V1.4 #325
Merged
V1.4 #325
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Changes to be committed: modified: data_dictionary/README.md
Changes to be committed: renamed: lib/covid-drdb/.gitignore -> covid-drdb/.gitignore renamed: lib/covid-drdb/Dockerfile -> covid-drdb/Dockerfile renamed: lib/covid-drdb/Makefile -> covid-drdb/Makefile renamed: lib/covid-drdb/Pipfile -> covid-drdb/Pipfile renamed: lib/covid-drdb/Pipfile.lock -> covid-drdb/Pipfile.lock renamed: lib/covid-drdb/README.md -> covid-drdb/README.md renamed: lib/covid-drdb/constraints_post-import.sql -> covid-drdb/constraints_post-import.sql renamed: lib/covid-drdb/constraints_pre-import.sql -> covid-drdb/constraints_pre-import.sql renamed: lib/covid-drdb/derived_tables/00_common_functions.sql -> covid-drdb/derived_tables/00_common_functions.sql renamed: lib/covid-drdb/derived_tables/01_rx_conv_plasma.sql -> covid-drdb/derived_tables/01_rx_conv_plasma.sql renamed: lib/covid-drdb/derived_tables/02_rx_vacc_plasma.sql -> covid-drdb/derived_tables/02_rx_vacc_plasma.sql renamed: lib/covid-drdb/derived_tables/03_invivo_selection_results.sql -> covid-drdb/derived_tables/03_invivo_selection_results.sql renamed: lib/covid-drdb/derived_tables/04_susc_results.sql -> covid-drdb/derived_tables/04_susc_results.sql renamed: lib/covid-drdb/derived_tables/05_isolate_pairs.sql -> covid-drdb/derived_tables/05_isolate_pairs.sql renamed: lib/covid-drdb/derived_tables/06_mab_resistance_mutations.sql -> covid-drdb/derived_tables/06_mab_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/07_3clpro_resistance_mutations.sql -> covid-drdb/derived_tables/07_3clpro_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/08_rdrp_resistance_mutations.sql -> covid-drdb/derived_tables/08_rdrp_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/09_susc_summary.sql -> covid-drdb/derived_tables/09_susc_summary.sql renamed: lib/covid-drdb/derived_tables/10_isolate_aggs.sql -> covid-drdb/derived_tables/10_isolate_aggs.sql renamed: lib/covid-drdb/docker-envfile.example -> covid-drdb/docker-envfile.example renamed: lib/covid-drdb/drdb/__init__.py -> covid-drdb/drdb/__init__.py renamed: lib/covid-drdb/drdb/cli.py -> covid-drdb/drdb/cli.py renamed: lib/covid-drdb/drdb/commands/__init__.py -> covid-drdb/drdb/commands/__init__.py renamed: lib/covid-drdb/drdb/commands/add_patients.py -> covid-drdb/drdb/commands/add_patients.py renamed: lib/covid-drdb/drdb/commands/autofill_payload.py -> covid-drdb/drdb/commands/autofill_payload.py renamed: lib/covid-drdb/drdb/commands/extract_gisaid_mutations.py -> covid-drdb/drdb/commands/extract_gisaid_mutations.py renamed: lib/covid-drdb/drdb/commands/extract_sierra_mutations.py -> covid-drdb/drdb/commands/extract_sierra_mutations.py renamed: lib/covid-drdb/drdb/commands/fetch_iedb_epitopes.py -> covid-drdb/drdb/commands/fetch_iedb_epitopes.py renamed: lib/covid-drdb/drdb/commands/gen_mutation_distance.py -> covid-drdb/drdb/commands/gen_mutation_distance.py renamed: lib/covid-drdb/drdb/commands/import_sra_info.py -> covid-drdb/drdb/commands/import_sra_info.py renamed: lib/covid-drdb/drdb/commands/merge_cpvp.py -> covid-drdb/drdb/commands/merge_cpvp.py renamed: lib/covid-drdb/drdb/commands/merge_expgroup.py -> covid-drdb/drdb/commands/merge_expgroup.py renamed: lib/covid-drdb/drdb/commands/merge_ptrx_and_plasma.py -> covid-drdb/drdb/commands/merge_ptrx_and_plasma.py renamed: lib/covid-drdb/drdb/commands/new_study.py -> covid-drdb/drdb/commands/new_study.py renamed: lib/covid-drdb/drdb/commands/refactor_sbj_history.py -> covid-drdb/drdb/commands/refactor_sbj_history.py renamed: lib/covid-drdb/drdb/commands/refactor_sbj_infections.py -> covid-drdb/drdb/commands/refactor_sbj_infections.py renamed: lib/covid-drdb/drdb/commands/update_glue_prevalence.py -> covid-drdb/drdb/commands/update_glue_prevalence.py renamed: lib/covid-drdb/drdb/commands/update_pt_history.py -> covid-drdb/drdb/commands/update_pt_history.py renamed: lib/covid-drdb/drdb/commands/update_ref_amino_acid.py -> covid-drdb/drdb/commands/update_ref_amino_acid.py renamed: lib/covid-drdb/drdb/commands/update_variant_consensus.py -> covid-drdb/drdb/commands/update_variant_consensus.py renamed: lib/covid-drdb/drdb/entry.py -> covid-drdb/drdb/entry.py renamed: lib/covid-drdb/drdb/utils/__init__.py -> covid-drdb/drdb/utils/__init__.py renamed: lib/covid-drdb/drdb/utils/codonutils.py -> covid-drdb/drdb/utils/codonutils.py renamed: lib/covid-drdb/drdb/utils/csvv.py -> covid-drdb/drdb/utils/csvv.py renamed: lib/covid-drdb/drdb/utils/gene_position.py -> covid-drdb/drdb/utils/gene_position.py renamed: lib/covid-drdb/drdb/utils/questionary_option.py -> covid-drdb/drdb/utils/questionary_option.py renamed: lib/covid-drdb/drop_views.sql -> covid-drdb/drop_views.sql renamed: lib/covid-drdb/er-diagram.drawio -> covid-drdb/er-diagram.drawio renamed: lib/covid-drdb/mypy.ini -> covid-drdb/mypy.ini renamed: lib/covid-drdb/payload -> covid-drdb/payload renamed: lib/covid-drdb/pipeline.drawio -> covid-drdb/pipeline.drawio renamed: lib/covid-drdb/pipeline.svg -> covid-drdb/pipeline.svg renamed: lib/covid-drdb/postgresql.conf -> covid-drdb/postgresql.conf renamed: lib/covid-drdb/schema.dbml -> covid-drdb/schema.dbml renamed: lib/covid-drdb/scripts/create-tag.sh -> covid-drdb/scripts/create-tag.sh renamed: lib/covid-drdb/scripts/db_to_sqlite.py -> covid-drdb/scripts/db_to_sqlite.py renamed: lib/covid-drdb/scripts/export-sqlite.sh -> covid-drdb/scripts/export-sqlite.sh renamed: lib/covid-drdb/scripts/export-sqls.sh -> covid-drdb/scripts/export-sqls.sh renamed: lib/covid-drdb/scripts/export-susc-summary.sh -> covid-drdb/scripts/export-susc-summary.sh renamed: lib/covid-drdb/scripts/github-release.sh -> covid-drdb/scripts/github-release.sh renamed: lib/covid-drdb/scripts/import_sierra_mutations.sh -> covid-drdb/scripts/import_sierra_mutations.sh renamed: lib/covid-drdb/scripts/make-drms-slim.sh -> covid-drdb/scripts/make-drms-slim.sh renamed: lib/covid-drdb/scripts/make-slim-version.sh -> covid-drdb/scripts/make-slim-version.sh renamed: lib/covid-drdb/scripts/make-variants-slim.sh -> covid-drdb/scripts/make-variants-slim.sh renamed: lib/covid-drdb/scripts/sync-to-s3.sh -> covid-drdb/scripts/sync-to-s3.sh renamed: lib/covid-drdb/scripts/watch-release.sh -> covid-drdb/scripts/watch-release.sh renamed: lib/covid-drdb/views/01_mab_view.sql -> covid-drdb/views/01_mab_view.sql renamed: lib/covid-drdb/views/02_rx_mab_view.sql -> covid-drdb/views/02_rx_mab_view.sql