"encoding/json"
"errors"
"fmt"
- "git.curoverse.com/arvados.git/sdk/go/arvados"
- "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
- "git.curoverse.com/arvados.git/sdk/go/keepclient"
- "git.curoverse.com/arvados.git/sdk/go/manifest"
- "github.com/curoverse/dockerclient"
- . "gopkg.in/check.v1"
"io"
"io/ioutil"
"os"
"syscall"
"testing"
"time"
+
+ "git.curoverse.com/arvados.git/sdk/go/arvados"
+ "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/keepclient"
+ "git.curoverse.com/arvados.git/sdk/go/manifest"
+ "github.com/curoverse/dockerclient"
+ . "gopkg.in/check.v1"
)
// Gocheck boilerplate
var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
-var normalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 27:5649:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt\n"
+var normalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt\n"
var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
+var denormalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt 0:10:subdir1/file1_in_subdir1.txt 10:17:subdir1/file2_in_subdir1.txt\n"
+var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
+
var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
output.(*arvados.Collection).ManifestText = otherManifest
} else if uuid == normalizedWithSubdirsPDH {
output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
+ } else if uuid == denormalizedWithSubdirsPDH {
+ output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
}
}
if resourceType == "containers" {
// Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
// dress rehearsal of the Run() function, starting from a JSON container record.
-func FullRunHelper(c *C, record string, extraMounts []string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner) {
+func FullRunHelper(c *C, record string, extraMounts []string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
rec := arvados.Container{}
err := json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
+ realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
+ c.Assert(err, IsNil)
+ defer os.RemoveAll(realTemp)
+
+ tempcount := 0
+ cr.MkTempDir = func(_ string, prefix string) (string, error) {
+ tempcount++
+ d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
+ err := os.Mkdir(d, os.ModePerm)
+ if err != nil && strings.Contains(err.Error(), ": file exists") {
+ // Test case must have pre-populated the tempdir
+ err = nil
+ }
+ return d, err
+ }
+
if extraMounts != nil && len(extraMounts) > 0 {
err := cr.SetupArvMountPoint("keep")
c.Check(err, IsNil)
}
func (s *TestSuite) TestFullRunHello(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["echo", "hello world"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestCrunchstat(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunStderr(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunSetCwd(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
}
-func (s *TestSuite) TestCancel(c *C) {
+func (s *TestSuite) TestStopOnSignal(c *C) {
+ s.testStopContainer(c, func(cr *ContainerRunner) {
+ go func() {
+ for cr.ContainerID == "" {
+ time.Sleep(time.Millisecond)
+ }
+ cr.SigChan <- syscall.SIGINT
+ }()
+ })
+}
+
+func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
+ s.testStopContainer(c, func(cr *ContainerRunner) {
+ cr.ArvMountExit = make(chan error)
+ go func() {
+ cr.ArvMountExit <- exec.Command("true").Run()
+ close(cr.ArvMountExit)
+ }()
+ })
+}
+
+func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
record := `{
"command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
api := &ArvTestClient{Container: rec}
cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
- am := &ArvMountCmdLine{}
- cr.RunArvMount = am.ArvMountTest
+ cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
+ setup(cr)
+ done := make(chan error)
go func() {
- for cr.ContainerID == "" {
- time.Sleep(time.Millisecond)
- }
- cr.SigChan <- syscall.SIGINT
+ done <- cr.Run()
}()
-
- err = cr.Run()
-
- c.Check(err, IsNil)
- if err != nil {
- for k, v := range api.Logs {
- c.Log(k)
- c.Log(v.String())
- }
+ select {
+ case <-time.After(20 * time.Second):
+ c.Fatal("timed out")
+ case err = <-done:
+ c.Check(err, IsNil)
+ }
+ for k, v := range api.Logs {
+ c.Log(k)
+ c.Log(v.String())
}
c.Check(api.CalledWith("container.log", nil), NotNil)
c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
-
}
func (s *TestSuite) TestFullRunSetEnv(c *C) {
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
"runtime_constraints": {}
}`
- api, _ := FullRunHelper(c, helperRecord, nil, func(t *TestDockerClient) {
+ api, _, _ := FullRunHelper(c, helperRecord, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
func (s *TestSuite) TestFullRunWithAPI(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
func (s *TestSuite) TestFullRunSetOutput(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _ := FullRunHelper(c, `{
+ api, _, _ := FullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
- api, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
"environment": {"FROBIZ": "bilbo"},
"mounts": {
"/tmp": {"kind": "tmp"},
- "/tmp/foo": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/"},
"/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
"/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
"/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
- "/tmp/foo/bar/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
+ "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
"stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
},
"output_path": "/tmp",
"runtime_constraints": {}
}`
- extraMounts := []string{"a0def87f80dd594d4675809e83bd4f15+367"}
+ extraMounts := []string{
+ "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
+ "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
+ }
- api, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
})
+ c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/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",
+ realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
+ })
+
c.Check(api.CalledWith("container.exit_code", 0), NotNil)
c.Check(api.CalledWith("container.state", "Complete"), NotNil)
for _, v := range api.Content {
if strings.Index(collection["name"].(string), "output") == 0 {
manifest := collection["manifest_text"].(string)
- c.Check(-1, Not(Equals), strings.Index(manifest, "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out"))
-
- origManifestWithDotReplacedAsFoo := strings.Replace(normalizedManifestWithSubdirs, "./", "./foo/", -1)
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo"+origManifestWithDotReplacedAsFoo[1:]))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:sub1file2"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo/bar 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2"))
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
+./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
+./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
+./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
+`)
}
}
}
}
-func (s *TestSuite) TestStdoutWithMountPointForFileUnderOutputDir(c *C) {
+func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
helperRecord := `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"environment": {"FROBIZ": "bilbo"},
"mounts": {
"/tmp": {"kind": "tmp"},
- "/tmp/foo": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"},
- "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt"},
- "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367/subdir1/"},
- "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
- "/tmp/foo/bar/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt"},
+ "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
"stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
},
"output_path": "/tmp",
}`
extraMounts := []string{
- "a0def87f80dd594d4675809e83bd4f15+367",
- "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
- "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
- "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
+ "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
}
- api, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
+ api, _, _ := FullRunHelper(c, helperRecord, extraMounts, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
if strings.Index(collection["name"].(string), "output") == 0 {
manifest := collection["manifest_text"].(string)
- c.Check(-1, Not(Equals), strings.Index(manifest, "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out"))
-
- origManifestWithDotReplacedAsFoo := strings.Replace(normalizedManifestWithSubdirs, "./", "./foo/", -1)
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo"+origManifestWithDotReplacedAsFoo[1:]))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:sub1file2"))
-
- c.Check(-1, Not(Equals), strings.Index(manifest, "./foo/bar 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2"))
+ c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
+./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
+`)
}
}
}
projects / arvados.git / blobdiff