qsar-report 1.0.0 → 1.0.1

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Files changed (5) hide show
  1. checksums.yaml +5 -5
  2. data/README.md +10 -5
  3. data/VERSION +1 -1
  4. data/example/example.rb +38 -32
  5. metadata +2 -3
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data/README.md CHANGED
@@ -1,14 +1,19 @@
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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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+ QMRF and QPRF reporting extension to OpenTox ruby modules and lazar.
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+ The QSAR-report gem was developed to extend the lazar and nano-lazar toxicity prediction application with QMRF and QPRF reporting features.
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+ The library gem is independent from lazar or nano-lazar and can also be used in any other ruby code.
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+
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  ## About
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- Class for QMRF and QPRF reporting.
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- * QMRF:
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+ Classes for QMRF and QPRF reporting.
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+
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+ * **OpenTox::QMRFReport**:
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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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+ * **OpenTox::QPRFReport**:
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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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+
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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
@@ -66,7 +71,7 @@ puts report.pretty_json
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  Installation
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  ------------
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- gem install qsar-report
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+ gem install qsar-report
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  Documentation
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  -------------
data/VERSION CHANGED
@@ -1 +1 @@
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- 1.0.0
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+ 1.0.1
data/example/example.rb CHANGED
@@ -10,7 +10,7 @@ prediction_model = Model::Prediction.find_by :model_id => params[:id]
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  validation_template = File.join(File.dirname(__FILE__),"../views/model_details.haml") #detailed validation results from lazar-rest
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- # Start filling the QMRF report
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+ # Start filling the QMRF report
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  # QSAR identifier (title) 1.1
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  report.value "QSAR_title", "Model for #{prediction_model.species} #{prediction_model.endpoint}"
@@ -22,10 +22,16 @@ report.ref_catalog :QSAR_software, :software_catalog, :firstsoftware
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  # Date of QMRF 2.1
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  report.value "qmrf_date", "#{Time.now.strftime('%d %B %Y')}"
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- # QMRF author(s) and contact details 2.1
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+ # QMRF author(s) and contact details 2.2
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  report.change_catalog :authors_catalog, :firstauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
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  report.ref_catalog :qmrf_authors, :authors_catalog, :firstauthor
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+ # Date of QMRF update(s) 2.3
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+ report.value "qmrf_date_revision", ""
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+
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+ # QMRF update(s) 2.4
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+ report.value "qmrf_revision", ""
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+
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  # Model developer(s) and contact details 2.5
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  report.change_catalog :authors_catalog, :modelauthor, {:name => "Christoph Helma", :affiliation => "in silico toxicology gmbh", :contact => "Contact Address", :email => "Contact Email", :number => "1", :url => "Web Page"}
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  report.ref_catalog :model_authors, :authors_catalog, :modelauthor
@@ -42,9 +48,9 @@ report.change_catalog :publications_catalog, :publications_catalog_2, {:title =>
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  report.ref_catalog :references, :publications_catalog, :publications_catalog_2
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  # Species 3.1
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- report.value "model_species", prediction_model.species
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+ report.value "model_species", prediction_model.species
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- # Endpoint 3.2
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+ # Endpoint 3.2
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  report.change_catalog :endpoints_catalog, :endpoints_catalog_1, {:name => prediction_model.endpoint, :group => ""}
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  report.ref_catalog :model_endpoint, :endpoints_catalog, :endpoints_catalog_1
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@@ -75,23 +81,23 @@ report.ref_catalog :descriptors_generation_software, :software_catalog, :softwar
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  # Chemicals/Descriptors ratio 4.7
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  report.value "descriptors_chemicals_ratio", "not applicable (classification based on activities of neighbors, descriptors are used for similarity calculation)"
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- # Some QMRF fields (tag contents) can have formatted HTML contents.
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- # These contents have to have a complete HTML document structure with basic surrounding tags like <html><body>.
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- # see Example below
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+ # Some QMRF fields (tag contents) can have formatted HTML contents.
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+ # These contents have to have a complete HTML document structure with basic surrounding tags like <html><body>.
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+ # see Example below
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  # Description of the applicability domain of the model 5.1
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  report.value "app_domain_description", "<html><head></head><body>
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  <p>
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- The applicability domain (AD) of the training set is characterized by
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- the confidence index of a prediction (high confidence index: close to
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- the applicability domain of the training set/reliable prediction, low
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- confidence: far from the applicability domain of the
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- trainingset/unreliable prediction). The confidence index considers (i)
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- the similarity and number of neighbors and (ii) contradictory examples
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+ The applicability domain (AD) of the training set is characterized by
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+ the confidence index of a prediction (high confidence index: close to
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+ the applicability domain of the training set/reliable prediction, low
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+ confidence: far from the applicability domain of the
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+ trainingset/unreliable prediction). The confidence index considers (i)
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+ the similarity and number of neighbors and (ii) contradictory examples
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  within the neighbors. A formal definition can be found in Helma 2006.
