tol-sdk 1.0.666__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (320) hide show
  1. tol_sdk-1.0.666/LICENSE +9 -0
  2. tol_sdk-1.0.666/MANIFEST.in +1 -0
  3. tol_sdk-1.0.666/PKG-INFO +73 -0
  4. tol_sdk-1.0.666/README.md +10 -0
  5. tol_sdk-1.0.666/pyproject.toml +75 -0
  6. tol_sdk-1.0.666/setup.cfg +4 -0
  7. tol_sdk-1.0.666/src/certs/cacert.pem +3276 -0
  8. tol_sdk-1.0.666/src/tol/__init__.py +3 -0
  9. tol_sdk-1.0.666/src/tol/api_base/__init__.py +10 -0
  10. tol_sdk-1.0.666/src/tol/api_base/action.py +196 -0
  11. tol_sdk-1.0.666/src/tol/api_base/auth/__init__.py +10 -0
  12. tol_sdk-1.0.666/src/tol/api_base/auth/abc/__init__.py +5 -0
  13. tol_sdk-1.0.666/src/tol/api_base/auth/abc/auth.py +69 -0
  14. tol_sdk-1.0.666/src/tol/api_base/auth/asserts.py +117 -0
  15. tol_sdk-1.0.666/src/tol/api_base/auth/blueprint.py +96 -0
  16. tol_sdk-1.0.666/src/tol/api_base/auth/composite.py +389 -0
  17. tol_sdk-1.0.666/src/tol/api_base/auth/config.py +51 -0
  18. tol_sdk-1.0.666/src/tol/api_base/auth/error.py +49 -0
  19. tol_sdk-1.0.666/src/tol/api_base/blueprint.py +356 -0
  20. tol_sdk-1.0.666/src/tol/api_base/controller.py +490 -0
  21. tol_sdk-1.0.666/src/tol/api_base/misc/__init__.py +13 -0
  22. tol_sdk-1.0.666/src/tol/api_base/misc/aggregation_body.py +30 -0
  23. tol_sdk-1.0.666/src/tol/api_base/misc/aggregation_parameters.py +28 -0
  24. tol_sdk-1.0.666/src/tol/api_base/misc/auth_context.py +95 -0
  25. tol_sdk-1.0.666/src/tol/api_base/misc/authenticate.py +67 -0
  26. tol_sdk-1.0.666/src/tol/api_base/misc/data_body.py +61 -0
  27. tol_sdk-1.0.666/src/tol/api_base/misc/filter_utils.py +29 -0
  28. tol_sdk-1.0.666/src/tol/api_base/misc/list_get_parameters.py +106 -0
  29. tol_sdk-1.0.666/src/tol/api_base/misc/relation_url.py +40 -0
  30. tol_sdk-1.0.666/src/tol/api_base/misc/stats_parameters.py +64 -0
  31. tol_sdk-1.0.666/src/tol/api_base/system.py +45 -0
  32. tol_sdk-1.0.666/src/tol/api_client/__init__.py +6 -0
  33. tol_sdk-1.0.666/src/tol/api_client/api_datasource.py +475 -0
  34. tol_sdk-1.0.666/src/tol/api_client/client.py +446 -0
  35. tol_sdk-1.0.666/src/tol/api_client/converter.py +167 -0
  36. tol_sdk-1.0.666/src/tol/api_client/exception.py +150 -0
  37. tol_sdk-1.0.666/src/tol/api_client/factory.py +139 -0
  38. tol_sdk-1.0.666/src/tol/api_client/filter.py +63 -0
  39. tol_sdk-1.0.666/src/tol/api_client/parser.py +211 -0
  40. tol_sdk-1.0.666/src/tol/api_client/validate.py +138 -0
  41. tol_sdk-1.0.666/src/tol/api_client/view.py +322 -0
  42. tol_sdk-1.0.666/src/tol/barcodes/__init__.py +8 -0
  43. tol_sdk-1.0.666/src/tol/barcodes/main.py +168 -0
  44. tol_sdk-1.0.666/src/tol/benchling/__init__.py +6 -0
  45. tol_sdk-1.0.666/src/tol/benchling/benchling_converter.py +750 -0
  46. tol_sdk-1.0.666/src/tol/benchling/benchling_datasource.py +964 -0
  47. tol_sdk-1.0.666/src/tol/benchling/benchling_warehouse_datasource.py +130 -0
  48. tol_sdk-1.0.666/src/tol/benchling/sql/__init__.py +3 -0
  49. tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_dna.sql +183 -0
  50. tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_lres.sql +47 -0
  51. tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_pooled_dna.sql +99 -0
  52. tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_rna.sql +89 -0
  53. tol_sdk-1.0.666/src/tol/benchling/sql/pacbio_prep.sql +92 -0
  54. tol_sdk-1.0.666/src/tol/benchling/sql/pooled_pacbio_prep.sql +93 -0
  55. tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_dna.sql +102 -0
  56. tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_pooled.sql +106 -0
  57. tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_rna.sql +87 -0
  58. tol_sdk-1.0.666/src/tol/benchling/sql/results_pacbio_prep.sql +126 -0
  59. tol_sdk-1.0.666/src/tol/benchling/sql/results_pacbio_prep_pooled.sql +130 -0
  60. tol_sdk-1.0.666/src/tol/benchling/sql/sample.sql +99 -0
  61. tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_hic.sql +95 -0
  62. tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_pacbio.sql +406 -0
  63. tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_rnaseq.sql +110 -0
  64. tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_wgs.sql +183 -0
  65. tol_sdk-1.0.666/src/tol/benchling/sql/tissue_prep.sql +144 -0
  66. tol_sdk-1.0.666/src/tol/board/__init__.py +5 -0
  67. tol_sdk-1.0.666/src/tol/board/blueprint.py +306 -0
  68. tol_sdk-1.0.666/src/tol/bold/__init__.py +6 -0
  69. tol_sdk-1.0.666/src/tol/bold/bold_datasource.py +144 -0
  70. tol_sdk-1.0.666/src/tol/bold/client.py +66 -0
  71. tol_sdk-1.0.666/src/tol/bold/converter.py +47 -0
  72. tol_sdk-1.0.666/src/tol/bold/factory.py +110 -0
  73. tol_sdk-1.0.666/src/tol/bold/parser.py +111 -0
  74. tol_sdk-1.0.666/src/tol/cli/__init__.py +5 -0
  75. tol_sdk-1.0.666/src/tol/cli/cli.py +416 -0
  76. tol_sdk-1.0.666/src/tol/copo/__init__.py +6 -0
  77. tol_sdk-1.0.666/src/tol/copo/client.py +116 -0
  78. tol_sdk-1.0.666/src/tol/copo/converter.py +52 -0
  79. tol_sdk-1.0.666/src/tol/copo/copo_datasource.py +182 -0
  80. tol_sdk-1.0.666/src/tol/copo/factory.py +105 -0
  81. tol_sdk-1.0.666/src/tol/copo/parser.py +116 -0
  82. tol_sdk-1.0.666/src/tol/core/__init__.py +36 -0
  83. tol_sdk-1.0.666/src/tol/core/attribute_metadata.py +140 -0
  84. tol_sdk-1.0.666/src/tol/core/core_converter.py +180 -0
  85. tol_sdk-1.0.666/src/tol/core/data_loader.py +377 -0
  86. tol_sdk-1.0.666/src/tol/core/data_object.py +122 -0
  87. tol_sdk-1.0.666/src/tol/core/data_object_converter.py +82 -0
  88. tol_sdk-1.0.666/src/tol/core/data_source_attribute_metadata.py +119 -0
  89. tol_sdk-1.0.666/src/tol/core/data_source_dict.py +59 -0
  90. tol_sdk-1.0.666/src/tol/core/datasource.py +185 -0
  91. tol_sdk-1.0.666/src/tol/core/datasource_error.py +60 -0
  92. tol_sdk-1.0.666/src/tol/core/datasource_filter.py +33 -0
  93. tol_sdk-1.0.666/src/tol/core/factory.py +303 -0
  94. tol_sdk-1.0.666/src/tol/core/http_client.py +85 -0
  95. tol_sdk-1.0.666/src/tol/core/operator/__init__.py +68 -0
  96. tol_sdk-1.0.666/src/tol/core/operator/_filterable.py +39 -0
  97. tol_sdk-1.0.666/src/tol/core/operator/_writer.py +84 -0
  98. tol_sdk-1.0.666/src/tol/core/operator/aggregator.py +33 -0
  99. tol_sdk-1.0.666/src/tol/core/operator/counter.py +32 -0
  100. tol_sdk-1.0.666/src/tol/core/operator/cursor.py +129 -0
  101. tol_sdk-1.0.666/src/tol/core/operator/declare.py +19 -0
  102. tol_sdk-1.0.666/src/tol/core/operator/deleter.py +33 -0
  103. tol_sdk-1.0.666/src/tol/core/operator/detail_getter.py +97 -0
  104. tol_sdk-1.0.666/src/tol/core/operator/enricher.py +106 -0
  105. tol_sdk-1.0.666/src/tol/core/operator/enum.py +77 -0
  106. tol_sdk-1.0.666/src/tol/core/operator/group_statter.py +32 -0
  107. tol_sdk-1.0.666/src/tol/core/operator/inserter.py +56 -0
  108. tol_sdk-1.0.666/src/tol/core/operator/list_getter.py +35 -0
  109. tol_sdk-1.0.666/src/tol/core/operator/operator_config.py +121 -0
  110. tol_sdk-1.0.666/src/tol/core/operator/page_getter.py +41 -0
  111. tol_sdk-1.0.666/src/tol/core/operator/relational.py +159 -0
  112. tol_sdk-1.0.666/src/tol/core/operator/statter.py +30 -0
  113. tol_sdk-1.0.666/src/tol/core/operator/summariser.py +195 -0
  114. tol_sdk-1.0.666/src/tol/core/operator/updater.py +40 -0
  115. tol_sdk-1.0.666/src/tol/core/operator/upserter.py +58 -0
  116. tol_sdk-1.0.666/src/tol/core/relationship.py +157 -0
