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base repository: FDA-ARGOS/data.argosdb
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base: v0.7
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head repository: FDA-ARGOS/data.argosdb
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compare: v.08
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  • 12 commits
  • 27 files changed
  • 3 contributors

Commits on Jun 9, 2022

  1. Fixes #70 - adds HIVE ID to file name

    @kerchner
    kerchner committed Jun 9, 2022
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  2. Merge pull request #71 from FDA-ARGOS/t70_hive_id 

    Fixes #70 - adds HIVE ID to file name
    @kee007ney
    kee007ney authored Jun 9, 2022
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  3. Add comment, remove pandas import 

    Pandas isn't used (and is a huge import).
    @kee007ney
    kee007ney authored Jun 9, 2022
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Commits on Jul 25, 2022

  1. Resolves #72 - new Python biosample data grabber

    @kerchner
    kerchner committed Jul 25, 2022
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  2. Merge pull request #73 from FDA-ARGOS/t72_biosample_datagrabber 

    Resolves #72 - new Python biosample data grabber
    @kee007ney
    kee007ney authored Jul 25, 2022
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  3. Reduce sleep time

    @kerchner
    kerchner committed Jul 25, 2022
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Commits on Jul 26, 2022

  1. Minor tweak to sleeptime

    @kee007ney
    kee007ney authored Jul 26, 2022
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  2. V0.7 (#75) 

    * Add data_sheet_validator and test files
Changes to be committed:
	modified:   data_files/SRA_ngsQCTEST.tsv
	deleted:    data_files/test_SRA_ngsQC.tsv
	new file:   lib/data_sheet_validator.py

* Add test files and test results

Changes to be committed:
	new file:   tests/test_files/SRA_assemblyQC.tsv
	new file:   tests/test_files/SRA_biosample.tsv
	new file:   tests/test_files/SRA_ngsQC.tsv
	new file:   tests/test_files/assemblyQC_HL.tsv
	new file:   tests/test_files/biosampleMeta_HL.tsv
	new file:   tests/test_files/ngsQC_Crandall.tsv
	new file:   tests/test_files/ngs_id_list.tsv
	new file:   tests/test_files/sars-cov-2_lineage_mutations.tsv
	new file:   tests/test_files/siteQC_HL.tsv
	new file:   tests/test_files/uniprot-proteome_UP000464024.csv
	new file:   tests/test_results/SRA_assemblyQC.json
	new file:   tests/test_results/SRA_biosample.json
	new file:   tests/test_results/SRA_ngsQC.json
	new file:   tests/test_results/assemblyQC.json
	new file:   tests/test_results/biosampleMeta_HL.json
	new file:   tests/test_results/ngsQC_Crandall.json
	new file:   tests/test_results/ngs_ID_list.json
	new file:   tests/test_results/sars-cov-2_lineage_mutations.json
	new file:   tests/test_results/siteQC_HL.json
	new file:   tests/test_results/uniprot-proteome_UP000464024.json

* Updated programs for v0.7 release

Changes to be committed:
	new file:   lib/__init__.py
	modified:   lib/csv2json.py
	modified:   lib/data_sheet_validator.py
	modified:   lib/dict_release_notes.py
	modified:   lib/dictionary_utils.py
	modified:   lib/headers.py
	new file:   lib/write_schema.py

* New data dictionary and release notes
Changes to be committed:
	new file:   data_dictionary/v0.7/README.tsv
	new file:   data_dictionary/v0.7/core_property_list.tsv
	new file:   data_dictionary/v0.7/non_core_property_list.tsv
	new file:   data_dictionary/v0.7/property_definition.tsv
	new file:   data_dictionary/v0.7/release_notes.tsv
	new file:   data_dictionary/v0.7/release_notes.txt

* New schemas
Changes to be committed:
	new file:   schema/v0.7/core/assemblyQC.json
	new file:   schema/v0.7/core/biosampleMeta.json
	new file:   schema/v0.7/core/ngsQC.json
	new file:   schema/v0.7/core/siteQC.json
	new file:   schema/v0.7/non-core/SRA_assemblyQC.json
	new file:   schema/v0.7/non-core/SRA_biosample.json
	new file:   schema/v0.7/non-core/SRA_ngsQC.json
	new file:   schema/v0.7/non-core/ngs_ID_list.json
	new file:   schema/v0.7/non-core/sars-cov-2_lineage_mutations.json
	new file:   schema/v0.7/non-core/uniprot-proteome_*.json

* Remove release_notes.txt
Changes to be committed:
	deleted:    data_dictionary/v0.7/release_notes.txt
    @HadleyKing
    HadleyKing authored Jul 26, 2022
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Commits on Jul 27, 2022

  1. Update biosample_datagrabber to v0.8 schema

    @kerchner
    kerchner committed Jul 27, 2022
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  2. Added ability to use NCBI API key, and automatically choose sleep time

    @kerchner
    kerchner committed Jul 27, 2022
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  3. Adds ability to pass in BCO ID, optionally

    @kerchner
    kerchner committed Jul 27, 2022
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Commits on Aug 3, 2022

  1. 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
    @HadleyKing
    HadleyKing authored Aug 3, 2022
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