opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #7049 from bernt-matthias/topic/doc-errors-detection

Browse Source 
doc: updated error parsing docs
This commit is contained in:
Martin Cech
2018-12-07 14:42:40 -05:00
committed by GitHub
parent f09d7b7d93 c4c8af036f
commit 1ca77d53ef
1 changed files with 5 additions and 12 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/tools/xsd/galaxy.xsd
+5 -12
View File
@@ -2699,20 +2699,13 @@ on the topic of ``GALAXY_SLOTS`` for more information and examples.
### Error detection
The ``detect_errors`` attribute of ``command``, if present, can be one of:
The ``detect_errors`` attribute of ``command``, if present, loads a preset of error detection checks (for exit codes and content of stdio to indicate fatal tool errors or fatal out of memory errors). It can be one of:
* ``default``: no-op fallback to ``stdio`` tags and erroring on standard error output (for legacy tools).
* ``exit_code``: error if tool exit code is not 0. (The @jmchilton recommendation).
* ``aggressive``: error if tool exit code is not 0 or ``Exception:``, ``Error:``, or
various messages related to being out of memory appear in the standard error or output.
(The @bgruening recommendation).
* ``default``: for non-legacy tools with absent stdio block non-zero exit codes are added. For legacy tools or if a stdio block is present nothing is added.
* ``exit_code``: adds checks for non zero exit codes (The @jmchilton recommendation). The ``oom_exit_code`` parameter can be used to add an additional out of memory indicating exit code.
* ``aggressive``: adds checks for non zero exit codes, and checks for ``Exception:``, ``Error:`` in the standard error. Additionally checks for messages in the standard error that indicate an out of memory error (``MemoryError``, ``std::bad_alloc``, ``java.lang.OutOfMemoryError``, ``Out of memory``). (The @bgruening recommendation).
For newer tools with ``profile>=16.04``, the default behavior is ``exit_code``.
Legacy tools default to ``default`` behavior described above (erroring if the tool
produces any standard error output).
See [pull request 117](https://github.com/galaxyproject/galaxy/pull/117) for more implementation
information and discussion on the ``detect_errors`` attribute.
Prior to Galaxy release 19.01 the stdio block has only been used for non-legacy tools using ``default``. From release 19.01 checks defined in the stdio tag are prepended to the checks defined by the presets loaded in the command block.
]]></xs:documentation>
</xs:annotation>
<xs:simpleContent>