Implement detect_errors attribute on command of tool XML.#117
Implement detect_errors attribute on command of tool XML.#117natefoo merged 1 commit intogalaxyproject:devfrom
detect_errors attribute on command of tool XML.#117Conversation
detect_errors attribute on XML.detect_errors attribute on tool XML.
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What about making it an attribute of |
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@nsoranzo Is there a reason you don't like |
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@jmchilton IMO how exits are handled aren't tool metadata, they're command metadata. my gut prefers @nsoranzo's suggestion. |
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Aggressive should probably allow case variants like ERROR as well as Error. |
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FWIW, there can only be one command tag now, but it'd be handy to be able to be able to define more in the future for things like map/reduce-type workflows in a single tool, or embarrassingly parallel steps in between serial steps. |
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+1 to the idea of potentially allowing multiple command tags. It might be nice to be able to put different failure modes on each command execution though. |
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@peterjc I consider @blankenberg, @natefoo so I am going to assume you guys are siding with @erasche and @nsoranzo that the |
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@jmchilton I'm fine with @peterjc suggestion to make it case insensitive. |
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Okay - I will make these two modifications then. Thanks for the input all! |
If present, it can be one of - "default", no-op fallback to stdio tags and erroring on standard error output. - "exit_code", error if tool exit code is not 0. (The @jmchilton recommendation). - "aggressive", error if tool exit code is not 0 or either Exception: or Error: appears in standard error/output. (The @bgruening recommendation). Refactoring and unit/functional tests to support and demonstrate this. Run functional test with: ./run_tests.sh -framework -id detect_errors_aggressive Run relevant unit tests: nosetests test/unit/tools/test_parsing.py Updated from original version to reflect comments on pull request galaxyproject#117 - in particular the ``detect_errors`` tag was moved from ``tool`` to ``command``.
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Okay - rebased and moved the tag and learned that these expressions have been case insensitive all along (though I made them lower case and added a comment to reflect this). |
Implement ``detect_errors`` attribute on tool XML.
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I think the title of this PR should be renamed |
detect_errors attribute on tool XML.detect_errors attribute on commamd of tool XML.
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Done. |
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Other than the typo, commamd [sic] --> command :( |
detect_errors attribute on commamd of tool XML.detect_errors attribute on command of tool XML.
Fix for galaxyproject#84 and documentation improvements
…ds for Galaxy release_15.01 or earlier.
If present, it can be one of
default, no-op fallback to stdio tags and erroring on standard error output.exit_code, error if tool exit code is not 0. (The @jmchilton recommendation).aggressive, error if tool exit code is not 0 or either Exception: or Error: appears in standard error/output. (The @bgruening recommendation).The
stdiotag is a very heavy solution when many (most?) tools use either thisexit_codeoraggressivestrategy leading to a lot of duplicated XML - and if there is one thing I like less than XML it is duplicated XML.Refactoring and unit/functional tests to support and demonstrate this.
Run relevant functional tests with:
Run relevant unit tests: