ncbi-datasets-pyclient 18.4.0__py3-none-any.whl → 18.13.0__py3-none-any.whl

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Files changed (302) hide show
  1. ncbi/datasets/openapi/__init__.py +603 -250
  2. ncbi/datasets/openapi/api/bio_sample_api.py +1 -2
  3. ncbi/datasets/openapi/api/gene_api.py +1331 -1011
  4. ncbi/datasets/openapi/api/genome_api.py +1129 -1303
  5. ncbi/datasets/openapi/api/organelle_api.py +1 -2
  6. ncbi/datasets/openapi/api/prokaryote_api.py +31 -32
  7. ncbi/datasets/openapi/api/taxonomy_api.py +105 -106
  8. ncbi/datasets/openapi/api/version_api.py +1 -2
  9. ncbi/datasets/openapi/api/virus_api.py +772 -830
  10. ncbi/datasets/openapi/api_client.py +14 -8
  11. ncbi/datasets/openapi/configuration.py +8 -9
  12. ncbi/datasets/openapi/exceptions.py +1 -2
  13. ncbi/datasets/openapi/models/__init__.py +53 -3
  14. ncbi/datasets/openapi/models/ncbiprotddv2_chain_footprint.py +93 -0
  15. ncbi/datasets/openapi/models/ncbiprotddv2_query_structure_definition.py +97 -0
  16. ncbi/datasets/openapi/models/ncbiprotddv2_redundancy_level.py +39 -0
  17. ncbi/datasets/openapi/models/ncbiprotddv2_sdid_request.py +87 -0
  18. ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_report.py +121 -0
  19. ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_report_page.py +99 -0
  20. ncbi/datasets/openapi/models/ncbiprotddv2_similar_structure_request.py +97 -0
  21. ncbi/datasets/openapi/models/ncbiprotddv2_sort_by_id.py +51 -0
  22. ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report.py +141 -0
  23. ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_biounit_chain.py +94 -0
  24. ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_experiment.py +89 -0
  25. ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_kind.py +42 -0
  26. ncbi/datasets/openapi/models/ncbiprotddv2_structure_data_report_ligand_chain.py +94 -0
  27. ncbi/datasets/openapi/models/ncbiprotddv2_structure_request.py +89 -0
  28. ncbi/datasets/openapi/models/ncbiprotddv2_vast_score.py +95 -0
  29. ncbi/datasets/openapi/models/protobuf_any.py +1 -2
  30. ncbi/datasets/openapi/models/rpc_status.py +1 -2
  31. ncbi/datasets/openapi/models/v2_accessions.py +87 -0
  32. ncbi/datasets/openapi/models/v2_annotation_for_assembly_type.py +2 -3
  33. ncbi/datasets/openapi/models/v2_annotation_for_organelle_type.py +2 -2
  34. ncbi/datasets/openapi/models/v2_assembly_accessions.py +1 -2
  35. ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_reply.py +1 -2
  36. ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_reply_histogram_interval.py +1 -2
  37. ncbi/datasets/openapi/models/v2_assembly_check_m_histogram_request.py +1 -2
  38. ncbi/datasets/openapi/models/v2_assembly_data_report_draft_request.py +87 -0
  39. ncbi/datasets/openapi/models/v2_assembly_dataset_availability.py +1 -2
  40. ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter.py +9 -10
  41. ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_assembly_source.py +1 -2
  42. ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_assembly_version.py +1 -2
  43. ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_metagenome_derived_filter.py +1 -2
  44. ncbi/datasets/openapi/models/v2_assembly_dataset_descriptors_filter_type_material_category.py +1 -2
  45. ncbi/datasets/openapi/models/v2_assembly_dataset_reports_request.py +5 -6
  46. ncbi/datasets/openapi/models/v2_assembly_dataset_reports_request_content_type.py +1 -2
  47. ncbi/datasets/openapi/models/v2_assembly_dataset_request.py +3 -4
  48. ncbi/datasets/openapi/models/v2_assembly_dataset_request_resolution.py +1 -2
  49. ncbi/datasets/openapi/models/v2_assembly_links_reply.py +1 -2
  50. ncbi/datasets/openapi/models/v2_assembly_links_reply_assembly_link.py +3 -4
  51. ncbi/datasets/openapi/models/v2_assembly_links_reply_assembly_link_type.py +3 -3
  52. ncbi/datasets/openapi/models/v2_assembly_links_request.py +1 -2
  53. ncbi/datasets/openapi/models/v2_assembly_revision_history.py +1 -2
  54. ncbi/datasets/openapi/models/v2_assembly_revision_history_request.py +1 -2
  55. ncbi/datasets/openapi/models/v2_assembly_sequence_reports_request.py +3 -4
  56. ncbi/datasets/openapi/models/v2_bio_sample_dataset_reports_request.py +87 -0
  57. ncbi/datasets/openapi/models/v2_catalog_api_version.py +38 -0
  58. ncbi/datasets/openapi/models/v2_dataset_request.py +1 -2
  59. ncbi/datasets/openapi/models/v2_download_summary.py +1 -2
  60. ncbi/datasets/openapi/models/v2_download_summary_available_files.py +1 -2
  61. ncbi/datasets/openapi/models/v2_download_summary_dehydrated.py +1 -2
  62. ncbi/datasets/openapi/models/v2_download_summary_file_summary.py +1 -2
  63. ncbi/datasets/openapi/models/v2_download_summary_hydrated.py +1 -2
  64. ncbi/datasets/openapi/models/v2_element_flank_config.py +87 -0
  65. ncbi/datasets/openapi/models/v2_fasta.py +1 -2
  66. ncbi/datasets/openapi/models/v2_file_file_type.py +57 -0
  67. ncbi/datasets/openapi/models/v2_gene_chromosome_summary_reply.py +1 -2
  68. ncbi/datasets/openapi/models/v2_gene_chromosome_summary_reply_gene_chromosome_summary.py +1 -2
  69. ncbi/datasets/openapi/models/v2_gene_chromosome_summary_request.py +89 -0
