Replace remote S3 paths with local paths for test_snake dryruns. #915
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yesimon
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Mar 1, 2019
Add support for krakenuniq, kaiju to replace kraken and diamond in default pipelines. Both rely on customized krakenuniq/kaiju packages for custom functionality, like loading database from pipe or printing out all taxa hits (kaiju). Krona fixed to use hit counts as scores in report files directly, instead of counting the individual read classifications (which takes a long time). Includes changes from #915 and also some pytest deprecation fixes: s/log.warn(/log.warning(/, runslow command line configuration.
Save time querying S3 remote file presence during dryruns. Since the files are not specified directly in config (they get operations to add suffixes in the rules), need to create a fake tree of files (or hardcode the paths to rewrite).
tomkinsc
requested changes
Mar 2, 2019
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| def translate_remote_s3(uri): | ||
| remote_path = uri[5:] | ||
| fake_s3_root = os.path.join(util.file.get_project_path(), 'test', 'input', 's3') |
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Maybe all of the empty placeholder files should be made dynamically as part of the tests?
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It's hard to determine what the filenames need to be dynamically. Either need to store a list of filenames to then create at runtime or create empty files - I'm ambivalent about these two.
tomkinsc
approved these changes
Mar 3, 2019
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Save time querying S3 remote file presence during dryruns. Since the files are not specified
directly in config (they get operations to add suffixes in the rules), need to create a fake tree
of files (or hardcode the paths to rewrite).