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
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.
@@ -58,18 +57,18 @@ class VirusApi:
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  @validate_call
59
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  def sars2_protein_download(
60
59
  self,
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- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
60
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
62
61
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
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62
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
64
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
65
- updated_since: Optional[datetime] = None,
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- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
67
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
68
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
69
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
70
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
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- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
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- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
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+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
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+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
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+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
66
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
67
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
68
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
69
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
70
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
71
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
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  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
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  _request_timeout: Union[
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  None,
@@ -84,33 +83,33 @@ class VirusApi:
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  _headers: Optional[Dict[StrictStr, Any]] = None,
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  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
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  ) -> bytearray:
87
- """Download SARS-CoV-2 protein and CDS datasets by protein name
86
+ """Get a SARS-CoV-2 protein data package by protein name
88
87
 
89
- Download SARS-CoV-2 protein datasets
88
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report by protein name.
90
89
 
91
- :param proteins: Which proteins to retrieve in the data package (required)
90
+ :param proteins: One or more SARS-CoV-2 protein names (required)
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  :type proteins: List[str]
93
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  :param refseq_only: If true, limit results to RefSeq genomes.
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  :type refseq_only: bool
95
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  :param annotated_only: If true, limit results to annotated genomes.
96
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  :type annotated_only: bool
97
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
96
+ :param released_since: Limit to genomes released on or after the specified date.
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  :type released_since: datetime
99
- :param updated_since:
98
+ :param updated_since: Limit to genomes updated on or after the specified date.
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  :type updated_since: datetime
101
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
100
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
102
101
  :type host: str
103
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
102
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
104
103
  :type pangolin_classification: str
105
- :param geo_location: Assemblies from this location (country or continent)
104
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
106
105
  :type geo_location: str
107
- :param usa_state: Assemblies from this state (official two letter code only)
106
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
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  :type usa_state: str
109
- :param complete_only: only include complete genomes.
108
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
110
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  :type complete_only: bool
111
- :param include_sequence: Specify which sequence files to include in the download
110
+ :param include_sequence: Specify which sequence files to include in the data package.
112
111
  :type include_sequence: List[V2ViralSequenceType]
113
- :param aux_report: List additional reports to include with download. Data report is included by default.
112
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
114
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  :type aux_report: List[V2VirusDatasetReportType]
115
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  :param filename: Output file name.
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  :type filename: str
@@ -173,18 +172,18 @@ class VirusApi:
173
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  @validate_call
174
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  def sars2_protein_download_with_http_info(
175
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  self,
176
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
175
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
177
176
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
178
177
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
179
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
180
- updated_since: Optional[datetime] = None,
181
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
182
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
183
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
184
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
185
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
186
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
187
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
178
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
179
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
180
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
181
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
182
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
183
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
184
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
185
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
186
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
188
187
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
189
188
  _request_timeout: Union[
190
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  None,
@@ -199,33 +198,33 @@ class VirusApi:
199
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  _headers: Optional[Dict[StrictStr, Any]] = None,
200
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  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
201
200
  ) -> ApiResponse[bytearray]:
202
- """Download SARS-CoV-2 protein and CDS datasets by protein name
201
+ """Get a SARS-CoV-2 protein data package by protein name
203
202
 
204
- Download SARS-CoV-2 protein datasets
203
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report by protein name.
205
204
 
206
- :param proteins: Which proteins to retrieve in the data package (required)
205
+ :param proteins: One or more SARS-CoV-2 protein names (required)
207
206
  :type proteins: List[str]
208
207
  :param refseq_only: If true, limit results to RefSeq genomes.
209
208
  :type refseq_only: bool
210
209
  :param annotated_only: If true, limit results to annotated genomes.
211
210
  :type annotated_only: bool
212
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
211
+ :param released_since: Limit to genomes released on or after the specified date.
213
212
  :type released_since: datetime
214
- :param updated_since:
213
+ :param updated_since: Limit to genomes updated on or after the specified date.
215
214
  :type updated_since: datetime
216
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
215
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
217
216
  :type host: str
218
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
217
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
219
218
  :type pangolin_classification: str
220
- :param geo_location: Assemblies from this location (country or continent)
219
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
221
220
  :type geo_location: str
222
- :param usa_state: Assemblies from this state (official two letter code only)
221
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
223
222
  :type usa_state: str
224
- :param complete_only: only include complete genomes.
223
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
225
224
  :type complete_only: bool
226
- :param include_sequence: Specify which sequence files to include in the download
225
+ :param include_sequence: Specify which sequence files to include in the data package.
227
226
  :type include_sequence: List[V2ViralSequenceType]
228
- :param aux_report: List additional reports to include with download. Data report is included by default.
227
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
229
228
  :type aux_report: List[V2VirusDatasetReportType]
230
229
  :param filename: Output file name.
231
230
  :type filename: str
@@ -288,18 +287,18 @@ class VirusApi:
288
287
  @validate_call
289
288
  def sars2_protein_download_without_preload_content(
290
289
  self,
291
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
290
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
292
291
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
293
292
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
294
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
295
- updated_since: Optional[datetime] = None,
296
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
297
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
298
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
299
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
300
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
301
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
302
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
293
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
294
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
295
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
296
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
297
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
298
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
299
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
300
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
301
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
303
302
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
304
303
  _request_timeout: Union[
305
304
  None,
@@ -314,33 +313,33 @@ class VirusApi:
314
313
  _headers: Optional[Dict[StrictStr, Any]] = None,
315
314
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
316
315
  ) -> RESTResponseType:
317
- """Download SARS-CoV-2 protein and CDS datasets by protein name
316
+ """Get a SARS-CoV-2 protein data package by protein name
318
317
 
319
- Download SARS-CoV-2 protein datasets
318
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report by protein name.
320
319
 
321
- :param proteins: Which proteins to retrieve in the data package (required)
320
+ :param proteins: One or more SARS-CoV-2 protein names (required)
322
321
  :type proteins: List[str]
323
322
  :param refseq_only: If true, limit results to RefSeq genomes.
324
323
  :type refseq_only: bool
325
324
  :param annotated_only: If true, limit results to annotated genomes.
326
325
  :type annotated_only: bool
327
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
326
+ :param released_since: Limit to genomes released on or after the specified date.
328
327
  :type released_since: datetime
329
- :param updated_since:
328
+ :param updated_since: Limit to genomes updated on or after the specified date.
330
329
  :type updated_since: datetime
331
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
330
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
332
331
  :type host: str
333
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
332
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
334
333
  :type pangolin_classification: str
335
- :param geo_location: Assemblies from this location (country or continent)
334
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
336
335
  :type geo_location: str
337
- :param usa_state: Assemblies from this state (official two letter code only)
336
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
338
337
  :type usa_state: str
339
- :param complete_only: only include complete genomes.
338
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
340
339
  :type complete_only: bool
341
- :param include_sequence: Specify which sequence files to include in the download
340
+ :param include_sequence: Specify which sequence files to include in the data package.
342
341
  :type include_sequence: List[V2ViralSequenceType]
343
- :param aux_report: List additional reports to include with download. Data report is included by default.
342
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
344
343
  :type aux_report: List[V2VirusDatasetReportType]
345
344
  :param filename: Output file name.
346
345
  :type filename: str
@@ -560,9 +559,9 @@ class VirusApi:
560
559
  _headers: Optional[Dict[StrictStr, Any]] = None,
561
560
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
562
561
  ) -> bytearray:
563
- """Download SARS-CoV-2 protein and CDS datasets by protein name by POST request
562
+ """Get a SARS-CoV-2 protein data package
564
563
 
565
- Download SARS-CoV-2 protein datasets POST request
564
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
566
565
 
567
566
  :param v2_sars2_protein_dataset_request: (required)
568
567
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -631,9 +630,9 @@ class VirusApi:
631
630
  _headers: Optional[Dict[StrictStr, Any]] = None,
632
631
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
633
632
  ) -> ApiResponse[bytearray]:
634
- """Download SARS-CoV-2 protein and CDS datasets by protein name by POST request
633
+ """Get a SARS-CoV-2 protein data package
635
634
 
636
- Download SARS-CoV-2 protein datasets POST request
635
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
637
636
 
638
637
  :param v2_sars2_protein_dataset_request: (required)
639
638
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -702,9 +701,9 @@ class VirusApi:
702
701
  _headers: Optional[Dict[StrictStr, Any]] = None,
703
702
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
704
703
  ) -> RESTResponseType:
705
- """Download SARS-CoV-2 protein and CDS datasets by protein name by POST request
704
+ """Get a SARS-CoV-2 protein data package
706
705
 
707
- Download SARS-CoV-2 protein datasets POST request
706
+ Download a SARS-CoV-2 protein data package including sequence, annotation, BioSample data and a detailed data report.
708
707
 
709
708
  :param v2_sars2_protein_dataset_request: (required)
710
709
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -837,18 +836,18 @@ class VirusApi:
837
836
  @validate_call
838
837
  def sars2_protein_summary(
839
838
  self,
840
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
839
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
841
840
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
842
841
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
843
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
844
- updated_since: Optional[datetime] = None,
845
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
846
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
847
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
848
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
849
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
850
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
851
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
842
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
843
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
844
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
845
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
846
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
847
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
848
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
849
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
850
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
852
851
  _request_timeout: Union[
853
852
  None,
854
853
  Annotated[StrictFloat, Field(gt=0)],
@@ -862,33 +861,33 @@ class VirusApi:
862
861
  _headers: Optional[Dict[StrictStr, Any]] = None,
863
862
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
864
863
  ) -> V2DownloadSummary:
865
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
864
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
866
865
 
867
- Download a summary of available SARS-CoV-2 protein datasets
866
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
868
867
 
869
- :param proteins: Which proteins to retrieve in the data package (required)
868
+ :param proteins: One or more SARS-CoV-2 protein names (required)
870
869
  :type proteins: List[str]
871
870
  :param refseq_only: If true, limit results to RefSeq genomes.
872
871
  :type refseq_only: bool
873
872
  :param annotated_only: If true, limit results to annotated genomes.
874
873
  :type annotated_only: bool
875
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
874
+ :param released_since: Limit to genomes released on or after the specified date.
876
875
  :type released_since: datetime
877
- :param updated_since:
876
+ :param updated_since: Limit to genomes updated on or after the specified date.
878
877
  :type updated_since: datetime
879
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
878
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
880
879
  :type host: str
881
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
880
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
882
881
  :type pangolin_classification: str
883
- :param geo_location: Assemblies from this location (country or continent)
882
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
884
883
  :type geo_location: str
885
- :param usa_state: Assemblies from this state (official two letter code only)
884
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
886
885
  :type usa_state: str
887
- :param complete_only: only include complete genomes.
886
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
888
887
  :type complete_only: bool
889
- :param include_sequence: Specify which sequence files to include in the download
888
+ :param include_sequence: Specify which sequence files to include in the data package.
890
889
  :type include_sequence: List[V2ViralSequenceType]
891
- :param aux_report: List additional reports to include with download. Data report is included by default.
890
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
892
891
  :type aux_report: List[V2VirusDatasetReportType]
893
892
  :param _request_timeout: timeout setting for this request. If one
894
893
  number provided, it will be total request
@@ -948,18 +947,18 @@ class VirusApi:
948
947
  @validate_call
949
948
  def sars2_protein_summary_with_http_info(
950
949
  self,
951
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
950
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
952
951
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
953
952
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
954
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
955
- updated_since: Optional[datetime] = None,
956
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
957
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
958
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
959
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
960
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
961
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
962
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
953
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
954
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
955
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
956
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
957
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
958
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
959
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
960
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
961
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
963
962
  _request_timeout: Union[
964
963
  None,
965
964
  Annotated[StrictFloat, Field(gt=0)],
@@ -973,33 +972,33 @@ class VirusApi:
973
972
  _headers: Optional[Dict[StrictStr, Any]] = None,
974
973
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
975
974
  ) -> ApiResponse[V2DownloadSummary]:
976
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
975
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
977
976
 
978
- Download a summary of available SARS-CoV-2 protein datasets
977
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
979
978
 
980
- :param proteins: Which proteins to retrieve in the data package (required)
979
+ :param proteins: One or more SARS-CoV-2 protein names (required)
981
980
  :type proteins: List[str]
982
981
  :param refseq_only: If true, limit results to RefSeq genomes.
983
982
  :type refseq_only: bool
984
983
  :param annotated_only: If true, limit results to annotated genomes.
985
984
  :type annotated_only: bool
986
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
985
+ :param released_since: Limit to genomes released on or after the specified date.
987
986
  :type released_since: datetime
988
- :param updated_since:
987
+ :param updated_since: Limit to genomes updated on or after the specified date.
989
988
  :type updated_since: datetime
990
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
989
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
991
990
  :type host: str
992
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
991
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
993
992
  :type pangolin_classification: str
994
- :param geo_location: Assemblies from this location (country or continent)
993
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
995
994
  :type geo_location: str
996
- :param usa_state: Assemblies from this state (official two letter code only)
995
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
997
996
  :type usa_state: str
998
- :param complete_only: only include complete genomes.
997
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
999
998
  :type complete_only: bool
1000
- :param include_sequence: Specify which sequence files to include in the download
999
+ :param include_sequence: Specify which sequence files to include in the data package.
1001
1000
  :type include_sequence: List[V2ViralSequenceType]
1002
- :param aux_report: List additional reports to include with download. Data report is included by default.
1001
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
1003
1002
  :type aux_report: List[V2VirusDatasetReportType]
1004
1003
  :param _request_timeout: timeout setting for this request. If one
1005
1004
  number provided, it will be total request
@@ -1059,18 +1058,18 @@ class VirusApi:
1059
1058
  @validate_call
1060
1059
  def sars2_protein_summary_without_preload_content(
1061
1060
  self,
1062
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
1061
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
1063
1062
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
1064
1063
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
1065
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
1066
- updated_since: Optional[datetime] = None,
1067
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
1068
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
1069
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
1070
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
1071
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
1072
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
1073
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
1064
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
1065
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
1066
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
1067
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
1068
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
1069
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
1070
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
1071
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
1072
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
1074
1073
  _request_timeout: Union[
1075
1074
  None,
1076
1075
  Annotated[StrictFloat, Field(gt=0)],
@@ -1084,33 +1083,33 @@ class VirusApi:
1084
1083
  _headers: Optional[Dict[StrictStr, Any]] = None,
1085
1084
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1086
1085
  ) -> RESTResponseType:
1087
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
1086
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
1088
1087
 
