oaklib 0.6.2__tar.gz → 0.6.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (318) hide show
  1. {oaklib-0.6.2 → oaklib-0.6.4}/PKG-INFO +2 -1
  2. {oaklib-0.6.2 → oaklib-0.6.4}/pyproject.toml +4 -3
  3. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/cli.py +294 -136
  4. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_obo_format_converter.py +41 -18
  5. oaklib-0.6.4/src/oaklib/datamodels/ontology_metadata.py +2179 -0
  6. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.yaml +27 -2
  7. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.py +221 -481
  8. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.yaml +20 -1
  9. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/llm_implementation.py +101 -1
  10. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/simple_obo_implementation.py +32 -5
  11. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/simple_obo_parser.py +18 -0
  12. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/interfaces/obograph_interface.py +55 -0
  13. oaklib-0.6.4/src/oaklib/interfaces/validator_interface.py +315 -0
  14. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/io/streaming_obo_writer.py +12 -44
  15. oaklib-0.6.4/src/oaklib/utilities/publication_utils/doi_wrapper.py +142 -0
  16. oaklib-0.6.4/src/oaklib/utilities/publication_utils/pubdb_wrapper.py +36 -0
  17. oaklib-0.6.4/src/oaklib/utilities/publication_utils/pubmed_wrapper.py +167 -0
  18. oaklib-0.6.4/src/oaklib/utilities/validation/__init__.py +0 -0
  19. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/utilities/validation/definition_ontology_rule.py +72 -50
  20. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/utilities/validation/rule_runner.py +2 -2
  21. oaklib-0.6.2/src/oaklib/datamodels/ontology_metadata.py +0 -3390
  22. oaklib-0.6.2/src/oaklib/interfaces/validator_interface.py +0 -122
  23. {oaklib-0.6.2 → oaklib-0.6.4}/LICENSE +0 -0
  24. {oaklib-0.6.2 → oaklib-0.6.4}/README.md +0 -0
  25. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/__init__.py +0 -0
  26. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/__init__.py +0 -0
  27. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/go-human-input-spec.yaml +0 -0
  28. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/go-pombase-input-spec.yaml +0 -0
  29. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/hpoa-g2p-input-spec.yaml +0 -0
  30. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/hpoa-input-spec.yaml +0 -0
  31. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/lexmatch-rules-oboinowl-default.yaml +0 -0
  32. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-g2d-input-spec.yaml +0 -0
  33. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-gencc-input-spec.yaml +0 -0
  34. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-hpoa-g2d-input-spec.yaml +0 -0
  35. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/mondo-medgen-g2d-input-spec.yaml +0 -0
  36. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/obograph-style.json +0 -0
  37. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/omo-to-skos.sssom.tsv +0 -0
  38. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/conf/value-set-expander.conf.yaml +0 -0
  39. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/constants.py +0 -0
  40. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/__init__.py +0 -0
  41. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/data_model_converter.py +0 -0
  42. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/logical_definition_flattener.py +0 -0
  43. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_cx_converter.py +0 -0
  44. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_fhir_converter.py +0 -0
  45. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/converters/obo_graph_to_rdf_owl_converter.py +0 -0
  46. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/__init__.py +0 -0
  47. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.owl.ttl +0 -0
  48. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.py +0 -0
  49. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/association.yaml +0 -0
  50. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.owl.ttl +0 -0
  51. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.py +0 -0
  52. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/class_enrichment.yaml +0 -0
  53. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.owl.ttl +0 -0
  54. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.py +0 -0
  55. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cross_ontology_diff.yaml +0 -0
  56. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cx.py +0 -0
  57. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/cx.yaml +0 -0
  58. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.owl.ttl +0 -0
  59. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.py +0 -0
  60. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/fhir.yaml +0 -0
  61. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/input_specification.py +0 -0
  62. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/input_specification.yaml +0 -0
  63. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/item_list.py +0 -0
  64. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/item_list.yaml +0 -0
  65. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.owl.ttl +0 -0
  66. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.py +0 -0
  67. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.schema.json +0 -0
  68. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/lexical_index.yaml +0 -0
  69. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_cluster_datamodel.py +0 -0
  70. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_cluster_datamodel.yaml +0 -0
  71. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.owl.ttl +0 -0
  72. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.py +0 -0
  73. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.schema.json +0 -0
  74. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/mapping_rules_datamodel.yaml +0 -0
  75. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.owl.ttl +0 -0
  76. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.py +0 -0
  77. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.schema.json +0 -0
  78. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/obograph.yaml +0 -0
  79. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.owl.ttl +0 -0
  80. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/ontology_metadata.schema.json +0 -0
  81. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.owl.ttl +0 -0
  82. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.py +0 -0
  83. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/oxo.yaml +0 -0
  84. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search.py +0 -0
  85. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.owl.ttl +0 -0
  86. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.py +0 -0
  87. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/search_datamodel.yaml +0 -0
  88. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/settings.py +0 -0
  89. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.owl.ttl +0 -0
  90. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.py +0 -0
  91. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/similarity.yaml +0 -0
  92. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.owl.ttl +0 -0
  93. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.py +0 -0
  94. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.schema.json +0 -0
  95. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/summary_statistics_datamodel.yaml +0 -0
