ngs from API #115
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ngs from API #115
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fix broken file names
HadleyKing
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Nov 14, 2022
* 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]>
HadleyKing
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Nov 21, 2022
* 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]>
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