1089
- Download a summary of available SARS-CoV-2 protein datasets
1088
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
1090
1089
 
1091
- :param proteins: Which proteins to retrieve in the data package (required)
1090
+ :param proteins: One or more SARS-CoV-2 protein names (required)
1092
1091
  :type proteins: List[str]
1093
1092
  :param refseq_only: If true, limit results to RefSeq genomes.
1094
1093
  :type refseq_only: bool
1095
1094
  :param annotated_only: If true, limit results to annotated genomes.
1096
1095
  :type annotated_only: bool
1097
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
1096
+ :param released_since: Limit to genomes released on or after the specified date.
1098
1097
  :type released_since: datetime
1099
- :param updated_since:
1098
+ :param updated_since: Limit to genomes updated on or after the specified date.
1100
1099
  :type updated_since: datetime
1101
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
1100
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
1102
1101
  :type host: str
1103
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
1102
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
1104
1103
  :type pangolin_classification: str
1105
- :param geo_location: Assemblies from this location (country or continent)
1104
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
1106
1105
  :type geo_location: str
1107
- :param usa_state: Assemblies from this state (official two letter code only)
1106
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
1108
1107
  :type usa_state: str
1109
- :param complete_only: only include complete genomes.
1108
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
1110
1109
  :type complete_only: bool
1111
- :param include_sequence: Specify which sequence files to include in the download
1110
+ :param include_sequence: Specify which sequence files to include in the data package.
1112
1111
  :type include_sequence: List[V2ViralSequenceType]
1113
- :param aux_report: List additional reports to include with download. Data report is included by default.
1112
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
1114
1113
  :type aux_report: List[V2VirusDatasetReportType]
1115
1114
  :param _request_timeout: timeout setting for this request. If one
1116
1115
  number provided, it will be total request
@@ -1321,9 +1320,9 @@ class VirusApi:
1321
1320
  _headers: Optional[Dict[StrictStr, Any]] = None,
1322
1321
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1323
1322
  ) -> V2DownloadSummary:
1324
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
1323
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
1325
1324
 
1326
- Download a summary of available SARS-CoV-2 protein datasets
1325
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
1327
1326
 
1328
1327
  :param v2_sars2_protein_dataset_request: (required)
1329
1328
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -1388,9 +1387,9 @@ class VirusApi:
1388
1387
  _headers: Optional[Dict[StrictStr, Any]] = None,
1389
1388
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1390
1389
  ) -> ApiResponse[V2DownloadSummary]:
1391
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
1390
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
1392
1391
 
1393
- Download a summary of available SARS-CoV-2 protein datasets
1392
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
1394
1393
 
1395
1394
  :param v2_sars2_protein_dataset_request: (required)
1396
1395
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -1455,9 +1454,9 @@ class VirusApi:
1455
1454
  _headers: Optional[Dict[StrictStr, Any]] = None,
1456
1455
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1457
1456
  ) -> RESTResponseType:
1458
- """Summary of SARS-CoV-2 protein and CDS datasets by protein name
1457
+ """Get a download summary of a SARS-CoV-2 protein data package by protein name
1459
1458
 
1460
- Download a summary of available SARS-CoV-2 protein datasets
1459
+ Get a download summary of a SARS-CoV-2 protein data package, including counts and file sizes, in JSON format.
1461
1460
 
1462
1461
  :param v2_sars2_protein_dataset_request: (required)
1463
1462
  :type v2_sars2_protein_dataset_request: V2Sars2ProteinDatasetRequest
@@ -1582,20 +1581,18 @@ class VirusApi:
1582
1581
  @validate_call
1583
1582
  def sars2_protein_table(
1584
1583
  self,
1585
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
1584
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
1586
1585
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
1587
1586
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
1588
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
1589
- updated_since: Optional[datetime] = None,
1590
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
1591
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
1592
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
1593
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
1594
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
1587
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
1588
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
1589
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
1590
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
1591
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
1592
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
1593
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
1595
1594
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
1596
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
1597
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
1598
- format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
1595
+ format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
1599
1596
  _request_timeout: Union[
1600
1597
  None,
1601
1598
  Annotated[StrictFloat, Field(gt=0)],
@@ -1609,37 +1606,33 @@ class VirusApi:
1609
1606
  _headers: Optional[Dict[StrictStr, Any]] = None,
1610
1607
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1611
1608
  ) -> V2TabularOutput:
1612
- """Get SARS-CoV-2 protein metadata in a tabular format.
1609
+ """Get SARS-CoV-2 protein metadata in a tabular format by protein name
1613
1610
 
1614
- Get protein metadata in tabular format for SARS-CoV-2 genomes.
1611
+ Get SARS-CoV-2 protein metadata in a tabular format by protein name.
1615
1612
 
1616
- :param proteins: Which proteins to retrieve in the data package (required)
1613
+ :param proteins: One or more SARS-CoV-2 protein names (required)
1617
1614
  :type proteins: List[str]
1618
1615
  :param refseq_only: If true, limit results to RefSeq genomes.
1619
1616
  :type refseq_only: bool
1620
1617
  :param annotated_only: If true, limit results to annotated genomes.
1621
1618
  :type annotated_only: bool
1622
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
1619
+ :param released_since: Limit to genomes released on or after the specified date.
1623
1620
  :type released_since: datetime
1624
- :param updated_since:
1621
+ :param updated_since: Limit to genomes updated on or after the specified date.
1625
1622
  :type updated_since: datetime
1626
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
1623
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
1627
1624
  :type host: str
1628
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
1625
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
1629
1626
  :type pangolin_classification: str
1630
- :param geo_location: Assemblies from this location (country or continent)
1627
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
1631
1628
  :type geo_location: str
1632
- :param usa_state: Assemblies from this state (official two letter code only)
1629
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
1633
1630
  :type usa_state: str
1634
- :param complete_only: only include complete genomes.
1631
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
1635
1632
  :type complete_only: bool
1636
1633
  :param table_fields: Specify which fields to include in the tabular report
1637
1634
  :type table_fields: List[V2VirusTableField]
1638
- :param include_sequence: Specify which sequence files to include in the download
1639
- :type include_sequence: List[V2ViralSequenceType]
1640
- :param aux_report: List additional reports to include with download. Data report is included by default.
1641
- :type aux_report: List[V2VirusDatasetReportType]
1642
- :param format: Choose download format (tsv, csv or jsonl)
1635
+ :param format: Specify output format
1643
1636
  :type format: V2TableFormat
1644
1637
  :param _request_timeout: timeout setting for this request. If one
1645
1638
  number provided, it will be total request
@@ -1675,8 +1668,6 @@ class VirusApi:
1675
1668
  usa_state=usa_state,
1676
1669
  complete_only=complete_only,
1677
1670
  table_fields=table_fields,
1678
- include_sequence=include_sequence,
1679
- aux_report=aux_report,
1680
1671
  format=format,
1681
1672
  _request_auth=_request_auth,
1682
1673
  _content_type=_content_type,
@@ -1701,20 +1692,18 @@ class VirusApi:
1701
1692
  @validate_call
1702
1693
  def sars2_protein_table_with_http_info(
1703
1694
  self,
1704
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
1695
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
1705
1696
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
1706
1697
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
1707
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
1708
- updated_since: Optional[datetime] = None,
1709
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
1710
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
1711
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
1712
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
1713
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
1698
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
1699
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
1700
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
1701
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
1702
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
1703
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
1704
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
1714
1705
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
1715
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
1716
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
1717
- format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
1706
+ format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
1718
1707
  _request_timeout: Union[
1719
1708
  None,
1720
1709
  Annotated[StrictFloat, Field(gt=0)],
@@ -1728,37 +1717,33 @@ class VirusApi:
1728
1717
  _headers: Optional[Dict[StrictStr, Any]] = None,
1729
1718
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1730
1719
  ) -> ApiResponse[V2TabularOutput]:
1731
- """Get SARS-CoV-2 protein metadata in a tabular format.
1720
+ """Get SARS-CoV-2 protein metadata in a tabular format by protein name
1732
1721
 
1733
- Get protein metadata in tabular format for SARS-CoV-2 genomes.
1722
+ Get SARS-CoV-2 protein metadata in a tabular format by protein name.
1734
1723
 
1735
- :param proteins: Which proteins to retrieve in the data package (required)
1724
+ :param proteins: One or more SARS-CoV-2 protein names (required)
1736
1725
  :type proteins: List[str]
1737
1726
  :param refseq_only: If true, limit results to RefSeq genomes.
1738
1727
  :type refseq_only: bool
1739
1728
  :param annotated_only: If true, limit results to annotated genomes.
1740
1729
  :type annotated_only: bool
1741
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
1730
+ :param released_since: Limit to genomes released on or after the specified date.
1742
1731
  :type released_since: datetime
1743
- :param updated_since:
1732
+ :param updated_since: Limit to genomes updated on or after the specified date.
1744
1733
  :type updated_since: datetime
1745
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
1734
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
1746
1735
  :type host: str
1747
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
1736
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
1748
1737
  :type pangolin_classification: str
1749
- :param geo_location: Assemblies from this location (country or continent)
1738
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
1750
1739
  :type geo_location: str
1751
- :param usa_state: Assemblies from this state (official two letter code only)
1740
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
1752
1741
  :type usa_state: str
1753
- :param complete_only: only include complete genomes.
1742
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
1754
1743
  :type complete_only: bool
1755
1744
  :param table_fields: Specify which fields to include in the tabular report
1756
1745
  :type table_fields: List[V2VirusTableField]
1757
- :param include_sequence: Specify which sequence files to include in the download
1758
- :type include_sequence: List[V2ViralSequenceType]
1759
- :param aux_report: List additional reports to include with download. Data report is included by default.
1760
- :type aux_report: List[V2VirusDatasetReportType]
1761
- :param format: Choose download format (tsv, csv or jsonl)
1746
+ :param format: Specify output format
1762
1747
  :type format: V2TableFormat
1763
1748
  :param _request_timeout: timeout setting for this request. If one
1764
1749
  number provided, it will be total request
@@ -1794,8 +1779,6 @@ class VirusApi:
1794
1779
  usa_state=usa_state,
1795
1780
  complete_only=complete_only,
1796
1781
  table_fields=table_fields,
1797
- include_sequence=include_sequence,
1798
- aux_report=aux_report,
1799
1782
  format=format,
1800
1783
  _request_auth=_request_auth,
1801
1784
  _content_type=_content_type,
@@ -1820,20 +1803,18 @@ class VirusApi:
1820
1803
  @validate_call
1821
1804
  def sars2_protein_table_without_preload_content(
1822
1805
  self,
1823
- proteins: Annotated[List[StrictStr], Field(description="Which proteins to retrieve in the data package")],
1806
+ proteins: Annotated[List[StrictStr], Field(description="One or more SARS-CoV-2 protein names")],
1824
1807
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
1825
1808
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
1826
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
1827
- updated_since: Optional[datetime] = None,
1828
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
1829
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
1830
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
1831
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
1832
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
1809
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
1810
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
1811
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
1812
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes with the specified Pango lineage.")] = None,
1813
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
1814
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
1815
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
1833
1816
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
1834
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the download")] = None,
1835
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="List additional reports to include with download. Data report is included by default.")] = None,
1836
- format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
1817
+ format: Annotated[Optional[V2TableFormat], Field(description="Specify output format")] = None,
1837
1818
  _request_timeout: Union[
1838
1819
  None,
1839
1820
  Annotated[StrictFloat, Field(gt=0)],
@@ -1847,37 +1828,33 @@ class VirusApi:
1847
1828
  _headers: Optional[Dict[StrictStr, Any]] = None,
1848
1829
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
1849
1830
  ) -> RESTResponseType:
1850
- """Get SARS-CoV-2 protein metadata in a tabular format.
1831
+ """Get SARS-CoV-2 protein metadata in a tabular format by protein name
1851
1832
 
1852
- Get protein metadata in tabular format for SARS-CoV-2 genomes.
1833
+ Get SARS-CoV-2 protein metadata in a tabular format by protein name.
1853
1834
 
1854
- :param proteins: Which proteins to retrieve in the data package (required)
1835
+ :param proteins: One or more SARS-CoV-2 protein names (required)
1855
1836
  :type proteins: List[str]
1856
1837
  :param refseq_only: If true, limit results to RefSeq genomes.
1857
1838
  :type refseq_only: bool
1858
1839
  :param annotated_only: If true, limit results to annotated genomes.
1859
1840
  :type annotated_only: bool
1860
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
1841
+ :param released_since: Limit to genomes released on or after the specified date.
1861
1842
  :type released_since: datetime
1862
- :param updated_since:
1843
+ :param updated_since: Limit to genomes updated on or after the specified date.
1863
1844
  :type updated_since: datetime
1864
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
1845
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
1865
1846
  :type host: str
1866
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
1847
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes with the specified Pango lineage.
1867
1848
  :type pangolin_classification: str
1868
- :param geo_location: Assemblies from this location (country or continent)
1849
+ :param geo_location: Limit to genomes collected from the specififed geographic location.
1869
1850
  :type geo_location: str
1870
- :param usa_state: Assemblies from this state (official two letter code only)
1851
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
1871
1852
  :type usa_state: str
1872
- :param complete_only: only include complete genomes.
1853
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
1873
1854
  :type complete_only: bool
1874
1855
  :param table_fields: Specify which fields to include in the tabular report
1875
1856
  :type table_fields: List[V2VirusTableField]
1876
- :param include_sequence: Specify which sequence files to include in the download
1877
- :type include_sequence: List[V2ViralSequenceType]
1878
- :param aux_report: List additional reports to include with download. Data report is included by default.
1879
- :type aux_report: List[V2VirusDatasetReportType]
1880
- :param format: Choose download format (tsv, csv or jsonl)
1857
+ :param format: Specify output format
1881
1858
  :type format: V2TableFormat
1882
1859
  :param _request_timeout: timeout setting for this request. If one
1883
1860
  number provided, it will be total request
@@ -1913,8 +1890,6 @@ class VirusApi:
1913
1890
  usa_state=usa_state,
1914
1891
  complete_only=complete_only,
1915
1892
  table_fields=table_fields,
1916
- include_sequence=include_sequence,
1917
- aux_report=aux_report,
1918
1893
  format=format,
1919
1894
  _request_auth=_request_auth,
1920
1895
  _content_type=_content_type,
@@ -1945,8 +1920,6 @@ class VirusApi:
1945
1920
  usa_state,
1946
1921
  complete_only,
1947
1922
  table_fields,
1948
- include_sequence,
1949
- aux_report,
1950
1923
  format,
1951
1924
  _request_auth,
1952
1925
  _content_type,
@@ -1959,8 +1932,6 @@ class VirusApi:
1959
1932
  _collection_formats: Dict[str, str] = {
1960
1933
  'proteins': 'csv',
1961
1934
  'table_fields': 'multi',
1962
- 'include_sequence': 'multi',
1963
- 'aux_report': 'multi',
1964
1935
  }
1965
1936
 