  70. ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_reply.py +1 -2
  71. ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_reply_gene_type_and_count.py +1 -2
  72. ncbi/datasets/openapi/models/v2_gene_counts_by_taxon_request.py +1 -2
  73. ncbi/datasets/openapi/models/v2_gene_dataset_reports_request.py +20 -9
  74. ncbi/datasets/openapi/models/v2_gene_dataset_reports_request_content_type.py +1 -3
  75. ncbi/datasets/openapi/models/v2_gene_dataset_reports_request_symbols_for_taxon.py +1 -2
  76. ncbi/datasets/openapi/models/v2_gene_dataset_request.py +5 -6
  77. ncbi/datasets/openapi/models/v2_gene_dataset_request_content_type.py +1 -2
  78. ncbi/datasets/openapi/models/v2_gene_dataset_request_gene_dataset_report_type.py +1 -2
  79. ncbi/datasets/openapi/models/v2_gene_links_reply.py +1 -2
  80. ncbi/datasets/openapi/models/v2_gene_links_reply_gene_link.py +3 -4
  81. ncbi/datasets/openapi/models/v2_gene_links_reply_gene_link_type.py +2 -2
  82. ncbi/datasets/openapi/models/v2_gene_links_request.py +1 -2
  83. ncbi/datasets/openapi/models/v2_gene_pubmed_ids_request.py +87 -0
  84. ncbi/datasets/openapi/models/v2_gene_pubmed_ids_response.py +87 -0
  85. ncbi/datasets/openapi/models/v2_gene_type.py +1 -2
  86. ncbi/datasets/openapi/models/v2_genome_annotation_request.py +5 -6
  87. ncbi/datasets/openapi/models/v2_genome_annotation_request_annotation_type.py +2 -2
  88. ncbi/datasets/openapi/models/v2_genome_annotation_request_genome_annotation_table_format.py +1 -2
  89. ncbi/datasets/openapi/models/v2_genome_annotation_table_summary_reply.py +1 -2
  90. ncbi/datasets/openapi/models/v2_http_body.py +1 -2
  91. ncbi/datasets/openapi/models/v2_image_size.py +1 -2
  92. ncbi/datasets/openapi/models/v2_include_tabular_header.py +1 -2
  93. ncbi/datasets/openapi/models/v2_micro_bigge_dataset_request.py +96 -0
  94. ncbi/datasets/openapi/models/v2_micro_bigge_dataset_request_file_type.py +39 -0
  95. ncbi/datasets/openapi/models/v2_mol_type.py +40 -0
  96. ncbi/datasets/openapi/models/v2_organelle_download_request.py +1 -2
  97. ncbi/datasets/openapi/models/v2_organelle_metadata_request.py +7 -8
  98. ncbi/datasets/openapi/models/v2_organelle_metadata_request_content_type.py +1 -2
  99. ncbi/datasets/openapi/models/v2_organelle_metadata_request_organelle_table_format.py +1 -2
  100. ncbi/datasets/openapi/models/v2_organelle_sort.py +3 -4
  101. ncbi/datasets/openapi/models/v2_organism_query_request.py +5 -6
  102. ncbi/datasets/openapi/models/v2_organism_query_request_tax_rank_filter.py +1 -2
  103. ncbi/datasets/openapi/models/v2_organism_query_request_taxon_resource_filter.py +1 -2
  104. ncbi/datasets/openapi/models/v2_ortholog_request.py +3 -4
  105. ncbi/datasets/openapi/models/v2_ortholog_request_content_type.py +1 -2
  106. ncbi/datasets/openapi/models/v2_prokaryote_gene_request.py +1 -2
  107. ncbi/datasets/openapi/models/v2_prokaryote_gene_request_gene_flank_config.py +1 -2
  108. ncbi/datasets/openapi/models/v2_ref_gene_catalog_dataset_request.py +96 -0
  109. ncbi/datasets/openapi/models/v2_ref_gene_catalog_dataset_request_file_type.py +38 -0
  110. ncbi/datasets/openapi/models/v2_sars2_protein_dataset_request.py +3 -4
  111. ncbi/datasets/openapi/models/v2_sci_name_and_ids.py +1 -2
  112. ncbi/datasets/openapi/models/v2_sci_name_and_ids_sci_name_and_id.py +3 -4
  113. ncbi/datasets/openapi/models/v2_seq_range.py +94 -0
  114. ncbi/datasets/openapi/models/v2_seq_reply.py +96 -0
  115. ncbi/datasets/openapi/models/v2_sequence_accession_request.py +1 -2
  116. ncbi/datasets/openapi/models/v2_sequence_report_page.py +1 -2
  117. ncbi/datasets/openapi/models/v2_sleep_reply.py +87 -0
  118. ncbi/datasets/openapi/models/v2_sleep_request.py +89 -0
  119. ncbi/datasets/openapi/models/v2_sort_direction.py +1 -2
  120. ncbi/datasets/openapi/models/v2_sort_field.py +3 -4
  121. ncbi/datasets/openapi/models/v2_table_format.py +1 -2
  122. ncbi/datasets/openapi/models/v2_tabular_output.py +1 -2
  123. ncbi/datasets/openapi/models/v2_taxonomy_dataset_request.py +1 -2
  124. ncbi/datasets/openapi/models/v2_taxonomy_dataset_request_taxonomy_report_type.py +1 -2
  125. ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_request.py +5 -4
  126. ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response.py +1 -2
  127. ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edge.py +3 -4
  128. ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edge_child_status.py +2 -2
  129. ncbi/datasets/openapi/models/v2_taxonomy_filtered_subtree_response_edges_entry.py +1 -2
  130. ncbi/datasets/openapi/models/v2_taxonomy_image_metadata_request.py +1 -2
  131. ncbi/datasets/openapi/models/v2_taxonomy_image_metadata_response.py +1 -2
  132. ncbi/datasets/openapi/models/v2_taxonomy_image_request.py +3 -4
  133. ncbi/datasets/openapi/models/v2_taxonomy_links_request.py +1 -2
  134. ncbi/datasets/openapi/models/v2_taxonomy_links_response.py +1 -2
  135. ncbi/datasets/openapi/models/v2_taxonomy_links_response_generic_link.py +1 -2
  136. ncbi/datasets/openapi/models/v2_taxonomy_match.py +1 -2
  137. ncbi/datasets/openapi/models/v2_taxonomy_metadata_request.py +7 -8
