qsar-report 0.0.3 → 0.0.5

checksums.yaml

@@ -1,7 +1,7 @@
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data/.gitignore

@@ -1,2 +1,3 @@
 *.*~
 *~
+tmp/

data/README.md

@@ -20,6 +20,9 @@ report = OpenTox::QMRFReport.new
 # add a title
 report.value "QSAR_title", "My QSAR Title"
 
+# change 6.2 'Available information for the training set' set inchi and smiles to Yes
+report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
+
 # 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"}
 

data/VERSION

@@ -1 +1 @@
-0.0.3
+0.0.5

data/lib/qmrf-report.rb

@@ -11,6 +11,7 @@ module OpenTox
   #  require "qsar-report"
   #  report = OpenTox::QMRFReport.new
   #  report.value "QSAR_title", "My QSAR Title"
+  #  report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
   #  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
@@ -20,6 +21,8 @@ module OpenTox
     SCHEMA_FILE   = File.join(File.dirname(__FILE__),"template/qmrf.xsd")
     # QMRF XML Template file
     TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml")
+    # QMRF XML tags with attributes to edit
+    ATTRIBUTE_TAGS = ["training_set_availability", "training_set_data", "training_set_descriptors", "dependent_var_availability", "validation_set_availability", "validation_set_data", "validation_set_descriptors", "validation_dependent_var_availability"]
     
     attr_accessor :xml, :report
 
@@ -55,6 +58,21 @@ module OpenTox
       t.content
     end
 
+    # Set attributes of an report XML tag
+    # e.G.: <training_set_data cas="Yes" chapter="6.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the training set" smiles="Yes"/>
+    #@example change_attributes
+    #  report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
+    # @param [String] key Nodename e.g.: "training_set_data"
+    # @param [Hash] valuehash Key-Value Hash of tag attributes to change.
+    # @return [Error]  returns Error message if fails
+    def change_attributes tagname, valuehash
+      raise "Can not edit the attributes of tag: #{tagname}." unless ATTRIBUTE_TAGS.include? tagname
+      tag = @report.at_css tagname
+      valuehash.each do |key, value|
+        tag.attributes["#{key}"].value = value
+      end
+    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.: "<software contact='mycontact@mydomain.dom' description="My QSAR Software " id="software_catalog_2" name="MySoftware" number="" url="https://mydomain.dom"/>
@@ -62,9 +80,9 @@ module OpenTox
     # @return [Error]  returns Error message if fails
     def change_catalog catalog, id, valuehash
       catalog_exists? catalog
-      if @report.at_css("#{catalog}").at("//*[@id='#{id}']")
+      if @report.at_css("#{catalog}").at("[@id='#{id}']")
         valuehash.each do |key, value|
-          @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"]= value
+          @report.at_css("#{catalog}").at("[@id='#{id}']")["#{key}"]= value
         end
       else
         cat = @report.at_css("#{catalog}")
@@ -88,7 +106,7 @@ module OpenTox
       catalog_exists? catalog
       if @report.at_css("#{catalog}").at("//*[@id='#{id}']")
         chap = @report.at_css("#{chapter}")
-        if chap.at("//*[@idref='#{id}']").nil?
+        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
@@ -105,8 +123,8 @@ module OpenTox
     # @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}"]
+      if @report.at_css("#{catalog}").at("[@id='#{id}']")
+        @report.at_css("#{catalog}").at("[@id='#{id}']")["#{key}"]
       else
         return false
       end

data/qsar-report.gemspec

@@ -3,7 +3,7 @@
 Gem::Specification.new do |s|
   s.name        = "qsar-report"
   s.version     = File.read("./VERSION")
-  s.date        = "2016-08-19"
+  s.date        = "2016-09-14"
   s.authors     = ["Micha Rautenberg"]
   s.email       = ["rautenberg@in-silico.ch"]
   s.homepage    = "http://github.com/opentox/qsar-report"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: qsar-report
 version: !ruby/object:Gem::Version
-  version: 0.0.3
+  version: 0.0.5
 platform: ruby
 authors:
 - Micha Rautenberg
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-19 00:00:00.000000000 Z
+date: 2016-09-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri