X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/9048749c1419cf5e130a4b5d992a2b9c5bafd9cf..8ed521f7fd1e48e1e415125745ed8c6627a62c91:/services/crunch-run/crunchrun.go diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go index 971cb3a27a..0b59f7df91 100644 --- a/services/crunch-run/crunchrun.go +++ b/services/crunch-run/crunchrun.go @@ -19,6 +19,7 @@ import ( "os/signal" "path" "path/filepath" + "sort" "strings" "sync" "syscall" @@ -40,7 +41,7 @@ var ErrCancelled = errors.New("Cancelled") // 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. @@ -94,7 +95,6 @@ type ContainerRunner struct { SigChan chan os.Signal ArvMountExit chan error finalState string - trashLifetime time.Duration statLogger io.WriteCloser statReporter *crunchstat.Reporter @@ -239,8 +239,15 @@ func (runner *ContainerRunner) ArvMountCmd(arvMountCmd []string, token string) ( return c, nil } +func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) { + if runner.ArvMountPoint == "" { + runner.ArvMountPoint, err = runner.MkTempDir("", prefix) + } + return +} + func (runner *ContainerRunner) SetupMounts() (err error) { - runner.ArvMountPoint, err = runner.MkTempDir("", "keep") + err = runner.SetupArvMountPoint("keep") if err != nil { return fmt.Errorf("While creating keep mount temp dir: %v", err) } @@ -259,7 +266,14 @@ func (runner *ContainerRunner) SetupMounts() (err error) { runner.Binds = nil needCertMount := true - for bind, mnt := range runner.Container.Mounts { + 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] if bind == "stdout" { // Is it a "file" mount kind? if mnt.Kind != "file" { @@ -275,10 +289,17 @@ func (runner *ContainerRunner) SetupMounts() (err error) { return fmt.Errorf("Stdout path does not start with OutputPath: %s, %s", mnt.Path, prefix) } } + if bind == "/etc/arvados/ca-certificates.crt" { needCertMount = false } + if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" { + if mnt.Kind != "collection" { + return fmt.Errorf("Only mount points of kind 'collection' are supported underneath the output_path: %v", bind) + } + } + switch { case mnt.Kind == "collection": var src string @@ -295,7 +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") @@ -305,6 +340,8 @@ func (runner *ContainerRunner) SetupMounts() (err error) { if mnt.Writable { if bind == runner.Container.OutputPath { runner.HostOutputDir = src + } else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") { + return fmt.Errorf("Writable mount points are not permitted underneath the output_path: %v", bind) } runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", src, bind)) } else { @@ -633,11 +670,44 @@ func (runner *ContainerRunner) CaptureOutput() error { 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{ "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) @@ -648,12 +718,45 @@ func (runner *ContainerRunner) CaptureOutput() error { return nil } -func (runner *ContainerRunner) loadDiscoveryVars() { - tl, err := runner.ArvClient.Discovery("defaultTrashLifetime") - if err != nil { - log.Fatalf("getting defaultTrashLifetime from discovery document: %s", err) +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 specified, +// return the entire manifest_text after replacing any "." with bindSuffix +// If mnt.Path corresponds to one stream, +// 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) { + 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 + } + + if collection.ManifestText == "" { + runner.CrunchLog.Printf("No manifest text for collection %v", collection.PortableDataHash) + return "", nil + } + + 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() { @@ -708,7 +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) @@ -903,7 +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 }