qsar-report 0.0.2

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data/.gitignore

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+*.*~
+*~

data/.yardopts

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+--readme README.md
+--title 'QMRF and QPRF reporting class for OpenTox'
+--charset utf-8
+yardoc  lib/*.rb - README.md ChangeLog VERSION LICENSE

data/ChangeLog

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+v0.0.2
+* add QPRF reporting
+* rename gem qmrf-report to qsar-report
+v0.0.1
+* initial version
+

data/Gemfile

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+source "https://rubygems.org"
+gemspec
+gem "nokogiri"
+gem "haml"
+gem "json"

data/LICENSE

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+

data/README.md

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+# QSAR-Report
+QMRF and QPRF reporting extension to OpenTox ruby modules and lazar
+## About
+Class for QMRF and QPRF reporting.
+* QMRF:
+  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/)
+* QPRF:
+  Provides a ruby OpenTox class to prepare an initial version of a QPRF report in JSON or HTML.
+
+## Usage
+### QMRF
+create a new QMRF report, add some content and show output:
+```ruby
+require "qsar-report"
+
+# create a new report
+report = OpenTox::QMRFReport.new
+
+# add a title
+report.change_qmrf_tag "QSAR_title", "My QSAR Title"
+
+# add a publication to the publication catalog
+report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
+
+# link/reference the publication to the report bibliography
+report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
+
+# output
+puts report.to_xml
+
+# validate a report (as created above) against qmrf.xsd
+report.validate
+```
+### QPRF
+create a new QPRF report, add some content and show output:
+```ruby
+require "qsar-report"
+
+# create a new QPRF report instance
+report = OpenTox::QPRFReport.new
+
+# Set Title of the report
+report.Title = "My QPRF Report"
+
+# Set Version
+report.Version = "1"
+
+# Set Date
+report.Date = Time.now.strftime("%Y/%m/%d")
+
+# Set the CAS number in chapter 1.1
+report.Value "1.1", "7732-18-5" # set CAS number for H²O
+
+# print HTML version
+puts report.to_html
+
+# print formated JSON version
+puts report.pretty_json
+
+```
+
+

data/VERSION

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+0.0.2

data/lib/qmrf-report.rb

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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.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
+
+    # 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
+
+    # 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