services/crunch-run/crunchrun_test.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "context"
   7         "crypto/md5"
   8         "encoding/json"
   9         "errors"
  10         "fmt"
  11         "io"
  12         "io/ioutil"
  13         "net"
  14         "os"
  15         "os/exec"
  16         "path/filepath"
  17         "runtime/pprof"
  18         "sort"
  19         "strings"
  20         "sync"
  21         "syscall"
  22         "testing"
  23         "time"
  24
  25         "git.curoverse.com/arvados.git/sdk/go/arvados"
  26         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  27         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  28         "git.curoverse.com/arvados.git/sdk/go/manifest"
  29
  30         dockertypes "github.com/docker/docker/api/types"
  31         dockercontainer "github.com/docker/docker/api/types/container"
  32         dockernetwork "github.com/docker/docker/api/types/network"
  33         . "gopkg.in/check.v1"
  34 )
  35
  36 // Gocheck boilerplate
  37 func TestCrunchExec(t *testing.T) {
  38         TestingT(t)
  39 }
  40
  41 type TestSuite struct{}
  42
  43 // Gocheck boilerplate
  44 var _ = Suite(&TestSuite{})
  45
  46 type ArvTestClient struct {
  47         Total   int64
  48         Calls   int
  49         Content []arvadosclient.Dict
  50         arvados.Container
  51         Logs map[string]*bytes.Buffer
  52         sync.Mutex
  53         WasSetRunning bool
  54 }
  55
  56 type KeepTestClient struct {
  57         Called  bool
  58         Content []byte
  59 }
  60
  61 var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0@569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
  62 var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
  63 var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
  64
  65 var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
  66 var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
  67
  68 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"
  69 var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
  70
  71 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"
  72 var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
  73
  74 var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
  75 var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
  76
  77 type TestDockerClient struct {
  78         imageLoaded string
  79         logReader   io.ReadCloser
  80         logWriter   io.WriteCloser
  81         fn          func(t *TestDockerClient)
  82         finish      int
  83         stop        chan bool
  84         cwd         string
  85         env         []string
  86         api         *ArvTestClient
  87 }
  88
  89 func NewTestDockerClient(exitCode int) *TestDockerClient {
  90         t := &TestDockerClient{}
  91         t.logReader, t.logWriter = io.Pipe()
  92         t.finish = exitCode
  93         t.stop = make(chan bool)
  94         t.cwd = "/"
  95         return t
  96 }
  97
  98 type MockConn struct {
  99         net.Conn
 100 }
 101
 102 func (m *MockConn) Write(b []byte) (int, error) {
 103         return len(b), nil
 104 }
 105
 106 func NewMockConn() *MockConn {
 107         c := &MockConn{}
 108         return c
 109 }
 110
 111 func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
 112         return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
 113 }
 114
 115 func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
 116         if config.WorkingDir != "" {
 117                 t.cwd = config.WorkingDir
 118         }
 119         t.env = config.Env
 120         return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
 121 }
 122
 123 func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 124         if container == "abcde" {
 125                 go t.fn(t)
 126                 return nil
 127         } else {
 128                 return errors.New("Invalid container id")
 129         }
 130 }
 131
 132 func (t *TestDockerClient) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
 133         t.stop <- true
 134         return nil
 135 }
 136
 137 func (t *TestDockerClient) ContainerWait(ctx context.Context, container string) (int64, error) {
 138         return int64(t.finish), nil
 139 }
 140
 141 func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 142         if t.imageLoaded == image {
 143                 return dockertypes.ImageInspect{}, nil, nil
 144         } else {
 145                 return dockertypes.ImageInspect{}, nil, errors.New("")
 146         }
 147 }
 148
 149 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 150         _, err := io.Copy(ioutil.Discard, input)
 151         if err != nil {
 152                 return dockertypes.ImageLoadResponse{}, err
 153         } else {
 154                 t.imageLoaded = hwImageId
 155                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 156         }
 157 }
 158
 159 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 160         return nil, nil
 161 }
 162
 163 func (client *ArvTestClient) Create(resourceType string,
 164         parameters arvadosclient.Dict,
 165         output interface{}) error {
 166
 167         client.Mutex.Lock()
 168         defer client.Mutex.Unlock()
 169
 170         client.Calls++
 171         client.Content = append(client.Content, parameters)
 172
 173         if resourceType == "logs" {
 174                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 175                 if client.Logs == nil {
 176                         client.Logs = make(map[string]*bytes.Buffer)
 177                 }
 178                 if client.Logs[et] == nil {
 179                         client.Logs[et] = &bytes.Buffer{}
 180                 }
 181                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 182         }
 183
 184         if resourceType == "collections" && output != nil {
 185                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 186                 outmap := output.(*arvados.Collection)
 187                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 188         }
 189
 190         return nil
 191 }
 192
 193 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 194         switch {
 195         case method == "GET" && resourceType == "containers" && action == "auth":
 196                 return json.Unmarshal([]byte(`{
 197                         "kind": "arvados#api_client_authorization",
 198                         "uuid": "`+fakeAuthUUID+`",
 199                         "api_token": "`+fakeAuthToken+`"
 200                         }`), output)
 201         default:
 202                 return fmt.Errorf("Not found")
 203         }
 204 }
 205
 206 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 207         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 208         j := []byte(`{
 209                 "command": ["sleep", "1"],
 210                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 211                 "cwd": ".",
 212                 "environment": {},
 213                 "mounts": {"/tmp": {"kind": "tmp"} },
 214                 "output_path": "/tmp",
 215                 "priority": 1,
 216                 "runtime_constraints": {}
 217         }`)
 218         return ioutil.NopCloser(bytes.NewReader(j)), nil
 219 }
 220
 221 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 222         if resourceType == "collections" {
 223                 if uuid == hwPDH {
 224                         output.(*arvados.Collection).ManifestText = hwManifest
 225                 } else if uuid == otherPDH {
 226                         output.(*arvados.Collection).ManifestText = otherManifest
 227                 } else if uuid == normalizedWithSubdirsPDH {
 228                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 229                 } else if uuid == denormalizedWithSubdirsPDH {
 230                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 231                 }
 232         }
 233         if resourceType == "containers" {
 234                 (*output.(*arvados.Container)) = client.Container
 235         }
 236         return nil
 237 }
 238
 239 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 240         client.Mutex.Lock()
 241         defer client.Mutex.Unlock()
 242         client.Calls++
 243         client.Content = append(client.Content, parameters)
 244         if resourceType == "containers" {
 245                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 246                         client.WasSetRunning = true
 247                 }
 248         }
 249         return nil
 250 }
 251
 252 var discoveryMap = map[string]interface{}{
 253         "defaultTrashLifetime":               float64(1209600),
 254         "crunchLimitLogBytesPerJob":          float64(67108864),
 255         "crunchLogThrottleBytes":             float64(65536),
 256         "crunchLogThrottlePeriod":            float64(60),
 257         "crunchLogThrottleLines":             float64(1024),
 258         "crunchLogPartialLineThrottlePeriod": float64(5),
 259         "crunchLogBytesPerEvent":             float64(4096),
 260         "crunchLogSecondsBetweenEvents":      float64(1),
 261 }
 262
 263 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 264         return discoveryMap[key], nil
 265 }
 266
 267 // CalledWith returns the parameters from the first API call whose
 268 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 269 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 270 // no call matches, it returns nil.
 271 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 272 call:
 273         for _, content := range client.Content {
 274                 var v interface{} = content
 275                 for _, k := range strings.Split(jpath, ".") {
 276                         if dict, ok := v.(arvadosclient.Dict); !ok {
 277                                 continue call
 278                         } else {
 279                                 v = dict[k]
 280                         }
 281                 }
 282                 if v == expect {
 283                         return content
 284                 }
 285         }
 286         return nil
 287 }
 288
 289 func (client *KeepTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 290         client.Content = buf
 291         return fmt.Sprintf("%s+%d", hash, len(buf)), len(buf), nil
 292 }
 293
 294 type FileWrapper struct {
 295         io.ReadCloser
 296         len uint64
 297 }
 298
 299 func (fw FileWrapper) Len() uint64 {
 300         return fw.len
 301 }
 302
 303 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 304         return 0, errors.New("not implemented")
 305 }
 306
 307 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 308         if filename == hwImageId+".tar" {
 309                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 310                 client.Called = true
 311                 return FileWrapper{rdr, 1321984}, nil
 312         } else if filename == "/file1_in_main.txt" {
 313                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 314                 client.Called = true
 315                 return FileWrapper{rdr, 3}, nil
 316         }
 317         return nil, nil
 318 }
 319
 320 func (s *TestSuite) TestLoadImage(c *C) {
 321         kc := &KeepTestClient{}
 322         docker := NewTestDockerClient(0)
 323         cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 324
 325         _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 326
 327         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 328         c.Check(err, NotNil)
 329
 330         cr.Container.ContainerImage = hwPDH
 331
 332         // (1) Test loading image from keep
 333         c.Check(kc.Called, Equals, false)
 334         c.Check(cr.ContainerConfig.Image, Equals, "")
 335
 336         err = cr.LoadImage()
 337
 338         c.Check(err, IsNil)
 339         defer func() {
 340                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 341         }()
 342
 343         c.Check(kc.Called, Equals, true)
 344         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 345
 346         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 347         c.Check(err, IsNil)
 348
 349         // (2) Test using image that's already loaded
 350         kc.Called = false
 351         cr.ContainerConfig.Image = ""
 352
 353         err = cr.LoadImage()
 354         c.Check(err, IsNil)
 355         c.Check(kc.Called, Equals, false)
 356         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 357
 358 }
 359
 360 type ArvErrorTestClient struct{}
 361
 362 func (ArvErrorTestClient) Create(resourceType string,
 363         parameters arvadosclient.Dict,
 364         output interface{}) error {
 365         return nil
 366 }
 367
 368 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 369         return errors.New("ArvError")
 370 }
 371
 372 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 373         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 374         return nil, errors.New("ArvError")
 375 }
 376
 377 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 378         return errors.New("ArvError")
 379 }
 380
 381 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 382         return nil
 383 }
 384
 385 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 386         return discoveryMap[key], nil
 387 }
 388
 389 type KeepErrorTestClient struct{}
 390
 391 func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 392         return "", 0, errors.New("KeepError")
 393 }
 394
 395 func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 396         return nil, errors.New("KeepError")
 397 }
 398
 399 type KeepReadErrorTestClient struct{}
 400
 401 func (KeepReadErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 402         return "", 0, nil
 403 }
 404
 405 type ErrorReader struct{}
 406
 407 func (ErrorReader) Read(p []byte) (n int, err error) {
 408         return 0, errors.New("ErrorReader")
 409 }
 410
 411 func (ErrorReader) Close() error {
 412         return nil
 413 }
 414
 415 func (ErrorReader) Len() uint64 {
 416         return 0
 417 }
 418
 419 func (ErrorReader) Seek(int64, int) (int64, error) {
 420         return 0, errors.New("ErrorReader")
 421 }
 422
 423 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 424         return ErrorReader{}, nil
 425 }
 426
 427 func (s *TestSuite) TestLoadImageArvError(c *C) {
 428         // (1) Arvados error
 429         cr := NewContainerRunner(ArvErrorTestClient{}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 430         cr.Container.ContainerImage = hwPDH
 431
 432         err := cr.LoadImage()
 433         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 434 }
 435
 436 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 437         // (2) Keep error
 438         docker := NewTestDockerClient(0)
 439         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 440         cr.Container.ContainerImage = hwPDH
 441
 442         err := cr.LoadImage()
 443         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 444 }
 445
 446 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 447         // (3) Collection doesn't contain image
 448         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 449         cr.Container.ContainerImage = otherPDH
 450
 451         err := cr.LoadImage()
 452         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 453 }
 454
