Tags: FDA-ARGOS/data.argosdb
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Create v1.6 schemas Changes to be committed: modified: README.md new file: data_dictionary/v1.6/README.tsv new file: data_dictionary/v1.6/annotation_property_list.tsv new file: data_dictionary/v1.6/core_property_list.tsv new file: data_dictionary/v1.6/property_definition.tsv new file: data_dictionary/v1.6/release_notes.tsv new file: schema/v1.6/annotation/DRM_all_orgs.json new file: schema/v1.6/core/assemblyQC.json new file: schema/v1.6/core/assemblyQC_HIVE.json new file: schema/v1.6/core/assemblyQC_NCBI.json new file: schema/v1.6/core/biosampleMeta_HIVE.json new file: schema/v1.6/core/biosampleMeta_NCBI.json new file: schema/v1.6/core/ngsQC.json new file: schema/v1.6/core/ngsQC_HIVE.json new file: schema/v1.6/core/ngsQC_NCBI.json new file: schema/v1.6/core/ngs_id_list.json new file: schema/v1.6/core/siteQC_HIVE.json
V1.4 (#325) * 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]> * update (#326) * 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> * Pre-release for v1.4 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 * fix Changes to be committed: modified: data_files/biosampleMeta_ncbi.tsv * readme links Changes to be committed: modified: schema/README.md * Update README.md * Update property lists and README 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 * Fix for Schemas 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 * Add v1.4 test files 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 * Testing results 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 * README Changes to be committed: modified: data_dictionary/README.md * Update docs Changes to be committed: modified: data_dictionary/README.md * V1.4 Data Files * Rename data_files/DRM_all_orgs.tsv to data_files/v1.4_data_files/DRM_all_orgs.tsv --------- 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>
V1.3 (#285) * Add BisampleMeta_ncbi Changes to be committed: new file: data_files/biosampleMeta_ncbi.tsv * Fixes for Review [Fixes for Review](#230 (comment)) Changes to be committed: modified: data_files/biosampleMeta_ncbi.tsv * v1.3 Data data_dictionary Changes to be committed: new file: data_dictionary/v1.3/README.tsv new file: data_dictionary/v1.3/core_property_list.tsv new file: data_dictionary/v1.3/non-core_property_list.tsv new file: data_dictionary/v1.3/property_definition.tsv new file: data_dictionary/v1.3/release_notes.tsv new file: schema/v1.3/core/.json new file: schema/v1.3/core/assemblyQC.json new file: schema/v1.3/core/assemblyQC_NCBI.json new file: schema/v1.3/core/biosampleMeta.json new file: schema/v1.3/core/ngsQC.json new file: schema/v1.3/core/ngsQC_NCBI.json new file: schema/v1.3/core/siteQC.json new file: schema/v1.3/non-core/.json new file: schema/v1.3/non-core/SRA_biosample.json new file: schema/v1.3/non-core/ngs_ID_list.json new file: schema/v1.3/non-core/sars-cov-2_lineage_mutations.json new file: schema/v1.3/non-core/uniprot-proteome_*.json * After Tests Changes to be committed: new file: lib/test_file_generation.sh new file: tests/v1.3/test_files/NC_045512_SARS-CoV-2_Wuhan.fasta new file: tests/v1.3/test_files/UP000001014_99287.fasta new file: tests/v1.3/test_files/UP000001014_99287_DNA.fasta new file: tests/v1.3/test_files/UP000009255_211044.fasta new file: tests/v1.3/test_files/UP000009255_211044_DNA.fasta new file: tests/v1.3/test_files/UP000009255_proteome_genome_metadata.csv new file: tests/v1.3/test_files/UP000180448_33727.fasta new file: tests/v1.3/test_files/UP000180448_33727_DNA.fasta new file: tests/v1.3/test_files/UP000464024_2697049.fasta new file: tests/v1.3/test_files/UP000464024_2697049_DNA.fasta new file: tests/v1.3/test_files/assemblyQC_HIVE.tsv