11693: Dereference symlinks to input files and add incorporate them into output colle...

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 2cd3417a5861b413c8ea99385ba2681ece5d1036..a7616192b810699c0a29f79e369d9aad55958272 100644 (file)
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -769,14 +769,14 @@ func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
                        if err != nil {
                                return nil, fmt.Errorf("While Stat on temp dir: %v", err)
                        }
-                       stdoutPath := path.Join(runner.HostOutputDir, subdirs)
+                       stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
                        err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
                        if err != nil {
                                return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
                        }
                }
        }
-       stdoutFile, err := os.Create(path.Join(runner.HostOutputDir, stdoutPath))
+       stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
        if err != nil {
                return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
        }
@@ -919,14 +919,74 @@ func (runner *ContainerRunner) CaptureOutput() error {
                return fmt.Errorf("While checking host output path: %v", err)
        }
 
+       // Pre-populate output from the configured mount points
+       var binds []string
+       for bind, _ := range runner.Container.Mounts {
+               binds = append(binds, bind)
+       }
+       sort.Strings(binds)
+
        var manifestText string
 
        collectionMetafile := fmt.Sprintf("%s/.arvados#collection", runner.HostOutputDir)
        _, err = os.Stat(collectionMetafile)
        if err != nil {
                // Regular directory
+
+               // Find symlinks to arv-mounted files & dirs.
+               err = filepath.Walk(runner.HostOutputDir, func(path string, info os.FileInfo, err error) error {
+                       if err != nil {
+                               return err
+                       }
+                       if info.Mode()&os.ModeSymlink == 0 {
+                               return nil
+                       }
+                       // read link to get container internal path
+                       var tgt string
+                       tgt, err = os.Readlink(path)
+                       if err != nil {
+                               return err
+                       }
+                       if !strings.HasPrefix(tgt, "/") {
+                               // Link is relative, don't handle it
+                               return nil
+                       }
+                       // go through mounts and reverse map to collection reference
+                       for _, bind := range binds {
+                               if tgt == bind || strings.HasPrefix(tgt, bind+"/") {
+                                       mnt := runner.Container.Mounts[bind]
+
+                                       // get path relative to bind
+                                       sourceSuffix := tgt[len(bind):]
+                                       // get path relative to output dir
+                                       bindSuffix := path[len(runner.HostOutputDir):]
+
+                                       // Copy mount and adjust the path to add path relative to the bind
+                                       adjustedMount := mnt
+                                       adjustedMount.Path = filepath.Join(adjustedMount.Path, sourceSuffix)
+
+                                       // get manifest text
+                                       var m string
+                                       m, err = runner.getCollectionManifestForPath(adjustedMount, bindSuffix)
+                                       if err != nil {
+                                               return err
+                                       }
+                                       manifestText = manifestText + m
+                                       // delete symlink so WriteTree won't try to to dereference it.
+                                       os.Remove(path)
+                                       return nil
+                               }
+                       }
+                       return nil
+               })
+               if err != nil {
+                       return fmt.Errorf("While checking output symlinks: %v", err)
+               }
+
                cw := CollectionWriter{0, runner.Kc, nil, nil, sync.Mutex{}}
-               manifestText, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
+               var m string
+               m, err = cw.WriteTree(runner.HostOutputDir, runner.CrunchLog.Logger)
+               manifestText = manifestText + m
                if err != nil {
                        return fmt.Errorf("While uploading output files: %v", err)
                }
@@ -946,13 +1006,6 @@ 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]