  138. ncbi/datasets/openapi/models/v2_taxonomy_metadata_request_content_type.py +1 -2
  139. ncbi/datasets/openapi/models/v2_taxonomy_metadata_request_table_format.py +1 -2
  140. ncbi/datasets/openapi/models/v2_taxonomy_metadata_response.py +1 -2
  141. ncbi/datasets/openapi/models/v2_taxonomy_node.py +3 -4
  142. ncbi/datasets/openapi/models/v2_taxonomy_node_count_by_type.py +3 -4
  143. ncbi/datasets/openapi/models/v2_taxonomy_related_id_request.py +1 -2
  144. ncbi/datasets/openapi/models/v2_taxonomy_tax_ids_page.py +1 -2
  145. ncbi/datasets/openapi/models/v2_version_reply.py +1 -2
  146. ncbi/datasets/openapi/models/v2_viral_sequence_type.py +1 -2
  147. ncbi/datasets/openapi/models/v2_virus_annotation_filter.py +1 -2
  148. ncbi/datasets/openapi/models/v2_virus_annotation_report_request.py +1 -2
  149. ncbi/datasets/openapi/models/v2_virus_availability.py +1 -2
  150. ncbi/datasets/openapi/models/v2_virus_availability_request.py +1 -2
  151. ncbi/datasets/openapi/models/v2_virus_data_report_request.py +3 -4
  152. ncbi/datasets/openapi/models/v2_virus_data_report_request_content_type.py +1 -2
  153. ncbi/datasets/openapi/models/v2_virus_dataset_filter.py +1 -2
  154. ncbi/datasets/openapi/models/v2_virus_dataset_report_type.py +1 -2
  155. ncbi/datasets/openapi/models/v2_virus_dataset_request.py +3 -4
  156. ncbi/datasets/openapi/models/v2_virus_table_field.py +1 -2
  157. ncbi/datasets/openapi/models/v2archive_affiliation.py +95 -0
  158. ncbi/datasets/openapi/models/v2archive_catalog.py +121 -0
  159. ncbi/datasets/openapi/models/v2archive_location.py +95 -0
  160. ncbi/datasets/openapi/models/v2archive_modifier.py +90 -0
  161. ncbi/datasets/openapi/models/v2archive_molecule_type.py +43 -0
  162. ncbi/datasets/openapi/models/v2archive_name.py +105 -0
  163. ncbi/datasets/openapi/models/v2archive_nuccore_request.py +87 -0
  164. ncbi/datasets/openapi/models/v2archive_sequence.py +90 -0
  165. ncbi/datasets/openapi/models/v2archive_sequence_length_units.py +39 -0
  166. ncbi/datasets/openapi/models/v2archive_submitter.py +105 -0
  167. ncbi/datasets/openapi/models/v2archive_taxonomy_node.py +118 -0
  168. ncbi/datasets/openapi/models/v2archive_taxonomy_subtype.py +77 -0
  169. ncbi/datasets/openapi/models/v2reports_additional_submitter.py +1 -2
  170. ncbi/datasets/openapi/models/v2reports_ani_match.py +3 -4
  171. ncbi/datasets/openapi/models/v2reports_ani_type_category.py +2 -3
  172. ncbi/datasets/openapi/models/v2reports_annotation.py +1 -2
  173. ncbi/datasets/openapi/models/v2reports_annotation_info.py +1 -2
  174. ncbi/datasets/openapi/models/v2reports_assembly_data_report.py +3 -4
  175. ncbi/datasets/openapi/models/v2reports_assembly_data_report_page.py +3 -4
  176. ncbi/datasets/openapi/models/v2reports_assembly_info.py +5 -6
  177. ncbi/datasets/openapi/models/v2reports_assembly_level.py +1 -2
  178. ncbi/datasets/openapi/models/v2reports_assembly_revision.py +8 -7
  179. ncbi/datasets/openapi/models/v2reports_assembly_stats.py +4 -3
  180. ncbi/datasets/openapi/models/v2reports_assembly_status.py +1 -2
  181. ncbi/datasets/openapi/models/v2reports_atypical_info.py +1 -2
  182. ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity.py +7 -8
  183. ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity_match_status.py +1 -2
  184. ncbi/datasets/openapi/models/v2reports_average_nucleotide_identity_taxonomy_check_status.py +1 -2
  185. ncbi/datasets/openapi/models/v2reports_bio_project.py +1 -2
  186. ncbi/datasets/openapi/models/v2reports_bio_project_lineage.py +1 -2
  187. ncbi/datasets/openapi/models/v2reports_bio_sample_attribute.py +1 -2
  188. ncbi/datasets/openapi/models/v2reports_bio_sample_contact.py +1 -2
  189. ncbi/datasets/openapi/models/v2reports_bio_sample_data_report.py +1 -2
  190. ncbi/datasets/openapi/models/v2reports_bio_sample_data_report_page.py +1 -2
  191. ncbi/datasets/openapi/models/v2reports_bio_sample_description.py +1 -2
  192. ncbi/datasets/openapi/models/v2reports_bio_sample_descriptor.py +1 -2
  193. ncbi/datasets/openapi/models/v2reports_bio_sample_id.py +1 -2
  194. ncbi/datasets/openapi/models/v2reports_bio_sample_owner.py +1 -2
  195. ncbi/datasets/openapi/models/v2reports_bio_sample_status.py +1 -2
  196. ncbi/datasets/openapi/models/v2reports_busco_stat.py +1 -2
  197. ncbi/datasets/openapi/models/v2reports_check_m.py +1 -2
  198. ncbi/datasets/openapi/models/v2reports_classification.py +8 -4
  199. ncbi/datasets/openapi/models/v2reports_collection_type.py +1 -2
  200. ncbi/datasets/openapi/models/v2reports_conserved_domain.py +1 -2
  201. ncbi/datasets/openapi/models/v2reports_content_type.py +1 -2
  202. ncbi/datasets/openapi/models/v2reports_count_type.py +1 -2
  203. ncbi/datasets/openapi/models/v2reports_error.py +11 -12
  204. ncbi/datasets/openapi/models/v2reports_error_assembly_error_code.py +1 -2
  205. ncbi/datasets/openapi/models/v2reports_error_gene_error_code.py +1 -2
  206. ncbi/datasets/openapi/models/v2reports_error_organelle_error_code.py +1 -2
  207. ncbi/datasets/openapi/models/v2reports_error_taxonomy_error_code.py +1 -2
  208. ncbi/datasets/openapi/models/v2reports_error_virus_error_code.py +1 -2
