// manifest, err := (&copier{...}).Copy()
type copier struct {
client *arvados.Client
- arvClient IArvadosClient
keepClient IKeepClient
hostOutputDir string
ctrOutputDir string
- binds []string
+ bindmounts map[string]bindmount
mounts map[string]arvados.Mount
secretMounts map[string]arvados.Mount
logger printfer
}
func (cp *copier) copyFile(fs arvados.CollectionFileSystem, f filetodo) (int64, error) {
- cp.logger.Printf("copying %q (%d bytes)", f.dst, f.size)
+ cp.logger.Printf("copying %q (%d bytes)", strings.TrimLeft(f.dst, "/"), f.size)
dst, err := fs.OpenFile(f.dst, os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return 0, err
// copy, relative to its mount point -- ".", "./foo.txt", ...
srcRelPath := filepath.Join(".", srcMount.Path, src[len(srcRoot):])
+ // outputRelPath is the path relative in the output directory
+ // that corresponds to the path in the output collection where
+ // the file will go, for logging
+ var outputRelPath = ""
+ if strings.HasPrefix(src, cp.ctrOutputDir) {
+ outputRelPath = strings.TrimPrefix(src[len(cp.ctrOutputDir):], "/")
+ }
+ if outputRelPath == "" {
+ // blank means copy a whole directory, so replace it
+ // with a wildcard to make it a little clearer what's
+ // going on since outputRelPath is only used for logging
+ outputRelPath = "*"
+ }
+
switch {
case srcMount.ExcludeFromOutput:
case srcMount.Kind == "tmp":
case srcMount.Kind != "collection":
return fmt.Errorf("%q: unsupported mount %q in output (kind is %q)", src, srcRoot, srcMount.Kind)
case !srcMount.Writable:
+ cp.logger.Printf("copying %q from %v/%v", outputRelPath, srcMount.PortableDataHash, strings.TrimPrefix(srcRelPath, "./"))
mft, err := cp.getManifest(srcMount.PortableDataHash)
if err != nil {
return err
}
cp.manifest += mft.Extract(srcRelPath, dest).Text
default:
+ cp.logger.Printf("copying %q", outputRelPath)
hostRoot, err := cp.hostRoot(srcRoot)
if err != nil {
return err
if ctrRoot == cp.ctrOutputDir {
return cp.hostOutputDir, nil
}
- for _, bind := range cp.binds {
- tokens := strings.Split(bind, ":")
- if len(tokens) >= 2 && tokens[1] == ctrRoot {
- return tokens[0], nil
- }
+ if mnt, ok := cp.bindmounts[ctrRoot]; ok {
+ return mnt.HostPath, nil
}
return "", fmt.Errorf("not bind-mounted: %q", ctrRoot)
}
return mft, nil
}
var coll arvados.Collection
- err := cp.arvClient.Get("collections", pdh, nil, &coll)
+ err := cp.client.RequestAndDecode(&coll, "GET", "arvados/v1/collections/"+pdh, nil, nil)
if err != nil {
return nil, fmt.Errorf("error retrieving collection record for %q: %s", pdh, err)
}