renamed: lib/covid-drdb/views/03_dms_mab_view.sql -> covid-drdb/views/03_dms_mab_view.sql renamed: lib/covid-drdb/views/04_rx_dms_mab_view.sql -> covid-drdb/views/04_rx_dms_mab_view.sql renamed: lib/covid-drdb/views/05_iso_view.sql -> covid-drdb/views/05_iso_view.sql renamed: lib/covid-drdb/views/06_rx_cp_view.sql -> covid-drdb/views/06_rx_cp_view.sql renamed: lib/covid-drdb/views/07_rx_vp_view.sql -> covid-drdb/views/07_rx_vp_view.sql renamed: lib/covid-drdb/views/08_susc_view.sql -> covid-drdb/views/08_susc_view.sql renamed: lib/covid-drdb/views/09_omicron_view.sql -> covid-drdb/views/09_omicron_view.sql renamed: lib/HIVEFileGrabber_V2.sh -> lib/shell/HIVEFileGrabber_V2.sh renamed: lib/HIVEFileGrabber_V3.1.sh -> lib/shell/HIVEFileGrabber_V3.1.sh renamed: lib/biosample_complete.sh -> lib/shell/biosample_complete.sh renamed: lib/efetch_bioproject_assemblies.sh -> lib/shell/efetch_bioproject_assemblies.sh renamed: lib/efetch_bioproject_biosample.sh -> lib/shell/efetch_bioproject_biosample.sh renamed: lib/efetch_bioproject_runs.sh -> lib/shell/efetch_bioproject_runs.sh renamed: lib/efetch_biosample_meta.sh -> lib/shell/efetch_biosample_meta.sh renamed: lib/efetch_biosample_runs.sh -> lib/shell/efetch_biosample_runs.sh renamed: lib/eutils.sh -> lib/shell/eutils.sh renamed: lib/eutils_SRAcurl_experiments.sh -> lib/shell/eutils_SRAcurl_experiments.sh renamed: lib/eutils_SRAfetch_experiments.sh -> lib/shell/eutils_SRAfetch_experiments.sh
Changes to be committed: renamed: schema/v1.0/non-core/uniprot-proteome_*.json -> schema/v1.0/non-core/uniprot-proteome_.json renamed: schema/v1.1/non-core/uniprot-proteome_*.json -> schema/v1.1/non-core/uniprot-proteome_.json renamed: schema/v1.2/non-core/uniprot-proteome_*.json -> schema/v1.2/non-core/uniprot-proteome_.json renamed: schema/v1.3/non-core/uniprot-proteome_*.json -> schema/v1.3/non-core/uniprot-proteome_.json
New ngs_id.py and associated files
Bumps [certifi](https://github.com/certifi/python-certifi) from 2021.10.8 to 2022.12.7. - [Commits](certifi/python-certifi@2021.10.08...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [certifi](https://github.com/certifi/python-certifi) from 2021.10.8 to 2022.12.7. - [Commits](certifi/python-certifi@2021.10.08...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [lxml](https://github.com/lxml/lxml) from 4.8.0 to 4.9.1. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](lxml/lxml@lxml-4.8.0...lxml-4.9.1) --- updated-dependencies: - dependency-name: lxml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.27.1...v2.31.0) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.27.1...v2.31.0) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]>
* Update docs Changes to be committed: modified: data_dictionary/README.md * Reorg Changes to be committed: renamed: lib/covid-drdb/.gitignore -> covid-drdb/.gitignore renamed: lib/covid-drdb/Dockerfile -> covid-drdb/Dockerfile renamed: lib/covid-drdb/Makefile -> covid-drdb/Makefile renamed: lib/covid-drdb/Pipfile -> covid-drdb/Pipfile renamed: lib/covid-drdb/Pipfile.lock -> covid-drdb/Pipfile.lock renamed: lib/covid-drdb/README.md -> covid-drdb/README.md renamed: lib/covid-drdb/constraints_post-import.sql -> covid-drdb/constraints_post-import.sql