 455 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 456         // (4) Collection doesn't contain image
 457         docker := NewTestDockerClient(0)
 458         cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 459         cr.Container.ContainerImage = hwPDH
 460
 461         err := cr.LoadImage()
 462         c.Check(err, NotNil)
 463 }
 464
 465 type ClosableBuffer struct {
 466         bytes.Buffer
 467 }
 468
 469 func (*ClosableBuffer) Close() error {
 470         return nil
 471 }
 472
 473 type TestLogs struct {
 474         Stdout ClosableBuffer
 475         Stderr ClosableBuffer
 476 }
 477
 478 func (tl *TestLogs) NewTestLoggingWriter(logstr string) io.WriteCloser {
 479         if logstr == "stdout" {
 480                 return &tl.Stdout
 481         }
 482         if logstr == "stderr" {
 483                 return &tl.Stderr
 484         }
 485         return nil
 486 }
 487
 488 func dockerLog(fd byte, msg string) []byte {
 489         by := []byte(msg)
 490         header := make([]byte, 8+len(by))
 491         header[0] = fd
 492         header[7] = byte(len(by))
 493         copy(header[8:], by)
 494         return header
 495 }
 496
 497 func (s *TestSuite) TestRunContainer(c *C) {
 498         docker := NewTestDockerClient(0)
 499         docker.fn = func(t *TestDockerClient) {
 500                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 501                 t.logWriter.Close()
 502         }
 503         cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 504
 505         var logs TestLogs
 506         cr.NewLogWriter = logs.NewTestLoggingWriter
 507         cr.Container.ContainerImage = hwPDH
 508         cr.Container.Command = []string{"./hw"}
 509         err := cr.LoadImage()
 510         c.Check(err, IsNil)
 511
 512         err = cr.CreateContainer()
 513         c.Check(err, IsNil)
 514
 515         err = cr.StartContainer()
 516         c.Check(err, IsNil)
 517
 518         err = cr.WaitFinish()
 519         c.Check(err, IsNil)
 520
 521         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 522         c.Check(logs.Stderr.String(), Equals, "")
 523 }
 524
 525 func (s *TestSuite) TestCommitLogs(c *C) {
 526         api := &ArvTestClient{}
 527         kc := &KeepTestClient{}
 528         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 529         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 530
 531         cr.CrunchLog.Print("Hello world!")
 532         cr.CrunchLog.Print("Goodbye")
 533         cr.finalState = "Complete"
 534
 535         err := cr.CommitLogs()
 536         c.Check(err, IsNil)
 537
 538         c.Check(api.Calls, Equals, 2)
 539         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 540         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 541         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 542         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 543 }
 544
 545 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 546         api := &ArvTestClient{}
 547         kc := &KeepTestClient{}
 548         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 549
 550         err := cr.UpdateContainerRunning()
 551         c.Check(err, IsNil)
 552
 553         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 554 }
 555
 556 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 557         api := &ArvTestClient{}
 558         kc := &KeepTestClient{}
 559         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 560
 561         cr.LogsPDH = new(string)
 562         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 563
 564         cr.ExitCode = new(int)
 565         *cr.ExitCode = 42
 566         cr.finalState = "Complete"
 567
 568         err := cr.UpdateContainerFinal()
 569         c.Check(err, IsNil)
 570
 571         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 572         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 573         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 574 }
 575
 576 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 577         api := &ArvTestClient{}
 578         kc := &KeepTestClient{}
 579         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 580         cr.cCancelled = true
 581         cr.finalState = "Cancelled"
 582
 583         err := cr.UpdateContainerFinal()
 584         c.Check(err, IsNil)
 585
 586         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 587         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 588         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 589 }
 590
 591 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 592 // dress rehearsal of the Run() function, starting from a JSON container record.
 593 func FullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 594         rec := arvados.Container{}
 595         err := json.Unmarshal([]byte(record), &rec)
 596         c.Check(err, IsNil)
 597
 598         docker := NewTestDockerClient(exitCode)
 599         docker.fn = fn
 600         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 601
 602         api = &ArvTestClient{Container: rec}
 603         docker.api = api
 604         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 605         cr.statInterval = 100 * time.Millisecond
 606         am := &ArvMountCmdLine{}
 607         cr.RunArvMount = am.ArvMountTest
 608
 609         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 610         c.Assert(err, IsNil)
 611         defer os.RemoveAll(realTemp)
 612
 613         tempcount := 0
 614         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 615                 tempcount++
 616                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 617                 err := os.Mkdir(d, os.ModePerm)
 618                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 619                         // Test case must have pre-populated the tempdir
 620                         err = nil
 621                 }
 622                 return d, err
 623         }
 624
