qsar-report 0.0.2 → 0.0.3

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data/README.md CHANGED
@@ -1,12 +1,12 @@
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  # QSAR-Report
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  QMRF and QPRF reporting extension to OpenTox ruby modules and lazar
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  ## About
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- Class for QMRF and QPRF reporting.
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+ Class for QMRF and QPRF reporting.
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  * QMRF:
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  Provides a ruby OpenTox class to prepare an initial version of a QMRF report.
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  The XML output is in QMRF version 1.3 and can be finalized with the QMRF editor 2.0 (https://sourceforge.net/projects/qmrf/)
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  * QPRF:
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- Provides a ruby OpenTox class to prepare an initial version of a QPRF report in JSON or HTML.
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+ Provides a ruby OpenTox class to prepare an initial version of a QPRF (version 1.1) report in JSON or HTML.
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  ## Usage
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  ### QMRF
@@ -18,7 +18,7 @@ require "qsar-report"
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  report = OpenTox::QMRFReport.new
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  # add a title
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- report.change_qmrf_tag "QSAR_title", "My QSAR Title"
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+ report.value "QSAR_title", "My QSAR Title"
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  # add a publication to the publication catalog
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  report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
@@ -50,7 +50,7 @@ report.Version = "1"
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  report.Date = Time.now.strftime("%Y/%m/%d")
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  # Set the CAS number in chapter 1.1
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- report.Value "1.1", "7732-18-5" # set CAS number for H²O
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+ report.value "1.1", "7732-18-5" # set CAS number for H²O
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  # print HTML version
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  puts report.to_html
@@ -60,4 +60,17 @@ puts report.pretty_json
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  ```
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+ Installation
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+ ------------
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+
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+ gem install qsar-report
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+
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+ Documentation
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+ -------------
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+ * [RubyDoc.info Code documentation](http://www.rubydoc.info/gems/qsar-report)
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+ * For full information on QSAR reporting see: [JRC QSAR Model Database and QSAR Model Reporting Formats](https://eurl-ecvam.jrc.ec.europa.eu/databases/jrc-qsar-model-database-and-qsar-model-reporting-formats)
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+
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+ Copyright
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+ ---------
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+ Copyright (c) 2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.0.2
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+ 0.0.3
data/lib/qmrf-report.rb CHANGED
@@ -10,7 +10,7 @@ module OpenTox
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  #@example Report
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  # require "qsar-report"
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  # report = OpenTox::QMRFReport.new
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- # report.change_qmrf_tag "QSAR_title", "My QSAR Title"
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+ # report.value "QSAR_title", "My QSAR Title"
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  # report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
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  # report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
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  # puts report.to_xml
@@ -48,7 +48,7 @@ module OpenTox
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  # @param [String] value Value to change. If not set the function returns the current value
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  # @return [Error] returns Error message if fails
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  # @return [String] returns value
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- def Value key, value=nil
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+ def value key, value=nil
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  raise "Can not edit attribute #{key} directly. Edit the catalog with 'report.change_catalog(catalog, key, value)'." if ["QSAR_software","QSAR_Algorithm", ""].include? key
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  t = @report.at_css key
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  t.content = value unless value.nil?
data/lib/qprf-report.rb CHANGED
@@ -14,7 +14,7 @@ module OpenTox
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  # report.Title = "My QPRF Report"
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  # report.Version = "1"
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  # report.Date = Time.now.strftime("%Y/%m/%d")
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- # report.Value "1.1", "7732-18-5" # set CAS number for H²O
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+ # report.value "1.1", "7732-18-5" # set CAS number for H²O
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  # puts report.to_html
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  class QPRFReport
@@ -56,12 +56,12 @@ module OpenTox
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  # Set or Get a value in the QPRF report
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  #@example for CAS Number
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  # report = OpenTox::QPRFReport.new
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- # report.Value "1.1", "7732-18-5"
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+ # report.value "1.1", "7732-18-5"
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  #
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  # @param [String] chapter Name of the chapter - e.g.: "1.1", "1.2", "1.3", "1.4", "1.5 General", "1.5 a.", "1.5 b.", "1.5 c.", "1.5 d.", "2.1" ...
