Enable local mode and improve podp mode #207
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The new design does not allow users to specify the path to their data files, instead they should always put data files to default paths defined by nplinker. To keep it simple, some settings are removed in the new config template. They could be added later if really needed.
- add function `transform_to_full_path` - add code to create download/extract dir if not exist - update docstrings to specify that the download/extract dir does not have to be exist
Transform `root_dir` to full path.
- add the support of PathLike path
- remove function `podp_run_bigscape` - updated function `run_bigscape`
- remove function `check_integrity` - update md5 checking in function `download_url`
- Add class `DatasetArranger` - Add dataset validation functions `validate_gnps`, `validate_antismash` and `validate_bigscape`
…inker/nplinker into refactor_project_folder_init
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Current dependencies on/for this PR: This stack of pull requests is managed by Graphite. |
CunliangGeng
changed the title
GNPS file mappings file could be tsv or csv file. - rename `gnps_file_mapping_tsv_file` to `gnps_file_mappings_file` - rename `tsv_file` to `gnps_file_mappings_file` - update relevant docstrings
- remove extension for `GNPS_FILE_MAPPINGS_FILENAME`
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redesign the template of config file
The new design does not allow users to specify the path to their data files, instead they should always put data files to default paths defined by nplinker.
To keep it simple, some settings are removed in the new config template. They could be added later if really needed.
update default values of config
add validations for all settings
remove config test demo2
update unit test for new configs
update utils.py
transform_to_full_pathUpdate config.py
Transform
root_dirto full path.Update mibig_downloader.py
add default data paths to globals
Update globals.py
move PFAM_PATH to where it is used
Update mibig_downloader.py
Update runbigscape.py
podp_run_bigscaperun_bigscapeupdate utils on checking md5
check_integritydownload_urlCreate arranger.py
DatasetArrangervalidate_gnps,validate_antismashandvalidate_bigscapeDelete downloader.py and its tests
remove running of bigscape in dataset loader
remove func
_start_downloadsfrom DatasetLoaderremove init paths from DatasetLoader
Merge branch 'refactor_project_folder_init' of https://github.com/NPLinker/nplinker into refactor_project_folder_init