├── .github └── workflows │ └── scala.yml ├── .gitignore ├── LICENSE ├── README.md ├── project ├── build.properties └── plugins.sbt └── src ├── main └── scala │ └── org │ └── monarchinitiative │ └── dosdp │ ├── Bindings.scala │ ├── DOSDP.scala │ ├── DOSDPEntityChecker.scala │ ├── DocsMarkdown.scala │ ├── ExpandedDOSDP.scala │ ├── Prefixes.scala │ ├── SPARQL.scala │ ├── SafeOWLEntityChecker.scala │ ├── SesameJena.scala │ ├── Utilities.scala │ └── cli │ ├── Config.scala │ ├── Docs.scala │ ├── Generate.scala │ ├── Main.scala │ ├── Prototype.scala │ ├── Query.scala │ ├── Terms.scala │ └── ZCaseApp.scala └── test ├── resources ├── org │ └── monarchinitiative │ │ └── dosdp │ │ ├── OverrideTest.ofn │ │ ├── OverrideTest.tsv │ │ ├── OverrideTest.yaml │ │ ├── QueryGeneratorRegexTest.yaml │ │ ├── QueryGeneratorTest.yaml │ │ ├── QueryLabelTest.ofn │ │ ├── QueryLabelTest.yaml │ │ ├── StandardPrefixes.yaml │ │ ├── internal_vars_test.ofn │ │ ├── internal_vars_test.tsv │ │ ├── internal_vars_test.yaml │ │ ├── missing_values_test.csv │ │ ├── missing_values_test.tsv │ │ ├── missing_values_test.yaml │ │ ├── test_annotation_parsing.yaml │ │ ├── test_blank_lines.tsv │ │ ├── test_blank_lines.yaml │ │ └── test_union.ofn └── tutorial │ ├── exposure_with_input.owl │ ├── exposure_with_input.tsv │ ├── exposure_with_input.yaml │ ├── exposure_with_input_with_role.owl │ ├── exposure_with_input_with_role.tsv │ ├── exposure_with_input_with_role.yaml │ └── prefixes.yaml └── scala └── org └── monarchinitiative └── dosdp ├── AxiomRestrictionsTest.scala ├── BlankLineTest.scala ├── ExpressionParsingTest.scala ├── IRIAnnotationValuesTest.scala ├── InternalVarsTest.scala ├── MissingValuesTest.scala ├── MultiClausePrintfTest.scala ├── MultipleLabelsTest.scala ├── OverrideTest.scala ├── ParseAnnotationsTest.scala ├── PrefixesTest.scala ├── QueryGeneratorRegexTest.scala ├── QueryGeneratorTest.scala ├── QueryLabelTest.scala ├── RegexTest.scala └── UnionQueryTest.scala /.github/workflows/scala.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/.github/workflows/scala.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/README.md -------------------------------------------------------------------------------- /project/build.properties: -------------------------------------------------------------------------------- 1 | sbt.version=1.6.2 2 | -------------------------------------------------------------------------------- /project/plugins.sbt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/project/plugins.sbt -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/Bindings.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/Bindings.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/DOSDP.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/DOSDP.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/DOSDPEntityChecker.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/DOSDPEntityChecker.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/DocsMarkdown.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/DocsMarkdown.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/ExpandedDOSDP.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/ExpandedDOSDP.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/Prefixes.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/Prefixes.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/SPARQL.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/SPARQL.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/SafeOWLEntityChecker.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/SafeOWLEntityChecker.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/SesameJena.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/SesameJena.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/Utilities.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/Utilities.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Config.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Config.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Docs.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Docs.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Generate.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Generate.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Main.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Main.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Prototype.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Prototype.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Query.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Query.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/Terms.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/Terms.scala -------------------------------------------------------------------------------- /src/main/scala/org/monarchinitiative/dosdp/cli/ZCaseApp.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/main/scala/org/monarchinitiative/dosdp/cli/ZCaseApp.scala -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/OverrideTest.ofn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/OverrideTest.ofn -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/OverrideTest.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/OverrideTest.tsv -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/OverrideTest.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/OverrideTest.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/QueryGeneratorRegexTest.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/QueryGeneratorRegexTest.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/QueryGeneratorTest.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/QueryGeneratorTest.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/QueryLabelTest.ofn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/QueryLabelTest.ofn -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/QueryLabelTest.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/QueryLabelTest.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/StandardPrefixes.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/StandardPrefixes.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.ofn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.ofn -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.tsv -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/internal_vars_test.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/missing_values_test.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/missing_values_test.csv -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/missing_values_test.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/missing_values_test.tsv -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/missing_values_test.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/missing_values_test.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/test_annotation_parsing.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/test_annotation_parsing.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/test_blank_lines.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/test_blank_lines.tsv -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/test_blank_lines.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/test_blank_lines.yaml -------------------------------------------------------------------------------- /src/test/resources/org/monarchinitiative/dosdp/test_union.ofn: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/org/monarchinitiative/dosdp/test_union.ofn -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/tutorial/exposure_with_input.owl -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/tutorial/exposure_with_input.tsv -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/tutorial/exposure_with_input.yaml -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input_with_role.owl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/tutorial/exposure_with_input_with_role.owl -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input_with_role.tsv: -------------------------------------------------------------------------------- 1 | defined_class input 2 | EXPOSO:4 CHEBI:50910 3 | -------------------------------------------------------------------------------- /src/test/resources/tutorial/exposure_with_input_with_role.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/resources/tutorial/exposure_with_input_with_role.yaml -------------------------------------------------------------------------------- /src/test/resources/tutorial/prefixes.yaml: -------------------------------------------------------------------------------- 1 | EXPOSO: http://example.org/exposure/ 2 | -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/AxiomRestrictionsTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/AxiomRestrictionsTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/BlankLineTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/BlankLineTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/ExpressionParsingTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/ExpressionParsingTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/IRIAnnotationValuesTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/IRIAnnotationValuesTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/InternalVarsTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/InternalVarsTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/MissingValuesTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/MissingValuesTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/MultiClausePrintfTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/MultiClausePrintfTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/MultipleLabelsTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/MultipleLabelsTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/OverrideTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/OverrideTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/ParseAnnotationsTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/ParseAnnotationsTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/PrefixesTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/PrefixesTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/QueryGeneratorRegexTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/QueryGeneratorRegexTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/QueryGeneratorTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/QueryGeneratorTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/QueryLabelTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/QueryLabelTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/RegexTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/RegexTest.scala -------------------------------------------------------------------------------- /src/test/scala/org/monarchinitiative/dosdp/UnionQueryTest.scala: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/INCATools/dosdp-tools/HEAD/src/test/scala/org/monarchinitiative/dosdp/UnionQueryTest.scala --------------------------------------------------------------------------------