qsar-report 0.0.2 → 0.0.3

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@@ -1,7 +1,7 @@
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data/README.md

@@ -1,12 +1,12 @@
 # QSAR-Report
 QMRF and QPRF reporting extension to OpenTox ruby modules and lazar
 ## About
-Class for QMRF and QPRF reporting.
+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.
+  Provides a ruby OpenTox class to prepare an initial version of a QPRF (version 1.1) report in JSON or HTML.
 
 ## Usage
 ### QMRF
@@ -18,7 +18,7 @@ require "qsar-report"
 report = OpenTox::QMRFReport.new
 
 # add a title
-report.change_qmrf_tag "QSAR_title", "My QSAR Title"
+report.value "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"}
@@ -50,7 +50,7 @@ report.Version = "1"
 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
+report.value "1.1", "7732-18-5" # set CAS number for H²O
 
 # print HTML version
 puts report.to_html
@@ -60,4 +60,17 @@ puts report.pretty_json
 
 ```
 
+Installation
+------------
+
+  gem install qsar-report
+
+Documentation
+-------------
+* [RubyDoc.info Code documentation](http://www.rubydoc.info/gems/qsar-report)
+* 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)
+
+Copyright
+---------
+Copyright (c) 2016 Christoph Helma, Micha Rautenberg, Denis Gebele. See LICENSE for details.
 

data/VERSION

@@ -1 +1 @@
-0.0.2
+0.0.3

data/lib/qmrf-report.rb

@@ -10,7 +10,7 @@ module OpenTox
   #@example Report
   #  require "qsar-report"
   #  report = OpenTox::QMRFReport.new
-  #  report.change_qmrf_tag "QSAR_title", "My QSAR Title"
+  #  report.value "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
@@ -48,7 +48,7 @@ module OpenTox
     # @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
+    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?

data/lib/qprf-report.rb

@@ -14,7 +14,7 @@ module OpenTox
   #  report.Title = "My QPRF Report"
   #  report.Version = "1"
   #  report.Date = Time.now.strftime("%Y/%m/%d")
-  #  report.Value "1.1", "7732-18-5" # set CAS number for H²O
+  #  report.value "1.1", "7732-18-5" # set CAS number for H²O
   #  puts report.to_html
 
   class QPRFReport
@@ -56,12 +56,12 @@ module OpenTox
     # Set or Get a value in the QPRF report
     #@example for CAS Number
     #  report = OpenTox::QPRFReport.new
-    #  report.Value "1.1", "7732-18-5"
+    #  report.value "1.1", "7732-18-5"
     #
     # @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" ...
     # @param [String] value Value to set. If not set the function returns the current value
     # @return [String]  returns Value
-    def Value chapter, value=nil
+    def value chapter, value=nil
       case chapter
       when /^1\.\d*/
         block = "1. Substance"

data/test/qmrf-report.rb

@@ -19,17 +19,17 @@ class QMRFReportTest < MiniTest::Test
 
   def test_3_write_some_values
     report = OpenTox::QMRFReport.new
-    report.Value "QSAR_title", "My QSAR Title"
-    report.Value "QSAR_models", "My QSAR Model"
-    assert_equal report.Value("QSAR_title"), "My QSAR Title"
-    assert_equal report.Value("QSAR_models"), "My QSAR Model"
-    refute_equal report.Value("QSAR_title"), "lazar"
+    report.value "QSAR_title", "My QSAR Title"
+    report.value "QSAR_models", "My QSAR Model"
+    assert_equal report.value("QSAR_title"), "My QSAR Title"
+    assert_equal report.value("QSAR_models"), "My QSAR Model"
+    refute_equal report.value("QSAR_title"), "lazar"
   end
 
   def test_4_write_check
     report = OpenTox::QMRFReport.new
-    report.Value "QSAR_title", "My QSAR Title"
-    report.Value "QSAR_models", "My QSAR Model"
+    report.value "QSAR_title", "My QSAR Title"
+    report.value "QSAR_models", "My QSAR Model"
     assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t4.xml")))
   end
 
@@ -52,8 +52,8 @@ class QMRFReportTest < MiniTest::Test
   
   def test_7_write_alot
     report = OpenTox::QMRFReport.new
-    report.Value "QSAR_title", "My QSAR Title"
-    report.Value "QSAR_models", "My QSAR Model"
+    report.value "QSAR_title", "My QSAR Title"
+    report.value "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"}

data/test/qprf-report.rb

@@ -25,7 +25,7 @@ class QMRFReportTest < MiniTest::Test
     assert_equal report.Title, "QSAR Prediction Reporting Format (QPRF)"
   end
   
-  def test_4_set_Values
+  def test_4_set_values
     report = OpenTox::QPRFReport.new
     report.Title = "My Test Title"
     report.Version = "12"
@@ -36,16 +36,16 @@ class QMRFReportTest < MiniTest::Test
 
   def test_5_get_11
     report = OpenTox::QPRFReport.new
-    report.Value "1.1", "7732-18-5"
-    assert_equal report.Value("1.1"), "7732-18-5"
+    report.value "1.1", "7732-18-5"
+    assert_equal report.value("1.1"), "7732-18-5"
   end
 
-  def test_6_set_more_Values
+  def test_6_set_more_values
     report = OpenTox::QPRFReport.new
     report.Title = "My QPRF Report"
     report.Version = "2.1"
     report.Date = "2016/08/21"
-    report.Value "1.1", "7732-18-5"
+    report.value "1.1", "7732-18-5"
     assert_equal report.pretty_json, File.read(File.join(DATA_DIR,'qprf-t6.json'))
   end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: qsar-report
 version: !ruby/object:Gem::Version
-  version: 0.0.2
+  version: 0.0.3
 platform: ruby
 authors:
 - Micha Rautenberg