+ if wantAPI := runner.Container.RuntimeConstraints.API; wantAPI != nil && *wantAPI {
+ // Output may have been set directly by the container, so
+ // refresh the container record to check.
+ err := runner.ArvClient.Get("containers", runner.Container.UUID,
+ nil, &runner.Container)
+ if err != nil {
+ return err
+ }
+ if runner.Container.Output != "" {
+ // Container output is already set.
+ runner.OutputPDH = &runner.Container.Output
+ return nil
+ }
+ }
+
+ if runner.HostOutputDir == "" {
+ return nil
+ }
+
+ _, err := os.Stat(runner.HostOutputDir)
+ if err != nil {
+ return fmt.Errorf("While checking host output path: %v", err)
+ }
+
+ var manifestText string
+
+ collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
+ _, err = os.Stat(collectionMetafile)
+ if err != nil {
+ // Regular directory
+ cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
+ manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
+ if err != nil {
+ return fmt.Errorf("While uploading output files: %v", err)
+ }
+ } else {
+ // FUSE mount directory
+ file, openerr := os.Open(collectionMetafile)
+ if openerr != nil {
+ return fmt.Errorf("While opening FUSE metafile: %v", err)
+ }
+ defer file.Close()
+
+ var rec arvados.Collection
+ err = json.NewDecoder(file).Decode(&rec)
+ if err != nil {
+ return fmt.Errorf("While reading FUSE metafile: %v", err)
+ }
+ manifestText = rec.ManifestText
+ }
+
+ // Pre-populate output from the configured mount points
+ var binds []string
+ for bind, _ := range runner.Container.Mounts {
+ binds = append(binds, bind)
+ }
+ sort.Strings(binds)
+
+ for _, bind := range binds {
+ mnt := runner.Container.Mounts[bind]
+
+ bindSuffix := strings.TrimPrefix(bind, runner.Container.OutputPath)
+
+ if bindSuffix == bind || len(bindSuffix) <= 0 {
+ // either does not start with OutputPath or is OutputPath itself
+ continue
+ }
+
+ if mnt.ExcludeFromOutput == true {
+ continue
+ }
+
+ // append to manifest_text
+ m, err := runner.getCollectionManifestForPath(mnt, bindSuffix)
+ if err != nil {
+ return err
+ }
+
+ manifestText = manifestText + m
+ }
+
+ // Save output
+ var response arvados.Collection
+ manifest := manifest.Manifest{Text: manifestText}
+ manifestText = manifest.Extract(".", ".").Text
+ err = runner.ArvClient.Create("collections",
+ arvadosclient.Dict{
+ "ensure_unique_name": true,
+ "collection": arvadosclient.Dict{
+ "is_trashed": true,
+ "name": "output for " + runner.Container.UUID,
+ "manifest_text": manifestText}},
+ &response)
+ if err != nil {
+ return fmt.Errorf("While creating output collection: %v", err)
+ }
+ runner.OutputPDH = &response.PortableDataHash