 625         if extraMounts != nil && len(extraMounts) > 0 {
 626                 err := cr.SetupArvMountPoint("keep")
 627                 c.Check(err, IsNil)
 628
 629                 for _, m := range extraMounts {
 630                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 631                 }
 632         }
 633
 634         err = cr.Run()
 635         c.Check(err, IsNil)
 636         c.Check(api.WasSetRunning, Equals, true)
 637
 638         c.Check(api.Content[api.Calls-1]["container"].(arvadosclient.Dict)["log"], NotNil)
 639
 640         if err != nil {
 641                 for k, v := range api.Logs {
 642                         c.Log(k)
 643                         c.Log(v.String())
 644                 }
 645         }
 646
 647         return
 648 }
 649
 650 func (s *TestSuite) TestFullRunHello(c *C) {
 651         api, _, _ := FullRunHelper(c, `{
 652     "command": ["echo", "hello world"],
 653     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 654     "cwd": ".",
 655     "environment": {},
 656     "mounts": {"/tmp": {"kind": "tmp"} },
 657     "output_path": "/tmp",
 658     "priority": 1,
 659     "runtime_constraints": {}
 660 }`, nil, 0, func(t *TestDockerClient) {
 661                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 662                 t.logWriter.Close()
 663         })
 664
 665         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 666         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 667         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 668
 669 }
 670
 671 func (s *TestSuite) TestCrunchstat(c *C) {
 672         api, _, _ := FullRunHelper(c, `{
 673                 "command": ["sleep", "1"],
 674                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 675                 "cwd": ".",
 676                 "environment": {},
 677                 "mounts": {"/tmp": {"kind": "tmp"} },
 678                 "output_path": "/tmp",
 679                 "priority": 1,
 680                 "runtime_constraints": {}
 681         }`, nil, 0, func(t *TestDockerClient) {
 682                 time.Sleep(time.Second)
 683                 t.logWriter.Close()
 684         })
 685
 686         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 687         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 688
 689         // We didn't actually start a container, so crunchstat didn't
 690         // find accounting files and therefore didn't log any stats.
 691         // It should have logged a "can't find accounting files"
 692         // message after one poll interval, though, so we can confirm
 693         // it's alive:
 694         c.Assert(api.Logs["crunchstat"], NotNil)
 695         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 696
 697         // The "files never appeared" log assures us that we called
 698         // (*crunchstat.Reporter)Stop(), and that we set it up with
 699         // the correct container ID "abcde":
 700         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 701 }
 702
 703 func (s *TestSuite) TestNodeInfoLog(c *C) {
 704         api, _, _ := FullRunHelper(c, `{
 705                 "command": ["sleep", "1"],
 706                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 707                 "cwd": ".",
 708                 "environment": {},
 709                 "mounts": {"/tmp": {"kind": "tmp"} },
 710                 "output_path": "/tmp",
 711                 "priority": 1,
 712                 "runtime_constraints": {}
 713         }`, nil, 0,
 714                 func(t *TestDockerClient) {
 715                         time.Sleep(time.Second)
 716                         t.logWriter.Close()
 717                 })
 718
 719         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 720         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 721
 722         c.Assert(api.Logs["node-info"], NotNil)
 723         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Host Information.*`)
 724         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*CPU Information.*`)
 725         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Memory Information.*`)
 726         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk Space.*`)
 727         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk INodes.*`)
 728 }
 729
 730 func (s *TestSuite) TestContainerRecordLog(c *C) {
 731         api, _, _ := FullRunHelper(c, `{
 732                 "command": ["sleep", "1"],
 733                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 734                 "cwd": ".",
 735                 "environment": {},
 736                 "mounts": {"/tmp": {"kind": "tmp"} },
 737                 "output_path": "/tmp",
 738                 "priority": 1,
 739                 "runtime_constraints": {}
 740         }`, nil, 0,
 741                 func(t *TestDockerClient) {
 742                         time.Sleep(time.Second)
 743                         t.logWriter.Close()
 744                 })
 745
 746         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 747         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 748
 749         c.Assert(api.Logs["container"], NotNil)
 750         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 751 }
 752
 753 func (s *TestSuite) TestFullRunStderr(c *C) {
 754         api, _, _ := FullRunHelper(c, `{
 755     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 756     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 757     "cwd": ".",
 758     "environment": {},
 759     "mounts": {"/tmp": {"kind": "tmp"} },
 760     "output_path": "/tmp",
 761     "priority": 1,
 762     "runtime_constraints": {}
 763 }`, nil, 1, func(t *TestDockerClient) {
 764                 t.logWriter.Write(dockerLog(1, "hello\n"))
 765                 t.logWriter.Write(dockerLog(2, "world\n"))
 766                 t.logWriter.Close()
 767         })
 768
 769         final := api.CalledWith("container.state", "Complete")