renamed: lib/covid-drdb/constraints_pre-import.sql -> covid-drdb/constraints_pre-import.sql renamed: lib/covid-drdb/derived_tables/00_common_functions.sql -> covid-drdb/derived_tables/00_common_functions.sql renamed: lib/covid-drdb/derived_tables/01_rx_conv_plasma.sql -> covid-drdb/derived_tables/01_rx_conv_plasma.sql renamed: lib/covid-drdb/derived_tables/02_rx_vacc_plasma.sql -> covid-drdb/derived_tables/02_rx_vacc_plasma.sql renamed: lib/covid-drdb/derived_tables/03_invivo_selection_results.sql -> covid-drdb/derived_tables/03_invivo_selection_results.sql renamed: lib/covid-drdb/derived_tables/04_susc_results.sql -> covid-drdb/derived_tables/04_susc_results.sql renamed: lib/covid-drdb/derived_tables/05_isolate_pairs.sql -> covid-drdb/derived_tables/05_isolate_pairs.sql renamed: lib/covid-drdb/derived_tables/06_mab_resistance_mutations.sql -> covid-drdb/derived_tables/06_mab_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/07_3clpro_resistance_mutations.sql -> covid-drdb/derived_tables/07_3clpro_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/08_rdrp_resistance_mutations.sql -> covid-drdb/derived_tables/08_rdrp_resistance_mutations.sql renamed: lib/covid-drdb/derived_tables/09_susc_summary.sql -> covid-drdb/derived_tables/09_susc_summary.sql renamed: lib/covid-drdb/derived_tables/10_isolate_aggs.sql -> covid-drdb/derived_tables/10_isolate_aggs.sql renamed: lib/covid-drdb/docker-envfile.example -> covid-drdb/docker-envfile.example renamed: lib/covid-drdb/drdb/__init__.py -> covid-drdb/drdb/__init__.py renamed: lib/covid-drdb/drdb/cli.py -> covid-drdb/drdb/cli.py renamed: lib/covid-drdb/drdb/commands/__init__.py -> covid-drdb/drdb/commands/__init__.py renamed: lib/covid-drdb/drdb/commands/add_patients.py -> covid-drdb/drdb/commands/add_patients.py renamed: lib/covid-drdb/drdb/commands/autofill_payload.py -> covid-drdb/drdb/commands/autofill_payload.py renamed: lib/covid-drdb/drdb/commands/extract_gisaid_mutations.py -> covid-drdb/drdb/commands/extract_gisaid_mutations.py renamed: lib/covid-drdb/drdb/commands/extract_sierra_mutations.py -> covid-drdb/drdb/commands/extract_sierra_mutations.py renamed: lib/covid-drdb/drdb/commands/fetch_iedb_epitopes.py -> covid-drdb/drdb/commands/fetch_iedb_epitopes.py renamed: lib/covid-drdb/drdb/commands/gen_mutation_distance.py -> covid-drdb/drdb/commands/gen_mutation_distance.py renamed: lib/covid-drdb/drdb/commands/import_sra_info.py -> covid-drdb/drdb/commands/import_sra_info.py renamed: lib/covid-drdb/drdb/commands/merge_cpvp.py -> covid-drdb/drdb/commands/merge_cpvp.py renamed: lib/covid-drdb/drdb/commands/merge_expgroup.py -> covid-drdb/drdb/commands/merge_expgroup.py renamed: lib/covid-drdb/drdb/commands/merge_ptrx_and_plasma.py -> covid-drdb/drdb/commands/merge_ptrx_and_plasma.py renamed: lib/covid-drdb/drdb/commands/new_study.py -> covid-drdb/drdb/commands/new_study.py renamed: lib/covid-drdb/drdb/commands/refactor_sbj_history.py -> covid-drdb/drdb/commands/refactor_sbj_history.py renamed: lib/covid-drdb/drdb/commands/refactor_sbj_infections.py -> covid-drdb/drdb/commands/refactor_sbj_infections.py renamed: lib/covid-drdb/drdb/commands/update_glue_prevalence.py -> covid-drdb/drdb/commands/update_glue_prevalence.py