  209. ncbi/datasets/openapi/models/v2reports_feature_counts.py +1 -2
  210. ncbi/datasets/openapi/models/v2reports_functional_site.py +97 -0
  211. ncbi/datasets/openapi/models/v2reports_gene_counts.py +1 -2
  212. ncbi/datasets/openapi/models/v2reports_gene_data_report_page.py +1 -2
  213. ncbi/datasets/openapi/models/v2reports_gene_descriptor.py +7 -8
  214. ncbi/datasets/openapi/models/v2reports_gene_group.py +1 -2
  215. ncbi/datasets/openapi/models/v2reports_gene_ontology.py +1 -2
  216. ncbi/datasets/openapi/models/v2reports_gene_report_match.py +1 -2
  217. ncbi/datasets/openapi/models/v2reports_gene_summary.py +1 -2
  218. ncbi/datasets/openapi/models/v2reports_gene_type.py +1 -2
  219. ncbi/datasets/openapi/models/v2reports_genome_annotation.py +7 -8
  220. ncbi/datasets/openapi/models/v2reports_genome_annotation_report_match.py +1 -2
  221. ncbi/datasets/openapi/models/v2reports_genome_annotation_report_page.py +1 -2
  222. ncbi/datasets/openapi/models/v2reports_genomic_location.py +1 -2
  223. ncbi/datasets/openapi/models/v2reports_genomic_region.py +3 -4
  224. ncbi/datasets/openapi/models/v2reports_genomic_region_genomic_region_type.py +1 -2
  225. ncbi/datasets/openapi/models/v2reports_infraspecific_names.py +1 -2
  226. ncbi/datasets/openapi/models/v2reports_isolate.py +1 -2
  227. ncbi/datasets/openapi/models/v2reports_lineage_organism.py +1 -2
  228. ncbi/datasets/openapi/models/v2reports_linked_assembly.py +3 -4
  229. ncbi/datasets/openapi/models/v2reports_linked_assembly_type.py +1 -2
  230. ncbi/datasets/openapi/models/v2reports_mature_peptide.py +1 -2
  231. ncbi/datasets/openapi/models/v2reports_message.py +1 -2
  232. ncbi/datasets/openapi/models/v2reports_name_and_authority.py +1 -2
  233. ncbi/datasets/openapi/models/v2reports_name_and_authority_note.py +3 -4
  234. ncbi/datasets/openapi/models/v2reports_name_and_authority_note_classifier.py +1 -2
  235. ncbi/datasets/openapi/models/v2reports_name_and_authority_publication.py +1 -2
  236. ncbi/datasets/openapi/models/v2reports_nomenclature_authority.py +1 -2
  237. ncbi/datasets/openapi/models/v2reports_organelle.py +5 -6
  238. ncbi/datasets/openapi/models/v2reports_organelle_biosample.py +1 -2
  239. ncbi/datasets/openapi/models/v2reports_organelle_data_reports.py +1 -2
  240. ncbi/datasets/openapi/models/v2reports_organelle_gene_counts.py +1 -2
  241. ncbi/datasets/openapi/models/v2reports_organelle_info.py +1 -2
  242. ncbi/datasets/openapi/models/v2reports_organelle_topology.py +1 -2
  243. ncbi/datasets/openapi/models/v2reports_organelle_type.py +1 -2
  244. ncbi/datasets/openapi/models/v2reports_organism.py +1 -2
  245. ncbi/datasets/openapi/models/v2reports_orientation.py +1 -2
  246. ncbi/datasets/openapi/models/v2reports_paired_assembly.py +7 -6
  247. ncbi/datasets/openapi/models/v2reports_process_metadata.py +1 -2
  248. ncbi/datasets/openapi/models/v2reports_product_descriptor.py +5 -6
  249. ncbi/datasets/openapi/models/v2reports_prokaryote_gene_location_completeness.py +37 -0
  250. ncbi/datasets/openapi/models/v2reports_protein.py +1 -2
  251. ncbi/datasets/openapi/models/v2reports_protein_conserved_domain.py +103 -0
  252. ncbi/datasets/openapi/models/v2reports_protein_data_report.py +127 -0
  253. ncbi/datasets/openapi/models/v2reports_protein_data_report_page.py +95 -0
  254. ncbi/datasets/openapi/models/v2reports_protein_family.py +95 -0
  255. ncbi/datasets/openapi/models/v2reports_purpose_of_sampling.py +1 -2
  256. ncbi/datasets/openapi/models/v2reports_range.py +3 -4
  257. ncbi/datasets/openapi/models/v2reports_rank_type.py +3 -2
  258. ncbi/datasets/openapi/models/v2reports_reference.py +1 -2
  259. ncbi/datasets/openapi/models/v2reports_rna_type.py +1 -2
  260. ncbi/datasets/openapi/models/v2reports_seq_range_set.py +1 -2
  261. ncbi/datasets/openapi/models/v2reports_seq_range_set_fasta.py +1 -2
  262. ncbi/datasets/openapi/models/v2reports_sequence_info.py +1 -2
  263. ncbi/datasets/openapi/models/v2reports_sequence_information.py +1 -2
  264. ncbi/datasets/openapi/models/v2reports_source_database.py +1 -2
  265. ncbi/datasets/openapi/models/v2reports_tax_data.py +1 -2
  266. ncbi/datasets/openapi/models/v2reports_taxonomy_data_report_page.py +1 -2
  267. ncbi/datasets/openapi/models/v2reports_taxonomy_names_data_report_page.py +1 -2
  268. ncbi/datasets/openapi/models/v2reports_taxonomy_names_descriptor.py +3 -4
  269. ncbi/datasets/openapi/models/v2reports_taxonomy_names_descriptor_citation.py +1 -2
  270. ncbi/datasets/openapi/models/v2reports_taxonomy_names_report_match.py +1 -2
  271. ncbi/datasets/openapi/models/v2reports_taxonomy_node.py +7 -6
  272. ncbi/datasets/openapi/models/v2reports_taxonomy_node_count_by_type.py +3 -4
  273. ncbi/datasets/openapi/models/v2reports_taxonomy_report_match.py +1 -2
  274. ncbi/datasets/openapi/models/v2reports_taxonomy_type_material.py +1 -2
  275. ncbi/datasets/openapi/models/v2reports_transcript.py +5 -6
  276. ncbi/datasets/openapi/models/v2reports_transcript_select_category.py +1 -2
  277. ncbi/datasets/openapi/models/v2reports_transcript_transcript_type.py +1 -2
