[ARVADOS] updated: 1.1.2-157-g23baab3

[Git user]

Summary of changes:
 services/crunch-run/crunchrun.go | 45 ++++++++++++++++++++--------------------
 1 file changed, 22 insertions(+), 23 deletions(-)

       via  23baab324564d36322b265c7fd904a0b4548c195 (commit)
       via  03c82ef2950a25085e8d8ec0dc5d261fa1ca7963 (commit)
      from  2eb85f70168d331e49e9d38bfbd2292d586dfcc1 (commit)

Those revisions listed above that are new to this repository have
not appeared on any other notification email; so we list those
revisions in full, below.


commit 23baab324564d36322b265c7fd904a0b4548c195
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Thu Feb 1 10:59:53 2018 -0500

    12764: Explicitly set desired permissions on copied files/dirs
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 63697b6..3230ca9 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -584,10 +584,19 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 				if walkerr != nil {
 					return walkerr
 				}
+				target := path.Join(cp.bind, walkpath[len(cp.src):])
 				if walkinfo.Mode().IsRegular() {
-					return copyfile(walkpath, path.Join(cp.bind, walkpath[len(cp.src):]))
+					copyerr := copyfile(walkpath, target)
+					if copyerr != nil {
+						return copyerr
+					}
+					return os.Chmod(target, walkinfo.Mode()|0777)
 				} else if walkinfo.Mode().IsDir() {
-					return os.MkdirAll(path.Join(cp.bind, walkpath[len(cp.src):]), 0777)
+					mkerr := os.MkdirAll(target, 0777)
+					if mkerr != nil {
+						return mkerr
+					}
+					return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
 				} else {
 					return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
 				}

commit 03c82ef2950a25085e8d8ec0dc5d261fa1ca7963
Author: Peter Amstutz <pamstutz at veritasgenetics.com>
Date:   Wed Jan 31 16:59:50 2018 -0500

    12764: Remove CleanupTempDir.  Better name for parent temp.
    
    Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz at veritasgenetics.com>

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 8d93560..63697b6 100644
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -103,17 +103,16 @@ type ContainerRunner struct {
 	LogsPDH       *string
 	RunArvMount
 	MkTempDir
-	ArvMount       *exec.Cmd
-	ArvMountPoint  string
-	HostOutputDir  string
-	CleanupTempDir []string
-	Binds          []string
-	Volumes        map[string]struct{}
-	OutputPDH      *string
-	SigChan        chan os.Signal
-	ArvMountExit   chan error
-	finalState     string
-	parentTemp     string
+	ArvMount      *exec.Cmd
+	ArvMountPoint string
+	HostOutputDir string
+	Binds         []string
+	Volumes       map[string]struct{}
+	OutputPDH     *string
+	SigChan       chan os.Signal
+	ArvMountExit  chan error
+	finalState    string
+	parentTemp    string
 
 	statLogger       io.WriteCloser
 	statReporter     *crunchstat.Reporter
@@ -503,7 +502,6 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 			if staterr != nil {
 				return fmt.Errorf("While Chmod temp dir: %v", err)
 			}
-			runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 			runner.Binds = append(runner.Binds, fmt.Sprintf("%s:%s", tmpdir, bind))
 			if bind == runner.Container.OutputPath {
 				runner.HostOutputDir = tmpdir
@@ -523,7 +521,6 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 			if err != nil {
 				return fmt.Errorf("creating temp dir: %v", err)
 			}
-			runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 			tmpfn := filepath.Join(tmpdir, "mountdata.json")
 			err = ioutil.WriteFile(tmpfn, jsondata, 0644)
 			if err != nil {
@@ -536,7 +533,6 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
 			if err != nil {
 				return fmt.Errorf("creating temp dir: %v", err)
 			}
-			runner.CleanupTempDir = append(runner.CleanupTempDir, tmpdir)
 			err = gitMount(mnt).extractTree(runner.ArvClient, tmpdir, token)
 			if err != nil {
 				return err
@@ -1428,12 +1424,6 @@ func (runner *ContainerRunner) CleanupDirs() {
 		}
 	}
 
-	for _, tmpdir := range runner.CleanupTempDir {
-		if rmerr := os.RemoveAll(tmpdir); rmerr != nil {
-			runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", tmpdir, rmerr)
-		}
-	}
-
 	if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
 		runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
 	}
@@ -1774,7 +1764,7 @@ func main() {
 		os.Exit(1)
 	}
 
-	parentTemp, tmperr := cr.MkTempDir("", "crunch-run")
+	parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerId+".")
 	if tmperr != nil {
 		log.Fatalf("%s: %v", containerId, tmperr)
 	}

-----------------------------------------------------------------------


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