  117. tol_sdk-1.0.666/src/tol/core/session.py +164 -0
  118. tol_sdk-1.0.666/src/tol/core/validate.py +135 -0
  119. tol_sdk-1.0.666/src/tol/elastic/__init__.py +6 -0
  120. tol_sdk-1.0.666/src/tol/elastic/elastic_datasource.py +1191 -0
  121. tol_sdk-1.0.666/src/tol/elastic/runtime_fields.py +135 -0
  122. tol_sdk-1.0.666/src/tol/eln/__init__.py +9 -0
  123. tol_sdk-1.0.666/src/tol/eln/auth.py +18 -0
  124. tol_sdk-1.0.666/src/tol/eln/eln_datasource.py +120 -0
  125. tol_sdk-1.0.666/src/tol/eln/entities.py +33 -0
  126. tol_sdk-1.0.666/src/tol/eln/generators.py +53 -0
  127. tol_sdk-1.0.666/src/tol/eln/sanitise.py +17 -0
  128. tol_sdk-1.0.666/src/tol/ena/__init__.py +6 -0
  129. tol_sdk-1.0.666/src/tol/ena/client.py +166 -0
  130. tol_sdk-1.0.666/src/tol/ena/converter.py +48 -0
  131. tol_sdk-1.0.666/src/tol/ena/ena_datasource.py +275 -0
  132. tol_sdk-1.0.666/src/tol/ena/ena_methods.py +264 -0
  133. tol_sdk-1.0.666/src/tol/ena/factory.py +160 -0
  134. tol_sdk-1.0.666/src/tol/ena/filter.py +86 -0
  135. tol_sdk-1.0.666/src/tol/ena/parser.py +104 -0
  136. tol_sdk-1.0.666/src/tol/excel/__init__.py +5 -0
  137. tol_sdk-1.0.666/src/tol/excel/excel.py +127 -0
  138. tol_sdk-1.0.666/src/tol/flows/__init__.py +6 -0
  139. tol_sdk-1.0.666/src/tol/flows/convert_functions/__init__.py +17 -0
  140. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_benchling_samples_to_data_object.py +10 -0
  141. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_bioscan_barcoding_run_data_to_data_object.py +9 -0
  142. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_bold_samples_to_data_object.py +34 -0
  143. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_elastic_samples_to_barcoding_run_data.py +16 -0
  144. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_portaldb_sequencing_request_events_to_sequencing_requests.py +13 -0
  145. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_species_lab_work_status_to_data_object.py +15 -0
  146. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_specimen_status_to_data_object.py +15 -0
  147. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_to_data_objects.py +9 -0
  148. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolid_species_to_data_object.py +21 -0
  149. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolid_specimen_to_data_object.py +14 -0
  150. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolqc_run_data_to_data_object.py +29 -0
  151. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolqc_samples_to_data_object.py +20 -0
  152. tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_treeofsex_species_to_data_object.py +54 -0
  153. tol_sdk-1.0.666/src/tol/flows/converters/__init__.py +50 -0
  154. tol_sdk-1.0.666/src/tol/flows/converters/benchling_entity_to_benchling_worklist_item_converter_factory.py +37 -0
  155. tol_sdk-1.0.666/src/tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py +30 -0
  156. tol_sdk-1.0.666/src/tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py +29 -0
  157. tol_sdk-1.0.666/src/tol/flows/converters/benchling_sample_casm_to_sts_sample_converter.py +42 -0
  158. tol_sdk-1.0.666/src/tol/flows/converters/benchling_sample_to_elastic_sample_converter.py +40 -0
  159. tol_sdk-1.0.666/src/tol/flows/converters/benchling_sequencing_request_to_elastic_sequencing_request_converter.py +38 -0
  160. tol_sdk-1.0.666/src/tol/flows/converters/benchling_tissue_prep_to_elastic_tissue_prep_converter.py +31 -0
  161. tol_sdk-1.0.666/src/tol/flows/converters/benchling_tissue_to_sts_sample_converter.py +42 -0
  162. tol_sdk-1.0.666/src/tol/flows/converters/bioscan_extra_pantheon_species_to_elastic_sample_update_converter.py +21 -0