  278. ncbi/datasets/openapi/models/v2reports_transcript_type_count.py +3 -4
  279. ncbi/datasets/openapi/models/v2reports_type_material.py +1 -2
  280. ncbi/datasets/openapi/models/v2reports_virus_annotation_report.py +1 -2
  281. ncbi/datasets/openapi/models/v2reports_virus_annotation_report_page.py +1 -2
  282. ncbi/datasets/openapi/models/v2reports_virus_assembly.py +5 -6
  283. ncbi/datasets/openapi/models/v2reports_virus_assembly_collection_location.py +1 -2
  284. ncbi/datasets/openapi/models/v2reports_virus_assembly_completeness.py +1 -2
  285. ncbi/datasets/openapi/models/v2reports_virus_assembly_submitter_info.py +1 -2
  286. ncbi/datasets/openapi/models/v2reports_virus_data_report_page.py +1 -2
  287. ncbi/datasets/openapi/models/v2reports_virus_gene.py +1 -2
  288. ncbi/datasets/openapi/models/v2reports_virus_peptide.py +3 -4
  289. ncbi/datasets/openapi/models/v2reports_virus_peptide_uni_prot_id.py +1 -2
  290. ncbi/datasets/openapi/models/v2reports_virus_peptide_viral_peptide_completeness.py +1 -2
  291. ncbi/datasets/openapi/models/v2reports_warning.py +3 -4
  292. ncbi/datasets/openapi/models/v2reports_warning_gene_warning_code.py +1 -2
  293. ncbi/datasets/openapi/models/v2reports_warning_replaced_id.py +1 -2
  294. ncbi/datasets/openapi/models/v2reports_wgs_info.py +1 -2
  295. ncbi/datasets/openapi/rest.py +1 -2
  296. ncbi_datasets_pyclient-18.13.0.dist-info/METADATA +537 -0
  297. ncbi_datasets_pyclient-18.13.0.dist-info/RECORD +305 -0
  298. ncbi_datasets_pyclient-18.4.0.dist-info/METADATA +0 -25
  299. ncbi_datasets_pyclient-18.4.0.dist-info/RECORD +0 -254
  300. {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/WHEEL +0 -0
  301. {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/licenses/LICENSE +0 -0
  302. {ncbi_datasets_pyclient-18.4.0.dist-info → ncbi_datasets_pyclient-18.13.0.dist-info}/top_level.txt +0 -0
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
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  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
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11
  Do not edit the class manually.
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
8
  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
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  Do not edit the class manually.
@@ -29,7 +28,7 @@ class V2OrthologRequest(BaseModel):
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  V2OrthologRequest
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  """ # noqa: E501
31
30
  gene_id: Optional[StrictInt] = None
32
- returned_content: Optional[V2OrthologRequestContentType] = None
31
+ returned_content: Optional[V2OrthologRequestContentType] = V2OrthologRequestContentType.COMPLETE
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32
  taxon_filter: Optional[List[StrictStr]] = None
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  page_size: Optional[StrictInt] = None
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  page_token: Optional[StrictStr] = None
@@ -87,7 +86,7 @@ class V2OrthologRequest(BaseModel):
87
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88
87
  _obj = cls.model_validate({
89
88
  "gene_id": obj.get("gene_id"),
90
- "returned_content": obj.get("returned_content"),
89
+ "returned_content": obj.get("returned_content") if obj.get("returned_content") is not None else V2OrthologRequestContentType.COMPLETE,
91
90
  "taxon_filter": obj.get("taxon_filter"),
92
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  "page_size": obj.get("page_size"),
93
92
  "page_token": obj.get("page_token")
@@ -3,10 +3,9 @@
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  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
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  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
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  Do not edit the class manually.
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
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  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
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  Do not edit the class manually.
@@ -3,10 +3,9 @@
3
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  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
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  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
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  Do not edit the class manually.
@@ -0,0 +1,96 @@
1
+ # coding: utf-8
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+
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+ """
4
+ NCBI Datasets API
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+
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+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
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+
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+ The version of the OpenAPI document: v2
9
+ Generated by OpenAPI Generator (https://openapi-generator.tech)
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+
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+ Do not edit the class manually.
