var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
+var subdirManifest = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6411234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 27:5649:qr1hi-8i9sb-6tjg516fx3dhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6415544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:19:file2_in_subdir2.txt\n"
+var subdirPDH = "a0def87f80dd594d4675809e83bd4f15+367"
+
var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
stop chan bool
cwd string
env []string
+ api *ArvTestClient
}
func NewTestDockerClient() *TestDockerClient {
output.(*arvados.Collection).ManifestText = hwManifest
} else if uuid == otherPDH {
output.(*arvados.Collection).ManifestText = otherManifest
+ } else if uuid == subdirPDH {
+ output.(*arvados.Collection).ManifestText = subdirManifest
}
}
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, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner) {
+func FullRunHelper(c *C, record string, extraMounts []string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner) {
rec := arvados.Container{}
err := json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
docker.RemoveImage(hwImageId, true)
api = &ArvTestClient{Container: rec}
+ docker.api = api
cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
cr.statInterval = 100 * time.Millisecond
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
+ if extraMounts != nil && len(extraMounts) > 0 {
+ err := cr.SetupArvMountPoint("keep")
+ c.Check(err, IsNil)
+
+ for _, m := range extraMounts {
+ os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
+ }
+ }
+
err = cr.Run()
c.Check(err, IsNil)
c.Check(api.WasSetRunning, Equals, true)
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, "hello world\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{}
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
- }`, func(t *TestDockerClient) {
+ }`, nil, func(t *TestDockerClient) {
time.Sleep(time.Second)
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{}
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, "hello\n"))
t.logWriter.Write(dockerLog(2, "world\n"))
t.logWriter.Close()
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
"output_path": "/tmp",
"priority": 1,
"runtime_constraints": {}
-}`, func(t *TestDockerClient) {
+}`, nil, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
t.finish <- dockerclient.WaitResult{ExitCode: 0}
return nil, nil
}
+func stubCert(temp string) string {
+ path := temp + "/ca-certificates.crt"
+ crt, _ := os.Create(path)
+ crt.Close()
+ arvadosclient.CertFiles = []string{path}
+ return path
+}
+
func (s *TestSuite) TestSetupMounts(c *C) {
api := &ArvTestClient{}
kc := &KeepTestClient{}
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
- realTemp, err := ioutil.TempDir("", "crunchrun_test-")
+ realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
+ c.Assert(err, IsNil)
+ certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
c.Assert(err, IsNil)
+ stubCertPath := stubCert(certTemp)
+
defer os.RemoveAll(realTemp)
+ defer os.RemoveAll(certTemp)
i := 0
cr.MkTempDir = func(_ string, prefix string) (string, error) {
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = make(map[string]arvados.Mount)
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.OutputPath = "/tmp"
{
i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
+ cr.OutputPath = "/tmp"
+
+ apiflag := true
+ cr.Container.RuntimeConstraints.API = &apiflag
+
+ err := cr.SetupMounts()
+ c.Check(err, IsNil)
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
+ cr.CleanupDirs()
+ checkEmpty()
+
+ apiflag = false
+ }
+
+ {
+ i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/keeptmp": {Kind: "collection", Writable: true},
}
{
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
"/keepout": {Kind: "collection", Writable: true},
checkEmpty()
}
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.RuntimeConstraints.KeepCacheRAM = 512
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
+ "/keepout": {Kind: "collection", Writable: true},
+ }
+ cr.OutputPath = "/keepout"
+
+ os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
+ os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
+
+ err := cr.SetupMounts()
+ c.Check(err, IsNil)
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ sort.StringSlice(cr.Binds).Sort()
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
+ realTemp + "/keep1/tmp0:/keepout"})
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
for _, test := range []struct {
in interface{}
out string
{in: map[string]int{"foo": 123}, out: `{"foo":123}`},
} {
i = 0
+ cr.ArvMountPoint = ""
cr.Container.Mounts = map[string]arvados.Mount{
"/mnt/test.json": {Kind: "json", Content: test.in},
}
cr.CleanupDirs()
checkEmpty()
}
+
+ // Read-only mount points are allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "collection"},
+ }
+ cr.OutputPath = "/tmp"
+
+ os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
+
+ err := cr.SetupMounts()
+ c.Check(err, IsNil)
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--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"})
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
+ // Writable mount points are not allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "collection", Writable: true},
+ }
+ cr.OutputPath = "/tmp"
+
+ err := cr.SetupMounts()
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
+ // Only mount points of kind 'collection' are allowed underneath output_dir mount point
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "json"},
+ }
+ cr.OutputPath = "/tmp"
+
+ err := cr.SetupMounts()
+ c.Check(err, NotNil)
+ c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
+ cr.CleanupDirs()
+ checkEmpty()
+ }
}
func (s *TestSuite) TestStdout(c *C) {
"runtime_constraints": {}
}`
- api, _ := FullRunHelper(c, helperRecord, 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}
c.Check(err, NotNil)
c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
}
+
+func (s *TestSuite) TestFullRunWithAPI(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
+ defer os.Unsetenv("ARVADOS_API_HOST")
+ api, _ := FullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {"API": true}
+}`, nil, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
+ t.logWriter.Close()
+ t.finish <- dockerclient.WaitResult{ExitCode: 0}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
+ c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
+}
+
+func (s *TestSuite) TestFullRunSetOutput(c *C) {
+ os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
+ defer os.Unsetenv("ARVADOS_API_HOST")
+ api, _ := FullRunHelper(c, `{
+ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {"API": true}
+}`, nil, func(t *TestDockerClient) {
+ t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
+ t.logWriter.Close()
+ t.finish <- dockerclient.WaitResult{ExitCode: 0}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
+}
+
+func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo": {"kind": "collection",
+ "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
+ "content": {"exclude_from_output": true}
+ },
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
+
+ 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}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
+}
+
+func (s *TestSuite) TestStdoutWithMountPointForFileUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo": {"kind": "collection", "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54/md5sum.txt"},
+ "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
+ },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54/md5sum.txt"}
+
+ 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}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ if strings.Index(collection["name"].(string), "output") == 0 {
+ streams := strings.Split(collection["manifest_text"].(string), "\n")
+ c.Check(streams[0], Equals, "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out")
+ c.Check(streams[1], Equals, ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:foo")
+ }
+ }
+ }
+}
+
+func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
+ helperRecord := `{
+ "command": ["/bin/sh", "-c", "echo $FROBIZ"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": "/bin",
+ "environment": {"FROBIZ": "bilbo"},
+ "mounts": {
+ "/tmp": {"kind": "tmp"},
+ "/tmp/foo": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"},
+ "/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/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",
+ "priority": 1,
+ "runtime_constraints": {}
+ }`
+
+ extraMounts := []string{"a0def87f80dd594d4675809e83bd4f15+367"}
+
+ 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}
+ })
+
+ c.Check(api.CalledWith("container.exit_code", 0), NotNil)
+ c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ for _, v := range api.Content {
+ if v["collection"] != nil {
+ collection := v["collection"].(arvadosclient.Dict)
+ 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(subdirManifest, "./", "./foo/", -1)
+ c.Check(-1, Not(Equals), strings.Index(manifest, "./foo"+origManifestWithDotReplacedAsFoo[1:]))
+
+ c.Check(-1, Not(Equals), strings.Index(manifest, "./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt"))
+
+ c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6419876543234@569fa8c4 9:18:sub1file2"))
+
+ c.Check(-1, Not(Equals), strings.Index(manifest, "./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0a18eda6415544332211@569fa8c5 9:19:sub2file2"))
+ }
+ }
+ }
+}
projects / arvados.git / blobdiff