new file: tests/v1.3/test_files/assemblyQC_NCBI.tsv new file: tests/v1.3/test_files/biosampleMeta_HIVE.tsv new file: tests/v1.3/test_files/biosampleMeta_ncbi.tsv new file: tests/v1.3/test_files/core_property_list.tsv new file: tests/v1.3/test_files/ngsQC_HIVE.tsv new file: tests/v1.3/test_files/ngsQC_NCBI.tsv new file: tests/v1.3/test_files/ngsQC_PL.tsv new file: tests/v1.3/test_files/ngs_id_list.tsv new file: tests/v1.3/test_files/non-core_property_list.tsv new file: tests/v1.3/test_files/property_definition.tsv new file: tests/v1.3/test_files/reference-guided_genome_assemblies_Galaxy.fasta new file: tests/v1.3/test_files/reference-guided_genome_assemblies_HIVE-Hexagon.fasta new file: tests/v1.3/test_files/sars-cov-2_lineage_mutations.tsv new file: tests/v1.3/test_files/siteQC_HIVE.tsv new file: tests/v1.3/test_files/temp_archive new file: tests/v1.3/test_files/uniprot-proteome_UP000001014.csv new file: tests/v1.3/test_files/uniprot-proteome_UP000180448.csv new file: tests/v1.3/test_files/uniprot-proteome_UP000464024.csv new file: tests/v1.3/test_results/assemblyQC_HIVE.json new file: tests/v1.3/test_results/assemblyQC_NCBI.json new file: tests/v1.3/test_results/biosampleMeta_HIVE.json new file: tests/v1.3/test_results/biosampleMeta_ncbi.json new file: tests/v1.3/test_results/core_property_list.json * README Changes to be committed: new file: data_dictionary/README.md
V1.2 (#205) * update assembly_qc_ncbi_.py Also created assemblyQC_ncbi_all.tsv * T124 biosample meta (#191) * resolved merge conflict * revert in order to facilitate rebasing * Repair after rebase * Adding README * revert in order to facilitate rebasing * More forgiving xpath * Fix for #131 Changes to be committed: deleted: Untitled Diagram.drawio new file: data_files/draft_galaxy_BCO_example.json new file: data_files/extsion_example.json modified: lib/galaxy_converter.py deleted: test.tsv * Improved documentation for galaxy_converter Changes to be committed: new file: data_files/final_galaxy_bco_result.json modified: lib/galaxy_converter.py * Remove failing CI actions * resolved merge conflict * revert in order to facilitate rebasing * Repair after rebase * Adding README * revert in order to facilitate rebasing * More forgiving xpath * Assembly QC Data flow 1st piece for #135 Changes to be committed: new file: docs/DataFlow.pptx new file: docs/DataFlow_assemblyQC_NCBI.pdf * Loop through a text file of biosample ids, create a single TSV file * Added lineage grab; reordered tsv columns to adhere to schema v1.0 Co-authored-by: [email protected] <[email protected]> * Fixes #162 * ngsQC_NCBI.tsv Fix #144 new file: lib/add_lineage.py modified: lib/efetch_bioproject_runs.sh modified: lib/eutils_SRAcurl_experiments.sh new file: lib/get_linage.py deleted: lib/linage.py new file: lib/sra_run_info_parser.py * Add ngsQC to data_files Fix #144 new file: data_files/ngsQC_NCBI.tsv * Sort assemblyQC_ncbi Changes to be committed: * ngsQC_ncbi_update modified: data_files/assemblyQC_NCBI.tsv new file: data_files/assemblyQC_NCBI_orig.tsv deleted: data_files/assemblyQC_ncbi_all.tsv modified: data_files/ngsQC_NCBI.tsv * update NCBI files Fix #144 Fix #145 Changes to be committed: modified: data_files/assemblyQC_NCBI.tsv modified: data_files/ngsQC_NCBI.tsv * Ngs qc ncbi update (#202) * ngsQC_NCBI.tsv Fix #144 new file: lib/add_lineage.py modified: lib/efetch_bioproject_runs.sh modified: lib/eutils_SRAcurl_experiments.sh new file: lib/get_linage.py deleted: lib/linage.py new file: lib/sra_run_info_parser.py * Add ngsQC to data_files Fix #144 new file: data_files/ngsQC_NCBI.tsv * Sort assemblyQC_ncbi Changes to be committed: * ngsQC_ncbi_update modified: data_files/assemblyQC_NCBI.tsv new file: data_files/assemblyQC_NCBI_orig.tsv deleted: data_files/assemblyQC_ncbi_all.tsv modified: data_files/ngsQC_NCBI.tsv * update NCBI files Fix #144 Fix #145 Changes to be committed: modified: data_files/assemblyQC_NCBI.tsv modified: data_files/ngsQC_NCBI.tsv * 1st commit new file: data_dictionary/v1.2/README.txt new file: data_dictionary/v1.2/core_property_list.txt new file: data_dictionary/v1.2/non-core_property_list.txt new file: data_dictionary/v1.2/property_definition.txt new file: data_dictionary/v1.2/release_notes.txt * Run schema generation For #201 Changes to be committed: renamed: data_dictionary/v1.2/README.txt -> data_dictionary/v1.2/README.tsv new file: data_dictionary/v1.2/core_property_list.tsv deleted: data_dictionary/v1.2/core_property_list.txt new file: data_dictionary/v1.2/non-core_property_list.tsv deleted: data_dictionary/v1.2/non-core_property_list.txt renamed: data_dictionary/v1.2/property_definition.txt -> data_dictionary/v1.2/property_definition.tsv renamed: data_dictionary/v1.2/release_notes.txt -> data_dictionary/v1.2/release_notes.tsv new file: schema/v1.2/core/assemblyQC.json new file: schema/v1.2/core/assemblyQC_NCBI.json new file: schema/v1.2/core/biosampleMeta.json new file: schema/v1.2/core/ngsQC.json new file: schema/v1.2/core/ngsQC_NCBI.json new file: schema/v1.2/core/siteQC.json new file: schema/v1.2/non-core/SRA_biosample.json new file: schema/v1.2/non-core/ngs_ID_list.json new file: schema/v1.2/non-core/sars-cov-2_lineage_mutations.json new file: schema/v1.2/non-core/uniprot-proteome_*.json * Testing data files * Testign data files Changes to be committed: new file: tests/v1.1/test_files/NC_045512_SARS-CoV-2_Wuhan.fasta new file: tests/v1.1/test_files/PRJNA231221_AssemblyUpdated.tsv new file: tests/v1.1/test_files/SRA_biosample.tsv new file: tests/v1.1/test_files/SRA_ngsQC.tsv new file: tests/v1.1/test_files/UP000001014_99287.fasta new file: tests/v1.1/test_files/UP000001014_99287_DNA.fasta new file: tests/v1.1/test_files/UP000009255_211044.fasta new file: tests/v1.1/test_files/UP000009255_211044_DNA.fasta new file: tests/v1.1/test_files/UP000009255_proteome_genome_metadata.csv new file: tests/v1.1/test_files/UP000180448_33727.fasta new file: tests/v1.1/test_files/UP000180448_33727_DNA.fasta new file: tests/v1.1/test_files/UP000464024_2697049.fasta new file: tests/v1.1/test_files/UP000464024_2697049_DNA.fasta new file: tests/v1.1/test_files/assemblyQC-Pond.tsv new file: tests/v1.1/test_files/assemblyQC_HL.tsv new file: tests/v1.1/test_files/assemblyQC_NCBI.tsv new file: tests/v1.1/test_files/biosampleMeta-Crandall.tsv new file: tests/v1.1/test_files/biosampleMeta_HL.tsv new file: tests/v1.1/test_files/core_property_list.tsv new file: tests/v1.1/test_files/ngsQC_Crandall.tsv new file: tests/v1.1/test_files/ngsQC_HL.tsv new file: tests/v1.1/test_files/ngs_id_list.tsv new file: tests/v1.1/test_files/non-core_property_list.tsv new file: tests/v1.1/test_files/property_definition.tsv new file: tests/v1.1/test_files/sars-cov-2_lineage_mutations.tsv new file: tests/v1.1/test_files/siteQC_HL.tsv new file: tests/v1.1/test_files/uniprot-proteome_UP000001014.csv new file: tests/v1.1/test_files/uniprot-proteome_UP000180448.csv new file: tests/v1.1/test_files/uniprot-proteome_UP000464024.csv --------- Co-authored-by: [email protected] <[email protected]>
