Added script for testing Java and Python SBOL2->SBOL3->SBOL2

Author: cjmyers

scripts/JavaFails

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+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence1.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence2.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence3.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence4.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_ref.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleModel.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleSequence.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/test_source_location.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/toggle.xml

scripts/JavaNotMatch.txt

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+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/act_example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ActivityTypeOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/AnnotationOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/attachment.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/BBa_I0462.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Cut_Example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CD_SA_Range_Example.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_cd_sa_comp.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl_noRange.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput_gl.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ComponentDefinitionOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/CreateAndRemoveModel.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/design_usa_act_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/EF587312.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/eukaryotic_transcriptional_cd_sa_gl.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/manifest
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Measure.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/memberAnnotations.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/ModuleDefinitionOutput.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/multipleSequences.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_left_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_casette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pIKE_right_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_left_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/partial_pTAK_right_cassette.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes_2.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_cassettes.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_left_right_cassettes.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/pIKE_pTAK_toggle_switches.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization_Agent_Act_CD.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_CodonOptimization.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag_Act.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_ag_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyCutOperation_Ag.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_SpecifyJoinOperation_act_us.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/Provenance_StrainDerivation.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence1.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence2.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence3.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/sequence4.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_plan_ann.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/simple_attachment_ref.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleCompDef_withSeq.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleModel.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/singleSequence.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/test_source_location.xml
+Java conversion DOES NOT match for /Users/myers/git/SBOLTestSuite/SBOL2/toggle.xml

scripts/java23.xml

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+<rdf:RDF
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:dcterms="http://purl.org/dc/terms/"
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:grn="urn:bbn.com:tasbe:grn/"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:annot="http://myannotation.org/"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/">
+   <sbol:Sequence rdf:about="http://www.async.ece.utah.edu/1.0/pLacSeq">
+      <sbol:encoding rdf:resource="https://identifiers.org/edam:format_1207"/>
+      <sbol:elements>ACGTURYSWKMBDHVN-.</sbol:elements>
+      <sbol:hasNamespace rdf:resource="http://www.async.ece.utah.edu"/>
+      <sbol:displayId>pLacSeq</sbol:displayId>
+   </sbol:Sequence>
+</rdf:RDF>

scripts/java32.xml

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+<?xml version="1.0" ?>
+<rdf:RDF xmlns:grn="urn:bbn.com:tasbe:grn/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:sbol="http://sbols.org/v2#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:annot="http://myannotation.org/" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/">
+  <sbol:Model rdf:about="http://www.async.ece.utah.edu/ToggleModel/1.0">
+    <sbol:persistentIdentity rdf:resource="http://www.async.ece.utah.edu/ToggleModel"/>
+    <sbol:displayId>ToggleModel</sbol:displayId>
+    <sbol:version>1.0</sbol:version>
+    <sbol:source rdf:resource="https://sbolstandard.org/SBOL3-Converter/ToggleModel_source"/>
+    <sbol:language rdf:resource="http://identifiers.org/edam/format_2585"/>
+    <sbol:framework rdf:resource="http://identifiers.org/biomodels.sbo/SBO:0000062"/>
+  </sbol:Model>
+</rdf:RDF>