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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 "qsar-report"
# report = OpenTox::QMRFReport.new
# report.value "QSAR_title", "My QSAR Title"
# report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
# 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")
# QMRF XML tags with attributes to edit
ATTRIBUTE_TAGS = ["training_set_availability", "training_set_data", "training_set_descriptors", "dependent_var_availability", "validation_set_availability", "validation_set_data", "validation_set_descriptors", "validation_dependent_var_availability"]
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
# Get or Set a value
# e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title>
# @param [String] key Nodename e.g.: "QSAR_title"
# @param [String] value Value to change. If not set the function returns the current value
# @return [Error] returns Error message if fails
# @return [String] returns value
def value key, value=nil
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 unless value.nil?
t.content
end
# Set attributes of an report XML tag
# e.G.: <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/>
#@example change_attributes
# report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
# @param [String] key Nodename e.g.: "training_set_data"
# @param [Hash] valuehash Key-Value Hash of tag attributes to change.
# @return [Error] returns Error message if fails
def change_attributes tagname, valuehash
raise "Can not edit the attributes of tag: #{tagname}." unless ATTRIBUTE_TAGS.include? tagname
tag = @report.at_css tagname
valuehash.each do |key, value|
tag.attributes["#{key}"].value = value
end
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 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'."
# @todo ignore case sensitivity error: error.message The value 'NO' is not an.Element of the set {'Yes', 'No'}.
end
return out
end
end
end
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