From 6e35e04712ca8046f27220d8db2d39ea217129bc Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Wed, 17 Oct 2018 15:43:15 -0400 Subject: [PATCH] 14366: Improve wording of "upgrading to containers API" section Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- doc/user/cwl/cwl-style.html.textile.liquid | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/doc/user/cwl/cwl-style.html.textile.liquid b/doc/user/cwl/cwl-style.html.textile.liquid index 07cb4aa909..fe53f4a454 100644 --- a/doc/user/cwl/cwl-style.html.textile.liquid +++ b/doc/user/cwl/cwl-style.html.textile.liquid @@ -178,7 +178,8 @@ steps: h2(#migrate). Migrating running CWL on jobs API to containers API -* When migrating from jobs API (--api=jobs) (sometimes referred to as "crunch v1") to the containers API (--api=containers) ("crunch v2") there are a few differences in behavior: -** The tool is limited to accessing only collections which are explicitly listed in the input, and further limited to only the subdirectories of collections listed in input. For example, given an explicit file input @/dir/subdir/file1.txt@, a tool will not be able to implicitly access the file @/dir/file2.txt@. Use @secondaryFiles@ or a @Directory@ input to describe trees of files. -** Files listed in @InitialWorkDirRequirement@ appear in the output directory as normal files (not symlinks) but cannot be moved, renamed or deleted. These files will be added to the output collection but without any additional copies of the underlying data. -** Tools are disallowed network access by default. Tools which require network access must include @arv:APIRequirement: {}@ in their @requirements@ section. +When migrating from jobs API (--api=jobs) (sometimes referred to as "crunch v1") to the containers API (--api=containers) ("crunch v2") there are a few differences in behavior: + +* A tool may fail to find an input file that could be found when run under the jobs API. This is because tools are limited to accessing collections explicitly listed in the input, and further limited to those individual files or subdirectories that are listed. For example, given an explicit file input @/dir/subdir/file1.txt@, a tool will not be allowed to implicitly access a file in the parent directory @/dir/file2.txt@. Use @secondaryFiles@ or a @Directory@ for files that need to be grouped together. +* A tool may fail when attempting to rename or delete a file in the output directory. This may happen because files listed in @InitialWorkDirRequirement@ appear in the output directory as normal files (not symlinks) but cannot be moved, renamed or deleted unless marked as "writable" in CWL. These files will be added to the output collection but without any additional copies of the underlying data. +* A tool may fail when attempting to access the network. This may happen because, unlike the jobs API, under the containers API network access is disabled by default. Tools which require network access should add @arv:APIRequirement: {}@ to the @requirements@ section. -- 2.30.2