1966
1937
  _path_params: Dict[str, str] = {}
@@ -2034,14 +2005,6 @@ class VirusApi:
2034
2005
 
2035
2006
  _query_params.append(('table_fields', table_fields))
2036
2007
 
2037
- if include_sequence is not None:
2038
-
2039
- _query_params.append(('include_sequence', include_sequence))
2040
-
2041
- if aux_report is not None:
2042
-
2043
- _query_params.append(('aux_report', aux_report))
2044
-
2045
2008
  if format is not None:
2046
2009
 
2047
2010
  _query_params.append(('format', format.value))
@@ -2101,9 +2064,9 @@ class VirusApi:
2101
2064
  _headers: Optional[Dict[StrictStr, Any]] = None,
2102
2065
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2103
2066
  ) -> V2VirusAvailability:
2104
- """Check available viruses by accession
2067
+ """Check the validity of a virus genome nucleotide accession
2105
2068
 
2106
- Check available viruses
2069
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2107
2070
 
2108
2071
  :param accessions: virus accessions (required)
2109
2072
  :type accessions: List[str]
@@ -2168,9 +2131,9 @@ class VirusApi:
2168
2131
  _headers: Optional[Dict[StrictStr, Any]] = None,
2169
2132
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2170
2133
  ) -> ApiResponse[V2VirusAvailability]:
2171
- """Check available viruses by accession
2134
+ """Check the validity of a virus genome nucleotide accession
2172
2135
 
2173
- Check available viruses
2136
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2174
2137
 
2175
2138
  :param accessions: virus accessions (required)
2176
2139
  :type accessions: List[str]
@@ -2235,9 +2198,9 @@ class VirusApi:
2235
2198
  _headers: Optional[Dict[StrictStr, Any]] = None,
2236
2199
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2237
2200
  ) -> RESTResponseType:
2238
- """Check available viruses by accession
2201
+ """Check the validity of a virus genome nucleotide accession
2239
2202
 
2240
- Check available viruses
2203
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2241
2204
 
2242
2205
  :param accessions: virus accessions (required)
2243
2206
  :type accessions: List[str]
@@ -2364,9 +2327,9 @@ class VirusApi:
2364
2327
  _headers: Optional[Dict[StrictStr, Any]] = None,
2365
2328
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2366
2329
  ) -> V2VirusAvailability:
2367
- """Check available viruses by accession
2330
+ """Check the validity of a virus genome nucleotide accession
2368
2331
 
2369
- Check available viruses
2332
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2370
2333
 
2371
2334
  :param v2_virus_availability_request: (required)
2372
2335
  :type v2_virus_availability_request: V2VirusAvailabilityRequest
@@ -2431,9 +2394,9 @@ class VirusApi:
2431
2394
  _headers: Optional[Dict[StrictStr, Any]] = None,
2432
2395
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2433
2396
  ) -> ApiResponse[V2VirusAvailability]:
2434
- """Check available viruses by accession
2397
+ """Check the validity of a virus genome nucleotide accession
2435
2398
 
2436
- Check available viruses
2399
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2437
2400
 
2438
2401
  :param v2_virus_availability_request: (required)
2439
2402
  :type v2_virus_availability_request: V2VirusAvailabilityRequest
@@ -2498,9 +2461,9 @@ class VirusApi:
2498
2461
  _headers: Optional[Dict[StrictStr, Any]] = None,
2499
2462
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2500
2463
  ) -> RESTResponseType:
2501
- """Check available viruses by accession
2464
+ """Check the validity of a virus genome nucleotide accession
2502
2465
 
2503
- Check available viruses
2466
+ Check the validity of a virus genome nucleotide accession. Output in JSON format.
2504
2467
 
2505
2468
  :param v2_virus_availability_request: (required)
2506
2469
  :type v2_virus_availability_request: V2VirusAvailabilityRequest
@@ -2625,19 +2588,19 @@ class VirusApi:
2625
2588
  @validate_call
2626
2589
  def virus_annotation_reports_by_acessions(
2627
2590
  self,
2628
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
2629
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
2630
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
2631
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
2632
- filter_updated_since: Optional[datetime] = None,
2633
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
2634
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
2635
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
2636
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
2637
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
2638
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
2591
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
2592
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
2593
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
2594
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
2595
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
2596
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
2597
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
2598
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
2599
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
2600
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
2601
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
2639
2602
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
2640
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2603
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2641
2604
  _request_timeout: Union[
2642
2605
  None,
2643
2606
  Annotated[StrictFloat, Field(gt=0)],
@@ -2651,35 +2614,35 @@ class VirusApi:
2651
2614
  _headers: Optional[Dict[StrictStr, Any]] = None,
2652
2615
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2653
2616
  ) -> V2reportsVirusAnnotationReportPage:
2654
- """Get virus annotation report by accession
2617
+ """Get a virus annotation report by nucleotide accession
2655
2618
 
2656
- Get virus annotation report by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
2619
+ Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
2657
2620
 
2658
- :param accessions: genome sequence accessions (required)
2621
+ :param accessions: One or more nucleotide sequence accessions (required)
2659
2622
  :type accessions: List[str]
2660
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
2623
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
2661
2624
  :type filter_refseq_only: bool
2662
- :param filter_annotated_only: If true, limit results to annotated genomes.
2625
+ :param filter_annotated_only: If true, limit to annotated genomes.
2663
2626
  :type filter_annotated_only: bool
2664
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
2627
+ :param filter_released_since: Limit to genomes released on or after the specified date.
2665
2628
  :type filter_released_since: datetime
2666
- :param filter_updated_since:
2629
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
2667
2630
  :type filter_updated_since: datetime
2668
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
2631
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
2669
2632
  :type filter_host: str
2670
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
2633
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
2671
2634
  :type filter_pangolin_classification: str
2672
- :param filter_geo_location: Assemblies from this location (country or continent)
2635
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
2673
2636
  :type filter_geo_location: str
2674
- :param filter_usa_state: Assemblies from this state (official two letter code only)
2637
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
2675
2638
  :type filter_usa_state: str
2676
- :param filter_complete_only: only include complete genomes.
2639
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
2677
2640
  :type filter_complete_only: bool
2678
- :param table_fields: Specify which fields to include in the tabular report
2641
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
2679
2642
  :type table_fields: List[str]
2680
2643
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
2681
2644
  :type page_size: int
2682
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2645
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2683
2646
  :type page_token: str
2684
2647
  :param _request_timeout: timeout setting for this request. If one
2685
2648
  number provided, it will be total request
@@ -2740,19 +2703,19 @@ class VirusApi:
2740
2703
  @validate_call
2741
2704
  def virus_annotation_reports_by_acessions_with_http_info(
2742
2705
  self,
2743
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
2744
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
2745
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
2746
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
2747
- filter_updated_since: Optional[datetime] = None,
2748
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
2749
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
2750
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
2751
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
2752
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
2753
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
2706
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
2707
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
2708
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
2709
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
2710
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
2711
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
2712
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
2713
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
2714
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
2715
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
2716
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
2754
2717
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
2755
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2718
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2756
2719
  _request_timeout: Union[
2757
2720
  None,
2758
2721
  Annotated[StrictFloat, Field(gt=0)],
@@ -2766,35 +2729,35 @@ class VirusApi:
2766
2729
  _headers: Optional[Dict[StrictStr, Any]] = None,
2767
2730
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2768
2731
  ) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
2769
- """Get virus annotation report by accession
2732
+ """Get a virus annotation report by nucleotide accession
2770
2733
 
2771
- Get virus annotation report by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
2734
+ Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
2772
2735
 
2773
- :param accessions: genome sequence accessions (required)
2736
+ :param accessions: One or more nucleotide sequence accessions (required)
2774
2737
  :type accessions: List[str]
2775
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
2738
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
2776
2739
  :type filter_refseq_only: bool
2777
- :param filter_annotated_only: If true, limit results to annotated genomes.
2740
+ :param filter_annotated_only: If true, limit to annotated genomes.
2778
2741
  :type filter_annotated_only: bool
2779
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
2742
+ :param filter_released_since: Limit to genomes released on or after the specified date.
2780
2743
  :type filter_released_since: datetime
2781
- :param filter_updated_since:
2744
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
2782
2745
  :type filter_updated_since: datetime
2783
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
2746
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
2784
2747
  :type filter_host: str
2785
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
2748
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
2786
2749
  :type filter_pangolin_classification: str
2787
- :param filter_geo_location: Assemblies from this location (country or continent)
2750
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
2788
2751
  :type filter_geo_location: str
2789
- :param filter_usa_state: Assemblies from this state (official two letter code only)
2752
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
2790
2753
  :type filter_usa_state: str
2791
- :param filter_complete_only: only include complete genomes.
2754
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
2792
2755
  :type filter_complete_only: bool
2793
- :param table_fields: Specify which fields to include in the tabular report
2756
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
2794
2757
  :type table_fields: List[str]
2795
2758
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
2796
2759
  :type page_size: int
2797
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2760
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2798
2761
  :type page_token: str
2799
2762
  :param _request_timeout: timeout setting for this request. If one
2800
2763
  number provided, it will be total request
@@ -2855,19 +2818,19 @@ class VirusApi:
2855
2818
  @validate_call
2856
2819
  def virus_annotation_reports_by_acessions_without_preload_content(
2857
2820
  self,
2858
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
2859
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
2860
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
2861
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
2862
- filter_updated_since: Optional[datetime] = None,
2863
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
2864
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
2865
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
2866
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
2867
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
2868
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
2821
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
2822
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
2823
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
2824
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
2825
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
2826
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
2827
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
2828
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
2829
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
2830
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
2831
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
2869
2832
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
2870
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2833
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
2871
2834
  _request_timeout: Union[
2872
2835
  None,
2873
2836
  Annotated[StrictFloat, Field(gt=0)],
@@ -2881,35 +2844,35 @@ class VirusApi:
2881
2844
  _headers: Optional[Dict[StrictStr, Any]] = None,
2882
2845
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
2883
2846
  ) -> RESTResponseType:
2884
- """Get virus annotation report by accession
2847
+ """Get a virus annotation report by nucleotide accession
2885
2848
 
2886
- Get virus annotation report by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
2849
+ Get a virus annotation report by nucleotide accesion. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
2887
2850
 
2888
- :param accessions: genome sequence accessions (required)
2851
+ :param accessions: One or more nucleotide sequence accessions (required)
2889
2852
  :type accessions: List[str]
2890
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
2853
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
2891
2854
  :type filter_refseq_only: bool
2892
- :param filter_annotated_only: If true, limit results to annotated genomes.
2855
+ :param filter_annotated_only: If true, limit to annotated genomes.
2893
2856
  :type filter_annotated_only: bool
2894
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
2857
+ :param filter_released_since: Limit to genomes released on or after the specified date.
2895
2858
  :type filter_released_since: datetime
2896
- :param filter_updated_since:
2859
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
2897
2860
  :type filter_updated_since: datetime
2898
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
2861
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
2899
2862
  :type filter_host: str
2900
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
2863
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
2901
2864
  :type filter_pangolin_classification: str
2902
- :param filter_geo_location: Assemblies from this location (country or continent)
2865
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
2903
2866
  :type filter_geo_location: str
2904
- :param filter_usa_state: Assemblies from this state (official two letter code only)
2867
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
2905
2868
  :type filter_usa_state: str
2906
- :param filter_complete_only: only include complete genomes.
2869
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
2907
2870
  :type filter_complete_only: bool
2908
- :param table_fields: Specify which fields to include in the tabular report
2871
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
2909
2872
  :type table_fields: List[str]
2910
2873
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
2911
2874
  :type page_size: int
2912
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2875
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
2913
2876
  :type page_token: str
2914
2877
  :param _request_timeout: timeout setting for this request. If one
2915
2878
  number provided, it will be total request
@@ -3127,9 +3090,9 @@ class VirusApi:
3127
3090
  _headers: Optional[Dict[StrictStr, Any]] = None,
3128
3091
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3129
3092
  ) -> V2reportsVirusAnnotationReportPage:
3130
- """Get virus annotation report by POST
3093
+ """Get a virus annotation report
3131
3094
 
3132
- Get virus annotation report. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3095
+ Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3133
3096
 
3134
3097
  :param v2_virus_annotation_report_request: (required)
3135
3098
  :type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
@@ -3194,9 +3157,9 @@ class VirusApi:
3194
3157
  _headers: Optional[Dict[StrictStr, Any]] = None,
3195
3158
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3196
3159
  ) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
3197
- """Get virus annotation report by POST
3160
+ """Get a virus annotation report
3198
3161
 
3199
- Get virus annotation report. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3162
+ Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3200
3163
 
3201
3164
  :param v2_virus_annotation_report_request: (required)
3202
3165
  :type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
@@ -3261,9 +3224,9 @@ class VirusApi:
3261
3224
  _headers: Optional[Dict[StrictStr, Any]] = None,
3262
3225
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3263
3226
  ) -> RESTResponseType:
3264
- """Get virus annotation report by POST
3227
+ """Get a virus annotation report
3265
3228
 
3266
- Get virus annotation report. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3229
+ Get a virus annotation report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3267
3230
 