  163. tol_sdk-1.0.666/src/tol/flows/converters/bioscan_qc_specimen_to_elastic_sample_update_converter.py +23 -0
  164. tol_sdk-1.0.666/src/tol/flows/converters/bioscan_qc_uksi_entry_to_elastic_sample_update_converter.py +22 -0
  165. tol_sdk-1.0.666/src/tol/flows/converters/bold_sample_to_elastic_sample_update_converter.py +21 -0
  166. tol_sdk-1.0.666/src/tol/flows/converters/elastic_object_to_portaldb_object_converter.py +35 -0
  167. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_benchling_tissue_converter.py +38 -0
  168. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_benchling_tissue_update_converter.py +76 -0
  169. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_bold_sample_converter.py +88 -0
  170. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_elastic_sequencing_request_update_converter.py +25 -0
  171. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_sts_sample_converter.py +25 -0
  172. tol_sdk-1.0.666/src/tol/flows/converters/elastic_sequencing_request_to_sts_sequencing_request_converter.py +31 -0
  173. tol_sdk-1.0.666/src/tol/flows/converters/elastic_species_to_sts_species_converter.py +38 -0
  174. tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_curation_update_converter.py +21 -0
  175. tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_genome_note_update_converter.py +25 -0
  176. tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_sample_update_converter.py +31 -0
  177. tol_sdk-1.0.666/src/tol/flows/converters/gap_assembly_to_elastic_assembly_analysis_converter.py +44 -0
  178. tol_sdk-1.0.666/src/tol/flows/converters/gap_assembly_to_elastic_assembly_converter.py +54 -0
  179. tol_sdk-1.0.666/src/tol/flows/converters/genome_notes_genome_note_to_elastic_genome_note_converter.py +42 -0
  180. tol_sdk-1.0.666/src/tol/flows/converters/goat_taxon_to_elastic_species_converter.py +34 -0
  181. tol_sdk-1.0.666/src/tol/flows/converters/grit_issue_to_elastic_curation_converter.py +108 -0
  182. tol_sdk-1.0.666/src/tol/flows/converters/labwhere_location_to_elastic_sample_update_converter.py +22 -0
  183. tol_sdk-1.0.666/src/tol/flows/converters/labwhere_location_to_sts_tray_converter.py +24 -0
  184. tol_sdk-1.0.666/src/tol/flows/converters/lrpacbio_sequencing_request_to_elastic_sequencing_request_converter.py +40 -0
  185. tol_sdk-1.0.666/src/tol/flows/converters/mlwh_extraction_to_elastic_extraction_converter.py +37 -0
  186. tol_sdk-1.0.666/src/tol/flows/converters/mlwh_run_data_to_elastic_run_data_converter.py +46 -0
  187. tol_sdk-1.0.666/src/tol/flows/converters/mlwh_sequencing_request_to_elastic_sequencing_request_converter.py +41 -0
  188. tol_sdk-1.0.666/src/tol/flows/converters/sts_banked_sample_to_elastic_sample_converter.py +25 -0
  189. tol_sdk-1.0.666/src/tol/flows/converters/sts_manifest_to_elastic_manifest_converter.py +39 -0
  190. tol_sdk-1.0.666/src/tol/flows/converters/sts_project_to_elastic_sample_update_converter.py +21 -0
  191. tol_sdk-1.0.666/src/tol/flows/converters/sts_sample_project_to_elastic_sample_converter.py +142 -0
  192. tol_sdk-1.0.666/src/tol/flows/converters/sts_sample_to_casm_benchling_converter.py +957 -0
  193. tol_sdk-1.0.666/src/tol/flows/converters/sts_sampleset_to_elastic_sampleset_converter.py +49 -0
  194. tol_sdk-1.0.666/src/tol/flows/converters/sts_species_to_elastic_species_converter.py +34 -0
  195. tol_sdk-1.0.666/src/tol/flows/converters/tolid_specimen_to_elastic_tolid_converter.py +35 -0
  196. tol_sdk-1.0.666/src/tol/flows/converters/tolqc_data_to_elastic_run_data_converter.py +66 -0
  197. tol_sdk-1.0.666/src/tol/flows/converters/tolqc_sample_to_elastic_sequencing_request_converter.py +32 -0
  198. tol_sdk-1.0.666/src/tol/flows/converters/tolqc_species_to_elastic_species_converter.py +45 -0
  199. tol_sdk-1.0.666/src/tol/flows/logger.py +9 -0
  200. tol_sdk-1.0.666/src/tol/flows/secrets.py +16 -0
  201. tol_sdk-1.0.666/src/tol/flows/sequencing_submissions.py +282 -0
  202. tol_sdk-1.0.666/src/tol/gap/__init__.py +5 -0
  203. tol_sdk-1.0.666/src/tol/gap/gap_datasource.py +116 -0
  204. tol_sdk-1.0.666/src/tol/goat/__init__.py +6 -0
  205. tol_sdk-1.0.666/src/tol/goat/client.py +108 -0
  206. tol_sdk-1.0.666/src/tol/goat/converter.py +50 -0
  207. tol_sdk-1.0.666/src/tol/goat/factory.py +125 -0
  208. tol_sdk-1.0.666/src/tol/goat/filter.py +82 -0
  209. tol_sdk-1.0.666/src/tol/goat/goat_datasource.py +205 -0
  210. tol_sdk-1.0.666/src/tol/goat/parser.py +118 -0
  211. tol_sdk-1.0.666/src/tol/google_sheets/__init__.py +5 -0
  212. tol_sdk-1.0.666/src/tol/google_sheets/google_sheet_datasource.py +184 -0
  213. tol_sdk-1.0.666/src/tol/irods/__init__.py +5 -0
  214. tol_sdk-1.0.666/src/tol/irods/irods_datasource.py +157 -0
  215. tol_sdk-1.0.666/src/tol/jira/__init__.py +9 -0
  216. tol_sdk-1.0.666/src/tol/jira/client.py +123 -0
  217. tol_sdk-1.0.666/src/tol/jira/converter.py +47 -0
  218. tol_sdk-1.0.666/src/tol/jira/factory.py +193 -0
  219. tol_sdk-1.0.666/src/tol/jira/filter.py +65 -0
  220. tol_sdk-1.0.666/src/tol/jira/jira_datasource.py +224 -0
  221. tol_sdk-1.0.666/src/tol/jira/mapper.py +24 -0
  222. tol_sdk-1.0.666/src/tol/jira/parser.py +162 -0
  223. tol_sdk-1.0.666/src/tol/jira/sort.py +44 -0
  224. tol_sdk-1.0.666/src/tol/json/__init__.py +6 -0
  225. tol_sdk-1.0.666/src/tol/json/json_datasource.py +130 -0
  226. tol_sdk-1.0.666/src/tol/json/s3_json_datasource.py +85 -0
  227. tol_sdk-1.0.666/src/tol/labwhere/__init__.py +6 -0
  228. tol_sdk-1.0.666/src/tol/labwhere/client.py +49 -0
  229. tol_sdk-1.0.666/src/tol/labwhere/converter.py +51 -0
  230. tol_sdk-1.0.666/src/tol/labwhere/factory.py +105 -0
  231. tol_sdk-1.0.666/src/tol/labwhere/labwhere_datasource.py +143 -0
  232. tol_sdk-1.0.666/src/tol/labwhere/parser.py +111 -0
  233. tol_sdk-1.0.666/src/tol/markdown.py +39 -0
  234. tol_sdk-1.0.666/src/tol/mlwh/__init__.py +5 -0
  235. tol_sdk-1.0.666/src/tol/mlwh/mlwh_datasource.py +565 -0
  236. tol_sdk-1.0.666/src/tol/prefect/__init__.py +6 -0
  237. tol_sdk-1.0.666/src/tol/prefect/converter.py +167 -0
  238. tol_sdk-1.0.666/src/tol/prefect/factory.py +103 -0
  239. tol_sdk-1.0.666/src/tol/prefect/filter.py +292 -0
  240. tol_sdk-1.0.666/src/tol/prefect/prefect_datasource.py +320 -0
  241. tol_sdk-1.0.666/src/tol/prefect/prefect_object.py +25 -0
  242. tol_sdk-1.0.666/src/tol/sciops/__init__.py +5 -0
  243. tol_sdk-1.0.666/src/tol/sciops/configuration.py +26 -0
  244. tol_sdk-1.0.666/src/tol/sciops/consumer.py +64 -0
  245. tol_sdk-1.0.666/src/tol/sciops/message_builder.py +140 -0
  246. tol_sdk-1.0.666/src/tol/sciops/messages.py +69 -0
  247. tol_sdk-1.0.666/src/tol/sciops/response_processors.py +76 -0
  248. tol_sdk-1.0.666/src/tol/sciops/sequencing_datasource.py +208 -0
  249. tol_sdk-1.0.666/src/tol/sources/__init__.py +3 -0
  250. tol_sdk-1.0.666/src/tol/sources/benchling.py +26 -0
  251. tol_sdk-1.0.666/src/tol/sources/benchling_warehouse.py +24 -0
  252. tol_sdk-1.0.666/src/tol/sources/bioscan.py +25 -0
  253. tol_sdk-1.0.666/src/tol/sources/bioscan_extra.py +67 -0
  254. tol_sdk-1.0.666/src/tol/sources/bioscan_qc.py +58 -0
  255. tol_sdk-1.0.666/src/tol/sources/bold.py +24 -0
  256. tol_sdk-1.0.666/src/tol/sources/copo.py +23 -0
  257. tol_sdk-1.0.666/src/tol/sources/defaults.py +48 -0
  258. tol_sdk-1.0.666/src/tol/sources/elastic.py +871 -0
  259. tol_sdk-1.0.666/src/tol/sources/ena.py +26 -0
  260. tol_sdk-1.0.666/src/tol/sources/gap.py +45 -0
  261. tol_sdk-1.0.666/src/tol/sources/genome_notes.py +65 -0
  262. tol_sdk-1.0.666/src/tol/sources/goat.py +23 -0
  263. tol_sdk-1.0.666/src/tol/sources/grit.py +23 -0
  264. tol_sdk-1.0.666/src/tol/sources/informatics.py +52 -0
  265. tol_sdk-1.0.666/src/tol/sources/labwhere.py +23 -0
  266. tol_sdk-1.0.666/src/tol/sources/lr_pacbio.py +67 -0
  267. tol_sdk-1.0.666/src/tol/sources/mlwh.py +18 -0
  268. tol_sdk-1.0.666/src/tol/sources/portal.py +26 -0
  269. tol_sdk-1.0.666/src/tol/sources/portal_attributes.py +63 -0
  270. tol_sdk-1.0.666/src/tol/sources/portaldb.py +23 -0
  271. tol_sdk-1.0.666/src/tol/sources/prefect.py +45 -0
  272. tol_sdk-1.0.666/src/tol/sources/sciops.py +32 -0
  273. tol_sdk-1.0.666/src/tol/sources/sts.py +25 -0
  274. tol_sdk-1.0.666/src/tol/sources/sts_legacy.py +21 -0
  275. tol_sdk-1.0.666/src/tol/sources/tolid.py +25 -0
  276. tol_sdk-1.0.666/src/tol/sources/tolqc.py +25 -0
  277. tol_sdk-1.0.666/src/tol/sources/tolqc_legacy.py +34 -0
  278. tol_sdk-1.0.666/src/tol/sources/uksi_qc.py.py +58 -0
  279. tol_sdk-1.0.666/src/tol/sources/workflows.py +25 -0
  280. tol_sdk-1.0.666/src/tol/sql/__init__.py +11 -0
  281. tol_sdk-1.0.666/src/tol/sql/action/__init__.py +6 -0
  282. tol_sdk-1.0.666/src/tol/sql/action/factory.py +141 -0
  283. tol_sdk-1.0.666/src/tol/sql/auth/__init__.py +7 -0
  284. tol_sdk-1.0.666/src/tol/sql/auth/blueprint.py +442 -0
  285. tol_sdk-1.0.666/src/tol/sql/auth/models.py +522 -0
  286. tol_sdk-1.0.666/src/tol/sql/board/__init__.py +5 -0
  287. tol_sdk-1.0.666/src/tol/sql/board/factory.py +331 -0
  288. tol_sdk-1.0.666/src/tol/sql/cast.py +28 -0
  289. tol_sdk-1.0.666/src/tol/sql/database.py +557 -0
  290. tol_sdk-1.0.666/src/tol/sql/ds_session.py +37 -0
  291. tol_sdk-1.0.666/src/tol/sql/exception.py +21 -0
  292. tol_sdk-1.0.666/src/tol/sql/ext.py +68 -0
  293. tol_sdk-1.0.666/src/tol/sql/factory.py +134 -0
  294. tol_sdk-1.0.666/src/tol/sql/filter.py +508 -0
  295. tol_sdk-1.0.666/src/tol/sql/loader/__init__.py +6 -0
  296. tol_sdk-1.0.666/src/tol/sql/loader/factory.py +141 -0
  297. tol_sdk-1.0.666/src/tol/sql/model.py +403 -0
  298. tol_sdk-1.0.666/src/tol/sql/relationship.py +112 -0
  299. tol_sdk-1.0.666/src/tol/sql/session.py +32 -0
  300. tol_sdk-1.0.666/src/tol/sql/sort.py +97 -0
  301. tol_sdk-1.0.666/src/tol/sql/sql_converter.py +221 -0
  302. tol_sdk-1.0.666/src/tol/sql/sql_datasource.py +524 -0
  303. tol_sdk-1.0.666/src/tol/sql/summary/__init__.py +6 -0
  304. tol_sdk-1.0.666/src/tol/sql/summary/factory.py +91 -0
  305. tol_sdk-1.0.666/src/tol/status/__init__.py +5 -0
  306. tol_sdk-1.0.666/src/tol/status/status_datasource.py +84 -0
  307. tol_sdk-1.0.666/src/tol/sts/__init__.py +7 -0
  308. tol_sdk-1.0.666/src/tol/sts/sts.py +44 -0
  309. tol_sdk-1.0.666/src/tol/sts/sts_datasource.py +170 -0
  310. tol_sdk-1.0.666/src/tol/sts/sts_requests.py +71 -0
  311. tol_sdk-1.0.666/src/tol/treeval/__init__.py +5 -0
  312. tol_sdk-1.0.666/src/tol/treeval/treeval_datasource.py +480 -0
  313. tol_sdk-1.0.666/src/tol/utils/__init__.py +5 -0
  314. tol_sdk-1.0.666/src/tol/utils/csv.py +19 -0
  315. tol_sdk-1.0.666/src/tol_sdk.egg-info/PKG-INFO +73 -0
  316. tol_sdk-1.0.666/src/tol_sdk.egg-info/SOURCES.txt +319 -0
  317. tol_sdk-1.0.666/src/tol_sdk.egg-info/dependency_links.txt +1 -0
  318. tol_sdk-1.0.666/src/tol_sdk.egg-info/entry_points.txt +2 -0
  319. tol_sdk-1.0.666/src/tol_sdk.egg-info/requires.txt +58 -0
  320. tol_sdk-1.0.666/src/tol_sdk.egg-info/top_level.txt +2 -0
@@ -0,0 +1,9 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2022 Genome Research Ltd.
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
6
+
7
+ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
8
+
9
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -0,0 +1 @@
1
+ include src/certs/cacert.pem
@@ -0,0 +1,73 @@
1
+ Metadata-Version: 2.4
2
+ Name: tol-sdk
3
+ Version: 1.0.666
4
+ Summary: SDK for interaction with ToL, Sanger and external services
5
+ Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
6
+ License: MIT
7
+ Project-URL: Homepage, https://gitlab.internal.sanger.ac.uk/tol/platforms/tol-sdk
8
+ Project-URL: Jira, https://jira.sanger.ac.uk/secure/RapidBoard.jspa?rapidView=32&projectKey=TOLP
9
+ Classifier: Programming Language :: Python :: 3
10
+ Classifier: License :: OSI Approved :: MIT License
11
+ Classifier: Operating System :: OS Independent
12
+ Requires-Python: >=3.10
13
+ Description-Content-Type: text/markdown
14
+ License-File: LICENSE
15
+ Requires-Dist: cachetools==5.3.3
16
+ Requires-Dist: case-converter==1.1.0
17
+ Requires-Dist: Click==8.1.7
18
+ Requires-Dist: more-itertools==10.2.0
19
+ Requires-Dist: python_dateutil>=2.8.1
20
+ Requires-Dist: python-dotenv>=1.0.1
21
+ Requires-Dist: requests==2.31.0
22
+ Requires-Dist: setuptools==69.0.3
23
+ Requires-Dist: dateparser==1.2.1
24
+ Provides-Extra: api-base
25
+ Requires-Dist: Flask==3.1.0; extra == "api-base"
26
+ Requires-Dist: Werkzeug==3.1.3; extra == "api-base"
27
+ Provides-Extra: benchling
28
+ Requires-Dist: benchling-sdk; extra == "benchling"
29
+ Provides-Extra: elastic
30
+ Requires-Dist: elasticsearch==7.17.9; extra == "elastic"
31
+ Provides-Extra: irods
32
+ Requires-Dist: python-irodsclient==3.1.0; extra == "irods"
33
+ Provides-Extra: jira
34
+ Requires-Dist: atlassian-python-api==3.41.14; extra == "jira"
35
+ Provides-Extra: json
36
+ Requires-Dist: minio==7.2.15; extra == "json"
37
+ Provides-Extra: mysql
38
+ Requires-Dist: mysql-connector-python; extra == "mysql"
39
+ Provides-Extra: postgresql
40
+ Requires-Dist: SQLAlchemy==2.0.35; extra == "postgresql"
41
+ Requires-Dist: psycopg2-binary==2.9.9; extra == "postgresql"
42
+ Provides-Extra: prefect
43
+ Requires-Dist: prefect==2.20.18; extra == "prefect"
44
+ Requires-Dist: griffe<1.0.0; extra == "prefect"
45
+ Provides-Extra: sheets
46
+ Requires-Dist: pandas==2.1.4; extra == "sheets"
47
+ Requires-Dist: openpyxl>=3.0.10; extra == "sheets"
48
+ Requires-Dist: XlsxWriter==3.1.9; extra == "sheets"
49
+ Requires-Dist: xlrd==2.0.1; extra == "sheets"
50
+ Requires-Dist: gspread>=5.12.0; extra == "sheets"
51
+ Provides-Extra: all
52
+ Requires-Dist: tol-sdk[api-base]; extra == "all"
53
+ Requires-Dist: tol-sdk[benchling]; extra == "all"
54
+ Requires-Dist: tol-sdk[elastic]; extra == "all"
55
+ Requires-Dist: tol-sdk[irods]; extra == "all"
56
+ Requires-Dist: tol-sdk[jira]; extra == "all"
57
+ Requires-Dist: tol-sdk[json]; extra == "all"
58
+ Requires-Dist: tol-sdk[mysql]; extra == "all"
59
+ Requires-Dist: tol-sdk[postgresql]; extra == "all"
60
+ Requires-Dist: tol-sdk[prefect]; extra == "all"
61
+ Requires-Dist: tol-sdk[sheets]; extra == "all"
62
+ Dynamic: license-file
63
+
64
+ <!--
65
+ SPDX-FileCopyrightText: 2022 Genome Research Ltd.