renamed: lib/covid-drdb/drdb/commands/update_pt_history.py -> covid-drdb/drdb/commands/update_pt_history.py renamed: lib/covid-drdb/drdb/commands/update_ref_amino_acid.py -> covid-drdb/drdb/commands/update_ref_amino_acid.py renamed: lib/covid-drdb/drdb/commands/update_variant_consensus.py -> covid-drdb/drdb/commands/update_variant_consensus.py renamed: lib/covid-drdb/drdb/entry.py -> covid-drdb/drdb/entry.py renamed: lib/covid-drdb/drdb/utils/__init__.py -> covid-drdb/drdb/utils/__init__.py renamed: lib/covid-drdb/drdb/utils/codonutils.py -> covid-drdb/drdb/utils/codonutils.py renamed: lib/covid-drdb/drdb/utils/csvv.py -> covid-drdb/drdb/utils/csvv.py renamed: lib/covid-drdb/drdb/utils/gene_position.py -> covid-drdb/drdb/utils/gene_position.py renamed: lib/covid-drdb/drdb/utils/questionary_option.py -> covid-drdb/drdb/utils/questionary_option.py renamed: lib/covid-drdb/drop_views.sql -> covid-drdb/drop_views.sql renamed: lib/covid-drdb/er-diagram.drawio -> covid-drdb/er-diagram.drawio renamed: lib/covid-drdb/mypy.ini -> covid-drdb/mypy.ini renamed: lib/covid-drdb/payload -> covid-drdb/payload renamed: lib/covid-drdb/pipeline.drawio -> covid-drdb/pipeline.drawio renamed: lib/covid-drdb/pipeline.svg -> covid-drdb/pipeline.svg renamed: lib/covid-drdb/postgresql.conf -> covid-drdb/postgresql.conf renamed: lib/covid-drdb/schema.dbml -> covid-drdb/schema.dbml renamed: lib/covid-drdb/scripts/create-tag.sh -> covid-drdb/scripts/create-tag.sh renamed: lib/covid-drdb/scripts/db_to_sqlite.py -> covid-drdb/scripts/db_to_sqlite.py renamed: lib/covid-drdb/scripts/export-sqlite.sh -> covid-drdb/scripts/export-sqlite.sh renamed: lib/covid-drdb/scripts/export-sqls.sh -> covid-drdb/scripts/export-sqls.sh renamed: lib/covid-drdb/scripts/export-susc-summary.sh -> covid-drdb/scripts/export-susc-summary.sh renamed: lib/covid-drdb/scripts/github-release.sh -> covid-drdb/scripts/github-release.sh renamed: lib/covid-drdb/scripts/import_sierra_mutations.sh -> covid-drdb/scripts/import_sierra_mutations.sh renamed: lib/covid-drdb/scripts/make-drms-slim.sh -> covid-drdb/scripts/make-drms-slim.sh renamed: lib/covid-drdb/scripts/make-slim-version.sh -> covid-drdb/scripts/make-slim-version.sh renamed: lib/covid-drdb/scripts/make-variants-slim.sh -> covid-drdb/scripts/make-variants-slim.sh renamed: lib/covid-drdb/scripts/sync-to-s3.sh -> covid-drdb/scripts/sync-to-s3.sh renamed: lib/covid-drdb/scripts/watch-release.sh -> covid-drdb/scripts/watch-release.sh renamed: lib/covid-drdb/views/01_mab_view.sql -> covid-drdb/views/01_mab_view.sql renamed: lib/covid-drdb/views/02_rx_mab_view.sql -> covid-drdb/views/02_rx_mab_view.sql renamed: lib/covid-drdb/views/03_dms_mab_view.sql -> covid-drdb/views/03_dms_mab_view.sql renamed: lib/covid-drdb/views/04_rx_dms_mab_view.sql -> covid-drdb/views/04_rx_dms_mab_view.sql renamed: lib/covid-drdb/views/05_iso_view.sql -> covid-drdb/views/05_iso_view.sql renamed: lib/covid-drdb/views/06_rx_cp_view.sql -> covid-drdb/views/06_rx_cp_view.sql renamed: lib/covid-drdb/views/07_rx_vp_view.sql -> covid-drdb/views/07_rx_vp_view.sql renamed: lib/covid-drdb/views/08_susc_view.sql -> covid-drdb/views/08_susc_view.sql renamed: lib/covid-drdb/views/09_omicron_view.sql -> covid-drdb/views/09_omicron_view.sql renamed: lib/HIVEFileGrabber_V2.sh -> lib/shell/HIVEFileGrabber_V2.sh renamed: lib/HIVEFileGrabber_V3.1.sh -> lib/shell/HIVEFileGrabber_V3.1.sh renamed: lib/biosample_complete.sh -> lib/shell/biosample_complete.sh renamed: lib/efetch_bioproject_assemblies.sh -> lib/shell/efetch_bioproject_assemblies.sh renamed: lib/efetch_bioproject_biosample.sh -> lib/shell/efetch_bioproject_biosample.sh renamed: lib/efetch_bioproject_runs.sh -> lib/shell/efetch_bioproject_runs.sh renamed: lib/efetch_biosample_meta.sh -> lib/shell/efetch_biosample_meta.sh renamed: lib/efetch_biosample_runs.sh -> lib/shell/efetch_biosample_runs.sh renamed: lib/eutils.sh -> lib/shell/eutils.sh renamed: lib/eutils_SRAcurl_experiments.sh -> lib/shell/eutils_SRAcurl_experiments.sh renamed: lib/eutils_SRAfetch_experiments.sh -> lib/shell/eutils_SRAfetch_experiments.sh * Rename lib/biosampleMDG.sh to lib/shell/biosampleMDG.sh * Rename lib/test_file_generation.sh to lib/shell/test_file_generation.sh * Update file names for schema files Changes to be committed: renamed: schema/v1.0/non-core/uniprot-proteome_*.json -> schema/v1.0/non-core/uniprot-proteome_.json renamed: schema/v1.1/non-core/uniprot-proteome_*.json -> schema/v1.1/non-core/uniprot-proteome_.json renamed: schema/v1.2/non-core/uniprot-proteome_*.json -> schema/v1.2/non-core/uniprot-proteome_.json renamed: schema/v1.3/non-core/uniprot-proteome_*.json -> schema/v1.3/non-core/uniprot-proteome_.json * test * Add files via upload New ngs_id.py and associated files * V1.4 Data Files * V1.4 Data Files * Create v1.4 * Rename data_files/DRM_all_orgs.tsv to data_files/v1.4_data_files/DRM_all_orgs.tsv * Bump certifi from 2021.10.8 to 2022.12.7 in /covid-drdb Bumps [certifi](https://github.com/certifi/python-certifi) from 2021.10.8 to 2022.12.7. - [Commits](certifi/python-certifi@2021.10.08...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> * Bump certifi from 2021.10.8 to 2022.12.7 Bumps [certifi](https://github.com/certifi/python-certifi) from 2021.10.8 to 2022.12.7. - [Commits](certifi/python-certifi@2021.10.08...2022.12.07) --- updated-dependencies: - dependency-name: certifi dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump lxml from 4.8.0 to 4.9.1 in /covid-drdb Bumps [lxml](https://github.com/lxml/lxml) from 4.8.0 to 4.9.1. - [Release notes](https://github.com/lxml/lxml/releases) - [Changelog](https://github.com/lxml/lxml/blob/master/CHANGES.txt) - [Commits](lxml/lxml@lxml-4.8.0...lxml-4.9.1) --- updated-dependencies: - dependency-name: lxml dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump requests from 2.27.1 to 2.31.0 in /covid-drdb Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.27.1...v2.31.0) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Bump requests from 2.27.1 to 2.31.0 Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0. - [Release notes](https://github.com/psf/requests/releases) - [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md) - [Commits](psf/requests@v2.27.1...v2.31.0) --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Stephanie Singleton <[email protected]> Co-authored-by: penningtonea <[email protected]> Co-authored-by: Jgergely11 <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Changes