3268
3231
  :param v2_virus_annotation_report_request: (required)
3269
3232
  :type v2_virus_annotation_report_request: V2VirusAnnotationReportRequest
@@ -3391,18 +3354,18 @@ class VirusApi:
3391
3354
  def virus_annotation_reports_by_taxon(
3392
3355
  self,
3393
3356
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
3394
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
3395
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
3396
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
3397
- filter_updated_since: Optional[datetime] = None,
3398
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
3399
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
3400
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
3401
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
3402
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
3403
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
3357
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
3358
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
3359
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
3360
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
3361
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
3362
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
3363
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
3364
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
3365
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
3366
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
3404
3367
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
3405
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3368
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3406
3369
  _request_timeout: Union[
3407
3370
  None,
3408
3371
  Annotated[StrictFloat, Field(gt=0)],
@@ -3416,35 +3379,35 @@ class VirusApi:
3416
3379
  _headers: Optional[Dict[StrictStr, Any]] = None,
3417
3380
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3418
3381
  ) -> V2reportsVirusAnnotationReportPage:
3419
- """Get virus annotation report by taxon
3382
+ """Get a virus annotation report by taxon
3420
3383
 
3421
- Get virus annotation report by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3384
+ Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3422
3385
 
3423
3386
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
3424
3387
  :type taxon: str
3425
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
3388
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
3426
3389
  :type filter_refseq_only: bool
3427
- :param filter_annotated_only: If true, limit results to annotated genomes.
3390
+ :param filter_annotated_only: If true, limit to annotated genomes.
3428
3391
  :type filter_annotated_only: bool
3429
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
3392
+ :param filter_released_since: Limit to genomes released on or after the specified date.
3430
3393
  :type filter_released_since: datetime
3431
- :param filter_updated_since:
3394
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
3432
3395
  :type filter_updated_since: datetime
3433
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
3396
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
3434
3397
  :type filter_host: str
3435
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
3398
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
3436
3399
  :type filter_pangolin_classification: str
3437
- :param filter_geo_location: Assemblies from this location (country or continent)
3400
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
3438
3401
  :type filter_geo_location: str
3439
- :param filter_usa_state: Assemblies from this state (official two letter code only)
3402
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
3440
3403
  :type filter_usa_state: str
3441
- :param filter_complete_only: only include complete genomes.
3404
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
3442
3405
  :type filter_complete_only: bool
3443
- :param table_fields: Specify which fields to include in the tabular report
3406
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
3444
3407
  :type table_fields: List[str]
3445
3408
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
3446
3409
  :type page_size: int
3447
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3410
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3448
3411
  :type page_token: str
3449
3412
  :param _request_timeout: timeout setting for this request. If one
3450
3413
  number provided, it will be total request
@@ -3506,18 +3469,18 @@ class VirusApi:
3506
3469
  def virus_annotation_reports_by_taxon_with_http_info(
3507
3470
  self,
3508
3471
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
3509
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
3510
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
3511
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
3512
- filter_updated_since: Optional[datetime] = None,
3513
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
3514
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
3515
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
3516
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
3517
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
3518
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
3472
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
3473
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
3474
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
3475
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
3476
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
3477
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
3478
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
3479
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
3480
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
3481
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
3519
3482
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
3520
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3483
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3521
3484
  _request_timeout: Union[
3522
3485
  None,
3523
3486
  Annotated[StrictFloat, Field(gt=0)],
@@ -3531,35 +3494,35 @@ class VirusApi:
3531
3494
  _headers: Optional[Dict[StrictStr, Any]] = None,
3532
3495
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3533
3496
  ) -> ApiResponse[V2reportsVirusAnnotationReportPage]:
3534
- """Get virus annotation report by taxon
3497
+ """Get a virus annotation report by taxon
3535
3498
 
3536
- Get virus annotation report by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3499
+ Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3537
3500
 
3538
3501
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
3539
3502
  :type taxon: str
3540
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
3503
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
3541
3504
  :type filter_refseq_only: bool
3542
- :param filter_annotated_only: If true, limit results to annotated genomes.
3505
+ :param filter_annotated_only: If true, limit to annotated genomes.
3543
3506
  :type filter_annotated_only: bool
3544
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
3507
+ :param filter_released_since: Limit to genomes released on or after the specified date.
3545
3508
  :type filter_released_since: datetime
3546
- :param filter_updated_since:
3509
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
3547
3510
  :type filter_updated_since: datetime
3548
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
3511
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
3549
3512
  :type filter_host: str
3550
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
3513
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
3551
3514
  :type filter_pangolin_classification: str
3552
- :param filter_geo_location: Assemblies from this location (country or continent)
3515
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
3553
3516
  :type filter_geo_location: str
3554
- :param filter_usa_state: Assemblies from this state (official two letter code only)
3517
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
3555
3518
  :type filter_usa_state: str
3556
- :param filter_complete_only: only include complete genomes.
3519
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
3557
3520
  :type filter_complete_only: bool
3558
- :param table_fields: Specify which fields to include in the tabular report
3521
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
3559
3522
  :type table_fields: List[str]
3560
3523
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
3561
3524
  :type page_size: int
3562
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3525
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3563
3526
  :type page_token: str
3564
3527
  :param _request_timeout: timeout setting for this request. If one
3565
3528
  number provided, it will be total request
@@ -3621,18 +3584,18 @@ class VirusApi:
3621
3584
  def virus_annotation_reports_by_taxon_without_preload_content(
3622
3585
  self,
3623
3586
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
3624
- filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
3625
- filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
3626
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
3627
- filter_updated_since: Optional[datetime] = None,
3628
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
3629
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
3630
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
3631
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
3632
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
3633
- table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
3587
+ filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit to RefSeq genomes.")] = None,
3588
+ filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit to annotated genomes.")] = None,
3589
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
3590
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
3591
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
3592
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
3593
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specififed geographic location.")] = None,
3594
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
3595
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
3596
+ table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.")] = None,
3634
3597
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
3635
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3598
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
3636
3599
  _request_timeout: Union[
3637
3600
  None,
3638
3601
  Annotated[StrictFloat, Field(gt=0)],
@@ -3646,35 +3609,35 @@ class VirusApi:
3646
3609
  _headers: Optional[Dict[StrictStr, Any]] = None,
3647
3610
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3648
3611
  ) -> RESTResponseType:
3649
- """Get virus annotation report by taxon
3612
+ """Get a virus annotation report by taxon
3650
3613
 
3651
- Get virus annotation report by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
3614
+ Get virus annotation report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
3652
3615
 
3653
3616
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
3654
3617
  :type taxon: str
3655
- :param filter_refseq_only: If true, limit results to RefSeq genomes.
3618
+ :param filter_refseq_only: If true, limit to RefSeq genomes.
3656
3619
  :type filter_refseq_only: bool
3657
- :param filter_annotated_only: If true, limit results to annotated genomes.
3620
+ :param filter_annotated_only: If true, limit to annotated genomes.
3658
3621
  :type filter_annotated_only: bool
3659
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
3622
+ :param filter_released_since: Limit to genomes released on or after the specified date.
3660
3623
  :type filter_released_since: datetime
3661
- :param filter_updated_since:
3624
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
3662
3625
  :type filter_updated_since: datetime
3663
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
3626
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
3664
3627
  :type filter_host: str
3665
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
3628
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
3666
3629
  :type filter_pangolin_classification: str
3667
- :param filter_geo_location: Assemblies from this location (country or continent)
3630
+ :param filter_geo_location: Limit to genomes collected from the specififed geographic location.
3668
3631
  :type filter_geo_location: str
3669
- :param filter_usa_state: Assemblies from this state (official two letter code only)
3632
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
3670
3633
  :type filter_usa_state: str
3671
- :param filter_complete_only: only include complete genomes.
3634
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
3672
3635
  :type filter_complete_only: bool
3673
- :param table_fields: Specify which fields to include in the tabular report
3636
+ :param table_fields: Specify which fields to include in the tabular report. Additional fields are described here: [virus annotation report fields](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/using-dataformat/virus-data-reports/#virus-annotation-report-fields). Use of this parameter requires the HTTP header, `accept: text/tab-separated-values`.
3674
3637
  :type table_fields: List[str]
3675
3638
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
3676
3639
  :type page_size: int
3677
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3640
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
3678
3641
  :type page_token: str
3679
3642
  :param _request_timeout: timeout setting for this request. If one
3680
3643
  number provided, it will be total request
@@ -3878,18 +3841,17 @@ class VirusApi:
3878
3841
  def virus_genome_download(
3879
3842
  self,
3880
3843
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
3881
- taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
3882
3844
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
3883
3845
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
3884
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
3885
- updated_since: Optional[datetime] = None,
3886
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
3887
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
3888
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
3889
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
3890
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
3891
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
3892
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
3846
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
3847
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
3848
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
3849
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
3850
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
3851
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
3852
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
3853
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
3854
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
3893
3855
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
3894
3856
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
3895
3857
  _request_timeout: Union[
@@ -3905,35 +3867,33 @@ class VirusApi:
3905
3867
  _headers: Optional[Dict[StrictStr, Any]] = None,
3906
3868
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
3907
3869
  ) -> bytearray:
3908
- """Download a virus genome dataset by taxon
3870
+ """Get a virus genome data package by taxon
3909
3871
 
3910
- Download a virus genome dataset by taxon
3872
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
3911
3873
 
3912
3874
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
3913
3875
  :type taxon: str
3914
- :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
3915
- :type taxons: List[str]
3916
3876
  :param refseq_only: If true, limit results to RefSeq genomes.
3917
3877
  :type refseq_only: bool
3918
3878
  :param annotated_only: If true, limit results to annotated genomes.
3919
3879
  :type annotated_only: bool
3920
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
3880
+ :param released_since: Limit to genomes released on or after the specified date.
3921
3881
  :type released_since: datetime
3922
- :param updated_since:
3882
+ :param updated_since: Limit to genomes updated on or after the specified date.
3923
3883
  :type updated_since: datetime
3924
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
3884
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
3925
3885
  :type host: str
3926
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
3886
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
3927
3887
  :type pangolin_classification: str
3928
- :param geo_location: Assemblies from this location (country or continent)
3888
+ :param geo_location: Limit to genomes collected from the specified geographic location.
3929
3889
  :type geo_location: str
3930
- :param usa_state: Assemblies from this state (official two letter code only)
3890
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
3931
3891
  :type usa_state: str
3932
- :param complete_only: only include complete genomes.
3892
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
3933
3893
  :type complete_only: bool
3934
- :param include_sequence: specify which sequence files to include in the download
3894
+ :param include_sequence: Specify which sequence files to include in the data package.
3935
3895
  :type include_sequence: List[V2ViralSequenceType]
3936
- :param aux_report: list additional reports to include with download. Data report is included by default.
3896
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
3937
3897
  :type aux_report: List[V2VirusDatasetReportType]
3938
3898
  :param use_psg: Experimental approach to retrieving sequence data.
3939
3899
  :type use_psg: bool
@@ -3963,7 +3923,6 @@ class VirusApi:
3963
3923
 
3964
3924
  _param = self._virus_genome_download_serialize(
3965
3925
  taxon=taxon,
3966
- taxons=taxons,
3967
3926
  refseq_only=refseq_only,
3968
3927
  annotated_only=annotated_only,
3969
3928
  released_since=released_since,
@@ -4001,18 +3960,17 @@ class VirusApi:
4001
3960
  def virus_genome_download_with_http_info(
4002
3961
  self,
4003
3962
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
4004
- taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
4005
3963
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
4006
3964
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
4007
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
4008
- updated_since: Optional[datetime] = None,
4009
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
4010
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
4011
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
4012
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
4013
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
4014
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
4015
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
3965
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
3966
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
3967
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
3968
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
3969
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
3970
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
3971
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
3972
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
3973
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
4016
3974
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
4017
3975
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
4018
3976
  _request_timeout: Union[
@@ -4028,35 +3986,33 @@ class VirusApi:
4028
3986
  _headers: Optional[Dict[StrictStr, Any]] = None,
4029
3987
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4030
3988
  ) -> ApiResponse[bytearray]:
4031
- """Download a virus genome dataset by taxon
3989
+ """Get a virus genome data package by taxon
4032
3990
 
4033
- Download a virus genome dataset by taxon
3991
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
4034
3992
 
4035
3993
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
4036
3994
  :type taxon: str
4037
- :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
4038
- :type taxons: List[str]
4039
3995
  :param refseq_only: If true, limit results to RefSeq genomes.
4040
3996
  :type refseq_only: bool
4041
3997
  :param annotated_only: If true, limit results to annotated genomes.
4042
3998
  :type annotated_only: bool
4043
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
3999
+ :param released_since: Limit to genomes released on or after the specified date.
4044
4000
  :type released_since: datetime
4045
- :param updated_since:
4001
+ :param updated_since: Limit to genomes updated on or after the specified date.
4046
4002
  :type updated_since: datetime
4047
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
4003
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
4048
4004
  :type host: str
4049
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
4005
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
4050
4006
  :type pangolin_classification: str
4051
- :param geo_location: Assemblies from this location (country or continent)
4007
+ :param geo_location: Limit to genomes collected from the specified geographic location.
4052
4008
  :type geo_location: str
4053
- :param usa_state: Assemblies from this state (official two letter code only)
4009
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
4054
4010
  :type usa_state: str
4055
- :param complete_only: only include complete genomes.
4011
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
4056
4012
  :type complete_only: bool
4057
- :param include_sequence: specify which sequence files to include in the download
4013
+ :param include_sequence: Specify which sequence files to include in the data package.
4058
4014
  :type include_sequence: List[V2ViralSequenceType]
4059
- :param aux_report: list additional reports to include with download. Data report is included by default.
4015
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
4060
4016
  :type aux_report: List[V2VirusDatasetReportType]
4061
4017
  :param use_psg: Experimental approach to retrieving sequence data.
4062
4018
  :type use_psg: bool
@@ -4086,7 +4042,6 @@ class VirusApi:
4086
4042
 