66
+
67
+ SPDX-License-Identifier: MIT
68
+ -->
69
+
70
+ # ToL SDK
71
+
72
+ A Python SDK for ToL services. Full documentation is available:
73
+ https://ssg-confluence.internal.sanger.ac.uk/display/TOL/ToL+SDK
@@ -0,0 +1,10 @@
1
+ <!--
2
+ SPDX-FileCopyrightText: 2022 Genome Research Ltd.
3
+
4
+ SPDX-License-Identifier: MIT
5
+ -->
6
+
7
+ # ToL SDK
8
+
9
+ A Python SDK for ToL services. Full documentation is available:
10
+ https://ssg-confluence.internal.sanger.ac.uk/display/TOL/ToL+SDK
@@ -0,0 +1,75 @@
1
+ # SPDX-FileCopyrightText: 2021 Genome Research Ltd.
2
+ #
3
+ # SPDX-License-Identifier: MIT
4
+
5
+ [build-system]
6
+ requires = ["setuptools>=42", "wheel"]
7
+ build-backend = "setuptools.build_meta"
8
+
9
+ [project]
10
+ name = "tol-sdk"
11
+ version = "1.0.666"
12
+ description = "SDK for interaction with ToL, Sanger and external services"
13
+ readme = "README.md"
14
+ authors = [
15
+ { name = "ToL Platforms Team", email = "tol-platforms@sanger.ac.uk" }
16
+ ]
17
+ license = { text = "MIT" }
18
+ requires-python = ">=3.10"
19
+ classifiers = [
20
+ "Programming Language :: Python :: 3",
21
+ "License :: OSI Approved :: MIT License",
22
+ "Operating System :: OS Independent"
23
+ ]
24
+ urls = { "Homepage" = "https://gitlab.internal.sanger.ac.uk/tol/platforms/tol-sdk", "Jira" = "https://jira.sanger.ac.uk/secure/RapidBoard.jspa?rapidView=32&projectKey=TOLP" }
25
+ dependencies = [
26
+ "cachetools == 5.3.3",
27
+ "case-converter == 1.1.0",
28
+ "Click == 8.1.7",
29
+ "more-itertools == 10.2.0",
30
+ "python_dateutil >= 2.8.1",
31
+ "python-dotenv >= 1.0.1",
32
+ "requests == 2.31.0",
33
+ "setuptools == 69.0.3",
34
+ "dateparser == 1.2.1"
35
+ ]
36
+
37
+ [project.optional-dependencies]
38
+ api-base = ["Flask == 3.1.0", "Werkzeug == 3.1.3"]
39
+ benchling = ["benchling-sdk"]
40
+ elastic = ["elasticsearch == 7.17.9"]
41
+ irods = ["python-irodsclient == 3.1.0"]
42
+ jira = ["atlassian-python-api==3.41.14"]
43
+ json = ["minio == 7.2.15"]
44
+ mysql = ["mysql-connector-python"]
45
+ postgresql = ["SQLAlchemy == 2.0.35", "psycopg2-binary == 2.9.9"]
46
+ prefect = ["prefect == 2.20.18", "griffe < 1.0.0"]
47
+ sheets = [
48
+ "pandas == 2.1.4",
49
+ "openpyxl >= 3.0.10",
50
+ "XlsxWriter == 3.1.9",
51
+ "xlrd == 2.0.1",
52
+ "gspread >= 5.12.0"
53
+ ]
54
+ all = [
55
+ "tol-sdk[api-base]",
56
+ "tol-sdk[benchling]",
57
+ "tol-sdk[elastic]",
58
+ "tol-sdk[irods]",
59
+ "tol-sdk[jira]",
60
+ "tol-sdk[json]",
61
+ "tol-sdk[mysql]",
62
+ "tol-sdk[postgresql]",
63
+ "tol-sdk[prefect]",
64
+ "tol-sdk[sheets]"
65
+ ]
66
+
67
+ [tool.setuptools.packages.find]
68
+ where = ["src"]
69
+
70
+ [tool.setuptools.package-data]
71
+ "tol" = ["../certs/cacert.pem"]
72
+ "tol.benchling.sql" = ["*.sql"]
73
+
74
+ [project.scripts]
75
+ tol = "tol.cli:cli"
@@ -0,0 +1,4 @@
1
+ [egg_info]
2
+ tag_build =
3
+ tag_date = 0
4
+