qsar-report 0.0.2 → 0.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- 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.tar.gz: 18a34a213877e2025b9aebe47ec61e4921a4152645dca17b742a3bda525dd1341eaceb954687dd3725d9e4a3ba507ccdcc6a8bbcc763d1ce46608d6b699ab07f
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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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#@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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# 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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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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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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