qsar-report 0.0.2 → 0.0.3
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- checksums.yaml +4 -4
- data/README.md +17 -4
- data/VERSION +1 -1
- data/lib/qmrf-report.rb +2 -2
- data/lib/qprf-report.rb +3 -3
- data/test/qmrf-report.rb +9 -9
- data/test/qprf-report.rb +5 -5
- metadata +1 -1
checksums.yaml
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data/README.md
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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
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report = OpenTox::QMRFReport.new
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# add a title
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report.
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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"}
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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.
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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
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```
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Installation
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------------
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gem install qsar-report
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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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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
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@@ -1 +1 @@
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1
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0.0.
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0.0.3
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data/lib/qmrf-report.rb
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@@ -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.
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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
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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
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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?
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data/lib/qprf-report.rb
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@@ -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.
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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
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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.
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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
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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"
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data/test/qmrf-report.rb
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@@ -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.
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report.
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assert_equal report.
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assert_equal report.
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refute_equal report.
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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.
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report.
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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.
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report.
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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"}
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data/test/qprf-report.rb
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assert_equal report.Title, "QSAR Prediction Reporting Format (QPRF)"
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end
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def
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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"
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def test_5_get_11
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report = OpenTox::QPRFReport.new
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report.
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assert_equal report.
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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
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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.
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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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