Issue151 use json for genome status file #157

CunliangGeng · 2023-07-05T07:42:06Z

Resolve #151.

👉 it's easier to review commit by commit.

instead you can use GenomeStatus.load_from_json.

src/nplinker/pairedomics/podp_antismash_downloader.py

CunliangGeng added 10 commits July 4, 2023 17:22

re-format code

eae4ccb

remove deprecated methods and unused varaibles

72a8483

refactor class GenomeStatus

8e485ca

remove private method _get_genome_status_log

6ef8c64

instead you can use GenomeStatus.load_from_json.

update GenomeStatus usage in podp antismash downloader

eab3b9d

Update __init__.py

14b0a3e

update GenomeStatus attribute names in tests

739bc60

remove tests for old GenomeStatus class

e6f9fb4

fix GenomeUsage usage in tests

43e6cb3

add unit tests for GenomeStatus class

e8d80ad

CunliangGeng requested a review from gcroci2 July 5, 2023 07:42

CunliangGeng added 4 commits July 5, 2023 14:14

rename method load_from_json to read_json

08774c8

rename method save_to_json to to_json

b2d88d0

change parameter output_dir to file for to_json method

6f4e123

enable to_json return string when output file is None

779465d

CunliangGeng marked this pull request as draft July 5, 2023 12:38

CunliangGeng marked this pull request as ready for review July 5, 2023 12:40

gcroci2 reviewed Jul 6, 2023

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gcroci2 reviewed Jul 6, 2023

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gcroci2 approved these changes Jul 6, 2023

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fix refseq id None

0594a48

CunliangGeng merged commit 0a74dcd into dev Jul 6, 2023
2 of 4 checks passed

CunliangGeng deleted the issue151_json_genome_status branch July 11, 2023 11:10

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