[ARVADOS] updated: a3562a62e6b23035543f08226479813d5d1c31ed
Git user
git at public.curoverse.com
Thu Oct 6 11:26:33 EDT 2016
Summary of changes:
sdk/cwl/arvados_cwl/arv-cwl-schema.yml | 2 +-
sdk/go/crunchrunner/crunchrunner.go | 18 ++++++++++--------
2 files changed, 11 insertions(+), 9 deletions(-)
via a3562a62e6b23035543f08226479813d5d1c31ed (commit)
from a3da8e980ccddf8312cec3e431517c212c964cd7 (commit)
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commit a3562a62e6b23035543f08226479813d5d1c31ed
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Thu Oct 6 11:25:53 2016 -0400
9307: Improve crunchrunner error handling. Fix typo.
diff --git a/sdk/cwl/arvados_cwl/arv-cwl-schema.yml b/sdk/cwl/arvados_cwl/arv-cwl-schema.yml
index fe3eadd..ee18347 100644
--- a/sdk/cwl/arvados_cwl/arv-cwl-schema.yml
+++ b/sdk/cwl/arvados_cwl/arv-cwl-schema.yml
@@ -22,7 +22,7 @@ $graph:
- |
local_output_dir: Use regular file system local to the compute node.
There must be sufficient local scratch space to store entire output;
- specify this this with `outdirMin` of `ResourceRequirement`. Files are
+ specify this with `outdirMin` of `ResourceRequirement`. Files are
batch uploaded to Keep when the process completes. Most compatible, but
upload step can be time consuming for very large files.
- |
diff --git a/sdk/go/crunchrunner/crunchrunner.go b/sdk/go/crunchrunner/crunchrunner.go
index 8dffd45..5e0e101 100644
--- a/sdk/go/crunchrunner/crunchrunner.go
+++ b/sdk/go/crunchrunner/crunchrunner.go
@@ -115,10 +115,12 @@ func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[
return "", "", "", err
}
if taskp.KeepTmpOutput {
- // Is there an os.Copy?
- copyFile(v, outdir+"/"+k)
+ err = copyFile(v, outdir+"/"+k)
} else {
- os.Symlink(v, outdir+"/"+k)
+ err = os.Symlink(v, outdir+"/"+k)
+ }
+ if err != nil {
+ return "", "", "", err
}
}
}
@@ -222,8 +224,8 @@ func getKeepTmp(outdir string) (manifest string, err error) {
return "", err
}
collection := arvados.Collection{}
- json.Unmarshal(buf, &collection)
- return collection.ManifestText, nil
+ err = json.Unmarshal(buf, &collection)
+ return collection.ManifestText, err
}
func runner(api IArvadosClient,
@@ -364,9 +366,9 @@ func runner(api IArvadosClient,
manifest, err = getKeepTmp(outdir)
} else {
manifest, err = WriteTree(kc, outdir)
- if err != nil {
- return TempFail{err}
- }
+ }
+ if err != nil {
+ return TempFail{err}
}
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