash.each do |key, value| + @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"]= value + end + else + cat = @report.at_css("#{catalog}") + newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'')}", self.report) + newentry["id"] = id + valuehash.each do |key, value| + newentry["#{key}"] = value + end + cat << newentry + end + end + + # Set reference to a catalog entry. + # e.g.: reference an author entry from authors_catalog to Chapter 2.2 QMRF authors + #@example ref_catalog + # report.ref_catalog 'qmrf_authors', 'authors_catalog', 'firstauthor' + # @param [String] chapter Name of the chapter to add the catalog reference. e.g.: qmrf_authors, model_authors, QSAR_software, ... + # @param [String] catalog Name of the catalog + # @param [String] id entry node in the catalog + def ref_catalog chapter, catalog, id + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + chap = @report.at_css("#{chapter}") + if chap.at("//*[@idref='#{id}']").nil? + newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'_ref')}", self.report) + newentry["idref"] = id + chap << newentry + end + else + raise "catalog entry with id: #{id} do not exist." + end + end + + # get value of a QMRF node + # @param [String] key Nodename e.g.: "QSAR_title" + # @return [String] returns value + def get_qmrf_tag key + t = @report.at_css key + t.content + end + + # get an attribute from a catalog entry + # @param [String] catalog Name of the catalog + # @param [String] id entry id in the catalog + # @param [String] key returns value of a key in a catalog node + # @return [String, false] returns value of a key in a catalog node or false if catalog entry do not exists. + def get_catalog_value catalog, id, key + catalog_exists? catalog + if @report.at_css("#{catalog}").at("//*[@id='#{id}']") + @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"] + else + return false + end + end + + # Check if a catalog exists in this QMRF version + # @param [String] catalog Catalog + # @return [Error, true] returns true or Error if a catalog do not exists + def catalog_exists? catalog + raise "Unknown catalog: #{catalog}" unless ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"].include? catalog.to_s + true + end + + # Validates a report instance against qmrf.xsd (XML Structure Definition) + def validate + xsd = Nokogiri::XML::Schema(File.read(SCHEMA_FILE)) + out = "" + xsd.validate(@report).each do |error| + out << error.message unless error.message == "Element 'algorithm', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'." || error.message == "Element 'descriptor', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'." + end + return out + end + + end +end
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