4087
4043
  _param = self._virus_genome_download_serialize(
4088
4044
  taxon=taxon,
4089
- taxons=taxons,
4090
4045
  refseq_only=refseq_only,
4091
4046
  annotated_only=annotated_only,
4092
4047
  released_since=released_since,
@@ -4124,18 +4079,17 @@ class VirusApi:
4124
4079
  def virus_genome_download_without_preload_content(
4125
4080
  self,
4126
4081
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
4127
- taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
4128
4082
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
4129
4083
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
4130
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
4131
- updated_since: Optional[datetime] = None,
4132
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
4133
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
4134
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
4135
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
4136
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
4137
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
4138
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
4084
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
4085
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
4086
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
4087
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
4088
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
4089
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
4090
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
4091
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
4092
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
4139
4093
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
4140
4094
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
4141
4095
  _request_timeout: Union[
@@ -4151,35 +4105,33 @@ class VirusApi:
4151
4105
  _headers: Optional[Dict[StrictStr, Any]] = None,
4152
4106
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4153
4107
  ) -> RESTResponseType:
4154
- """Download a virus genome dataset by taxon
4108
+ """Get a virus genome data package by taxon
4155
4109
 
4156
- Download a virus genome dataset by taxon
4110
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.
4157
4111
 
4158
4112
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
4159
4113
  :type taxon: str
4160
- :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
4161
- :type taxons: List[str]
4162
4114
  :param refseq_only: If true, limit results to RefSeq genomes.
4163
4115
  :type refseq_only: bool
4164
4116
  :param annotated_only: If true, limit results to annotated genomes.
4165
4117
  :type annotated_only: bool
4166
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
4118
+ :param released_since: Limit to genomes released on or after the specified date.
4167
4119
  :type released_since: datetime
4168
- :param updated_since:
4120
+ :param updated_since: Limit to genomes updated on or after the specified date.
4169
4121
  :type updated_since: datetime
4170
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
4122
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
4171
4123
  :type host: str
4172
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
4124
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
4173
4125
  :type pangolin_classification: str
4174
- :param geo_location: Assemblies from this location (country or continent)
4126
+ :param geo_location: Limit to genomes collected from the specified geographic location.
4175
4127
  :type geo_location: str
4176
- :param usa_state: Assemblies from this state (official two letter code only)
4128
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
4177
4129
  :type usa_state: str
4178
- :param complete_only: only include complete genomes.
4130
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
4179
4131
  :type complete_only: bool
4180
- :param include_sequence: specify which sequence files to include in the download
4132
+ :param include_sequence: Specify which sequence files to include in the data package.
4181
4133
  :type include_sequence: List[V2ViralSequenceType]
4182
- :param aux_report: list additional reports to include with download. Data report is included by default.
4134
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
4183
4135
  :type aux_report: List[V2VirusDatasetReportType]
4184
4136
  :param use_psg: Experimental approach to retrieving sequence data.
4185
4137
  :type use_psg: bool
@@ -4209,7 +4161,6 @@ class VirusApi:
4209
4161
 
4210
4162
  _param = self._virus_genome_download_serialize(
4211
4163
  taxon=taxon,
4212
- taxons=taxons,
4213
4164
  refseq_only=refseq_only,
4214
4165
  annotated_only=annotated_only,
4215
4166
  released_since=released_since,
@@ -4242,7 +4193,6 @@ class VirusApi:
4242
4193
  def _virus_genome_download_serialize(
4243
4194
  self,
4244
4195
  taxon,
4245
- taxons,
4246
4196
  refseq_only,
4247
4197
  annotated_only,
4248
4198
  released_since,
@@ -4265,7 +4215,6 @@ class VirusApi:
4265
4215
  _host = None
4266
4216
 
4267
4217
  _collection_formats: Dict[str, str] = {
4268
- 'taxons': 'multi',
4269
4218
  'include_sequence': 'multi',
4270
4219
  'aux_report': 'multi',
4271
4220
  }
@@ -4283,10 +4232,6 @@ class VirusApi:
4283
4232
  if taxon is not None:
4284
4233
  _path_params['taxon'] = taxon
4285
4234
  # process the query parameters
4286
- if taxons is not None:
4287
-
4288
- _query_params.append(('taxons', taxons))
4289
-
4290
4235
  if refseq_only is not None:
4291
4236
 
4292
4237
  _query_params.append(('refseq_only', refseq_only))
@@ -4398,19 +4343,19 @@ class VirusApi:
4398
4343
  @validate_call
4399
4344
  def virus_genome_download_accession(
4400
4345
  self,
4401
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
4346
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
4402
4347
  taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
4403
4348
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
4404
4349
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
4405
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
4406
- updated_since: Optional[datetime] = None,
4407
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
4408
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
4409
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
4410
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
4411
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
4412
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
4413
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
4350
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
4351
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
4352
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
4353
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
4354
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
4355
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
4356
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
4357
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
4358
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
4414
4359
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
4415
4360
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
4416
4361
  _request_timeout: Union[
@@ -4426,11 +4371,11 @@ class VirusApi:
4426
4371
  _headers: Optional[Dict[StrictStr, Any]] = None,
4427
4372
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4428
4373
  ) -> bytearray:
4429
- """Download a virus genome dataset by accession
4374
+ """Get a virus genome data package by nucleotide accession
4430
4375
 
4431
- Download a virus genome dataset by accession
4376
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
4432
4377
 
4433
- :param accessions: genome sequence accessions (required)
4378
+ :param accessions: One or more nucleotide sequence accessions (required)
4434
4379
  :type accessions: List[str]
4435
4380
  :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
4436
4381
  :type taxons: List[str]
@@ -4438,23 +4383,23 @@ class VirusApi:
4438
4383
  :type refseq_only: bool
4439
4384
  :param annotated_only: If true, limit results to annotated genomes.
4440
4385
  :type annotated_only: bool
4441
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
4386
+ :param released_since: Limit to genomes released on or after the specified date.
4442
4387
  :type released_since: datetime
4443
- :param updated_since:
4388
+ :param updated_since: Limit to genomes updated on or after the specified date.
4444
4389
  :type updated_since: datetime
4445
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
4390
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
4446
4391
  :type host: str
4447
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
4392
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
4448
4393
  :type pangolin_classification: str
4449
- :param geo_location: Assemblies from this location (country or continent)
4394
+ :param geo_location: Limit to genomes collected from the specified geographic location.
4450
4395
  :type geo_location: str
4451
- :param usa_state: Assemblies from this state (official two letter code only)
4396
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
4452
4397
  :type usa_state: str
4453
- :param complete_only: only include complete genomes.
4398
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
4454
4399
  :type complete_only: bool
4455
- :param include_sequence: specify which sequence files to include in the download
4400
+ :param include_sequence: Specify which sequence files to include in the data package.
4456
4401
  :type include_sequence: List[V2ViralSequenceType]
4457
- :param aux_report: list additional reports to include with download. Data report is included by default.
4402
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
4458
4403
  :type aux_report: List[V2VirusDatasetReportType]
4459
4404
  :param use_psg: Experimental approach to retrieving sequence data.
4460
4405
  :type use_psg: bool
@@ -4521,19 +4466,19 @@ class VirusApi:
4521
4466
  @validate_call
4522
4467
  def virus_genome_download_accession_with_http_info(
4523
4468
  self,
4524
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
4469
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
4525
4470
  taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
4526
4471
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
4527
4472
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
4528
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
4529
- updated_since: Optional[datetime] = None,
4530
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
4531
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
4532
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
4533
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
4534
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
4535
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
4536
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
4473
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
4474
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
4475
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
4476
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
4477
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
4478
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
4479
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
4480
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
4481
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
4537
4482
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
4538
4483
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
4539
4484
  _request_timeout: Union[
@@ -4549,11 +4494,11 @@ class VirusApi:
4549
4494
  _headers: Optional[Dict[StrictStr, Any]] = None,
4550
4495
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4551
4496
  ) -> ApiResponse[bytearray]:
4552
- """Download a virus genome dataset by accession
4497
+ """Get a virus genome data package by nucleotide accession
4553
4498
 
4554
- Download a virus genome dataset by accession
4499
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
4555
4500
 
4556
- :param accessions: genome sequence accessions (required)
4501
+ :param accessions: One or more nucleotide sequence accessions (required)
4557
4502
  :type accessions: List[str]
4558
4503
  :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
4559
4504
  :type taxons: List[str]
@@ -4561,23 +4506,23 @@ class VirusApi:
4561
4506
  :type refseq_only: bool
4562
4507
  :param annotated_only: If true, limit results to annotated genomes.
4563
4508
  :type annotated_only: bool
4564
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
4509
+ :param released_since: Limit to genomes released on or after the specified date.
4565
4510
  :type released_since: datetime
4566
- :param updated_since:
4511
+ :param updated_since: Limit to genomes updated on or after the specified date.
4567
4512
  :type updated_since: datetime
4568
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
4513
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
4569
4514
  :type host: str
4570
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
4515
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
4571
4516
  :type pangolin_classification: str
4572
- :param geo_location: Assemblies from this location (country or continent)
4517
+ :param geo_location: Limit to genomes collected from the specified geographic location.
4573
4518
  :type geo_location: str
4574
- :param usa_state: Assemblies from this state (official two letter code only)
4519
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
4575
4520
  :type usa_state: str
4576
- :param complete_only: only include complete genomes.
4521
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
4577
4522
  :type complete_only: bool
4578
- :param include_sequence: specify which sequence files to include in the download
4523
+ :param include_sequence: Specify which sequence files to include in the data package.
4579
4524
  :type include_sequence: List[V2ViralSequenceType]
4580
- :param aux_report: list additional reports to include with download. Data report is included by default.
4525
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
4581
4526
  :type aux_report: List[V2VirusDatasetReportType]
4582
4527
  :param use_psg: Experimental approach to retrieving sequence data.
4583
4528
  :type use_psg: bool
@@ -4644,19 +4589,19 @@ class VirusApi:
4644
4589
  @validate_call
4645
4590
  def virus_genome_download_accession_without_preload_content(
4646
4591
  self,
4647
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
4592
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
4648
4593
  taxons: Annotated[Optional[List[StrictStr]], Field(description="NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank")] = None,
4649
4594
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
4650
4595
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
4651
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
4652
- updated_since: Optional[datetime] = None,
4653
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
4654
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
4655
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
4656
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
4657
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
4658
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
4659
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
4596
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
4597
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
4598
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
4599
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
4600
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
4601
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
4602
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
4603
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
4604
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
4660
4605
  use_psg: Annotated[Optional[StrictBool], Field(description="Experimental approach to retrieving sequence data.")] = None,
4661
4606
  filename: Annotated[Optional[StrictStr], Field(description="Output file name.")] = None,
4662
4607
  _request_timeout: Union[
@@ -4672,11 +4617,11 @@ class VirusApi:
4672
4617
  _headers: Optional[Dict[StrictStr, Any]] = None,
4673
4618
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4674
4619
  ) -> RESTResponseType:
4675
- """Download a virus genome dataset by accession
4620
+ """Get a virus genome data package by nucleotide accession
4676
4621
 
4677
- Download a virus genome dataset by accession
4622
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
4678
4623
 
4679
- :param accessions: genome sequence accessions (required)
4624
+ :param accessions: One or more nucleotide sequence accessions (required)
4680
4625
  :type accessions: List[str]
4681
4626
  :param taxons: NCBI Taxonomy IDs or names (common or scientific) at any taxonomic rank
4682
4627
  :type taxons: List[str]
@@ -4684,23 +4629,23 @@ class VirusApi:
4684
4629
  :type refseq_only: bool
4685
4630
  :param annotated_only: If true, limit results to annotated genomes.
4686
4631
  :type annotated_only: bool
4687
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
4632
+ :param released_since: Limit to genomes released on or after the specified date.
4688
4633
  :type released_since: datetime
4689
- :param updated_since:
4634
+ :param updated_since: Limit to genomes updated on or after the specified date.
4690
4635
  :type updated_since: datetime
4691
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
4636
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
4692
4637
  :type host: str
4693
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
4638
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
4694
4639
  :type pangolin_classification: str
4695
- :param geo_location: Assemblies from this location (country or continent)
4640
+ :param geo_location: Limit to genomes collected from the specified geographic location.
4696
4641
  :type geo_location: str
4697
- :param usa_state: Assemblies from this state (official two letter code only)
4642
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
4698
4643
  :type usa_state: str
4699
- :param complete_only: only include complete genomes.
4644
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
4700
4645
  :type complete_only: bool
4701
- :param include_sequence: specify which sequence files to include in the download
4646
+ :param include_sequence: Specify which sequence files to include in the data package.
4702
4647
  :type include_sequence: List[V2ViralSequenceType]
4703
- :param aux_report: list additional reports to include with download. Data report is included by default.
4648
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
4704
4649
  :type aux_report: List[V2VirusDatasetReportType]
4705
4650
  :param use_psg: Experimental approach to retrieving sequence data.
4706
4651
  :type use_psg: bool
@@ -4935,9 +4880,9 @@ class VirusApi:
4935
4880
  _headers: Optional[Dict[StrictStr, Any]] = None,
4936
4881
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
4937
4882
  ) -> bytearray:
4938
- """Get a virus genome dataset by post
4883
+ """Get a virus genome data package
4939
4884
 
4940
- The 'GET' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request.
4885
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
4941
4886
 
4942
4887
  :param v2_virus_dataset_request: (required)
4943
4888
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5006,9 +4951,9 @@ class VirusApi:
5006
4951
  _headers: Optional[Dict[StrictStr, Any]] = None,
5007
4952
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5008
4953
  ) -> ApiResponse[bytearray]:
5009
- """Get a virus genome dataset by post
4954
+ """Get a virus genome data package
5010
4955
 
5011
- The 'GET' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request.
4956
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
5012
4957
 
5013
4958
  :param v2_virus_dataset_request: (required)
5014
4959
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5077,9 +5022,9 @@ class VirusApi:
5077
5022
  _headers: Optional[Dict[StrictStr, Any]] = None,
5078
5023
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5079
5024
  ) -> RESTResponseType:
5080
- """Get a virus genome dataset by post
5025
+ """Get a virus genome data package
5081
5026
 
5082
- The 'GET' version of download is limited by the size of the GET URL (2KB, which works out to about 140 genomic accessions). The POST operation is provided to allow users to supply a larger number of accessions in a single request.
5027
+ Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by nucleotide accession.
5083
5028
 