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+ """ # noqa: E501
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+
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+
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+ from __future__ import annotations
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+ import pprint
17
+ import re # noqa: F401
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+ import json
19
+
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+ from pydantic import BaseModel, ConfigDict, StrictStr
21
+ from typing import Any, ClassVar, Dict, List, Optional
22
+ from ncbi.datasets.openapi.models.v2_element_flank_config import V2ElementFlankConfig
23
+ from ncbi.datasets.openapi.models.v2_ref_gene_catalog_dataset_request_file_type import V2RefGeneCatalogDatasetRequestFileType
24
+ from typing import Optional, Set
25
+ from typing_extensions import Self
26
+
27
+ class V2RefGeneCatalogDatasetRequest(BaseModel):
28
+ """
29
+ V2RefGeneCatalogDatasetRequest
30
+ """ # noqa: E501
31
+ opaque_solr_query: Optional[StrictStr] = None
32
+ files: Optional[List[V2RefGeneCatalogDatasetRequestFileType]] = None
33
+ element_flank_config: Optional[V2ElementFlankConfig] = None
34
+ __properties: ClassVar[List[str]] = ["opaque_solr_query", "files", "element_flank_config"]
35
+
36
+ model_config = ConfigDict(
37
+ populate_by_name=True,
38
+ validate_assignment=True,
39
+ protected_namespaces=(),
40
+ )
41
+
42
+
43
+ def to_str(self) -> str:
44
+ """Returns the string representation of the model using alias"""
45
+ return pprint.pformat(self.model_dump(by_alias=True))
46
+
47
+ def to_json(self) -> str:
48
+ """Returns the JSON representation of the model using alias"""
49
+ # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
50
+ return json.dumps(self.to_dict())
51
+
52
+ @classmethod
53
+ def from_json(cls, json_str: str) -> Optional[Self]:
54
+ """Create an instance of V2RefGeneCatalogDatasetRequest from a JSON string"""
55
+ return cls.from_dict(json.loads(json_str))
56
+
57
+ def to_dict(self) -> Dict[str, Any]:
58
+ """Return the dictionary representation of the model using alias.
59
+
60
+ This has the following differences from calling pydantic's
61
+ `self.model_dump(by_alias=True)`:
62
+
63
+ * `None` is only added to the output dict for nullable fields that
64
+ were set at model initialization. Other fields with value `None`
65
+ are ignored.
66
+ """
67
+ excluded_fields: Set[str] = set([
68
+ ])
69
+
70
+ _dict = self.model_dump(
71
+ by_alias=True,
72
+ exclude=excluded_fields,
73
+ exclude_none=True,
74
+ )
75
+ # override the default output from pydantic by calling `to_dict()` of element_flank_config
76
+ if self.element_flank_config:
77
+ _dict['element_flank_config'] = self.element_flank_config.to_dict()
78
+ return _dict
79
+
80
+ @classmethod
81
+ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
82
+ """Create an instance of V2RefGeneCatalogDatasetRequest from a dict"""
83
+ if obj is None:
84
+ return None
85
+
86
+ if not isinstance(obj, dict):
87
+ return cls.model_validate(obj)
88
+
89
+ _obj = cls.model_validate({
90
+ "opaque_solr_query": obj.get("opaque_solr_query"),
91
+ "files": obj.get("files"),
92
+ "element_flank_config": V2ElementFlankConfig.from_dict(obj["element_flank_config"]) if obj.get("element_flank_config") is not None else None
93
+ })
94
+ return _obj
95
+
96
+
@@ -0,0 +1,38 @@
1
+ # coding: utf-8
2
+
3
+ """
4
+ NCBI Datasets API
5
+
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+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
+
8
+ The version of the OpenAPI document: v2
9
+ Generated by OpenAPI Generator (https://openapi-generator.tech)
10
+
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+ Do not edit the class manually.
12
+ """ # noqa: E501
13
+
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+
15
+ from __future__ import annotations
16
+ import json
17
+ from enum import Enum
18
+ from typing_extensions import Self
19
+
20
+
21
+ class V2RefGeneCatalogDatasetRequestFileType(str, Enum):
22
+ """
23
+ V2RefGeneCatalogDatasetRequestFileType
24
+ """
25
+
26
+ """
27
+ allowed enum values
28
+ """
29
+ FILE_TYPE_NUCLEOTIDE = 'FILE_TYPE_NUCLEOTIDE'
30
+ FILE_TYPE_NUCLEOTIDE_WITH_FLANK = 'FILE_TYPE_NUCLEOTIDE_WITH_FLANK'
31
+ FILE_TYPE_PROTEIN = 'FILE_TYPE_PROTEIN'
32
+
33
+ @classmethod
34
+ def from_json(cls, json_str: str) -> Self:
35
+ """Create an instance of V2RefGeneCatalogDatasetRequestFileType from a JSON string"""
36
+ return cls(json.loads(json_str))
37
+
38
+
@@ -3,10 +3,9 @@
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  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
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  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
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  Do not edit the class manually.
@@ -45,7 +44,7 @@ class V2Sars2ProteinDatasetRequest(BaseModel):
45
44
  table_fields: Optional[List[V2VirusTableField]] = None
46
45
  include_sequence: Optional[List[V2ViralSequenceType]] = None
47
46
  aux_report: Optional[List[V2VirusDatasetReportType]] = None
48
- format: Optional[V2TableFormat] = None
47
+ format: Optional[V2TableFormat] = V2TableFormat.TSV
49
48
  __properties: ClassVar[List[str]] = ["proteins", "refseq_only", "annotated_only", "released_since", "updated_since", "host", "pangolin_classification", "geo_location", "usa_state", "complete_only", "table_fields", "include_sequence", "aux_report", "format"]
50
49
 
51
50
  model_config = ConfigDict(
@@ -112,7 +111,7 @@ class V2Sars2ProteinDatasetRequest(BaseModel):
112
111
  "table_fields": obj.get("table_fields"),
113
112
  "include_sequence": obj.get("include_sequence"),
114
113
  "aux_report": obj.get("aux_report"),
115
- "format": obj.get("format")
114
+ "format": obj.get("format") if obj.get("format") is not None else V2TableFormat.TSV
116
115
  })
117
116
  return _obj
118
117
 
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
8
  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
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  Do not edit the class manually.
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
8
  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
12
11
  Do not edit the class manually.
@@ -32,7 +31,7 @@ class V2SciNameAndIdsSciNameAndId(BaseModel):
32
31
  tax_id: Optional[StrictStr] = None
33
32
  common_name: Optional[StrictStr] = None
34
33
  matched_term: Optional[StrictStr] = None
35
- rank: Optional[V2reportsRankType] = None
34
+ rank: Optional[V2reportsRankType] = V2reportsRankType.NO_RANK
36
35
  group_name: Optional[StrictStr] = None
37
36
  __properties: ClassVar[List[str]] = ["sci_name", "tax_id", "common_name", "matched_term", "rank", "group_name"]
38
37
 
@@ -91,7 +90,7 @@ class V2SciNameAndIdsSciNameAndId(BaseModel):
91
90
  "tax_id": obj.get("tax_id"),
92
91
  "common_name": obj.get("common_name"),
93
92
  "matched_term": obj.get("matched_term"),
94
- "rank": obj.get("rank"),
93
+ "rank": obj.get("rank") if obj.get("rank") is not None else V2reportsRankType.NO_RANK,
95
94
  "group_name": obj.get("group_name")
96
95
  })
97
96
  return _obj
@@ -0,0 +1,94 @@
1
+ # coding: utf-8
2
+
3
+ """
4
+ NCBI Datasets API
5
+
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
+
8
+ The version of the OpenAPI document: v2
9
+ Generated by OpenAPI Generator (https://openapi-generator.tech)
10
+
11
+ Do not edit the class manually.
12
+ """ # noqa: E501
13
+
14
+
15
+ from __future__ import annotations
16
+ import pprint
17
+ import re # noqa: F401
18
+ import json
19
+
20
+ from pydantic import BaseModel, ConfigDict, StrictStr
21
+ from typing import Any, ClassVar, Dict, List, Optional
22
+ from ncbi.datasets.openapi.models.v2reports_orientation import V2reportsOrientation
23
+ from typing import Optional, Set
24
+ from typing_extensions import Self
25
+
26
+ class V2SeqRange(BaseModel):
27
+ """
28
+ V2SeqRange
29
+ """ # noqa: E501
30
+ accession: Optional[StrictStr] = None
31
+ begin: Optional[StrictStr] = None
32
+ end: Optional[StrictStr] = None
33
+ orientation: Optional[V2reportsOrientation] = V2reportsOrientation.NONE
34
+ __properties: ClassVar[List[str]] = ["accession", "begin", "end", "orientation"]
35
+
36
+ model_config = ConfigDict(
37
+ populate_by_name=True,
38
+ validate_assignment=True,
39
+ protected_namespaces=(),
40
+ )
41
+
42
+
43
+ def to_str(self) -> str:
44
+ """Returns the string representation of the model using alias"""
45
+ return pprint.pformat(self.model_dump(by_alias=True))
46
+
47
+ def to_json(self) -> str:
48
+ """Returns the JSON representation of the model using alias"""
49
+ # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
50
+ return json.dumps(self.to_dict())
51
+
52
+ @classmethod
53
+ def from_json(cls, json_str: str) -> Optional[Self]:
54
+ """Create an instance of V2SeqRange from a JSON string"""
55
+ return cls.from_dict(json.loads(json_str))
56
+
57
+ def to_dict(self) -> Dict[str, Any]:
58
+ """Return the dictionary representation of the model using alias.
59
+
60
+ This has the following differences from calling pydantic's
61
+ `self.model_dump(by_alias=True)`:
62
+
63
+ * `None` is only added to the output dict for nullable fields that
64
+ were set at model initialization. Other fields with value `None`
65
+ are ignored.
66
+ """
67
+ excluded_fields: Set[str] = set([
68
+ ])
69
+
70
+ _dict = self.model_dump(
71
+ by_alias=True,
72
+ exclude=excluded_fields,
73
+ exclude_none=True,
74
+ )
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+ return _dict
76
+
77
+ @classmethod
78
+ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
79
+ """Create an instance of V2SeqRange from a dict"""
80
+ if obj is None:
81
+ return None
82
+
83
+ if not isinstance(obj, dict):
84
+ return cls.model_validate(obj)
85
+
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+ _obj = cls.model_validate({
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+ "accession": obj.get("accession"),
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+ "begin": obj.get("begin"),
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+ "end": obj.get("end"),
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+ "orientation": obj.get("orientation") if obj.get("orientation") is not None else V2reportsOrientation.NONE
91
+ })
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+ return _obj
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+
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+
@@ -0,0 +1,96 @@
1
+ # coding: utf-8
2
+
3
+ """
4
+ NCBI Datasets API
5
+
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
+
8
+ The version of the OpenAPI document: v2
9
+ Generated by OpenAPI Generator (https://openapi-generator.tech)
10
+
11
+ Do not edit the class manually.
