qsar-report 0.0.5 → 1.0.0

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Files changed (15) hide show
  1. checksums.yaml +4 -4
  2. data/.yardopts +1 -1
  3. data/ChangeLog +6 -2
  4. data/LICENSE +619 -285
  5. data/README.md +7 -1
  6. data/VERSION +1 -1
  7. data/example/example.rb +175 -0
  8. data/lib/qmrf-report.rb +17 -9
  9. data/qsar-report.gemspec +5 -5
  10. data/test/all.rb +2 -2
  11. data/test/data/qmrf_t9n.xml +146 -0
  12. data/test/data/qmrf_t9y.xml +146 -0
  13. data/test/qmrf-report.rb +8 -0
  14. data/test/qprf-report.rb +1 -1
  15. metadata +8 -4
data/test/data/qmrf_t9y.xml ADDED
@@ -0,0 +1,146 @@
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+ <?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+ <!DOCTYPE QMRF PUBLIC "http://qmrf.sourceforge.net/qmrf.dtd" "qmrf.dtd">
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+ <QMRF author="Joint Research Centre, European Commission" contact="Joint Research Centre, European Commission" date="July 2007" email="JRC-IHCP-COMPUTOX@ec.europa.eu" name="(Q)SAR Model Reporting Format" schema_version="1.0" url="http://ihcp.jrc.ec.europa.eu/" version="1.3">
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+ <QMRF_chapters>
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+ <QSAR_identifier chapter="1" help="" name="QSAR identifier">
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+ <QSAR_title chapter="1.1" help="" name="QSAR identifier (title)"/>
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+ <QSAR_models chapter="1.2" help="" name="Other related models"/>
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+ <QSAR_software chapter="1.3" help="" name="Software coding the model">
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+
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+ <software_ref idref="firstsoftware"/>
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+ </QSAR_software>
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+ </QSAR_identifier>
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+ <QSAR_General_information chapter="2" help="" name="General information">
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+ <qmrf_date chapter="2.1" help="" name="Date of QMRF"/>
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+ <qmrf_authors chapter="2.2" help="" name="QMRF author(s) and contact details">
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+
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+ <author_ref idref="firstauthor"/>
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+ </qmrf_authors>
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+ <qmrf_date_revision chapter="2.3" help="" name="Date of QMRF update(s)"/>
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+ <qmrf_revision chapter="2.4" help="" name="QMRF update(s)"/>
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+ <model_authors chapter="2.5" help="" name="Model developer(s) and contact details">
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+
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+ <author_ref idref="modelauthor"/>
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+ </model_authors>
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+ <model_date chapter="2.6" help="" name="Date of model development and/or publication"/>
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+ <references chapter="2.7" help="" name="Reference(s) to main scientific papers and/or software package">
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+
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+ </references>
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+ <info_availability chapter="2.8" help="" name="Availability of information about the model"/>
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+ <related_models chapter="2.9" help="" name="Availability of another QMRF for exactly the same model"/>
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+ </QSAR_General_information>
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+ <QSAR_Endpoint chapter="3" help="" name="Defining the endpoint - OECD Principle 1">
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+ <model_species chapter="3.1" help="" name="Species"/>
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+ <model_endpoint chapter="3.2" help="" name="Endpoint">
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+
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+ </model_endpoint>
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+ <endpoint_comments chapter="3.3" help="" name="Comment on endpoint"/>
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+ <endpoint_units chapter="3.4" help="" name="Endpoint units"/>
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+ <endpoint_variable chapter="3.5" help="" name="Dependent variable"/>
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+ <endpoint_protocol chapter="3.6" help="" name="Experimental protocol"/>
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+ <endpoint_data_quality chapter="3.7" help="" name="Endpoint data quality and variability"/>
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+ </QSAR_Endpoint>
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+ <QSAR_Algorithm chapter="4" help="" name="Defining the algorithm - OECD Principle 2">
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+ <algorithm_type chapter="4.1" help="" name="Type of model"/>
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+ <algorithm_explicit chapter="4.2" help="" name="Explicit algorithm">
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+ <algorithm_ref idref="algorithms_catalog_1"/>
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+ <equation/>
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+ </algorithm_explicit>
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+ <algorithms_descriptors chapter="4.3" help="" name="Descriptors in the model">
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+
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+ <descriptor_ref idref="descriptors_catalog_1"/>
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+ </algorithms_descriptors>
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+ <descriptors_selection chapter="4.4" help="" name="Descriptor selection"/>
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+ <descriptors_generation chapter="4.5" help="" name="Algorithm and descriptor generation"/>
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+ <descriptors_generation_software chapter="4.6" help="" name="Software name and version for descriptor generation" options="">
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+
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+ <software_ref idref="software_catalog_2"/>
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+ </descriptors_generation_software>
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+ <descriptors_chemicals_ratio chapter="4.7" help="" name="Chemicals/Descriptors ratio"/>
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+ </QSAR_Algorithm>