V1.0 (#121) * updating (#119) * fix broken file names * Added ngs_id_script.py and template docs * Added ngs_id_script.py and template dataset * Bump numpy from 1.21.4 to 1.22.0 Bumps [numpy](https://github.com/numpy/numpy) from 1.21.4 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.21.4...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * ngs from API (#115) * fix broken file names * Added ngs_id_script.py and template docs * Added ngs_id_script.py and template dataset * message Please enter the commit message for your changes. Lines starting * updated script Co-authored-by: hadleyking <[email protected]> * Update galaxy_converter.py * ARGOSDB API argosdb_api_query Changes to be committed: new file: lib/argosdb_api_query.py modified: lib/assembly_qc_ncbi_.py * saving changes * make argosdb_api_query.py script Fix #95 Changes to be committed: modified: lib/assembly_qc_ncbi_.py Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: jgergely11 <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jgergely11 <[email protected]> * V1.0 Version 1.0 docs Changes to be committed: modified: .gitignore new file: data_dictionary/v1.0/README.tsv new file: data_dictionary/v1.0/core_property_list.tsv new file: data_dictionary/v1.0/non-core_property_list.tsv new file: data_dictionary/v1.0/property_definition.tsv new file: data_dictionary/v1.0/release_notes.tsv modified: lib/assembly_qc_ncbi_.py modified: lib/data_sheet_validator.py modified: lib/dict_release_notes.py modified: lib/dictionary_utils.py new file: schema/README.md modified: schema/v0.9/core/siteQC.json new file: schema/v1.0/core/assemblyQC.json new file: schema/v1.0/core/biosampleMeta.json new file: schema/v1.0/core/ngsQC.json new file: schema/v1.0/core/siteQC.json new file: schema/v1.0/non-core/SRA_assemblyQC.json new file: schema/v1.0/non-core/SRA_biosample.json new file: schema/v1.0/non-core/SRA_ngsQC.json new file: schema/v1.0/non-core/ngs_ID_list.json new file: schema/v1.0/non-core/sars-cov-2_lineage_mutations.json new file: schema/v1.0/non-core/uniprot-proteome_*.json * Release for v1.0 Includes test files and test results Changes to be committed: modified: .gitignore modified: lib/argosdb_api_query.py modified: lib/data_sheet_validator.py new file: tests/v1.0/test_files/PRJNA231221_AssemblyUpdated.tsv new file: tests/v1.0/test_files/SRA_biosample.tsv new file: tests/v1.0/test_files/SRA_ngsQC.tsv new file: tests/v1.0/test_files/UP000001014_99287.fasta new file: tests/v1.0/test_files/UP000001014_99287_DNA.fasta new file: tests/v1.0/test_files/UP000009255_211044.fasta new file: tests/v1.0/test_files/UP000009255_211044_DNA.fasta new file: tests/v1.0/test_files/UP000009255_proteome_genome_metadata.csv new file: tests/v1.0/test_files/UP000180448_33727.fasta new file: tests/v1.0/test_files/UP000180448_33727_DNA.fasta new file: tests/v1.0/test_files/UP000464024_2697049.fasta new file: tests/v1.0/test_files/UP000464024_2697049_DNA.fasta new file: tests/v1.0/test_files/assemblyQC-Pond.tsv new file: tests/v1.0/test_files/assemblyQC_HL.tsv new file: tests/v1.0/test_files/assemblyQC_NCBI.tsv new file: tests/v1.0/test_files/biosampleMeta-Crandall.tsv new file: tests/v1.0/test_files/biosampleMeta_HL.tsv new file: tests/v1.0/test_files/core_property_list.tsv new file: tests/v1.0/test_files/ngsQC_Crandall.tsv new file: tests/v1.0/test_files/ngsQC_HL.tsv new file: tests/v1.0/test_files/ngs_ID_list.tsv new file: tests/v1.0/test_files/non-core_property_list.tsv new file: tests/v1.0/test_files/property_definition.tsv new file: tests/v1.0/test_files/sars-cov-2_lineage_mutations.tsv new file: tests/v1.0/test_files/siteQC_HL.tsv new file: tests/v1.0/test_files/uniprot-proteome_UP000001014.csv new file: tests/v1.0/test_files/uniprot-proteome_UP000180448.csv new file: tests/v1.0/test_files/uniprot-proteome_UP000464024.csv new file: tests/v1.0/test_results/SRA_biosample.json new file: tests/v1.0/test_results/SRA_ngsQC.json new file: tests/v1.0/test_results/assemblyQC-Pond.json new file: tests/v1.0/test_results/assemblyQC_HL.json new file: tests/v1.0/test_results/assemblyQC_NCBI.json new file: tests/v1.0/test_results/biosampleMeta-Crandall.json new file: tests/v1.0/test_results/biosampleMeta_HL.json new file: tests/v1.0/test_results/ngsQC_Crandall.json new file: tests/v1.0/test_results/ngsQC_HL.json new file: tests/v1.0/test_results/ngs_ID_list.json new file: tests/v1.0/test_results/sars-cov-2_lineage_mutations.json new file: tests/v1.0/test_results/siteQC_HL.json new file: tests/v1.0/test_results/uniprot-proteome_UP000001014.json new file: tests/v1.0/test_results/uniprot-proteome_UP000180448.json new file: tests/v1.0/test_results/uniprot-proteome_UP000464024.json Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: jgergely11 <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jgergely11 <[email protected]>
V0.9 (#82) * Create ngsDataGrabber.py This is a copy of ngsDataGrabber_V0.6.py and it has been renamed to something more generic for ngsQC protocol. * Create assemblyQC_data_grabber.py file This file is created in order to extract numbers of unspecified nucleotides from the backend. * Update assemblyQC_data_grabber.py * Bump numpy from 1.21.6 to 1.22.0 in /lib Bumps [numpy](https://github.com/numpy/numpy) from 1.21.6 to 1.22.0. - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v1.21.6...v1.22.0) --- updated-dependencies: - dependency-name: numpy dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> * Created assemblyQC_NCBI.tsv Changes to be committed: new file: data_files/assemblyQC_NCBI.tsv new file: lib/assembly_qc_ncbi_.py * Update requirements.txt Changes to be committed: modified: requirements.txt * Publish v0.9 Changes to be committed: new file: data_dictionary/v0.9/README.tsv new file: data_dictionary/v0.9/core_property_list.tsv new file: data_dictionary/v0.9/non_core_property_list.tsv new file: data_dictionary/v0.9/property_definition.tsv new file: data_dictionary/v0.9/release_notes.tsv new file: schema/v0.9/core/assemblyQC.json new file: schema/v0.9/core/biosampleMeta.json new file: schema/v0.9/core/ngsQC.json new file: schema/v0.9/core/siteQC.json new file: schema/v0.9/non-core/SRA_assemblyQC.json new file: schema/v0.9/non-core/SRA_biosample.json new file: schema/v0.9/non-core/SRA_ngsQC.json new file: schema/v0.9/non-core/ngs_ID_list.json new file: schema/v0.9/non-core/sars-cov-2_lineage_mutations.json new file: schema/v0.9/non-core/uniprot-proteome_*.json Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Jingyue Wu <[email protected]> Co-authored-by: penningtonea <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
v0.8 files added (#76) Changes to be committed: new file: data_dictionary/v0.8/README.tsv new file: data_dictionary/v0.8/core_property_list.tsv new file: data_dictionary/v0.8/non-core_property_list.tsv new file: data_dictionary/v0.8/property_definition.tsv new file: data_dictionary/v0.8/release_notes.tsv renamed: data_files/SRA_AssemblyUpdated.tsv -> data_files/SRA_Assembly.tsv modified: data_files/SRA_biosample.tsv modified: data_files/SRA_ngsQC.tsv deleted: data_files/SRA_ngsQCTEST.tsv modified: lib/write_schema.py modified: schema/v0.7/core/assemblyQC.json modified: schema/v0.7/core/biosampleMeta.json modified: schema/v0.7/core/ngsQC.json modified: schema/v0.7/core/siteQC.json new file: schema/v0.8/core/assemblyQC.json new file: schema/v0.8/core/biosampleMeta.json new file: schema/v0.8/core/ngsQC.json new file: schema/v0.8/core/siteQC.json new file: schema/v0.8/non-core/SRA_assemblyQC.json new file: schema/v0.8/non-core/SRA_biosample.json new file: schema/v0.8/non-core/SRA_ngsQC.json new file: schema/v0.8/non-core/ngs_ID_list.json new file: schema/v0.8/non-core/sars-cov-2_lineage_mutations.json new file: schema/v0.8/non-core/uniprot-proteome_*.json
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