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.
- tol_sdk-1.0.666/LICENSE +9 -0
- tol_sdk-1.0.666/MANIFEST.in +1 -0
- tol_sdk-1.0.666/PKG-INFO +73 -0
- tol_sdk-1.0.666/README.md +10 -0
- tol_sdk-1.0.666/pyproject.toml +75 -0
- tol_sdk-1.0.666/setup.cfg +4 -0
- tol_sdk-1.0.666/src/certs/cacert.pem +3276 -0
- tol_sdk-1.0.666/src/tol/__init__.py +3 -0
- tol_sdk-1.0.666/src/tol/api_base/__init__.py +10 -0
- tol_sdk-1.0.666/src/tol/api_base/action.py +196 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/__init__.py +10 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/abc/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/abc/auth.py +69 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/asserts.py +117 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/blueprint.py +96 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/composite.py +389 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/config.py +51 -0
- tol_sdk-1.0.666/src/tol/api_base/auth/error.py +49 -0
- tol_sdk-1.0.666/src/tol/api_base/blueprint.py +356 -0
- tol_sdk-1.0.666/src/tol/api_base/controller.py +490 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/__init__.py +13 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/aggregation_body.py +30 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/aggregation_parameters.py +28 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/auth_context.py +95 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/authenticate.py +67 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/data_body.py +61 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/filter_utils.py +29 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/list_get_parameters.py +106 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/relation_url.py +40 -0
- tol_sdk-1.0.666/src/tol/api_base/misc/stats_parameters.py +64 -0
- tol_sdk-1.0.666/src/tol/api_base/system.py +45 -0
- tol_sdk-1.0.666/src/tol/api_client/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/api_client/api_datasource.py +475 -0
- tol_sdk-1.0.666/src/tol/api_client/client.py +446 -0
- tol_sdk-1.0.666/src/tol/api_client/converter.py +167 -0
- tol_sdk-1.0.666/src/tol/api_client/exception.py +150 -0
- tol_sdk-1.0.666/src/tol/api_client/factory.py +139 -0
- tol_sdk-1.0.666/src/tol/api_client/filter.py +63 -0
- tol_sdk-1.0.666/src/tol/api_client/parser.py +211 -0
- tol_sdk-1.0.666/src/tol/api_client/validate.py +138 -0
- tol_sdk-1.0.666/src/tol/api_client/view.py +322 -0
- tol_sdk-1.0.666/src/tol/barcodes/__init__.py +8 -0
- tol_sdk-1.0.666/src/tol/barcodes/main.py +168 -0
- tol_sdk-1.0.666/src/tol/benchling/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/benchling/benchling_converter.py +750 -0
- tol_sdk-1.0.666/src/tol/benchling/benchling_datasource.py +964 -0
- tol_sdk-1.0.666/src/tol/benchling/benchling_warehouse_datasource.py +130 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/__init__.py +3 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_dna.sql +183 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_lres.sql +47 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_pooled_dna.sql +99 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/extraction_extraction_type_rna.sql +89 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/pacbio_prep.sql +92 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/pooled_pacbio_prep.sql +93 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_dna.sql +102 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_pooled.sql +106 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/results_extraction_rna.sql +87 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/results_pacbio_prep.sql +126 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/results_pacbio_prep_pooled.sql +130 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/sample.sql +99 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_hic.sql +95 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_pacbio.sql +406 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_rnaseq.sql +110 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/sequencing_request_sequencing_platform_wgs.sql +183 -0
- tol_sdk-1.0.666/src/tol/benchling/sql/tissue_prep.sql +144 -0
- tol_sdk-1.0.666/src/tol/board/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/board/blueprint.py +306 -0
- tol_sdk-1.0.666/src/tol/bold/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/bold/bold_datasource.py +144 -0
- tol_sdk-1.0.666/src/tol/bold/client.py +66 -0
- tol_sdk-1.0.666/src/tol/bold/converter.py +47 -0
- tol_sdk-1.0.666/src/tol/bold/factory.py +110 -0
- tol_sdk-1.0.666/src/tol/bold/parser.py +111 -0
- tol_sdk-1.0.666/src/tol/cli/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/cli/cli.py +416 -0
- tol_sdk-1.0.666/src/tol/copo/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/copo/client.py +116 -0
- tol_sdk-1.0.666/src/tol/copo/converter.py +52 -0
- tol_sdk-1.0.666/src/tol/copo/copo_datasource.py +182 -0
- tol_sdk-1.0.666/src/tol/copo/factory.py +105 -0
- tol_sdk-1.0.666/src/tol/copo/parser.py +116 -0
- tol_sdk-1.0.666/src/tol/core/__init__.py +36 -0
- tol_sdk-1.0.666/src/tol/core/attribute_metadata.py +140 -0
- tol_sdk-1.0.666/src/tol/core/core_converter.py +180 -0
- tol_sdk-1.0.666/src/tol/core/data_loader.py +377 -0
- tol_sdk-1.0.666/src/tol/core/data_object.py +122 -0
- tol_sdk-1.0.666/src/tol/core/data_object_converter.py +82 -0
- tol_sdk-1.0.666/src/tol/core/data_source_attribute_metadata.py +119 -0
- tol_sdk-1.0.666/src/tol/core/data_source_dict.py +59 -0
- tol_sdk-1.0.666/src/tol/core/datasource.py +185 -0
- tol_sdk-1.0.666/src/tol/core/datasource_error.py +60 -0
- tol_sdk-1.0.666/src/tol/core/datasource_filter.py +33 -0
- tol_sdk-1.0.666/src/tol/core/factory.py +303 -0
- tol_sdk-1.0.666/src/tol/core/http_client.py +85 -0
- tol_sdk-1.0.666/src/tol/core/operator/__init__.py +68 -0
- tol_sdk-1.0.666/src/tol/core/operator/_filterable.py +39 -0
- tol_sdk-1.0.666/src/tol/core/operator/_writer.py +84 -0
- tol_sdk-1.0.666/src/tol/core/operator/aggregator.py +33 -0
- tol_sdk-1.0.666/src/tol/core/operator/counter.py +32 -0
- tol_sdk-1.0.666/src/tol/core/operator/cursor.py +129 -0
- tol_sdk-1.0.666/src/tol/core/operator/declare.py +19 -0
- tol_sdk-1.0.666/src/tol/core/operator/deleter.py +33 -0
- tol_sdk-1.0.666/src/tol/core/operator/detail_getter.py +97 -0
- tol_sdk-1.0.666/src/tol/core/operator/enricher.py +106 -0
- tol_sdk-1.0.666/src/tol/core/operator/enum.py +77 -0
- tol_sdk-1.0.666/src/tol/core/operator/group_statter.py +32 -0
- tol_sdk-1.0.666/src/tol/core/operator/inserter.py +56 -0
- tol_sdk-1.0.666/src/tol/core/operator/list_getter.py +35 -0
- tol_sdk-1.0.666/src/tol/core/operator/operator_config.py +121 -0
- tol_sdk-1.0.666/src/tol/core/operator/page_getter.py +41 -0
- tol_sdk-1.0.666/src/tol/core/operator/relational.py +159 -0
- tol_sdk-1.0.666/src/tol/core/operator/statter.py +30 -0
- tol_sdk-1.0.666/src/tol/core/operator/summariser.py +195 -0
- tol_sdk-1.0.666/src/tol/core/operator/updater.py +40 -0
- tol_sdk-1.0.666/src/tol/core/operator/upserter.py +58 -0
- tol_sdk-1.0.666/src/tol/core/relationship.py +157 -0
- tol_sdk-1.0.666/src/tol/core/session.py +164 -0
- tol_sdk-1.0.666/src/tol/core/validate.py +135 -0
- tol_sdk-1.0.666/src/tol/elastic/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/elastic/elastic_datasource.py +1191 -0
- tol_sdk-1.0.666/src/tol/elastic/runtime_fields.py +135 -0
- tol_sdk-1.0.666/src/tol/eln/__init__.py +9 -0
- tol_sdk-1.0.666/src/tol/eln/auth.py +18 -0
- tol_sdk-1.0.666/src/tol/eln/eln_datasource.py +120 -0
- tol_sdk-1.0.666/src/tol/eln/entities.py +33 -0
- tol_sdk-1.0.666/src/tol/eln/generators.py +53 -0
- tol_sdk-1.0.666/src/tol/eln/sanitise.py +17 -0
- tol_sdk-1.0.666/src/tol/ena/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/ena/client.py +166 -0
- tol_sdk-1.0.666/src/tol/ena/converter.py +48 -0
- tol_sdk-1.0.666/src/tol/ena/ena_datasource.py +275 -0
- tol_sdk-1.0.666/src/tol/ena/ena_methods.py +264 -0
- tol_sdk-1.0.666/src/tol/ena/factory.py +160 -0
- tol_sdk-1.0.666/src/tol/ena/filter.py +86 -0
- tol_sdk-1.0.666/src/tol/ena/parser.py +104 -0
- tol_sdk-1.0.666/src/tol/excel/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/excel/excel.py +127 -0
- tol_sdk-1.0.666/src/tol/flows/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/__init__.py +17 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_benchling_samples_to_data_object.py +10 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_bioscan_barcoding_run_data_to_data_object.py +9 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_bold_samples_to_data_object.py +34 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_elastic_samples_to_barcoding_run_data.py +16 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_portaldb_sequencing_request_events_to_sequencing_requests.py +13 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_species_lab_work_status_to_data_object.py +15 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_specimen_status_to_data_object.py +15 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_to_data_objects.py +9 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolid_species_to_data_object.py +21 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolid_specimen_to_data_object.py +14 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolqc_run_data_to_data_object.py +29 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_tolqc_samples_to_data_object.py +20 -0
- tol_sdk-1.0.666/src/tol/flows/convert_functions/convert_treeofsex_species_to_data_object.py +54 -0
- tol_sdk-1.0.666/src/tol/flows/converters/__init__.py +50 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_entity_to_benchling_worklist_item_converter_factory.py +37 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_extraction_to_elastic_extraction_converter.py +30 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_extraction_to_elastic_sequencing_request_converter.py +29 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_sample_casm_to_sts_sample_converter.py +42 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_sample_to_elastic_sample_converter.py +40 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_sequencing_request_to_elastic_sequencing_request_converter.py +38 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_tissue_prep_to_elastic_tissue_prep_converter.py +31 -0
- tol_sdk-1.0.666/src/tol/flows/converters/benchling_tissue_to_sts_sample_converter.py +42 -0
- tol_sdk-1.0.666/src/tol/flows/converters/bioscan_extra_pantheon_species_to_elastic_sample_update_converter.py +21 -0
- tol_sdk-1.0.666/src/tol/flows/converters/bioscan_qc_specimen_to_elastic_sample_update_converter.py +23 -0
- tol_sdk-1.0.666/src/tol/flows/converters/bioscan_qc_uksi_entry_to_elastic_sample_update_converter.py +22 -0
- tol_sdk-1.0.666/src/tol/flows/converters/bold_sample_to_elastic_sample_update_converter.py +21 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_object_to_portaldb_object_converter.py +35 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_benchling_tissue_converter.py +38 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_benchling_tissue_update_converter.py +76 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_bold_sample_converter.py +88 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_elastic_sequencing_request_update_converter.py +25 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sample_to_sts_sample_converter.py +25 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_sequencing_request_to_sts_sequencing_request_converter.py +31 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_species_to_sts_species_converter.py +38 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_curation_update_converter.py +21 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_genome_note_update_converter.py +25 -0
- tol_sdk-1.0.666/src/tol/flows/converters/elastic_tolid_to_elastic_sample_update_converter.py +31 -0
- tol_sdk-1.0.666/src/tol/flows/converters/gap_assembly_to_elastic_assembly_analysis_converter.py +44 -0
- tol_sdk-1.0.666/src/tol/flows/converters/gap_assembly_to_elastic_assembly_converter.py +54 -0
- tol_sdk-1.0.666/src/tol/flows/converters/genome_notes_genome_note_to_elastic_genome_note_converter.py +42 -0
- tol_sdk-1.0.666/src/tol/flows/converters/goat_taxon_to_elastic_species_converter.py +34 -0
- tol_sdk-1.0.666/src/tol/flows/converters/grit_issue_to_elastic_curation_converter.py +108 -0
- tol_sdk-1.0.666/src/tol/flows/converters/labwhere_location_to_elastic_sample_update_converter.py +22 -0
- tol_sdk-1.0.666/src/tol/flows/converters/labwhere_location_to_sts_tray_converter.py +24 -0
- tol_sdk-1.0.666/src/tol/flows/converters/lrpacbio_sequencing_request_to_elastic_sequencing_request_converter.py +40 -0
- tol_sdk-1.0.666/src/tol/flows/converters/mlwh_extraction_to_elastic_extraction_converter.py +37 -0
- tol_sdk-1.0.666/src/tol/flows/converters/mlwh_run_data_to_elastic_run_data_converter.py +46 -0
- tol_sdk-1.0.666/src/tol/flows/converters/mlwh_sequencing_request_to_elastic_sequencing_request_converter.py +41 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_banked_sample_to_elastic_sample_converter.py +25 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_manifest_to_elastic_manifest_converter.py +39 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_project_to_elastic_sample_update_converter.py +21 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_sample_project_to_elastic_sample_converter.py +142 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_sample_to_casm_benchling_converter.py +957 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_sampleset_to_elastic_sampleset_converter.py +49 -0
- tol_sdk-1.0.666/src/tol/flows/converters/sts_species_to_elastic_species_converter.py +34 -0
- tol_sdk-1.0.666/src/tol/flows/converters/tolid_specimen_to_elastic_tolid_converter.py +35 -0
- tol_sdk-1.0.666/src/tol/flows/converters/tolqc_data_to_elastic_run_data_converter.py +66 -0
- tol_sdk-1.0.666/src/tol/flows/converters/tolqc_sample_to_elastic_sequencing_request_converter.py +32 -0
- tol_sdk-1.0.666/src/tol/flows/converters/tolqc_species_to_elastic_species_converter.py +45 -0
- tol_sdk-1.0.666/src/tol/flows/logger.py +9 -0
- tol_sdk-1.0.666/src/tol/flows/secrets.py +16 -0
- tol_sdk-1.0.666/src/tol/flows/sequencing_submissions.py +282 -0
- tol_sdk-1.0.666/src/tol/gap/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/gap/gap_datasource.py +116 -0
- tol_sdk-1.0.666/src/tol/goat/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/goat/client.py +108 -0
- tol_sdk-1.0.666/src/tol/goat/converter.py +50 -0
- tol_sdk-1.0.666/src/tol/goat/factory.py +125 -0
- tol_sdk-1.0.666/src/tol/goat/filter.py +82 -0
- tol_sdk-1.0.666/src/tol/goat/goat_datasource.py +205 -0
- tol_sdk-1.0.666/src/tol/goat/parser.py +118 -0
- tol_sdk-1.0.666/src/tol/google_sheets/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/google_sheets/google_sheet_datasource.py +184 -0
- tol_sdk-1.0.666/src/tol/irods/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/irods/irods_datasource.py +157 -0
- tol_sdk-1.0.666/src/tol/jira/__init__.py +9 -0
- tol_sdk-1.0.666/src/tol/jira/client.py +123 -0
- tol_sdk-1.0.666/src/tol/jira/converter.py +47 -0
- tol_sdk-1.0.666/src/tol/jira/factory.py +193 -0
- tol_sdk-1.0.666/src/tol/jira/filter.py +65 -0
- tol_sdk-1.0.666/src/tol/jira/jira_datasource.py +224 -0
- tol_sdk-1.0.666/src/tol/jira/mapper.py +24 -0
- tol_sdk-1.0.666/src/tol/jira/parser.py +162 -0
- tol_sdk-1.0.666/src/tol/jira/sort.py +44 -0
- tol_sdk-1.0.666/src/tol/json/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/json/json_datasource.py +130 -0
- tol_sdk-1.0.666/src/tol/json/s3_json_datasource.py +85 -0
- tol_sdk-1.0.666/src/tol/labwhere/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/labwhere/client.py +49 -0
- tol_sdk-1.0.666/src/tol/labwhere/converter.py +51 -0
- tol_sdk-1.0.666/src/tol/labwhere/factory.py +105 -0
- tol_sdk-1.0.666/src/tol/labwhere/labwhere_datasource.py +143 -0
- tol_sdk-1.0.666/src/tol/labwhere/parser.py +111 -0
- tol_sdk-1.0.666/src/tol/markdown.py +39 -0
- tol_sdk-1.0.666/src/tol/mlwh/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/mlwh/mlwh_datasource.py +565 -0
- tol_sdk-1.0.666/src/tol/prefect/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/prefect/converter.py +167 -0
- tol_sdk-1.0.666/src/tol/prefect/factory.py +103 -0
- tol_sdk-1.0.666/src/tol/prefect/filter.py +292 -0
- tol_sdk-1.0.666/src/tol/prefect/prefect_datasource.py +320 -0
- tol_sdk-1.0.666/src/tol/prefect/prefect_object.py +25 -0
- tol_sdk-1.0.666/src/tol/sciops/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/sciops/configuration.py +26 -0
- tol_sdk-1.0.666/src/tol/sciops/consumer.py +64 -0
- tol_sdk-1.0.666/src/tol/sciops/message_builder.py +140 -0
- tol_sdk-1.0.666/src/tol/sciops/messages.py +69 -0
- tol_sdk-1.0.666/src/tol/sciops/response_processors.py +76 -0
- tol_sdk-1.0.666/src/tol/sciops/sequencing_datasource.py +208 -0
- tol_sdk-1.0.666/src/tol/sources/__init__.py +3 -0
- tol_sdk-1.0.666/src/tol/sources/benchling.py +26 -0
- tol_sdk-1.0.666/src/tol/sources/benchling_warehouse.py +24 -0
- tol_sdk-1.0.666/src/tol/sources/bioscan.py +25 -0
- tol_sdk-1.0.666/src/tol/sources/bioscan_extra.py +67 -0
- tol_sdk-1.0.666/src/tol/sources/bioscan_qc.py +58 -0
- tol_sdk-1.0.666/src/tol/sources/bold.py +24 -0
- tol_sdk-1.0.666/src/tol/sources/copo.py +23 -0
- tol_sdk-1.0.666/src/tol/sources/defaults.py +48 -0
- tol_sdk-1.0.666/src/tol/sources/elastic.py +871 -0
- tol_sdk-1.0.666/src/tol/sources/ena.py +26 -0
- tol_sdk-1.0.666/src/tol/sources/gap.py +45 -0
- tol_sdk-1.0.666/src/tol/sources/genome_notes.py +65 -0
- tol_sdk-1.0.666/src/tol/sources/goat.py +23 -0
- tol_sdk-1.0.666/src/tol/sources/grit.py +23 -0
- tol_sdk-1.0.666/src/tol/sources/informatics.py +52 -0
- tol_sdk-1.0.666/src/tol/sources/labwhere.py +23 -0
- tol_sdk-1.0.666/src/tol/sources/lr_pacbio.py +67 -0
- tol_sdk-1.0.666/src/tol/sources/mlwh.py +18 -0
- tol_sdk-1.0.666/src/tol/sources/portal.py +26 -0
- tol_sdk-1.0.666/src/tol/sources/portal_attributes.py +63 -0
- tol_sdk-1.0.666/src/tol/sources/portaldb.py +23 -0
- tol_sdk-1.0.666/src/tol/sources/prefect.py +45 -0
- tol_sdk-1.0.666/src/tol/sources/sciops.py +32 -0
- tol_sdk-1.0.666/src/tol/sources/sts.py +25 -0
- tol_sdk-1.0.666/src/tol/sources/sts_legacy.py +21 -0
- tol_sdk-1.0.666/src/tol/sources/tolid.py +25 -0
- tol_sdk-1.0.666/src/tol/sources/tolqc.py +25 -0
- tol_sdk-1.0.666/src/tol/sources/tolqc_legacy.py +34 -0
- tol_sdk-1.0.666/src/tol/sources/uksi_qc.py.py +58 -0
- tol_sdk-1.0.666/src/tol/sources/workflows.py +25 -0
- tol_sdk-1.0.666/src/tol/sql/__init__.py +11 -0
- tol_sdk-1.0.666/src/tol/sql/action/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/sql/action/factory.py +141 -0
- tol_sdk-1.0.666/src/tol/sql/auth/__init__.py +7 -0
- tol_sdk-1.0.666/src/tol/sql/auth/blueprint.py +442 -0
- tol_sdk-1.0.666/src/tol/sql/auth/models.py +522 -0
- tol_sdk-1.0.666/src/tol/sql/board/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/sql/board/factory.py +331 -0
- tol_sdk-1.0.666/src/tol/sql/cast.py +28 -0
- tol_sdk-1.0.666/src/tol/sql/database.py +557 -0
- tol_sdk-1.0.666/src/tol/sql/ds_session.py +37 -0
- tol_sdk-1.0.666/src/tol/sql/exception.py +21 -0
- tol_sdk-1.0.666/src/tol/sql/ext.py +68 -0
- tol_sdk-1.0.666/src/tol/sql/factory.py +134 -0
- tol_sdk-1.0.666/src/tol/sql/filter.py +508 -0
- tol_sdk-1.0.666/src/tol/sql/loader/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/sql/loader/factory.py +141 -0
- tol_sdk-1.0.666/src/tol/sql/model.py +403 -0
- tol_sdk-1.0.666/src/tol/sql/relationship.py +112 -0
- tol_sdk-1.0.666/src/tol/sql/session.py +32 -0
- tol_sdk-1.0.666/src/tol/sql/sort.py +97 -0
- tol_sdk-1.0.666/src/tol/sql/sql_converter.py +221 -0
- tol_sdk-1.0.666/src/tol/sql/sql_datasource.py +524 -0
- tol_sdk-1.0.666/src/tol/sql/summary/__init__.py +6 -0
- tol_sdk-1.0.666/src/tol/sql/summary/factory.py +91 -0
- tol_sdk-1.0.666/src/tol/status/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/status/status_datasource.py +84 -0
- tol_sdk-1.0.666/src/tol/sts/__init__.py +7 -0
- tol_sdk-1.0.666/src/tol/sts/sts.py +44 -0
- tol_sdk-1.0.666/src/tol/sts/sts_datasource.py +170 -0
- tol_sdk-1.0.666/src/tol/sts/sts_requests.py +71 -0
- tol_sdk-1.0.666/src/tol/treeval/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/treeval/treeval_datasource.py +480 -0
- tol_sdk-1.0.666/src/tol/utils/__init__.py +5 -0
- tol_sdk-1.0.666/src/tol/utils/csv.py +19 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/PKG-INFO +73 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/SOURCES.txt +319 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/dependency_links.txt +1 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/entry_points.txt +2 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/requires.txt +58 -0
- tol_sdk-1.0.666/src/tol_sdk.egg-info/top_level.txt +2 -0
tol_sdk-1.0.666/LICENSE
ADDED
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@@ -0,0 +1,9 @@
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MIT License
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Copyright (c) 2022 Genome Research Ltd.
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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:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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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.
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include src/certs/cacert.pem
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tol_sdk-1.0.666/PKG-INFO
ADDED
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Metadata-Version: 2.4
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Name: tol-sdk
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Version: 1.0.666
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Summary: SDK for interaction with ToL, Sanger and external services
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Author-email: ToL Platforms Team <tol-platforms@sanger.ac.uk>
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License: MIT
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Project-URL: Homepage, https://gitlab.internal.sanger.ac.uk/tol/platforms/tol-sdk
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Project-URL: Jira, https://jira.sanger.ac.uk/secure/RapidBoard.jspa?rapidView=32&projectKey=TOLP
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Classifier: Programming Language :: Python :: 3
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Classifier: License :: OSI Approved :: MIT License
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Classifier: Operating System :: OS Independent
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: cachetools==5.3.3
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Requires-Dist: case-converter==1.1.0
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Requires-Dist: Click==8.1.7
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Requires-Dist: more-itertools==10.2.0
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Requires-Dist: python_dateutil>=2.8.1
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Requires-Dist: python-dotenv>=1.0.1
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Requires-Dist: requests==2.31.0
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Requires-Dist: setuptools==69.0.3
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Requires-Dist: dateparser==1.2.1
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Provides-Extra: api-base
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Requires-Dist: Flask==3.1.0; extra == "api-base"
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Requires-Dist: Werkzeug==3.1.3; extra == "api-base"
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Provides-Extra: benchling
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Requires-Dist: benchling-sdk; extra == "benchling"
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Provides-Extra: elastic
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Requires-Dist: elasticsearch==7.17.9; extra == "elastic"
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Provides-Extra: irods
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Requires-Dist: python-irodsclient==3.1.0; extra == "irods"
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Provides-Extra: jira
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Requires-Dist: atlassian-python-api==3.41.14; extra == "jira"
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Provides-Extra: json
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Requires-Dist: minio==7.2.15; extra == "json"
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Provides-Extra: mysql
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Provides-Extra: postgresql
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Requires-Dist: SQLAlchemy==2.0.35; extra == "postgresql"
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Requires-Dist: psycopg2-binary==2.9.9; extra == "postgresql"
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Provides-Extra: prefect
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Requires-Dist: prefect==2.20.18; extra == "prefect"
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Requires-Dist: griffe<1.0.0; extra == "prefect"
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Provides-Extra: sheets
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Requires-Dist: pandas==2.1.4; extra == "sheets"
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Requires-Dist: openpyxl>=3.0.10; extra == "sheets"
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Requires-Dist: XlsxWriter==3.1.9; extra == "sheets"
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Requires-Dist: xlrd==2.0.1; extra == "sheets"
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Requires-Dist: gspread>=5.12.0; extra == "sheets"
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Provides-Extra: all
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Requires-Dist: tol-sdk[api-base]; extra == "all"
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Requires-Dist: tol-sdk[benchling]; extra == "all"
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Requires-Dist: tol-sdk[elastic]; extra == "all"
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Requires-Dist: tol-sdk[irods]; extra == "all"
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Requires-Dist: tol-sdk[jira]; extra == "all"
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Requires-Dist: tol-sdk[json]; extra == "all"
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Requires-Dist: tol-sdk[mysql]; extra == "all"
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Requires-Dist: tol-sdk[postgresql]; extra == "all"
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Requires-Dist: tol-sdk[prefect]; extra == "all"
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Requires-Dist: tol-sdk[sheets]; extra == "all"
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Dynamic: license-file
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<!--
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SPDX-FileCopyrightText: 2022 Genome Research Ltd.