 770         c.Assert(final, NotNil)
 771         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 772         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 773
 774         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 775         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 776 }
 777
 778 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 779         api, _, _ := FullRunHelper(c, `{
 780     "command": ["pwd"],
 781     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 782     "cwd": ".",
 783     "environment": {},
 784     "mounts": {"/tmp": {"kind": "tmp"} },
 785     "output_path": "/tmp",
 786     "priority": 1,
 787     "runtime_constraints": {}
 788 }`, nil, 0, func(t *TestDockerClient) {
 789                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 790                 t.logWriter.Close()
 791         })
 792
 793         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 794         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 795         c.Log(api.Logs["stdout"])
 796         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 797 }
 798
 799 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 800         api, _, _ := FullRunHelper(c, `{
 801     "command": ["pwd"],
 802     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 803     "cwd": "/bin",
 804     "environment": {},
 805     "mounts": {"/tmp": {"kind": "tmp"} },
 806     "output_path": "/tmp",
 807     "priority": 1,
 808     "runtime_constraints": {}
 809 }`, nil, 0, func(t *TestDockerClient) {
 810                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 811                 t.logWriter.Close()
 812         })
 813
 814         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 815         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 816         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 817 }
 818
 819 func (s *TestSuite) TestStopOnSignal(c *C) {
 820         s.testStopContainer(c, func(cr *ContainerRunner) {
 821                 go func() {
 822                         for !cr.cStarted {
 823                                 time.Sleep(time.Millisecond)
 824                         }
 825                         cr.SigChan <- syscall.SIGINT
 826                 }()
 827         })
 828 }
 829
 830 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 831         s.testStopContainer(c, func(cr *ContainerRunner) {
 832                 cr.ArvMountExit = make(chan error)
 833                 go func() {
 834                         cr.ArvMountExit <- exec.Command("true").Run()
 835                         close(cr.ArvMountExit)
 836                 }()
 837         })
 838 }
 839
 840 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 841         record := `{
 842     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 843     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 844     "cwd": ".",
 845     "environment": {},
 846     "mounts": {"/tmp": {"kind": "tmp"} },
 847     "output_path": "/tmp",
 848     "priority": 1,
 849     "runtime_constraints": {}
 850 }`
 851
 852         rec := arvados.Container{}
 853         err := json.Unmarshal([]byte(record), &rec)
 854         c.Check(err, IsNil)
 855
 856         docker := NewTestDockerClient(0)
 857         docker.fn = func(t *TestDockerClient) {
 858                 <-t.stop
 859                 t.logWriter.Write(dockerLog(1, "foo\n"))
 860                 t.logWriter.Close()
 861         }
 862         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 863
 864         api := &ArvTestClient{Container: rec}
 865         cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 866         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
 867         setup(cr)
 868
 869         done := make(chan error)
 870         go func() {
 871                 done <- cr.Run()
 872         }()
 873         select {
 874         case <-time.After(20 * time.Second):
 875                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
 876                 c.Fatal("timed out")
 877         case err = <-done:
 878                 c.Check(err, IsNil)
 879         }
 880         for k, v := range api.Logs {
 881                 c.Log(k)
 882                 c.Log(v.String())
 883         }
 884
 885         c.Check(api.CalledWith("container.log", nil), NotNil)
 886         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
 887         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
 888 }
 889
 890 func (s *TestSuite) TestFullRunSetEnv(c *C) {
 891         api, _, _ := FullRunHelper(c, `{
 892     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
 893     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 894     "cwd": "/bin",
 895     "environment": {"FROBIZ": "bilbo"},
 896     "mounts": {"/tmp": {"kind": "tmp"} },
 897     "output_path": "/tmp",
 898     "priority": 1,
 899     "runtime_constraints": {}
 900 }`, nil, 0, func(t *TestDockerClient) {
 901                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
 902                 t.logWriter.Close()
 903         })
 904
 905         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 906         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 907         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
 908 }
 909
 910 type ArvMountCmdLine struct {
 911         Cmd   []string
 912         token string
 913 }
 914
 915 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
 916         am.Cmd = c
 917         am.token = token
 918         return nil, nil
 919 }
 920
 921 func stubCert(temp string) string {
 922         path := temp + "/ca-certificates.crt"
 923         crt, _ := os.Create(path)
 924         crt.Close()
 925         arvadosclient.CertFiles = []string{path}
 926         return path
 927 }
 928
 929 func (s *TestSuite) TestSetupMounts(c *C) {
 930         api := &ArvTestClient{}
 931         kc := &KeepTestClient{}
 932         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 933         am := &ArvMountCmdLine{}