5084
5029
  :param v2_virus_dataset_request: (required)
5085
5030
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5213,18 +5158,18 @@ class VirusApi:
5213
5158
  def virus_genome_summary(
5214
5159
  self,
5215
5160
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
5216
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
5161
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
5217
5162
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
5218
5163
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
5219
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
5220
- updated_since: Optional[datetime] = None,
5221
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
5222
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
5223
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
5224
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
5225
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
5226
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
5227
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
5164
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
5165
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
5166
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
5167
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
5168
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
5169
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
5170
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
5171
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
5172
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
5228
5173
  _request_timeout: Union[
5229
5174
  None,
5230
5175
  Annotated[StrictFloat, Field(gt=0)],
@@ -5238,35 +5183,35 @@ class VirusApi:
5238
5183
  _headers: Optional[Dict[StrictStr, Any]] = None,
5239
5184
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5240
5185
  ) -> V2DownloadSummary:
5241
- """Get summary data for virus genomes by taxon
5186
+ """Get a download summary of a virus genome data package by taxon
5242
5187
 
5243
- Get summary data and download by command line instructions for virus genomes by taxon.
5188
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5244
5189
 
5245
5190
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
5246
5191
  :type taxon: str
5247
- :param accessions: genome sequence accessions
5192
+ :param accessions: One or more nucleotide sequence accessions
5248
5193
  :type accessions: List[str]
5249
5194
  :param refseq_only: If true, limit results to RefSeq genomes.
5250
5195
  :type refseq_only: bool
5251
5196
  :param annotated_only: If true, limit results to annotated genomes.
5252
5197
  :type annotated_only: bool
5253
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
5198
+ :param released_since: Limit to genomes released on or after the specified date.
5254
5199
  :type released_since: datetime
5255
- :param updated_since:
5200
+ :param updated_since: Limit to genomes updated on or after the specified date.
5256
5201
  :type updated_since: datetime
5257
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
5202
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
5258
5203
  :type host: str
5259
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
5204
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
5260
5205
  :type pangolin_classification: str
5261
- :param geo_location: Assemblies from this location (country or continent)
5206
+ :param geo_location: Limit to genomes collected from the specified geographic location.
5262
5207
  :type geo_location: str
5263
- :param usa_state: Assemblies from this state (official two letter code only)
5208
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
5264
5209
  :type usa_state: str
5265
- :param complete_only: only include complete genomes.
5210
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
5266
5211
  :type complete_only: bool
5267
- :param include_sequence: specify which sequence files to include in the download
5212
+ :param include_sequence: Specify which sequence files to include in the data package.
5268
5213
  :type include_sequence: List[V2ViralSequenceType]
5269
- :param aux_report: list additional reports to include with download. Data report is included by default.
5214
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
5270
5215
  :type aux_report: List[V2VirusDatasetReportType]
5271
5216
  :param _request_timeout: timeout setting for this request. If one
5272
5217
  number provided, it will be total request
@@ -5328,18 +5273,18 @@ class VirusApi:
5328
5273
  def virus_genome_summary_with_http_info(
5329
5274
  self,
5330
5275
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
5331
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
5276
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
5332
5277
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
5333
5278
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
5334
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
5335
- updated_since: Optional[datetime] = None,
5336
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
5337
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
5338
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
5339
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
5340
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
5341
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
5342
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
5279
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
5280
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
5281
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
5282
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
5283
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
5284
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
5285
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
5286
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
5287
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
5343
5288
  _request_timeout: Union[
5344
5289
  None,
5345
5290
  Annotated[StrictFloat, Field(gt=0)],
@@ -5353,35 +5298,35 @@ class VirusApi:
5353
5298
  _headers: Optional[Dict[StrictStr, Any]] = None,
5354
5299
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5355
5300
  ) -> ApiResponse[V2DownloadSummary]:
5356
- """Get summary data for virus genomes by taxon
5301
+ """Get a download summary of a virus genome data package by taxon
5357
5302
 
5358
- Get summary data and download by command line instructions for virus genomes by taxon.
5303
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5359
5304
 
5360
5305
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
5361
5306
  :type taxon: str
5362
- :param accessions: genome sequence accessions
5307
+ :param accessions: One or more nucleotide sequence accessions
5363
5308
  :type accessions: List[str]
5364
5309
  :param refseq_only: If true, limit results to RefSeq genomes.
5365
5310
  :type refseq_only: bool
5366
5311
  :param annotated_only: If true, limit results to annotated genomes.
5367
5312
  :type annotated_only: bool
5368
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
5313
+ :param released_since: Limit to genomes released on or after the specified date.
5369
5314
  :type released_since: datetime
5370
- :param updated_since:
5315
+ :param updated_since: Limit to genomes updated on or after the specified date.
5371
5316
  :type updated_since: datetime
5372
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
5317
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
5373
5318
  :type host: str
5374
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
5319
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
5375
5320
  :type pangolin_classification: str
5376
- :param geo_location: Assemblies from this location (country or continent)
5321
+ :param geo_location: Limit to genomes collected from the specified geographic location.
5377
5322
  :type geo_location: str
5378
- :param usa_state: Assemblies from this state (official two letter code only)
5323
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
5379
5324
  :type usa_state: str
5380
- :param complete_only: only include complete genomes.
5325
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
5381
5326
  :type complete_only: bool
5382
- :param include_sequence: specify which sequence files to include in the download
5327
+ :param include_sequence: Specify which sequence files to include in the data package.
5383
5328
  :type include_sequence: List[V2ViralSequenceType]
5384
- :param aux_report: list additional reports to include with download. Data report is included by default.
5329
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
5385
5330
  :type aux_report: List[V2VirusDatasetReportType]
5386
5331
  :param _request_timeout: timeout setting for this request. If one
5387
5332
  number provided, it will be total request
@@ -5443,18 +5388,18 @@ class VirusApi:
5443
5388
  def virus_genome_summary_without_preload_content(
5444
5389
  self,
5445
5390
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
5446
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
5391
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
5447
5392
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
5448
5393
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
5449
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
5450
- updated_since: Optional[datetime] = None,
5451
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
5452
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
5453
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
5454
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
5455
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
5456
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
5457
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
5394
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
5395
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
5396
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
5397
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
5398
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
5399
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
5400
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
5401
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
5402
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
5458
5403
  _request_timeout: Union[
5459
5404
  None,
5460
5405
  Annotated[StrictFloat, Field(gt=0)],
@@ -5468,35 +5413,35 @@ class VirusApi:
5468
5413
  _headers: Optional[Dict[StrictStr, Any]] = None,
5469
5414
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5470
5415
  ) -> RESTResponseType:
5471
- """Get summary data for virus genomes by taxon
5416
+ """Get a download summary of a virus genome data package by taxon
5472
5417
 
5473
- Get summary data and download by command line instructions for virus genomes by taxon.
5418
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5474
5419
 
5475
5420
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
5476
5421
  :type taxon: str
5477
- :param accessions: genome sequence accessions
5422
+ :param accessions: One or more nucleotide sequence accessions
5478
5423
  :type accessions: List[str]
5479
5424
  :param refseq_only: If true, limit results to RefSeq genomes.
5480
5425
  :type refseq_only: bool
5481
5426
  :param annotated_only: If true, limit results to annotated genomes.
5482
5427
  :type annotated_only: bool
5483
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
5428
+ :param released_since: Limit to genomes released on or after the specified date.
5484
5429
  :type released_since: datetime
5485
- :param updated_since:
5430
+ :param updated_since: Limit to genomes updated on or after the specified date.
5486
5431
  :type updated_since: datetime
5487
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
5432
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
5488
5433
  :type host: str
5489
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
5434
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
5490
5435
  :type pangolin_classification: str
5491
- :param geo_location: Assemblies from this location (country or continent)
5436
+ :param geo_location: Limit to genomes collected from the specified geographic location.
5492
5437
  :type geo_location: str
5493
- :param usa_state: Assemblies from this state (official two letter code only)
5438
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
5494
5439
  :type usa_state: str
5495
- :param complete_only: only include complete genomes.
5440
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
5496
5441
  :type complete_only: bool
5497
- :param include_sequence: specify which sequence files to include in the download
5442
+ :param include_sequence: Specify which sequence files to include in the data package.
5498
5443
  :type include_sequence: List[V2ViralSequenceType]
5499
- :param aux_report: list additional reports to include with download. Data report is included by default.
5444
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
5500
5445
  :type aux_report: List[V2VirusDatasetReportType]
5501
5446
  :param _request_timeout: timeout setting for this request. If one
5502
5447
  number provided, it will be total request
@@ -5713,9 +5658,9 @@ class VirusApi:
5713
5658
  _headers: Optional[Dict[StrictStr, Any]] = None,
5714
5659
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5715
5660
  ) -> V2DownloadSummary:
5716
- """Get summary data for virus genomes by post
5661
+ """Get a download summary of a virus genome data package
5717
5662
 
5718
- Get summary data and download by command line instructions for virus genomes by taxon.
5663
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5719
5664
 
5720
5665
  :param v2_virus_dataset_request: (required)
5721
5666
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5780,9 +5725,9 @@ class VirusApi:
5780
5725
  _headers: Optional[Dict[StrictStr, Any]] = None,
5781
5726
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5782
5727
  ) -> ApiResponse[V2DownloadSummary]:
5783
- """Get summary data for virus genomes by post
5728
+ """Get a download summary of a virus genome data package
5784
5729
 
5785
- Get summary data and download by command line instructions for virus genomes by taxon.
5730
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5786
5731
 
5787
5732
  :param v2_virus_dataset_request: (required)
5788
5733
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5847,9 +5792,9 @@ class VirusApi:
5847
5792
  _headers: Optional[Dict[StrictStr, Any]] = None,
5848
5793
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
5849
5794
  ) -> RESTResponseType:
5850
- """Get summary data for virus genomes by post
5795
+ """Get a download summary of a virus genome data package
5851
5796
 
5852
- Get summary data and download by command line instructions for virus genomes by taxon.
5797
+ Get a download summary of a virus genome data package, including counts and file sizes, in JSON format.
5853
5798
 
5854
5799
  :param v2_virus_dataset_request: (required)
5855
5800
  :type v2_virus_dataset_request: V2VirusDatasetRequest
@@ -5975,19 +5920,19 @@ class VirusApi:
5975
5920
  def virus_genome_table(
5976
5921
  self,
5977
5922
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
5978
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
5923
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
5979
5924
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
5980
5925
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
5981
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
5982
- updated_since: Optional[datetime] = None,
5983
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
5984
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
5985
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
5986
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
5987
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
5926
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
5927
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
5928
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
5929
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
5930
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
5931
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
5932
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
5988
5933
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
5989
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
5990
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
5934
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
5935
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
5991
5936
  format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
5992
5937
  _request_timeout: Union[
5993
5938
  None,
@@ -6002,37 +5947,37 @@ class VirusApi:
6002
5947
  _headers: Optional[Dict[StrictStr, Any]] = None,
6003
5948
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6004
5949
  ) -> V2TabularOutput:
6005
- """(Deprecated) Get virus genome metadata in a tabular format.
5950
+ """Get virus genome metadata in a tabular format (deprecated)
6006
5951
 
6007
5952
  Get virus genome metadata in tabular format for virus genomes by taxon.
6008
5953
 
6009
5954
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
6010
5955
  :type taxon: str
6011
- :param accessions: genome sequence accessions
5956
+ :param accessions: One or more nucleotide sequence accessions
6012
5957
  :type accessions: List[str]
6013
5958
  :param refseq_only: If true, limit results to RefSeq genomes.
6014
5959
  :type refseq_only: bool
6015
5960
  :param annotated_only: If true, limit results to annotated genomes.
6016
5961
  :type annotated_only: bool
6017
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
5962
+ :param released_since: Limit to genomes released on or after the specified date.
6018
5963
  :type released_since: datetime
6019
- :param updated_since:
5964
+ :param updated_since: Limit to genomes updated on or after the specified date.
6020
5965
  :type updated_since: datetime
6021
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
5966
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6022
5967
  :type host: str
6023
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
5968
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6024
5969
  :type pangolin_classification: str
6025
- :param geo_location: Assemblies from this location (country or continent)
5970
+ :param geo_location: Limit to genomes collected from the specified geographic location.
6026
5971
  :type geo_location: str
6027
- :param usa_state: Assemblies from this state (official two letter code only)
5972
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6028
5973
  :type usa_state: str
6029
- :param complete_only: only include complete genomes.
5974
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
6030
5975
  :type complete_only: bool
6031
5976
  :param table_fields: Specify which fields to include in the tabular report
6032
5977
  :type table_fields: List[V2VirusTableField]
6033
- :param include_sequence: specify which sequence files to include in the download
5978
+ :param include_sequence: Specify which sequence files to include in the data package.
6034
5979
  :type include_sequence: List[V2ViralSequenceType]
6035
- :param aux_report: list additional reports to include with download. Data report is included by default.
5980
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
6036
5981
  :type aux_report: List[V2VirusDatasetReportType]
6037
5982
  :param format: Choose download format (tsv, csv or jsonl)
6038
5983
  :type format: V2TableFormat
@@ -6057,7 +6002,6 @@ class VirusApi:
6057
6002
  :type _host_index: int, optional
6058
6003
  :return: Returns the result object.
6059
6004
  """ # noqa: E501
6060
- warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
6061
6005
 
6062
6006
  _param = self._virus_genome_table_serialize(
6063
6007
  taxon=taxon,
@@ -6099,19 +6043,19 @@ class VirusApi:
6099
6043
  def virus_genome_table_with_http_info(
6100
6044
  self,
6101
6045
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
6102
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
6046
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
6103
6047
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
6104
6048
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
6105
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
6106
- updated_since: Optional[datetime] = None,
6107
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
6108
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
6109
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
6110
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
6111
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
6049
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
6050
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
6051
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
6052
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
6053
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
6054
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
6055
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
6112
6056
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
6113
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
6114
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
6057
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
6058
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
6115
6059
  format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
6116
6060
  _request_timeout: Union[
6117
6061
  None,
@@ -6126,37 +6070,37 @@ class VirusApi:
6126
6070
  _headers: Optional[Dict[StrictStr, Any]] = None,
6127
6071
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6128
6072
  ) -> ApiResponse[V2TabularOutput]:
6129
- """(Deprecated) Get virus genome metadata in a tabular format.
6073
+ """Get virus genome metadata in a tabular format (deprecated)
6130
6074
 
6131
6075
  Get virus genome metadata in tabular format for virus genomes by taxon.
6132
6076
 
