qsar-report 0.0.2

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+ *.*~
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+ *~
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+ --readme README.md
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+ --title 'QMRF and QPRF reporting class for OpenTox'
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+ --charset utf-8
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+ yardoc lib/*.rb - README.md ChangeLog VERSION LICENSE
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+ v0.0.2
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+ * add QPRF reporting
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+ * rename gem qmrf-report to qsar-report
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+ v0.0.1
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+ * initial version
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+
data/Gemfile ADDED
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+ source "https://rubygems.org"
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+ gemspec
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+ gem "nokogiri"
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+ gem "haml"
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+ gem "json"
data/LICENSE ADDED
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+ GNU GENERAL PUBLIC LICENSE
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+ Version 2, June 1991
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+
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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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+ * 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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+
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+ ## Usage
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+ ### QMRF
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+ create a new QMRF report, add some content and show output:
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+ ```ruby
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+ require "qsar-report"
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+
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+ # create a new report
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+ report = OpenTox::QMRFReport.new
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+
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+ # add a title
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+ report.change_qmrf_tag "QSAR_title", "My QSAR Title"
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+
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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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+
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+ # link/reference the publication to the report bibliography
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+ report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
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+
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+ # output
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+ puts report.to_xml
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+
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+ # validate a report (as created above) against qmrf.xsd
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+ report.validate
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+ ```
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+ ### QPRF
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+ create a new QPRF report, add some content and show output:
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+ ```ruby
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+ require "qsar-report"
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+
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+ # create a new QPRF report instance
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+ report = OpenTox::QPRFReport.new
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+
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+ # Set Title of the report
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+ report.Title = "My QPRF Report"
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+
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+ # Set Version
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+ report.Version = "1"
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+
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+ # Set Date
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+ report.Date = Time.now.strftime("%Y/%m/%d")
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+
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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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+
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+ # print HTML version
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+ puts report.to_html
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+
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+ # print formated JSON version
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+ puts report.pretty_json
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+
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+ ```
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+
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+
data/VERSION ADDED
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+ 0.0.2
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+ require "nokogiri"
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+
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+ # OpenTox module
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+ module OpenTox
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+
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+ #Class for QMRF reporting.
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+ #
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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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+ #@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.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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+
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+ class QMRFReport
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+ # QMRF XML Schema file
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+ SCHEMA_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xsd")
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+ # QMRF XML Template file
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+ TEMPLATE_FILE = File.join(File.dirname(__FILE__),"template/qmrf.xml")
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+
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+ attr_accessor :xml, :report
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+
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+ # Open an existing QMRF xml report
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+ # @param [String] file Name of the file
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+ def open file
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+ xml = File.read("#{file}")
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+ @report = Nokogiri.XML(xml)
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+ end
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+
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+ # Initialize a new report instance from qmrf template
34
+ def initialize
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+ xml = File.read(TEMPLATE_FILE)
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+ @report = Nokogiri.XML(xml)
37
+ end
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+
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+ # returns XML representation (QMRF XML report) of report instance
40
+ # @return [String] returns XML
41
+ def to_xml
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+ @report.to_xml
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+ end
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+
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+ # Get or Set a value
46
+ # e.G.: <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)">Title of My QSAR</QSAR_title>
47
+ # @param [String] key Nodename e.g.: "QSAR_title"
48
+ # @param [String] value Value to change. If not set the function returns the current value
49
+ # @return [Error] returns Error message if fails
50
+ # @return [String] returns value
51
+ def Value key, value=nil
52
+ 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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+ t.content
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+ end
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+
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+ # Change a catalog
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+ # @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
60
+ # @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"/>
61
+ # @param [Hash] valuehash Key-Value Hash with attributes for a single catalog node
62
+ # @return [Error] returns Error message if fails
63
+ def change_catalog catalog, id, valuehash
64
+ catalog_exists? catalog
65
+ if @report.at_css("#{catalog}").at("//*[@id='#{id}']")
66
+ valuehash.each do |key, value|
67
+ @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"]= value
68
+ end
69
+ else
70
+ cat = @report.at_css("#{catalog}")
71
+ newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'')}", self.report)
72
+ newentry["id"] = id
73
+ valuehash.each do |key, value|
74
+ newentry["#{key}"] = value
75
+ end
76
+ cat << newentry
77
+ end
78
+ end
79
+
80
+ # Set reference to a catalog entry.
81
+ # e.g.: reference an author entry from authors_catalog to Chapter 2.2 QMRF authors
82
+ #@example ref_catalog
83
+ # report.ref_catalog 'qmrf_authors', 'authors_catalog', 'firstauthor'
84
+ # @param [String] chapter Name of the chapter to add the catalog reference. e.g.: qmrf_authors, model_authors, QSAR_software, ...
85
+ # @param [String] catalog Name of the catalog
86
+ # @param [String] id entry node in the catalog
87
+ def ref_catalog chapter, catalog, id
88
+ catalog_exists? catalog
89
+ if @report.at_css("#{catalog}").at("//*[@id='#{id}']")
90
+ chap = @report.at_css("#{chapter}")
91
+ if chap.at("//*[@idref='#{id}']").nil?
92
+ newentry = Nokogiri::XML::Node.new("#{catalog.to_s.gsub(/s?_catalog/,'_ref')}", self.report)
93
+ newentry["idref"] = id
94
+ chap << newentry
95
+ end
96
+ else
97
+ raise "catalog entry with id: #{id} do not exist."
98
+ end
99
+ end
100
+
101
+ # get an attribute from a catalog entry
102
+ # @param [String] catalog Name of the catalog
103
+ # @param [String] id entry id in the catalog
104
+ # @param [String] key returns value of a key in a catalog node
105
+ # @return [String, false] returns value of a key in a catalog node or false if catalog entry do not exists.
106
+ def get_catalog_value catalog, id, key
107
+ catalog_exists? catalog
108
+ if @report.at_css("#{catalog}").at("//*[@id='#{id}']")
109
+ @report.at_css("#{catalog}").at("//*[@id='#{id}']")["#{key}"]
110
+ else
111
+ return false
112
+ end
113
+ end
114
+
115
+ # Check if a catalog exists in this QMRF version
116
+ # @param [String] catalog Catalog
117
+ # @return [Error, true] returns true or Error if a catalog do not exists
118
+ def catalog_exists? catalog
119
+ raise "Unknown catalog: #{catalog}" unless ["software_catalog", "algorithms_catalog", "descriptors_catalog", "endpoints_catalog", "publications_catalog", "authors_catalog"].include? catalog.to_s
120
+ true
121
+ end
122
+
123
+ # Validates a report instance against qmrf.xsd (XML Structure Definition)
124
+ def validate
125
+ xsd = Nokogiri::XML::Schema(File.read(SCHEMA_FILE))
126
+ out = ""
127
+ xsd.validate(@report).each do |error|
128
+ out << error.message unless error.message == "Element 'algorithm', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'." || error.message == "Element 'descriptor', attribute 'publication_ref': '' is not a valid value of the atomic type 'xs:IDREF'."
129
+ # @todo ignore case sensitivity error: error.message The value 'NO' is not an.Element of the set {'Yes', 'No'}.
130
+ end
131
+ return out
132
+ end
133
+
134
+ end
135
+ end