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+ <QSAR_Applicability_domain chapter="5" help="" name="Defining the applicability domain - OECD Principle 3">
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+ <app_domain_description chapter="5.1" help="" name="Description of the applicability domain of the model"/>
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+ <app_domain_method chapter="5.2" help="" name="Method used to assess the applicability domain"/>
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+ <app_domain_software chapter="5.3" help="" name="Software name and version for applicability domain assessment">
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+
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+ <software_ref idref="software_catalog_3"/>
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+ </app_domain_software>
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+ <applicability_limits chapter="5.4" help="" name="Limits of applicability"/>
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+ </QSAR_Applicability_domain>
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+ <QSAR_Robustness chapter="6" help="" name="Internal validation - OECD Principle 4">
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+ <training_set_availability answer="Yes" chapter="6.1" help="" name="Availability of the training set"/>
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+ <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"/>
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+ <training_set_descriptors answer="All" chapter="6.3" help="" name="Data for each descriptor variable for the training set"/>
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+ <dependent_var_availability answer="All" chapter="6.4" help="" name="Data for the dependent variable for the training set"/>
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+ <other_info chapter="6.5" help="" name="Other information about the training set"/>
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+ <preprocessing chapter="6.6" help="" name="Pre-processing of data before modelling"/>
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+ <goodness_of_fit chapter="6.7" help="" name="Statistics for goodness-of-fit"/>
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+ <loo chapter="6.8" help="" name="Robustness - Statistics obtained by leave-one-out cross-validation"/>
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+ <lmo chapter="6.9" help="" name="Robustness - Statistics obtained by leave-many-out cross-validation"/>
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+ <yscrambling chapter="6.10" help="" name="Robustness - Statistics obtained by Y-scrambling"/>
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+ <bootstrap chapter="6.11" help="" name="Robustness - Statistics obtained by bootstrap"/>
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+ <other_statistics chapter="6.12" help="" name="Robustness - Statistics obtained by other methods"/>
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+ </QSAR_Robustness>
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+ <QSAR_Predictivity chapter="7" help="" name="External validation - OECD Principle 4">
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+ <validation_set_availability answer="Yes" chapter="7.1" help="" name="Availability of the external validation set"/>
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+ <validation_set_data cas="Yes" chapter="7.2" chemname="Yes" formula="Yes" help="" inchi="Yes" mol="Yes" name="Available information for the external validation set" smiles="Yes"/>
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+ <validation_set_descriptors answer="All" chapter="7.3" help="" name="Data for each descriptor variable for the external validation set"/>
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+ <validation_dependent_var_availability answer="All" chapter="7.4" help="" name="Data for the dependent variable for the external validation set"/>
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+ <validation_other_info chapter="7.5" help="" name="Other information about the external validation set"/>
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+ <experimental_design chapter="7.6" help="" name="Experimental design of test set"/>
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+ <validation_predictivity chapter="7.7" help="" name="Predictivity - Statistics obtained by external validation"/>
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+ <validation_assessment chapter="7.8" help="" name="Predictivity - Assessment of the external validation set"/>
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+ <validation_comments chapter="7.9" help="" name="Comments on the external validation of the model"/>
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+ </QSAR_Predictivity>
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+ <QSAR_Interpretation chapter="8" help="" name="Providing a mechanistic interpretation - OECD Principle 5">
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+ <mechanistic_basis chapter="8.1" help="" name="Mechanistic basis of the model"/>
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+ <mechanistic_basis_comments chapter="8.2" help="" name="A priori or a posteriori mechanistic interpretation"/>
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+ <mechanistic_basis_info chapter="8.3" help="" name="Other information about the mechanistic interpretation"/>
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+ </QSAR_Interpretation>
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+ <QSAR_Miscelaneous chapter="9" help="" name="Miscellaneous information">
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+ <comments chapter="9.1" help="" name="Comments"/>
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+ <bibliography chapter="9.2" help="" name="Bibliography">
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+
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+ <publication_ref idref="publications_catalog_1"/>
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+ </bibliography>
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+ <attachments chapter="9.3" help="" name="Supporting information">
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+
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+
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+
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+
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+
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+
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+ <attachment_training_data/>
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+ <attachment_validation_data/>
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+ <attachment_documents/>
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+ </attachments>
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+ </QSAR_Miscelaneous>
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+ <QMRF_Summary chapter="10" help="" name="Summary (JRC QSAR Model Database)">
