// IKeepClient is the minimal Keep API methods used by crunch-run.
type IKeepClient interface {
PutHB(hash string, buf []byte) (string, int, error)
- ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error)
+ ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error)
}
// NewLogWriter is a factory function to create a new log writer.
SigChan chan os.Signal
ArvMountExit chan error
finalState string
- trashLifetime time.Duration
statLogger io.WriteCloser
statReporter *crunchstat.Reporter
return c, nil
}
-var tmpBackedOutputDir = false
-
func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
if runner.ArvMountPoint == "" {
runner.ArvMountPoint, err = runner.MkTempDir("", prefix)
if mnt.Writable {
return fmt.Errorf("Can never write to a collection specified by portable data hash")
}
+ idx := strings.Index(mnt.PortableDataHash, "/")
+ if idx > 0 {
+ mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
+ mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
+ runner.Container.Mounts[bind] = mnt
+ }
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
+ if mnt.Path != "" && mnt.Path != "." {
+ if strings.HasPrefix(mnt.Path, "./") {
+ mnt.Path = mnt.Path[2:]
+ } else if strings.HasPrefix(mnt.Path, "/") {
+ mnt.Path = mnt.Path[1:]
+ }
+ src += "/" + mnt.Path
+ }
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp")
}
runner.CleanupTempDir = append(runner.CleanupTempDir, runner.HostOutputDir)
runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", runner.HostOutputDir, bind))
- tmpBackedOutputDir = true
case mnt.Kind == "tmp":
runner.Binds = append(runner.Binds, bind)
bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
if bindSuffix == bind || len(bindSuffix) <= 0 {
- // either doesn't start with OutputPath or is OutputPath itself
+ // either does not start with OutputPath or is OutputPath itself
continue
}
- if strings.Index(bindSuffix, "/") != 0 {
- return fmt.Errorf("Expected bind to be of the format '%v/*' but found: %v", runner.Container.OutputPath, bind)
- }
-
- jsondata, err := json.Marshal(mnt.Content)
- if err != nil {
- return fmt.Errorf("While marshal of mount content: %v", err)
- }
- var content map[string]interface{}
- err = json.Unmarshal(jsondata, &content)
- if err != nil {
- return fmt.Errorf("While unmarshal of mount content: %v", err)
- }
-
- if content["exclude_from_output"] == true {
+ if mnt.ExcludeFromOutput == true {
continue
}
- idx := strings.Index(mnt.PortableDataHash, "/")
- if idx > 0 {
- mnt.Path = mnt.PortableDataHash[idx:]
- mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
- }
-
// append to manifest_text
m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
if err != nil {
// Save output
var response arvados.Collection
+ manifest := manifest.Manifest{Text: manifestText}
+ manifestText = manifest.Extract(".", ".").Text
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
"collection": arvadosclient.Dict{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "output for " + runner.Container.UUID,
"manifest_text": manifestText}},
&response)
return nil
}
+var outputCollections = make(map[string]arvados.Collection)
+
// Fetch the collection for the mnt.PortableDataHash
// Return the manifest_text fragment corresponding to the specified mnt.Path
// after making any required updates.
// Ex:
-// If mnt.Path is not speficied,
+// If mnt.Path is not specified,
// return the entire manifest_text after replacing any "." with bindSuffix
// If mnt.Path corresponds to one stream,
-// return the manitest_text for that stream after replacing that stream name with bindSuffix
-// Otherwise, check if a filename in any one stream is being sought. Return the manitest_text
-// for that stream after replacing that stream name and file name using bindSuffix components.
+// return the manifest_text for that stream after replacing that stream name with bindSuffix
+// Otherwise, check if a filename in any one stream is being sought. Return the manifest_text
+// for that stream after replacing stream name with bindSuffix minus the last word
+// and the file name with last word of the bindSuffix
+// Allowed path examples:
+// "path":"/"
+// "path":"/subdir1"
+// "path":"/subdir1/subdir2"
+// "path":"/subdir/filename" etc
func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, bindSuffix string) (string, error) {
- var collection arvados.Collection
- err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
- if err != nil {
- return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
- }
-
- manifestText := ""
- if mnt.Path == "" {
- // no path specified; return the entire manifest text
- manifestText = collection.ManifestText
- manifestText = strings.Replace(manifestText, "./", "."+bindSuffix+"/", -1)
- manifestText = strings.Replace(manifestText, ". ", "."+bindSuffix+" ", -1)
- } else {
- // either a single stream or file from a stream is being sought
- bindIdx := strings.LastIndex(bindSuffix, "/")
- var bindSubdir, bindFileName string
- if bindIdx >= 0 {
- bindSubdir = bindSuffix[0:bindIdx]
- bindFileName = bindSuffix[bindIdx+1:]
- }
- pathIdx := strings.LastIndex(mnt.Path, "/")
- var pathSubdir, pathFileName string
- if pathIdx >= 0 {
- pathSubdir = mnt.Path[0:pathIdx]
- pathFileName = mnt.Path[pathIdx+1:]
- }
- streams := strings.Split(collection.ManifestText, "\n")
- for _, stream := range streams {
- tokens := strings.Split(stream, " ")
- if tokens[0] == "."+mnt.Path {
- // path refers to this stream
- adjustedStream := strings.Replace(stream, mnt.Path, bindSuffix, -1)
- manifestText = adjustedStream + "\n"
- break
- } else {
- // look for a matching file in this stream
- if tokens[0] == "."+pathSubdir {
- // path refers to a file in this stream
- for _, token := range tokens {
- if strings.Index(token, ":"+pathFileName) > 0 {
- // found the file in the stream; discard all other file tokens
- for _, t := range tokens {
- if strings.Index(t, ":") == -1 {
- manifestText += (" " + t)
- } else {
- break // done reading all non-file tokens
- }
- }
- manifestText = strings.Trim(manifestText, " ")
- token = strings.Replace(token, pathFileName, bindFileName, -1)
- manifestText += (" " + token + "\n")
- manifestText = strings.Replace(manifestText, pathSubdir, bindSubdir, -1)
- break
- }
- }
- }
- }
+ collection := outputCollections[mnt.PortableDataHash]
+ if collection.PortableDataHash == "" {
+ err := runner.ArvClient.Get("collections", mnt.PortableDataHash, nil, &collection)
+ if err != nil {
+ return "", fmt.Errorf("While getting collection for %v: %v", mnt.PortableDataHash, err)
}
+ outputCollections[mnt.PortableDataHash] = collection
}
- return manifestText, nil
-}
+ if collection.ManifestText == "" {
+ runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash)
+ return "", nil
+ }
-func (runner *ContainerRunner) loadDiscoveryVars() {
- tl, err := runner.ArvClient.Discovery("defaultTrashLifetime")
- if err != nil {
- log.Fatalf("getting defaultTrashLifetime from discovery document: %s", err)
+ mft := manifest.Manifest{Text: collection.ManifestText}
+ extracted := mft.Extract(mnt.Path, bindSuffix)
+ if extracted.Err != nil {
+ return "", fmt.Errorf("Error parsing manifest for %v: %v", mnt.PortableDataHash, extracted.Err.Error())
}
- runner.trashLifetime = time.Duration(tl.(float64)) * time.Second
+ return extracted.Text, nil
}
func (runner *ContainerRunner) CleanupDirs() {
err = runner.ArvClient.Create("collections",
arvadosclient.Dict{
"collection": arvadosclient.Dict{
- "trash_at": time.Now().Add(runner.trashLifetime).Format(time.RFC3339),
+ "is_trashed": true,
"name": "logs for " + runner.Container.UUID,
"manifest_text": mt}},
&response)
cr.Container.UUID = containerUUID
cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
- cr.loadDiscoveryVars()
return cr
}
projects / arvados.git / blobdiff