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  # @param [String] value Value to set. If not set the function returns the current value
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  # @return [String] returns Value
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- def Value chapter, value=nil
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+ def value chapter, value=nil
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  case chapter
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  when /^1\.\d*/
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  block = "1. Substance"
data/test/qmrf-report.rb CHANGED
@@ -19,17 +19,17 @@ class QMRFReportTest < MiniTest::Test
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  def test_3_write_some_values
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  report = OpenTox::QMRFReport.new
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- report.Value "QSAR_title", "My QSAR Title"
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- report.Value "QSAR_models", "My QSAR Model"
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- assert_equal report.Value("QSAR_title"), "My QSAR Title"
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- assert_equal report.Value("QSAR_models"), "My QSAR Model"
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- refute_equal report.Value("QSAR_title"), "lazar"
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+ report.value "QSAR_title", "My QSAR Title"
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+ report.value "QSAR_models", "My QSAR Model"
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+ assert_equal report.value("QSAR_title"), "My QSAR Title"
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+ assert_equal report.value("QSAR_models"), "My QSAR Model"
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+ refute_equal report.value("QSAR_title"), "lazar"
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  end
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  def test_4_write_check
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  report = OpenTox::QMRFReport.new
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- report.Value "QSAR_title", "My QSAR Title"
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- report.Value "QSAR_models", "My QSAR Model"
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+ report.value "QSAR_title", "My QSAR Title"
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+ report.value "QSAR_models", "My QSAR Model"
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  assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t4.xml")))
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  end
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@@ -52,8 +52,8 @@ class QMRFReportTest < MiniTest::Test
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  def test_7_write_alot
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  report = OpenTox::QMRFReport.new
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- report.Value "QSAR_title", "My QSAR Title"
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- report.Value "QSAR_models", "My QSAR Model"
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+ report.value "QSAR_title", "My QSAR Title"
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+ report.value "QSAR_models", "My QSAR Model"
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  report.change_catalog :software_catalog, :firstsoftware, {:name => "lazar", :contact => "in-silico toxicology gmbh", :url => "https://lazar.in-silico.ch", :description => "lazar toxicity predictions"}
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  report.change_catalog :publications_catalog, :publications_catalog_1, {:title => "MyName M (2016) My Publication Title, QSAR News, 10, 14-22", :url => "http://myqsarnewsmag.dom"}
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  report.change_catalog :publications_catalog, :publications_catalog_2, {:title => "MyName M (2016) My Second Publication Title, Hornblower, 101ff.", :url => "http://hornblower.dom"}
data/test/qprf-report.rb CHANGED
@@ -25,7 +25,7 @@ class QMRFReportTest < MiniTest::Test
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  assert_equal report.Title, "QSAR Prediction Reporting Format (QPRF)"
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  end
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- def test_4_set_Values
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+ def test_4_set_values
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  report = OpenTox::QPRFReport.new
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  report.Title = "My Test Title"
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  report.Version = "12"
@@ -36,16 +36,16 @@ class QMRFReportTest < MiniTest::Test
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  def test_5_get_11
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  report = OpenTox::QPRFReport.new
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- report.Value "1.1", "7732-18-5"
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- assert_equal report.Value("1.1"), "7732-18-5"
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+ report.value "1.1", "7732-18-5"
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+ assert_equal report.value("1.1"), "7732-18-5"
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  end
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- def test_6_set_more_Values
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+ def test_6_set_more_values
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  report = OpenTox::QPRFReport.new
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  report.Title = "My QPRF Report"
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  report.Version = "2.1"
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  report.Date = "2016/08/21"
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- report.Value "1.1", "7732-18-5"
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+ report.value "1.1", "7732-18-5"
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  assert_equal report.pretty_json, File.read(File.join(DATA_DIR,'qprf-t6.json'))
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  end
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metadata CHANGED
@@ -1,7 +1,7 @@
1
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  --- !ruby/object:Gem::Specification
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  name: qsar-report
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  version: !ruby/object:Gem::Version
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- version: 0.0.2
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+ version: 0.0.3
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  platform: ruby
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  authors:
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  - Micha Rautenberg