to be committed: modified: data_dictionary/README.md deleted: data_dictionary/v1.4 new file: data_dictionary/v1.4/README.tsv new file: data_dictionary/v1.4/annotation_property_list.tsv new file: data_dictionary/v1.4/core_property_list.tsv new file: data_dictionary/v1.4/property_definition.tsv new file: data_dictionary/v1.4/release_notes.tsv modified: lib/dictionary_utils.py new file: schema/v1.4/annotation/DRM_all_orgs.json new file: schema/v1.4/core/assemblyQC_HIVE.json new file: schema/v1.4/core/assemblyQC_NCBI.json new file: schema/v1.4/core/biosampleMeta_HIVE.json new file: schema/v1.4/core/biosampleMeta_NCBI.json new file: schema/v1.4/core/ngsQC_HIVE.json new file: schema/v1.4/core/ngsQC_NCBI.json new file: schema/v1.4/core/ngs_id_list.json new file: schema/v1.4/core/siteQC_HIVE.json
Changes to be committed: modified: schema/README.md
Changes to be committed: modified: data_dictionary/README.md modified: data_dictionary/v1.4/annotation_property_list.tsv modified: data_dictionary/v1.4/core_property_list.tsv new file: tests/README.md
Changes to be committed: modified: schema/v1.4/annotation/DRM_all_orgs.json modified: schema/v1.4/core/assemblyQC_HIVE.json modified: schema/v1.4/core/assemblyQC_NCBI.json modified: schema/v1.4/core/biosampleMeta_HIVE.json modified: schema/v1.4/core/biosampleMeta_NCBI.json modified: schema/v1.4/core/ngsQC_HIVE.json modified: schema/v1.4/core/ngsQC_NCBI.json modified: schema/v1.4/core/ngs_id_list.json modified: schema/v1.4/core/siteQC_HIVE.json
Changes to be committed: new file: tests/v1.4/test_files/DRM_all_orgs.tsv new file: tests/v1.4/test_files/NC_045512_SARS-CoV-2_Wuhan.fasta new file: tests/v1.4/test_files/annotation_property_list.tsv new file: tests/v1.4/test_files/assemblyQC_HIVE.tsv new file: tests/v1.4/test_files/assemblyQC_NCBI.tsv new file: tests/v1.4/test_files/biosampleMeta_HIVE.tsv new file: tests/v1.4/test_files/biosampleMeta_NCBI.tsv new file: tests/v1.4/test_files/core_property_list.tsv new file: tests/v1.4/test_files/ngsQC_HIVE.tsv new file: tests/v1.4/test_files/ngsQC_NCBI.tsv new file: tests/v1.4/test_files/ngs_id_list.tsv new file: tests/v1.4/test_files/property_definition.tsv new file: tests/v1.4/test_files/reference-guided_genome_assemblies_Galaxy.fasta new file: tests/v1.4/test_files/reference-guided_genome_assemblies_HIVE-Hexagon.fasta new file: tests/v1.4/test_files/siteQC_HIVE.tsv new file: tests/v1.4/test_files/temp_archive
Changes to be committed: modified: lib/data_sheet_validator.py new file: tests/v1.4/test_results/DRM_all_orgs.json renamed: tests/README.md -> tests/v1.4/test_results/README.md new file: tests/v1.4/test_results/assemblyQC_HIVE.json new file: tests/v1.4/test_results/assemblyQC_NCBI.json new file: tests/v1.4/test_results/biosampleMeta_HIVE.json new file: tests/v1.4/test_results/biosampleMeta_NCBI.json new file: tests/v1.4/test_results/ngsQC_HIVE.json new file: tests/v1.4/test_results/ngsQC_NCBI.json new file: tests/v1.4/test_results/ngs_id_list.json new file: tests/v1.4/test_results/siteQC_HIVE.json new file: tests/v1.4/test_results/summary.txt
Changes to be committed: modified: data_dictionary/README.md
2 tasks
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.