From c05766e3e87319dde06bace83c5aac5620d76be7 Mon Sep 17 00:00:00 2001 From: rautenberg Date: Fri, 19 Aug 2016 16:24:44 +0200 Subject: iniitial commit --- .gitignore | 2 + .yardopts | 4 + ChangeLog | 3 + Gemfile | 3 + LICENSE | 340 +++++++++ README.md | 32 + VERSION | 1 + lib/qmrf-report.rb | 140 ++++ lib/template/qmrf.xml | 146 ++++ lib/template/qmrf.xsd | 2018 +++++++++++++++++++++++++++++++++++++++++++++++++ qmrf-report.gemspec | 21 + test/data/qmrf_t4.xml | 146 ++++ test/data/qmrf_t7.xml | 146 ++++ test/data/qmrf_t8.xml | 146 ++++ test/report.rb | 74 ++ test/setup.rb | 7 + 16 files changed, 3229 insertions(+) create mode 100644 .gitignore create mode 100644 .yardopts create mode 100644 ChangeLog create mode 100644 Gemfile create mode 100644 LICENSE create mode 100644 README.md create mode 100644 VERSION create mode 100644 lib/qmrf-report.rb create mode 100644 lib/template/qmrf.xml create mode 100644 lib/template/qmrf.xsd create mode 100644 qmrf-report.gemspec create mode 100644 test/data/qmrf_t4.xml create mode 100644 test/data/qmrf_t7.xml create mode 100644 test/data/qmrf_t8.xml create mode 100644 test/report.rb create mode 100644 test/setup.rb diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..1931eb9 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +*.*~ +*~ diff --git a/.yardopts b/.yardopts new file mode 100644 index 0000000..f4a7b90 --- /dev/null +++ b/.yardopts @@ -0,0 +1,4 @@ +--readme README.md +--title 'QMRF reporting class for opentox' +--charset utf-8 +yardoc lib/*.rb - README.md ChangeLog VERSION LICENSE diff --git a/ChangeLog b/ChangeLog new file mode 100644 index 0000000..7b71772 --- /dev/null +++ b/ChangeLog @@ -0,0 +1,3 @@ +v0.0.1 +* initial version + diff --git a/Gemfile b/Gemfile new file mode 100644 index 0000000..6109aa6 --- /dev/null +++ b/Gemfile @@ -0,0 +1,3 @@ +source "https://rubygems.org" +gemspec +gem "nokogiri" \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..8cdb845 --- /dev/null +++ b/LICENSE @@ -0,0 +1,340 @@ + GNU GENERAL PUBLIC LICENSE + Version 2, June 1991 + + Copyright (C) 1989, 1991 Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The licenses for most software are designed to take away your +freedom to share and change it. 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See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + {signature of Ty Coon}, 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. + diff --git a/README.md b/README.md new file mode 100644 index 0000000..47483bc --- /dev/null +++ b/README.md @@ -0,0 +1,32 @@ +# lazar-report +QMRF reporting extension to OpenTox ruby modules and lazar +## About +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/) + + + +## Usage +create a new report, add some content and show output: +```ruby +require "" + +# 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 +``` diff --git a/VERSION b/VERSION new file mode 100644 index 0000000..8a9ecc2 --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +0.0.1 \ No newline at end of file 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.: Title of My QSAR + # @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.: " + # @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 \ No newline at end of file diff --git a/lib/template/qmrf.xml b/lib/template/qmrf.xml new file mode 100644 index 0000000..56dee5e --- /dev/null +++ b/lib/template/qmrf.xml @@ -0,0 +1,146 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +To be entered by JRC +To be entered by JRC +To be entered by JRC +To be entered by JRC + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/lib/template/qmrf.xsd b/lib/template/qmrf.xsd new file mode 100644 index 0000000..4dd8fa1 --- /dev/null +++ b/lib/template/qmrf.xsd @@ -0,0 +1,2018 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/qmrf-report.gemspec b/qmrf-report.gemspec new file mode 100644 index 0000000..2472dba --- /dev/null +++ b/qmrf-report.gemspec @@ -0,0 +1,21 @@ +# -*- encoding: utf-8 -*- + +Gem::Specification.new do |s| + s.name = "qmrf-report" + s.version = File.read("./VERSION") + s.date = "2016-08-19" + s.authors = ["Micha Rautenberg"] + s.email = ["rautenberg@in-silico.ch"] + s.homepage = "http://github.com/opentox/qmrf-report" + s.summary = %q{qmrf-report} + s.description = %q{QMRF reporting for OpenTox ruby module and Lazar Toxicology Predictions} + s.license = 'GPL-3' + + #s.rubyforge_project = "qmrf-report" + + s.files = `git ls-files`.split("\n") + s.required_ruby_version = '>= 2.0.0' + + s.add_runtime_dependency "nokogiri" + +end \ No newline at end of file diff --git a/test/data/qmrf_t4.xml b/test/data/qmrf_t4.xml new file mode 100644 index 0000000..16a12bf --- /dev/null +++ b/test/data/qmrf_t4.xml @@ -0,0 +1,146 @@ + + + + + +My QSAR Title +My QSAR Model + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +To be entered by JRC +To be entered by JRC +To be entered by JRC +To be entered by JRC + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/data/qmrf_t7.xml b/test/data/qmrf_t7.xml new file mode 100644 index 0000000..038110e --- /dev/null +++ b/test/data/qmrf_t7.xml @@ -0,0 +1,146 @@ + + + + + +My QSAR Title +My QSAR Model + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +To be entered by JRC +To be entered by JRC +To be entered by JRC +To be entered by JRC + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/data/qmrf_t8.xml b/test/data/qmrf_t8.xml new file mode 100644 index 0000000..76e2973 --- /dev/null +++ b/test/data/qmrf_t8.xml @@ -0,0 +1,146 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +To be entered by JRC +To be entered by JRC +To be entered by JRC +To be entered by JRC + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/test/report.rb b/test/report.rb new file mode 100644 index 0000000..b9a6c54 --- /dev/null +++ b/test/report.rb @@ -0,0 +1,74 @@ +require_relative "setup.rb" + +class QMRFReportTest < MiniTest::Test + + def test_0_self + puts "MiniTest start OK" + end + + def test_1_base + report = OpenTox::QMRFReport.new + assert report + assert_kind_of(OpenTox::QMRFReport, report) + end + + def test_2_validate + report = OpenTox::QMRFReport.new + assert_empty report.validate + end + + def test_3_write_some_values + report = OpenTox::QMRFReport.new + report.change_qmrf_tag "QSAR_title", "My QSAR Title" + report.change_qmrf_tag "QSAR_models", "My QSAR Model" + assert_equal report.get_qmrf_tag("QSAR_title"), "My QSAR Title" + assert_equal report.get_qmrf_tag("QSAR_models"), "My QSAR Model" + refute_equal report.get_qmrf_tag("QSAR_title"), "lazar" + end + + def test_4_write_check + report = OpenTox::QMRFReport.new + report.change_qmrf_tag "QSAR_title", "My QSAR Title" + report.change_qmrf_tag "QSAR_models", "My QSAR Model" + assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t4.xml"))) + end + + def test_5_write_catalog + report = OpenTox::QMRFReport.new + report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :contact => "in-silico toxicology gmbh", :url => "https://lazar.in-silico.ch", :description => "lazar toxicity predictions"} + assert "in-silico toxicology gmbh", report.get_catalog_value(:software_catalog, :firstsoftware, :contact) + assert "lazar", report.get_catalog_value(:software_catalog, :firstsoftware, :name) + assert "https://lazar.in-silico.ch", report.get_catalog_value(:software_catalog, :firstsoftware, :url) + assert "lazar toxicity predictions", report.get_catalog_value(:software_catalog, :firstsoftware, :description) + end + + def test_6_check_catalog_exists + report = OpenTox::QMRFReport.new + assert_raises RuntimeError do + report.catalog_exists? :noexist_catalog + end + assert report.catalog_exists? :software_catalog + end + + def test_7_write_alot + report = OpenTox::QMRFReport.new + report.change_qmrf_tag "QSAR_title", "My QSAR Title" + report.change_qmrf_tag "QSAR_models", "My QSAR Model" + report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :contact => "in-silico toxicology gmbh", :url => "https://lazar.in-silico.ch", :description => "lazar toxicity predictions"} + 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.change_catalog :publications_catalog, :publications_catalog_2, {:title => "MyName M (2016) My Second Publication Title, Hornblower, 101ff.", :url => "http://hornblower.dom"} + assert_equal report.to_xml, File.read(File.join(File.join(File.dirname(__FILE__),"data/qmrf_t7.xml"))) + report.change_catalog :publications_catalog, :publications_catalog_3, {:title => "MyName M (2016) My Third Publication Title, Somewhereelse, 43f.", :url => "http://somewhereelse.dom"} + refute_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t7.xml"))) + end + + def test_8_ref_catalog_entry + report = OpenTox::QMRFReport.new + report.change_catalog :authors_catalog, :firstauthor, {:name => "Dr. My MyName", :url => "http://myauthor.dom", :email => "myauthor@myauthor.dom"} + report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor + report.change_catalog :authors_catalog, :secondauthor, {:name => "Dr. Mysec MysecName", :url => "http://myauthor.dom", :email => "myauthor@myauthor.dom"} + report.ref_catalog :qmrf_authors, :authors_catalog, :secondauthor + assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t8.xml"))) + end + +end diff --git a/test/setup.rb b/test/setup.rb new file mode 100644 index 0000000..5d61c1c --- /dev/null +++ b/test/setup.rb @@ -0,0 +1,7 @@ +ENV["LAZAR_ENV"] = "development" +require 'minitest/autorun' +require_relative '../lib/qmrf-report.rb' +#require 'lazar' +include OpenTox +TEST_DIR ||= File.expand_path(File.dirname(__FILE__)) +DATA_DIR ||= File.join(TEST_DIR,"data") \ No newline at end of file -- cgit v1.2.3