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SPDX-License-Identifier: MIT
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-->
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# ToL SDK
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A Python SDK for ToL services. Full documentation is available:
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https://ssg-confluence.internal.sanger.ac.uk/display/TOL/ToL+SDK
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# SPDX-FileCopyrightText: 2021 Genome Research Ltd.
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#
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# SPDX-License-Identifier: MIT
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[build-system]
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requires = ["setuptools>=42", "wheel"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "tol-sdk"
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version = "1.0.666"
|
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description = "SDK for interaction with ToL, Sanger and external services"
|
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13
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readme = "README.md"
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authors = [
|
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{ name = "ToL Platforms Team", email = "tol-platforms@sanger.ac.uk" }
|
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]
|
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license = { text = "MIT" }
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requires-python = ">=3.10"
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classifiers = [
|
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"Programming Language :: Python :: 3",
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"License :: OSI Approved :: MIT License",
|
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"Operating System :: OS Independent"
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]
|
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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" }
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dependencies = [
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"cachetools == 5.3.3",
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"case-converter == 1.1.0",
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"Click == 8.1.7",
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"more-itertools == 10.2.0",
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"python_dateutil >= 2.8.1",
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"python-dotenv >= 1.0.1",
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"requests == 2.31.0",
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"setuptools == 69.0.3",
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"dateparser == 1.2.1"
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]
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[project.optional-dependencies]
|
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api-base = ["Flask == 3.1.0", "Werkzeug == 3.1.3"]
|
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benchling = ["benchling-sdk"]
|
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elastic = ["elasticsearch == 7.17.9"]
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irods = ["python-irodsclient == 3.1.0"]
|
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jira = ["atlassian-python-api==3.41.14"]
|
|
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json = ["minio == 7.2.15"]
|
|
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mysql = ["mysql-connector-python"]
|
|
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postgresql = ["SQLAlchemy == 2.0.35", "psycopg2-binary == 2.9.9"]
|
|
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prefect = ["prefect == 2.20.18", "griffe < 1.0.0"]
|
|
47
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sheets = [
|
|
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"pandas == 2.1.4",
|
|
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+
"openpyxl >= 3.0.10",
|
|
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"XlsxWriter == 3.1.9",
|
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"xlrd == 2.0.1",
|
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"gspread >= 5.12.0"
|
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]
|
|
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all = [
|
|
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"tol-sdk[api-base]",
|
|
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"tol-sdk[benchling]",
|
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"tol-sdk[elastic]",
|
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"tol-sdk[irods]",
|
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"tol-sdk[jira]",
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"tol-sdk[json]",
|
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"tol-sdk[mysql]",
|
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"tol-sdk[postgresql]",
|
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"tol-sdk[prefect]",
|
|
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"tol-sdk[sheets]"
|
|
65
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]
|
|
66
|
+
|
|
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|
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[tool.setuptools.packages.find]
|
|
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|
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where = ["src"]
|
|
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|
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[tool.setuptools.package-data]
|
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"tol" = ["../certs/cacert.pem"]
|
|
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|
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"tol.benchling.sql" = ["*.sql"]
|
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|
|
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[project.scripts]
|
|
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|
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tol = "tol.cli:cli"
|