12
+ """ # noqa: E501
13
+
14
+
15
+ from __future__ import annotations
16
+ import pprint
17
+ import re # noqa: F401
18
+ import json
19
+
20
+ from pydantic import BaseModel, ConfigDict, StrictStr
21
+ from typing import Any, ClassVar, Dict, List, Optional
22
+ from ncbi.datasets.openapi.models.v2_mol_type import V2MolType
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+ from typing import Optional, Set
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+ from typing_extensions import Self
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+
26
+ class V2SeqReply(BaseModel):
27
+ """
28
+ V2SeqReply
29
+ """ # noqa: E501
30
+ accession: Optional[StrictStr] = None
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+ seq_length: Optional[StrictStr] = None
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+ mol_type: Optional[V2MolType] = V2MolType.MOL_UNSPECIFIED
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+ defline: Optional[StrictStr] = None
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+ sequence: Optional[StrictStr] = None
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+ __properties: ClassVar[List[str]] = ["accession", "seq_length", "mol_type", "defline", "sequence"]
36
+
37
+ model_config = ConfigDict(
38
+ populate_by_name=True,
39
+ validate_assignment=True,
40
+ protected_namespaces=(),
41
+ )
42
+
43
+
44
+ def to_str(self) -> str:
45
+ """Returns the string representation of the model using alias"""
46
+ return pprint.pformat(self.model_dump(by_alias=True))
47
+
48
+ def to_json(self) -> str:
49
+ """Returns the JSON representation of the model using alias"""
50
+ # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
51
+ return json.dumps(self.to_dict())
52
+
53
+ @classmethod
54
+ def from_json(cls, json_str: str) -> Optional[Self]:
55
+ """Create an instance of V2SeqReply from a JSON string"""
56
+ return cls.from_dict(json.loads(json_str))
57
+
58
+ def to_dict(self) -> Dict[str, Any]:
59
+ """Return the dictionary representation of the model using alias.
60
+
61
+ This has the following differences from calling pydantic's
62
+ `self.model_dump(by_alias=True)`:
63
+
64
+ * `None` is only added to the output dict for nullable fields that
65
+ were set at model initialization. Other fields with value `None`
66
+ are ignored.
67
+ """
68
+ excluded_fields: Set[str] = set([
69
+ ])
70
+
71
+ _dict = self.model_dump(
72
+ by_alias=True,
73
+ exclude=excluded_fields,
74
+ exclude_none=True,
75
+ )
76
+ return _dict
77
+
78
+ @classmethod
79
+ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
80
+ """Create an instance of V2SeqReply from a dict"""
81
+ if obj is None:
82
+ return None
83
+
84
+ if not isinstance(obj, dict):
85
+ return cls.model_validate(obj)
86
+
87
+ _obj = cls.model_validate({
88
+ "accession": obj.get("accession"),
89
+ "seq_length": obj.get("seq_length"),
90
+ "mol_type": obj.get("mol_type") if obj.get("mol_type") is not None else V2MolType.MOL_UNSPECIFIED,
91
+ "defline": obj.get("defline"),
92
+ "sequence": obj.get("sequence")
93
+ })
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+ return _obj
95
+
96
+
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
8
  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
12
11
  Do not edit the class manually.
@@ -3,10 +3,9 @@
3
3
  """
4
4
  NCBI Datasets API
5
5
 
6
- ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The Datasets version 2 API is still in alpha, and we're updating it often to add new functionality, iron out bugs and enhance usability. For some larger downloads, you may want to download a [dehydrated zip archive](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/how-tos/genomes/large-download/), and retrieve the individual data files at a later time.
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
7
 
8
8
  The version of the OpenAPI document: v2
9
- Contact: help@ncbi.nlm.nih.gov
10
9
  Generated by OpenAPI Generator (https://openapi-generator.tech)
11
10
 
12
11
  Do not edit the class manually.
@@ -0,0 +1,87 @@
1
+ # coding: utf-8
2
+
3
+ """
4
+ NCBI Datasets API
5
+
6
+ ### NCBI Datasets is a resource that lets you easily gather data from NCBI. The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.
7
+
8
+ The version of the OpenAPI document: v2
9
+ Generated by OpenAPI Generator (https://openapi-generator.tech)
10
+
11
+ Do not edit the class manually.
12
+ """ # noqa: E501
13
+
14
+
15
+ from __future__ import annotations
16
+ import pprint
17
+ import re # noqa: F401
18
+ import json
19
+
20
+ from pydantic import BaseModel, ConfigDict, StrictStr
21
+ from typing import Any, ClassVar, Dict, List, Optional
22
+ from typing import Optional, Set
23
+ from typing_extensions import Self
24
+
25
+ class V2SleepReply(BaseModel):
26
+ """
27
+ V2SleepReply
28
+ """ # noqa: E501
29
+ reply: Optional[StrictStr] = None
30
+ __properties: ClassVar[List[str]] = ["reply"]
31
+
32
+ model_config = ConfigDict(
33
+ populate_by_name=True,
34
+ validate_assignment=True,
35
+ protected_namespaces=(),
36
+ )
37
+
38
+
39
+ def to_str(self) -> str:
40
+ """Returns the string representation of the model using alias"""
41
+ return pprint.pformat(self.model_dump(by_alias=True))
42
+
43
+ def to_json(self) -> str:
44
+ """Returns the JSON representation of the model using alias"""
45
+ # TODO: pydantic v2: use .model_dump_json(by_alias=True, exclude_unset=True) instead
46
+ return json.dumps(self.to_dict())
47
+
48
+ @classmethod
49
+ def from_json(cls, json_str: str) -> Optional[Self]:
50
+ """Create an instance of V2SleepReply from a JSON string"""
51
+ return cls.from_dict(json.loads(json_str))
52
+
53
+ def to_dict(self) -> Dict[str, Any]:
54
+ """Return the dictionary representation of the model using alias.
55
+
56
+ This has the following differences from calling pydantic's
57
+ `self.model_dump(by_alias=True)`:
58
+
59
+ * `None` is only added to the output dict for nullable fields that
60
+ were set at model initialization. Other fields with value `None`
61
+ are ignored.
62
+ """
63
+ excluded_fields: Set[str] = set([
64
+ ])
65
+
66
+ _dict = self.model_dump(
67
+ by_alias=True,
68
+ exclude=excluded_fields,
69
+ exclude_none=True,
70
+ )
71
+ return _dict
72
+
73
+ @classmethod
74
+ def from_dict(cls, obj: Optional[Dict[str, Any]]) -> Optional[Self]:
75
+ """Create an instance of V2SleepReply from a dict"""
76
+ if obj is None:
77
+ return None
78
+
79
+ if not isinstance(obj, dict):
80
+ return cls.model_validate(obj)
81
+
82
+ _obj = cls.model_validate({
83
+ "reply": obj.get("reply")
84
+ })
85
+ return _obj
86
+
87
+