6133
6077
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
6134
6078
  :type taxon: str
6135
- :param accessions: genome sequence accessions
6079
+ :param accessions: One or more nucleotide sequence accessions
6136
6080
  :type accessions: List[str]
6137
6081
  :param refseq_only: If true, limit results to RefSeq genomes.
6138
6082
  :type refseq_only: bool
6139
6083
  :param annotated_only: If true, limit results to annotated genomes.
6140
6084
  :type annotated_only: bool
6141
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
6085
+ :param released_since: Limit to genomes released on or after the specified date.
6142
6086
  :type released_since: datetime
6143
- :param updated_since:
6087
+ :param updated_since: Limit to genomes updated on or after the specified date.
6144
6088
  :type updated_since: datetime
6145
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
6089
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6146
6090
  :type host: str
6147
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
6091
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6148
6092
  :type pangolin_classification: str
6149
- :param geo_location: Assemblies from this location (country or continent)
6093
+ :param geo_location: Limit to genomes collected from the specified geographic location.
6150
6094
  :type geo_location: str
6151
- :param usa_state: Assemblies from this state (official two letter code only)
6095
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6152
6096
  :type usa_state: str
6153
- :param complete_only: only include complete genomes.
6097
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
6154
6098
  :type complete_only: bool
6155
6099
  :param table_fields: Specify which fields to include in the tabular report
6156
6100
  :type table_fields: List[V2VirusTableField]
6157
- :param include_sequence: specify which sequence files to include in the download
6101
+ :param include_sequence: Specify which sequence files to include in the data package.
6158
6102
  :type include_sequence: List[V2ViralSequenceType]
6159
- :param aux_report: list additional reports to include with download. Data report is included by default.
6103
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
6160
6104
  :type aux_report: List[V2VirusDatasetReportType]
6161
6105
  :param format: Choose download format (tsv, csv or jsonl)
6162
6106
  :type format: V2TableFormat
@@ -6181,7 +6125,6 @@ class VirusApi:
6181
6125
  :type _host_index: int, optional
6182
6126
  :return: Returns the result object.
6183
6127
  """ # noqa: E501
6184
- warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
6185
6128
 
6186
6129
  _param = self._virus_genome_table_serialize(
6187
6130
  taxon=taxon,
@@ -6223,19 +6166,19 @@ class VirusApi:
6223
6166
  def virus_genome_table_without_preload_content(
6224
6167
  self,
6225
6168
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
6226
- accessions: Annotated[Optional[List[StrictStr]], Field(description="genome sequence accessions")] = None,
6169
+ accessions: Annotated[Optional[List[StrictStr]], Field(description="One or more nucleotide sequence accessions")] = None,
6227
6170
  refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
6228
6171
  annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
6229
- released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
6230
- updated_since: Optional[datetime] = None,
6231
- host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
6232
- pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
6233
- geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
6234
- usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
6235
- complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
6172
+ released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
6173
+ updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
6174
+ host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
6175
+ pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
6176
+ geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
6177
+ usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
6178
+ complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
6236
6179
  table_fields: Annotated[Optional[List[V2VirusTableField]], Field(description="Specify which fields to include in the tabular report")] = None,
6237
- include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="specify which sequence files to include in the download")] = None,
6238
- aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="list additional reports to include with download. Data report is included by default.")] = None,
6180
+ include_sequence: Annotated[Optional[List[V2ViralSequenceType]], Field(description="Specify which sequence files to include in the data package.")] = None,
6181
+ aux_report: Annotated[Optional[List[V2VirusDatasetReportType]], Field(description="Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.")] = None,
6239
6182
  format: Annotated[Optional[V2TableFormat], Field(description="Choose download format (tsv, csv or jsonl)")] = None,
6240
6183
  _request_timeout: Union[
6241
6184
  None,
@@ -6250,37 +6193,37 @@ class VirusApi:
6250
6193
  _headers: Optional[Dict[StrictStr, Any]] = None,
6251
6194
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6252
6195
  ) -> RESTResponseType:
6253
- """(Deprecated) Get virus genome metadata in a tabular format.
6196
+ """Get virus genome metadata in a tabular format (deprecated)
6254
6197
 
6255
6198
  Get virus genome metadata in tabular format for virus genomes by taxon.
6256
6199
 
6257
6200
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
6258
6201
  :type taxon: str
6259
- :param accessions: genome sequence accessions
6202
+ :param accessions: One or more nucleotide sequence accessions
6260
6203
  :type accessions: List[str]
6261
6204
  :param refseq_only: If true, limit results to RefSeq genomes.
6262
6205
  :type refseq_only: bool
6263
6206
  :param annotated_only: If true, limit results to annotated genomes.
6264
6207
  :type annotated_only: bool
6265
- :param released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
6208
+ :param released_since: Limit to genomes released on or after the specified date.
6266
6209
  :type released_since: datetime
6267
- :param updated_since:
6210
+ :param updated_since: Limit to genomes updated on or after the specified date.
6268
6211
  :type updated_since: datetime
6269
- :param host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
6212
+ :param host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6270
6213
  :type host: str
6271
- :param pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
6214
+ :param pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6272
6215
  :type pangolin_classification: str
6273
- :param geo_location: Assemblies from this location (country or continent)
6216
+ :param geo_location: Limit to genomes collected from the specified geographic location.
6274
6217
  :type geo_location: str
6275
- :param usa_state: Assemblies from this state (official two letter code only)
6218
+ :param usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6276
6219
  :type usa_state: str
6277
- :param complete_only: only include complete genomes.
6220
+ :param complete_only: Limit to genomes designated as complete, as defined by the submitter.
6278
6221
  :type complete_only: bool
6279
6222
  :param table_fields: Specify which fields to include in the tabular report
6280
6223
  :type table_fields: List[V2VirusTableField]
6281
- :param include_sequence: specify which sequence files to include in the download
6224
+ :param include_sequence: Specify which sequence files to include in the data package.
6282
6225
  :type include_sequence: List[V2ViralSequenceType]
6283
- :param aux_report: list additional reports to include with download. Data report is included by default.
6226
+ :param aux_report: Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.
6284
6227
  :type aux_report: List[V2VirusDatasetReportType]
6285
6228
  :param format: Choose download format (tsv, csv or jsonl)
6286
6229
  :type format: V2TableFormat
@@ -6305,7 +6248,6 @@ class VirusApi:
6305
6248
  :type _host_index: int, optional
6306
6249
  :return: Returns the result object.
6307
6250
  """ # noqa: E501
6308
- warnings.warn("GET /virus/taxon/{taxon}/genome/table is deprecated.", DeprecationWarning)
6309
6251
 
6310
6252
  _param = self._virus_genome_table_serialize(
6311
6253
  taxon=taxon,
@@ -6499,20 +6441,20 @@ class VirusApi:
6499
6441
  @validate_call
6500
6442
  def virus_reports_by_acessions(
6501
6443
  self,
6502
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
6444
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
6503
6445
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
6504
6446
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
6505
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
6506
- filter_updated_since: Optional[datetime] = None,
6507
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
6508
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
6509
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
6510
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
6511
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
6512
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
6447
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
6448
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
6449
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
6450
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
6451
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
6452
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
6453
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
6454
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
6513
6455
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
6514
6456
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
6515
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6457
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6516
6458
  _request_timeout: Union[
6517
6459
  None,
6518
6460
  Annotated[StrictFloat, Field(gt=0)],
@@ -6526,37 +6468,37 @@ class VirusApi:
6526
6468
  _headers: Optional[Dict[StrictStr, Any]] = None,
6527
6469
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6528
6470
  ) -> V2reportsVirusDataReportPage:
6529
- """Get virus metadata by accession
6471
+ """Get a virus data report by nucleotide accession
6530
6472
 
6531
- Get virus metadata by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
6473
+ Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
6532
6474
 
6533
- :param accessions: genome sequence accessions (required)
6475
+ :param accessions: One or more nucleotide sequence accessions (required)
6534
6476
  :type accessions: List[str]
6535
6477
  :param filter_refseq_only: If true, limit results to RefSeq genomes.
6536
6478
  :type filter_refseq_only: bool
6537
6479
  :param filter_annotated_only: If true, limit results to annotated genomes.
6538
6480
  :type filter_annotated_only: bool
6539
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
6481
+ :param filter_released_since: Limit to genomes released on or after the specified date.
6540
6482
  :type filter_released_since: datetime
6541
- :param filter_updated_since:
6483
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
6542
6484
  :type filter_updated_since: datetime
6543
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
6485
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6544
6486
  :type filter_host: str
6545
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
6487
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6546
6488
  :type filter_pangolin_classification: str
6547
- :param filter_geo_location: Assemblies from this location (country or continent)
6489
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
6548
6490
  :type filter_geo_location: str
6549
- :param filter_usa_state: Assemblies from this state (official two letter code only)
6491
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6550
6492
  :type filter_usa_state: str
6551
- :param filter_complete_only: only include complete genomes.
6493
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
6552
6494
  :type filter_complete_only: bool
6553
- :param returned_content: Return either virus genome accessions, or complete virus metadata
6495
+ :param returned_content: Return complete virus reports or nucleotide accessions only
6554
6496
  :type returned_content: V2VirusDataReportRequestContentType
6555
6497
  :param table_fields: Specify which fields to include in the tabular report
6556
6498
  :type table_fields: List[str]
6557
6499
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
6558
6500
  :type page_size: int
6559
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6501
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6560
6502
  :type page_token: str
6561
6503
  :param _request_timeout: timeout setting for this request. If one
6562
6504
  number provided, it will be total request
@@ -6618,20 +6560,20 @@ class VirusApi:
6618
6560
  @validate_call
6619
6561
  def virus_reports_by_acessions_with_http_info(
6620
6562
  self,
6621
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
6563
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
6622
6564
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
6623
6565
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
6624
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
6625
- filter_updated_since: Optional[datetime] = None,
6626
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
6627
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
6628
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
6629
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
6630
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
6631
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
6566
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
6567
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
6568
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
6569
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
6570
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
6571
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
6572
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
6573
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
6632
6574
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
6633
6575
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
6634
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6576
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6635
6577
  _request_timeout: Union[
6636
6578
  None,
6637
6579
  Annotated[StrictFloat, Field(gt=0)],
@@ -6645,37 +6587,37 @@ class VirusApi:
6645
6587
  _headers: Optional[Dict[StrictStr, Any]] = None,
6646
6588
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6647
6589
  ) -> ApiResponse[V2reportsVirusDataReportPage]:
6648
- """Get virus metadata by accession
6590
+ """Get a virus data report by nucleotide accession
6649
6591
 
6650
- Get virus metadata by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
6592
+ Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
6651
6593
 
6652
- :param accessions: genome sequence accessions (required)
6594
+ :param accessions: One or more nucleotide sequence accessions (required)
6653
6595
  :type accessions: List[str]
6654
6596
  :param filter_refseq_only: If true, limit results to RefSeq genomes.
6655
6597
  :type filter_refseq_only: bool
6656
6598
  :param filter_annotated_only: If true, limit results to annotated genomes.
6657
6599
  :type filter_annotated_only: bool
6658
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
6600
+ :param filter_released_since: Limit to genomes released on or after the specified date.
6659
6601
  :type filter_released_since: datetime
6660
- :param filter_updated_since:
6602
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
6661
6603
  :type filter_updated_since: datetime
6662
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
6604
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6663
6605
  :type filter_host: str
6664
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
6606
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6665
6607
  :type filter_pangolin_classification: str
6666
- :param filter_geo_location: Assemblies from this location (country or continent)
6608
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
6667
6609
  :type filter_geo_location: str
6668
- :param filter_usa_state: Assemblies from this state (official two letter code only)
6610
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6669
6611
  :type filter_usa_state: str
6670
- :param filter_complete_only: only include complete genomes.
6612
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
6671
6613
  :type filter_complete_only: bool
6672
- :param returned_content: Return either virus genome accessions, or complete virus metadata
6614
+ :param returned_content: Return complete virus reports or nucleotide accessions only
6673
6615
  :type returned_content: V2VirusDataReportRequestContentType
6674
6616
  :param table_fields: Specify which fields to include in the tabular report
6675
6617
  :type table_fields: List[str]
6676
6618
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
6677
6619
  :type page_size: int
6678
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6620
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6679
6621
  :type page_token: str
6680
6622
  :param _request_timeout: timeout setting for this request. If one
6681
6623
  number provided, it will be total request
@@ -6737,20 +6679,20 @@ class VirusApi:
6737
6679
  @validate_call
6738
6680
  def virus_reports_by_acessions_without_preload_content(
6739
6681
  self,
6740
- accessions: Annotated[List[StrictStr], Field(description="genome sequence accessions")],
6682
+ accessions: Annotated[List[StrictStr], Field(description="One or more nucleotide sequence accessions")],
6741
6683
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
6742
6684
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
6743
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
6744
- filter_updated_since: Optional[datetime] = None,
6745
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
6746
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
6747
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
6748
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
6749
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
6750
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
6685
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
6686
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
6687
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
6688
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
6689
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
6690
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
6691
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
6692
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
6751
6693
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
6752
6694
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
6753
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6695
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
6754
6696
  _request_timeout: Union[
6755
6697
  None,
6756
6698
  Annotated[StrictFloat, Field(gt=0)],
@@ -6764,37 +6706,37 @@ class VirusApi:
6764
6706
  _headers: Optional[Dict[StrictStr, Any]] = None,
6765
6707
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
6766
6708
  ) -> RESTResponseType:
6767
- """Get virus metadata by accession
6709
+ """Get a virus data report by nucleotide accession
6768
6710
 
6769
- Get virus metadata by accesion. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
6711
+ Get a virus data report by nucleotide accession. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
6770
6712
 