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  </p>
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  <p>
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- The reliability of predictions decreases gradually with increasing
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+ The reliability of predictions decreases gradually with increasing
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  distance from the applicability domain (i.e. decreasing confidence index)
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  </p>
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  </body>
@@ -100,7 +106,7 @@ report.value "app_domain_description", "<html><head></head><body>
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  # Method used to assess the applicability domain 5.2
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  report.value "app_domain_method", "see Helma 2006 and Maunz 2008"
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- # Software name and version for applicability domain assessment 5.3
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+ # Software name and version for applicability domain assessment 5.3
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  report.change_catalog :software_catalog, :software_catalog_3, {:name => "lazar, submitted version: #{lazar_commit}", :description => "integrated into main lazar algorithm", :number => "3", :url => "https://lazar.in-silico.ch", :contact => "Contact Email"}
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  report.ref_catalog :app_domain_software, :software_catalog, :software_catalog_3
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@@ -135,10 +141,10 @@ end
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  # Mechanistic basis of the model 8.1
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  report.value "mechanistic_basis","<html><head></head><body>
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  <p>
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- Compounds with similar structures (neighbors) are assumed to have
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- similar activities as the query compound. For the determination of
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- activity specific similarities only statistically relevant subtructures
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- (paths) are used. For this reason there is a priori no bias towards
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+ Compounds with similar structures (neighbors) are assumed to have
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+ similar activities as the query compound. For the determination of
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+ activity specific similarities only statistically relevant subtructures
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+ (paths) are used. For this reason there is a priori no bias towards
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  specific mechanistic hypothesis.
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  </p>
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  </body>
@@ -148,22 +154,22 @@ report.value "mechanistic_basis","<html><head></head><body>
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  report.value "mechanistic_basis_comments","a posteriori for individual predictions"
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  # Other information about the mechanistic interpretation 8.3
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- report.value "mechanistic_basis_info","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual
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+ report.value "mechanistic_basis_info","<html><head></head><body><p>Hypothesis about biochemical mechanisms can be derived from individual
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  predictions by inspecting neighbors and relevant fragments.</p>
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- <p>Neighbors are compounds that are similar in respect to a certain
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- endpoint and it is likely that compounds with high similarity act by
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- similar mechanisms as the query compound. Links at the webinterface
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- prove an easy access to additional experimental data and literature
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+ <p>Neighbors are compounds that are similar in respect to a certain
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+ endpoint and it is likely that compounds with high similarity act by
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+ similar mechanisms as the query compound. Links at the webinterface
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+ prove an easy access to additional experimental data and literature
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  citations for the neighbors and the query structure.</p>
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- <p>Activating and deactivating parts of the query compound are highlighted
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- in red and green on the webinterface. Fragments that are unknown (or too
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- infrequent for statistical evaluation are marked in yellow and
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- additional statistical information about the individual fragments can be
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- retrieved. Please note that lazar predictions are based on neighbors and
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- not on fragments. Fragments and their statistical significance are used
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+ <p>Activating and deactivating parts of the query compound are highlighted
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+ in red and green on the webinterface. Fragments that are unknown (or too
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+ infrequent for statistical evaluation are marked in yellow and
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+ additional statistical information about the individual fragments can be
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+ retrieved. Please note that lazar predictions are based on neighbors and
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+ not on fragments. Fragments and their statistical significance are used
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  for the calculation of activity specific similarities.</p>"
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- # Reference all publications to the bibliography
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+ # Reference all publications to the bibliography
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  # Bibliography 9.2
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  report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_1
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  report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_2
@@ -172,4 +178,4 @@ report.ref_catalog :bibliography, :publications_catalog, :publications_catalog_3
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  # output
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  response['Content-Type'] = "application/xml"
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- return report.to_xml
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+ return report.to_xml
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: qsar-report
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  version: !ruby/object:Gem::Version
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- version: 1.0.0
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+ version: 1.0.1
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  platform: ruby
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  authors:
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  - Micha Rautenberg
@@ -107,8 +107,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  - !ruby/object:Gem::Version
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  version: '0'
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  requirements: []
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- rubyforge_project:
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- rubygems_version: 2.5.1
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+ rubygems_version: 3.0.6
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  signing_key:
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  specification_version: 4
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  summary: qsar-report