  96. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/synonymizer_datamodel.py +0 -0
  97. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/synonymizer_datamodel.yaml +0 -0
  98. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.owl.ttl +0 -0
  99. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.py +0 -0
  100. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/taxon_constraints.yaml +0 -0
  101. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.owl.ttl +0 -0
  102. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.py +0 -0
  103. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.schema.json +0 -0
  104. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/text_annotator.yaml +0 -0
  105. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.owl.ttl +0 -0
  106. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/validation_datamodel.schema.json +0 -0
  107. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.owl.ttl +0 -0
  108. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.py +0 -0
  109. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/value_set_configuration.yaml +0 -0
  110. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/datamodels/vocabulary.py +0 -0
  111. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/__init__.py +0 -0
  112. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/aggregator/__init__.py +0 -0
  113. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/aggregator/aggregator_implementation.py +0 -0
  114. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/agrkb/__init__.py +0 -0
  115. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/agrkb/agrkb_implementation.py +0 -0
  116. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/amigo/__init__.py +0 -0
  117. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/amigo/amigo_implementation.py +0 -0
  118. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/cx/__init__.py +0 -0
  119. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/cx/cx_implementation.py +0 -0
  120. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/__init__.py +0 -0
  121. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/eutils_implementation.py +0 -0
  122. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/eutils/pubmed_implementation.py +0 -0
  123. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/fhir/__init__.py +0 -0
  124. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/funowl/__init__.py +0 -0
  125. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/funowl/funowl_implementation.py +0 -0
  126. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/gilda.py +0 -0
  127. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/kgx/__init__.py +0 -0
  128. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/kgx/kgx_implementation.py +0 -0
  129. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/monarch/__init__.py +0 -0
  130. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/monarch/monarch_implementation.py +0 -0
  131. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ncbi/__init__.py +0 -0
  132. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ncbi/ncbi_gene_implementation.py +0 -0
  133. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/neo4j/__init__.py +0 -0
  134. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/obograph/__init__.py +0 -0
  135. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/obograph/obograph_implementation.py +0 -0
  136. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/__init__.py +0 -0
  137. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/constants.py +0 -0
  138. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/ols_implementation.py +0 -0
  139. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ols/oxo_utils.py +0 -0
  140. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontobee/__init__.py +0 -0
  141. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontobee/ontobee_implementation.py +0 -0
  142. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/__init__.py +0 -0
  143. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/agroportal_implementation.py +0 -0
  144. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/bioportal_implementation.py +0 -0
  145. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/ecoportal_implementation.py +0 -0
  146. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/matportal_implementation.py +0 -0
  147. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/ontoportal/ontoportal_implementation_base.py +0 -0
  148. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/owlery/__init__.py +0 -0
  149. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/owlery/owlery_implementation.py +0 -0
  150. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pantherdb/__init__.py +0 -0
  151. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pantherdb/pantherdb_implementation.py +0 -0
  152. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pronto/__init__.py +0 -0
  153. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/pronto/pronto_implementation.py +0 -0
  154. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/robot/__init__.py +0 -0
  155. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/scigraph/__init__.py +0 -0
  156. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/__init__.py +0 -0
  157. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/profiler.py +0 -0
  158. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/semsimian/semsimian_implementation.py +0 -0
  159. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/simpleobo/__init__.py +0 -0
  160. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/skos/__init__.py +0 -0
  161. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/solor/__init__.py +0 -0
  162. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/solr/__init__.py +0 -0
  163. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/__init__.py +0 -0
  164. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/abstract_sparql_implementation.py +0 -0
  165. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/lov_implementation.py +0 -0
  166. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/oak_metamodel_implementation.py +0 -0
  167. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/sparql_implementation.py +0 -0
  168. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sparql/sparql_query.py +0 -0
  169. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/__init__.py +0 -0
  170. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/sql_implementation.py +0 -0
  171. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/sqldb/sqlite_utils.py +0 -0
  172. {oaklib-0.6.2 → oaklib-0.6.4}/src/oaklib/implementations/tabular/__init__.py +0 -0
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  Metadata-Version: 2.1
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  Name: oaklib
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- Version: 0.6.2
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  Summary: Ontology Access Kit: Python library for common ontology operations over a variety of backends
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  Author: cmungall
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  Author-email: cjm@berkeleybop.org
@@ -26,6 +26,7 @@ Requires-Dist: curies (>=0.6.6)
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  [tool.poetry]
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  name = "oaklib"
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- version = "v0.6.2"
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