6771
- :param accessions: genome sequence accessions (required)
6713
+ :param accessions: One or more nucleotide sequence accessions (required)
6772
6714
  :type accessions: List[str]
6773
6715
  :param filter_refseq_only: If true, limit results to RefSeq genomes.
6774
6716
  :type filter_refseq_only: bool
6775
6717
  :param filter_annotated_only: If true, limit results to annotated genomes.
6776
6718
  :type filter_annotated_only: bool
6777
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
6719
+ :param filter_released_since: Limit to genomes released on or after the specified date.
6778
6720
  :type filter_released_since: datetime
6779
- :param filter_updated_since:
6721
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
6780
6722
  :type filter_updated_since: datetime
6781
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
6723
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
6782
6724
  :type filter_host: str
6783
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
6725
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
6784
6726
  :type filter_pangolin_classification: str
6785
- :param filter_geo_location: Assemblies from this location (country or continent)
6727
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
6786
6728
  :type filter_geo_location: str
6787
- :param filter_usa_state: Assemblies from this state (official two letter code only)
6729
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
6788
6730
  :type filter_usa_state: str
6789
- :param filter_complete_only: only include complete genomes.
6731
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
6790
6732
  :type filter_complete_only: bool
6791
- :param returned_content: Return either virus genome accessions, or complete virus metadata
6733
+ :param returned_content: Return complete virus reports or nucleotide accessions only
6792
6734
  :type returned_content: V2VirusDataReportRequestContentType
6793
6735
  :param table_fields: Specify which fields to include in the tabular report
6794
6736
  :type table_fields: List[str]
6795
6737
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
6796
6738
  :type page_size: int
6797
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6739
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
6798
6740
  :type page_token: str
6799
6741
  :param _request_timeout: timeout setting for this request. If one
6800
6742
  number provided, it will be total request
@@ -7018,9 +6960,9 @@ class VirusApi:
7018
6960
  _headers: Optional[Dict[StrictStr, Any]] = None,
7019
6961
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7020
6962
  ) -> V2reportsVirusDataReportPage:
7021
- """Get virus metadata by POST
6963
+ """Get a virus data report
7022
6964
 
7023
- Get virus metadata. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
6965
+ Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7024
6966
 
7025
6967
  :param v2_virus_data_report_request: (required)
7026
6968
  :type v2_virus_data_report_request: V2VirusDataReportRequest
@@ -7085,9 +7027,9 @@ class VirusApi:
7085
7027
  _headers: Optional[Dict[StrictStr, Any]] = None,
7086
7028
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7087
7029
  ) -> ApiResponse[V2reportsVirusDataReportPage]:
7088
- """Get virus metadata by POST
7030
+ """Get a virus data report
7089
7031
 
7090
- Get virus metadata. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
7032
+ Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7091
7033
 
7092
7034
  :param v2_virus_data_report_request: (required)
7093
7035
  :type v2_virus_data_report_request: V2VirusDataReportRequest
@@ -7152,9 +7094,9 @@ class VirusApi:
7152
7094
  _headers: Optional[Dict[StrictStr, Any]] = None,
7153
7095
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7154
7096
  ) -> RESTResponseType:
7155
- """Get virus metadata by POST
7097
+ """Get a virus data report
7156
7098
 
7157
- Get virus metadata. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
7099
+ Get a virus data report. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7158
7100
 
7159
7101
  :param v2_virus_data_report_request: (required)
7160
7102
  :type v2_virus_data_report_request: V2VirusDataReportRequest
@@ -7284,17 +7226,17 @@ class VirusApi:
7284
7226
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
7285
7227
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
7286
7228
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
7287
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
7288
- filter_updated_since: Optional[datetime] = None,
7289
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
7290
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
7291
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
7292
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
7293
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
7294
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
7229
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
7230
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
7231
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
7232
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
7233
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
7234
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
7235
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
7236
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
7295
7237
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
7296
7238
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
7297
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7239
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7298
7240
  _request_timeout: Union[
7299
7241
  None,
7300
7242
  Annotated[StrictFloat, Field(gt=0)],
@@ -7308,9 +7250,9 @@ class VirusApi:
7308
7250
  _headers: Optional[Dict[StrictStr, Any]] = None,
7309
7251
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7310
7252
  ) -> V2reportsVirusDataReportPage:
7311
- """Get virus metadata by taxon
7253
+ """Get a virus data report by taxon
7312
7254
 
7313
- Get virus metadata by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
7255
+ Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7314
7256
 
7315
7257
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
7316
7258
  :type taxon: str
@@ -7318,27 +7260,27 @@ class VirusApi:
7318
7260
  :type filter_refseq_only: bool
7319
7261
  :param filter_annotated_only: If true, limit results to annotated genomes.
7320
7262
  :type filter_annotated_only: bool
7321
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
7263
+ :param filter_released_since: Limit to genomes released on or after the specified date.
7322
7264
  :type filter_released_since: datetime
7323
- :param filter_updated_since:
7265
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
7324
7266
  :type filter_updated_since: datetime
7325
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
7267
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
7326
7268
  :type filter_host: str
7327
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
7269
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
7328
7270
  :type filter_pangolin_classification: str
7329
- :param filter_geo_location: Assemblies from this location (country or continent)
7271
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
7330
7272
  :type filter_geo_location: str
7331
- :param filter_usa_state: Assemblies from this state (official two letter code only)
7273
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
7332
7274
  :type filter_usa_state: str
7333
- :param filter_complete_only: only include complete genomes.
7275
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
7334
7276
  :type filter_complete_only: bool
7335
- :param returned_content: Return either virus genome accessions, or complete virus metadata
7277
+ :param returned_content: Return complete virus reports or nucleotide accessions only
7336
7278
  :type returned_content: V2VirusDataReportRequestContentType
7337
7279
  :param table_fields: Specify which fields to include in the tabular report
7338
7280
  :type table_fields: List[str]
7339
7281
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
7340
7282
  :type page_size: int
7341
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7283
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7342
7284
  :type page_token: str
7343
7285
  :param _request_timeout: timeout setting for this request. If one
7344
7286
  number provided, it will be total request
@@ -7403,17 +7345,17 @@ class VirusApi:
7403
7345
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
7404
7346
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
7405
7347
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
7406
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
7407
- filter_updated_since: Optional[datetime] = None,
7408
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
7409
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
7410
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
7411
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
7412
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
7413
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
7348
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
7349
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
7350
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
7351
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
7352
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
7353
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
7354
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
7355
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
7414
7356
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
7415
7357
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
7416
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7358
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7417
7359
  _request_timeout: Union[
7418
7360
  None,
7419
7361
  Annotated[StrictFloat, Field(gt=0)],
@@ -7427,9 +7369,9 @@ class VirusApi:
7427
7369
  _headers: Optional[Dict[StrictStr, Any]] = None,
7428
7370
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7429
7371
  ) -> ApiResponse[V2reportsVirusDataReportPage]:
7430
- """Get virus metadata by taxon
7372
+ """Get a virus data report by taxon
7431
7373
 
7432
- Get virus metadata by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
7374
+ Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7433
7375
 
7434
7376
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
7435
7377
  :type taxon: str
@@ -7437,27 +7379,27 @@ class VirusApi:
7437
7379
  :type filter_refseq_only: bool
7438
7380
  :param filter_annotated_only: If true, limit results to annotated genomes.
7439
7381
  :type filter_annotated_only: bool
7440
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
7382
+ :param filter_released_since: Limit to genomes released on or after the specified date.
7441
7383
  :type filter_released_since: datetime
7442
- :param filter_updated_since:
7384
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
7443
7385
  :type filter_updated_since: datetime
7444
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
7386
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
7445
7387
  :type filter_host: str
7446
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
7388
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
7447
7389
  :type filter_pangolin_classification: str
7448
- :param filter_geo_location: Assemblies from this location (country or continent)
7390
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
7449
7391
  :type filter_geo_location: str
7450
- :param filter_usa_state: Assemblies from this state (official two letter code only)
7392
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
7451
7393
  :type filter_usa_state: str
7452
- :param filter_complete_only: only include complete genomes.
7394
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
7453
7395
  :type filter_complete_only: bool
7454
- :param returned_content: Return either virus genome accessions, or complete virus metadata
7396
+ :param returned_content: Return complete virus reports or nucleotide accessions only
7455
7397
  :type returned_content: V2VirusDataReportRequestContentType
7456
7398
  :param table_fields: Specify which fields to include in the tabular report
7457
7399
  :type table_fields: List[str]
7458
7400
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
7459
7401
  :type page_size: int
7460
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7402
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7461
7403
  :type page_token: str
7462
7404
  :param _request_timeout: timeout setting for this request. If one
7463
7405
  number provided, it will be total request
@@ -7522,17 +7464,17 @@ class VirusApi:
7522
7464
  taxon: Annotated[StrictStr, Field(description="NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank")],
7523
7465
  filter_refseq_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to RefSeq genomes.")] = None,
7524
7466
  filter_annotated_only: Annotated[Optional[StrictBool], Field(description="If true, limit results to annotated genomes.")] = None,
7525
- filter_released_since: Annotated[Optional[datetime], Field(description="If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'")] = None,
7526
- filter_updated_since: Optional[datetime] = None,
7527
- filter_host: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default")] = None,
7528
- filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="If set, limit results to genomes classified to this lineage by the PangoLearn tool.")] = None,
7529
- filter_geo_location: Annotated[Optional[StrictStr], Field(description="Assemblies from this location (country or continent)")] = None,
7530
- filter_usa_state: Annotated[Optional[StrictStr], Field(description="Assemblies from this state (official two letter code only)")] = None,
7531
- filter_complete_only: Annotated[Optional[StrictBool], Field(description="only include complete genomes.")] = None,
7532
- returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return either virus genome accessions, or complete virus metadata")] = None,
7467
+ filter_released_since: Annotated[Optional[datetime], Field(description="Limit to genomes released on or after the specified date.")] = None,
7468
+ filter_updated_since: Annotated[Optional[datetime], Field(description="Limit to genomes updated on or after the specified date.")] = None,
7469
+ filter_host: Annotated[Optional[StrictStr], Field(description="Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).")] = None,
7470
+ filter_pangolin_classification: Annotated[Optional[StrictStr], Field(description="Limit to SARS-CoV-2 genomes from the specified Pango lineage.")] = None,
7471
+ filter_geo_location: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified geographic location.")] = None,
7472
+ filter_usa_state: Annotated[Optional[StrictStr], Field(description="Limit to genomes collected from the specified U.S. state (two-letter abbreviation).")] = None,
7473
+ filter_complete_only: Annotated[Optional[StrictBool], Field(description="Limit to genomes designated as complete, as defined by the submitter.")] = None,
7474
+ returned_content: Annotated[Optional[V2VirusDataReportRequestContentType], Field(description="Return complete virus reports or nucleotide accessions only")] = None,
7533
7475
  table_fields: Annotated[Optional[List[StrictStr]], Field(description="Specify which fields to include in the tabular report")] = None,
7534
7476
  page_size: Annotated[Optional[StrictInt], Field(description="The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.")] = None,
7535
- page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7477
+ page_token: Annotated[Optional[StrictStr], Field(description="A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.")] = None,
7536
7478
  _request_timeout: Union[
7537
7479
  None,
7538
7480
  Annotated[StrictFloat, Field(gt=0)],
@@ -7546,9 +7488,9 @@ class VirusApi:
7546
7488
  _headers: Optional[Dict[StrictStr, Any]] = None,
7547
7489
  _host_index: Annotated[StrictInt, Field(ge=0, le=0)] = 0,
7548
7490
  ) -> RESTResponseType:
7549
- """Get virus metadata by taxon
7491
+ """Get a virus data report by taxon
7550
7492
 
7551
- Get virus metadata by taxon. By default, in paged JSON format, but also available as tabular (accept: text/tab-separated-values) or json-lines (accept: application/x-ndjson)
7493
+ Get a virus data report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.
7552
7494
 
7553
7495
  :param taxon: NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank (required)
7554
7496
  :type taxon: str
@@ -7556,27 +7498,27 @@ class VirusApi:
7556
7498
  :type filter_refseq_only: bool
7557
7499
  :param filter_annotated_only: If true, limit results to annotated genomes.
7558
7500
  :type filter_annotated_only: bool
7559
- :param filter_released_since: If set, limit results to viral genomes that have been released after a specified date (and optionally, time). April 1, 2020 midnight UTC should be formatted as '2020-04-01T00:00:00.000Z'
7501
+ :param filter_released_since: Limit to genomes released on or after the specified date.
7560
7502
  :type filter_released_since: datetime
7561
- :param filter_updated_since:
7503
+ :param filter_updated_since: Limit to genomes updated on or after the specified date.
7562
7504
  :type filter_updated_since: datetime
7563
- :param filter_host: If set, limit results to genomes extracted from this host (Taxonomy ID or name) All hosts by default
7505
+ :param filter_host: Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).
7564
7506
  :type filter_host: str
7565
- :param filter_pangolin_classification: If set, limit results to genomes classified to this lineage by the PangoLearn tool.
7507
+ :param filter_pangolin_classification: Limit to SARS-CoV-2 genomes from the specified Pango lineage.
7566
7508
  :type filter_pangolin_classification: str
7567
- :param filter_geo_location: Assemblies from this location (country or continent)
7509
+ :param filter_geo_location: Limit to genomes collected from the specified geographic location.
7568
7510
  :type filter_geo_location: str
7569
- :param filter_usa_state: Assemblies from this state (official two letter code only)
7511
+ :param filter_usa_state: Limit to genomes collected from the specified U.S. state (two-letter abbreviation).
7570
7512
  :type filter_usa_state: str
7571
- :param filter_complete_only: only include complete genomes.
7513
+ :param filter_complete_only: Limit to genomes designated as complete, as defined by the submitter.
7572
7514
  :type filter_complete_only: bool
7573
- :param returned_content: Return either virus genome accessions, or complete virus metadata
7515
+ :param returned_content: Return complete virus reports or nucleotide accessions only
7574
7516
  :type returned_content: V2VirusDataReportRequestContentType
7575
7517
  :param table_fields: Specify which fields to include in the tabular report
7576
7518
  :type table_fields: List[str]
7577
7519
  :param page_size: The maximum number of virus data reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, `page_token` can be used to retrieve the remaining results.
7578
7520
  :type page_size: int
7579
- :param page_token: A page token is returned from a `GetVirusDataReports` call with more than `page_size` results. Use this token, along with the previous `VirusDataReportRequest` parameters, to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7521
+ :param page_token: A page token is returned when the results count exceeds `page size`. Use this token along with previous request parameters to retrieve the next page of results. When `page_token` is empty, all results have been retrieved.
7580
7522
  :type page_token: str
7581
7523
  :param _request_timeout: timeout setting for this request. If one
7582
7524
  number provided, it will be total request