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+ <QMRF_number chapter="10.1" help="" name="QMRF number">To be entered by JRC</QMRF_number>
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+ <date_publication chapter="10.2" help="" name="Publication date">To be entered by JRC</date_publication>
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+ <keywords chapter="10.3" help="" name="Keywords">To be entered by JRC</keywords>
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+ <summary_comments chapter="10.4" help="" name="Comments">To be entered by JRC</summary_comments>
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+ </QMRF_Summary>
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+ </QMRF_chapters>
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+ <Catalogs>
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+ <software_catalog>
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+ <software contact="" description="" id="firstsoftware" name="" number="" url=""/>
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+ <software contact="" description="" id="software_catalog_2" name="" number="" url=""/>
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+ <software contact="" description="" id="software_catalog_3" name="" number="" url=""/>
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+ </software_catalog>
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+ <algorithms_catalog>
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+ <algorithm definition="" description="" id="algorithms_catalog_1" publication_ref=""/>
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+ </algorithms_catalog>
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+ <descriptors_catalog>
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+ <descriptor description="" id="descriptors_catalog_1" name="" publication_ref="" units=""/>
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+ </descriptors_catalog>
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+ <endpoints_catalog/>
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+ <publications_catalog>
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+ <publication id="publications_catalog_1" title="" url=""/>
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+ </publications_catalog>
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+ <authors_catalog>
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+ <author affiliation="" contact="" email="" id="firstauthor" name="" number="" url=""/>
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+ <author affiliation="" contact="" email="" id="modelauthor" name="" number="" url=""/>
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+ </authors_catalog>
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+ </Catalogs>
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+ </QMRF>
data/test/qmrf-report.rb CHANGED
@@ -71,4 +71,12 @@ class QMRFReportTest < MiniTest::Test
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  assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t8.xml")))
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  end
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+ def test_9_set_attributes
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+ report = OpenTox::QMRFReport.new
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+ report.change_attributes "training_set_data", {:inchi => "Yes", :smiles => "Yes"}
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+ assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t9y.xml")))
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+ report.change_attributes "training_set_data", {:inchi => "No", :smiles => "No"}
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+ assert_equal report.to_xml, File.read(File.join(File.join(DATA_DIR, "qmrf_t9n.xml")))
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+ end
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+
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  end
data/test/qprf-report.rb CHANGED
@@ -1,6 +1,6 @@
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  require_relative "setup.rb"
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- class QMRFReportTest < MiniTest::Test
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+ class QPRFReportTest < MiniTest::Test
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  def test_0_self
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  puts "MiniTest #{self.class} start OK"
metadata CHANGED
@@ -1,14 +1,14 @@
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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: 0.0.5
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+ version: 1.0.0
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  platform: ruby
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  authors:
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  - Micha Rautenberg
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2016-09-14 00:00:00.000000000 Z
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+ date: 2016-09-16 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: nokogiri
@@ -67,6 +67,7 @@ files:
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  - LICENSE
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  - README.md
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  - VERSION
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+ - example/example.rb
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  - lib/qmrf-report.rb
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  - lib/qprf-report.rb
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  - lib/qsar-report.rb
@@ -80,14 +81,17 @@ files:
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  - test/data/qmrf_t4.xml
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  - test/data/qmrf_t7.xml
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  - test/data/qmrf_t8.xml
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+ - test/data/qmrf_t9n.xml
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+ - test/data/qmrf_t9y.xml
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  - test/data/qprf-t6.json
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  - test/qmrf-report.rb
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  - test/qprf-report.rb
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  - test/setup.rb
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- homepage: http://github.com/opentox/qsar-report
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+ homepage: https://github.com/opentox/qsar-report
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  licenses:
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  - GPL-3.0
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- metadata: {}
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+ metadata:
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+ issue_tracker: https://github.com/opentox/qsar-report/issues
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  post_install_message:
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  rdoc_options: []
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  require_paths: