12764: Set mode on copied single files. Fix tests.

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <pamstutz@veritasgenetics.com>

diff --git a/services/crunch-run/crunchrun.go b/services/crunch-run/crunchrun.go
index 3230ca98affefc49bf875bd54f674427d46014c7..a9f1c25d37fa1714868d371c245dc7aa8d041543 100644 (file)
--- a/services/crunch-run/crunchrun.go
+++ b/services/crunch-run/crunchrun.go
@@ -575,11 +575,11 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
        }
 
        for _, cp := range copyFiles {
-               dir, err := os.Stat(cp.src)
+               st, err := os.Stat(cp.src)
                if err != nil {
                        return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)
                }
-               if dir.IsDir() {
+               if st.IsDir() {
                        err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
                                if walkerr != nil {
                                        return walkerr
@@ -601,8 +601,11 @@ func (runner *ContainerRunner) SetupMounts() (err error) {
                                        return fmt.Errorf("Source %q is not a regular file or directory", cp.src)
                                }
                        })
-               } else {
+               } else if st.Mode().IsRegular() {
                        err = copyfile(cp.src, cp.bind)
+                       if err == nil {
+                               err = os.Chmod(cp.bind, st.Mode()|0777)
+                       }
                }
                if err != nil {
                        return fmt.Errorf("While staging writable file from %q to %q: %v", cp.src, cp.bind, err)

diff --git a/services/crunch-run/crunchrun_test.go b/services/crunch-run/crunchrun_test.go
index ed31adecf8caa39ec7523076678a46a8e039f6c7..94b713355dd10a13e2563f701589f39874d8ac12 100644 (file)
--- a/services/crunch-run/crunchrun_test.go
+++ b/services/crunch-run/crunchrun_test.go
@@ -16,7 +16,6 @@ import (
        "net"
        "os"
        "os/exec"
-       "path/filepath"
        "runtime/pprof"
        "sort"
        "strings"
@@ -1029,6 +1028,8 @@ func (s *TestSuite) TestSetupMounts(c *C) {
        c.Assert(err, IsNil)
        stubCertPath := stubCert(certTemp)
 
+       cr.parentTemp = realTemp
+
        defer os.RemoveAll(realTemp)
        defer os.RemoveAll(certTemp)
 
@@ -1045,11 +1046,12 @@ func (s *TestSuite) TestSetupMounts(c *C) {
        }
 
        checkEmpty := func() {
-               filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
-                       c.Check(path, Equals, realTemp)
-                       c.Check(err, IsNil)
-                       return nil
-               })
+               // Should be deleted.
+               _, err := os.Stat(realTemp)
+               c.Assert(os.IsNotExist(err), Equals, true)
+
+               // Now recreate it for the next test.
+               c.Assert(os.Mkdir(realTemp, 0777), IsNil)
        }
 
        {
@@ -1064,7 +1066,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
                        "--read-write", "--crunchstat-interval=5",
                        "--mount-by-pdh", "by_id", realTemp + "/keep1"})
-               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
+               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
                os.RemoveAll(cr.ArvMountPoint)
                cr.CleanupDirs()
                checkEmpty()
@@ -1083,7 +1085,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
                        "--read-write", "--crunchstat-interval=5",
                        "--mount-by-pdh", "by_id", realTemp + "/keep1"})
-               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/out", realTemp + "/3:/tmp"})
+               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
                os.RemoveAll(cr.ArvMountPoint)
                cr.CleanupDirs()
                checkEmpty()
@@ -1104,7 +1106,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
                        "--read-write", "--crunchstat-interval=5",
                        "--mount-by-pdh", "by_id", realTemp + "/keep1"})
-               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
+               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
                os.RemoveAll(cr.ArvMountPoint)
                cr.CleanupDirs()
                checkEmpty()
@@ -1200,8 +1202,8 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                err := cr.SetupMounts()
                c.Check(err, IsNil)
                sort.StringSlice(cr.Binds).Sort()
-               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
-               content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
+               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
+               content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
                c.Check(err, IsNil)
                c.Check(content, DeepEquals, []byte(test.out))
                os.RemoveAll(cr.ArvMountPoint)
@@ -1227,7 +1229,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
                        "--read-write", "--crunchstat-interval=5",
                        "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
-               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
+               c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
                os.RemoveAll(cr.ArvMountPoint)
                cr.CleanupDirs()
                checkEmpty()
@@ -1539,7 +1541,7 @@ func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
                t.logWriter.Close()
        })
 
-       c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
+       c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
                realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
                realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
                realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
@@ -1628,11 +1630,11 @@ func (s *TestSuite) TestOutputSymlinkToInput(c *C) {
        }
 
        api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
-               os.Symlink("/keep/foo/sub1file2", t.realTemp+"/2/baz")
-               os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz2")
-               os.Symlink("/keep/foo2/subdir1", t.realTemp+"/2/baz3")
-               os.Mkdir(t.realTemp+"/2/baz4", 0700)
-               os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz4/baz5")
+               os.Symlink("/keep/foo/sub1file2", t.realTemp+"/tmp2/baz")
+               os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz2")
+               os.Symlink("/keep/foo2/subdir1", t.realTemp+"/tmp2/baz3")
+               os.Mkdir(t.realTemp+"/tmp2/baz4", 0700)
+               os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz4/baz5")
                t.logWriter.Close()
        })
 
@@ -1670,7 +1672,7 @@ func (s *TestSuite) TestOutputError(c *C) {
        extraMounts := []string{}
 
        api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
-               os.Symlink("/etc/hosts", t.realTemp+"/2/baz")
+               os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
                t.logWriter.Close()
        })
 
@@ -1694,21 +1696,21 @@ func (s *TestSuite) TestOutputSymlinkToOutput(c *C) {
        extraMounts := []string{}
 
        api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
-               rf, _ := os.Create(t.realTemp + "/2/realfile")
+               rf, _ := os.Create(t.realTemp + "/tmp2/realfile")
                rf.Write([]byte("foo"))
                rf.Close()
 
-               os.Mkdir(t.realTemp+"/2/realdir", 0700)
-               rf, _ = os.Create(t.realTemp + "/2/realdir/subfile")
+               os.Mkdir(t.realTemp+"/tmp2/realdir", 0700)
+               rf, _ = os.Create(t.realTemp + "/tmp2/realdir/subfile")
                rf.Write([]byte("bar"))
                rf.Close()
 
-               os.Symlink("/tmp/realfile", t.realTemp+"/2/file1")
-               os.Symlink("realfile", t.realTemp+"/2/file2")
-               os.Symlink("/tmp/file1", t.realTemp+"/2/file3")
-               os.Symlink("file2", t.realTemp+"/2/file4")
-               os.Symlink("realdir", t.realTemp+"/2/dir1")
-               os.Symlink("/tmp/realdir", t.realTemp+"/2/dir2")
+               os.Symlink("/tmp/realfile", t.realTemp+"/tmp2/file1")
+               os.Symlink("realfile", t.realTemp+"/tmp2/file2")
+               os.Symlink("/tmp/file1", t.realTemp+"/tmp2/file3")
+               os.Symlink("file2", t.realTemp+"/tmp2/file4")
+               os.Symlink("realdir", t.realTemp+"/tmp2/dir1")
+               os.Symlink("/tmp/realdir", t.realTemp+"/tmp2/dir2")
                t.logWriter.Close()
        })