X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/85c684122fd678dc24035d58236dd5734aed50e5..8ed521f7fd1e48e1e415125745ed8c6627a62c91:/services/crunch-run/crunchrun.go

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index f73ec73466..0b59f7df91 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -95,7 +95,6 @@ type ContainerRunner struct {
 	SigChan        chan os.Signal
 	ArvMountExit   chan error
 	finalState     string
-	trashLifetime  time.Duration
 
 	statLogger   io.WriteCloser
 	statReporter *crunchstat.Reporter
@@ -317,7 +316,21 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 				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")
@@ -674,20 +687,10 @@ func (runner *ContainerRunner) CaptureOutput() error {
 			continue
 		}
 
-		if strings.HasPrefix(bindSuffix, "/") == false {
-			bindSuffix = "/" + bindSuffix
-		}
-
 		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 {
@@ -699,11 +702,12 @@ func (runner *ContainerRunner) CaptureOutput() error {
 
 	// Save output
 	var response arvados.Collection
-	manifestText := manifest.Manifest{Text: manifestText}.NormalizedText()
+	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)
@@ -747,17 +751,12 @@ func (runner *ContainerRunner) getCollectionManifestForPath(mnt arvados.Mount, b
 		return "", nil
 	}
 
-	manifest := manifest.Manifest{Text: collection.ManifestText}
-	manifestText := manifest.ManifestTextForPath(mnt.Path, bindSuffix)
-	return manifestText, 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() {
@@ -812,7 +811,7 @@ func (runner *ContainerRunner) CommitLogs() error {
 	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)
@@ -1007,7 +1006,6 @@ func NewContainerRunner(api IArvadosClient,
 	cr.Container.UUID = containerUUID
 	cr.CrunchLog = NewThrottledLogger(cr.NewLogWriter("crunch-run"))
 	cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
-	cr.loadDiscoveryVars()
 	return cr
 }