 934         cr.RunArvMount = am.ArvMountTest
 935
 936         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
 937         c.Assert(err, IsNil)
 938         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
 939         c.Assert(err, IsNil)
 940         stubCertPath := stubCert(certTemp)
 941
 942         defer os.RemoveAll(realTemp)
 943         defer os.RemoveAll(certTemp)
 944
 945         i := 0
 946         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 947                 i++
 948                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
 949                 err := os.Mkdir(d, os.ModePerm)
 950                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 951                         // Test case must have pre-populated the tempdir
 952                         err = nil
 953                 }
 954                 return d, err
 955         }
 956
 957         checkEmpty := func() {
 958                 filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
 959                         c.Check(path, Equals, realTemp)
 960                         c.Check(err, IsNil)
 961                         return nil
 962                 })
 963         }
 964
 965         {
 966                 i = 0
 967                 cr.ArvMountPoint = ""
 968                 cr.Container.Mounts = make(map[string]arvados.Mount)
 969                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
 970                 cr.OutputPath = "/tmp"
 971
 972                 err := cr.SetupMounts()
 973                 c.Check(err, IsNil)
 974                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
 975                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
 976                 cr.CleanupDirs()
 977                 checkEmpty()
 978         }
 979
 980         {
 981                 i = 0
 982                 cr.ArvMountPoint = ""
 983                 cr.Container.Mounts = make(map[string]arvados.Mount)
 984                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
 985                 cr.OutputPath = "/tmp"
 986
 987                 apiflag := true
 988                 cr.Container.RuntimeConstraints.API = &apiflag
 989
 990                 err := cr.SetupMounts()
 991                 c.Check(err, IsNil)
 992                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
 993                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
 994                 cr.CleanupDirs()
 995                 checkEmpty()
 996
 997                 apiflag = false
 998         }
 999
1000         {
1001                 i = 0
1002                 cr.ArvMountPoint = ""
1003                 cr.Container.Mounts = map[string]arvados.Mount{
1004                         "/keeptmp": {Kind: "collection", Writable: true},
1005                 }
1006                 cr.OutputPath = "/keeptmp"
1007
1008                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1009
1010                 err := cr.SetupMounts()
1011                 c.Check(err, IsNil)
1012                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1013                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1014                 cr.CleanupDirs()
1015                 checkEmpty()
1016         }
1017
1018         {
1019                 i = 0
1020                 cr.ArvMountPoint = ""
1021                 cr.Container.Mounts = map[string]arvados.Mount{
1022                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1023                         "/keepout": {Kind: "collection", Writable: true},
1024                 }
1025                 cr.OutputPath = "/keepout"
1026
1027                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1028                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1029
1030                 err := cr.SetupMounts()
1031                 c.Check(err, IsNil)
1032                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1033                 sort.StringSlice(cr.Binds).Sort()
1034                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1035                         realTemp + "/keep1/tmp0:/keepout"})
1036                 cr.CleanupDirs()
1037                 checkEmpty()
1038         }
1039
1040         {
1041                 i = 0
1042                 cr.ArvMountPoint = ""
1043                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1044                 cr.Container.Mounts = map[string]arvados.Mount{
1045                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1046                         "/keepout": {Kind: "collection", Writable: true},
1047                 }
1048                 cr.OutputPath = "/keepout"
1049
1050                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1051                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1052
1053                 err := cr.SetupMounts()
1054                 c.Check(err, IsNil)
1055                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1056                 sort.StringSlice(cr.Binds).Sort()
1057                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1058                         realTemp + "/keep1/tmp0:/keepout"})
1059                 cr.CleanupDirs()
1060                 checkEmpty()
1061         }
1062
1063         for _, test := range []struct {
1064                 in  interface{}
1065                 out string
1066         }{
1067                 {in: "foo", out: `"foo"`},
1068                 {in: nil, out: `null`},
1069                 {in: map[string]int{"foo": 123}, out: `{"foo":123}`},
1070         } {
1071                 i = 0
1072                 cr.ArvMountPoint = ""
1073                 cr.Container.Mounts = map[string]arvados.Mount{
1074                         "/mnt/test.json": {Kind: "json", Content: test.in},
1075                 }
1076                 err := cr.SetupMounts()
1077                 c.Check(err, IsNil)
1078                 sort.StringSlice(cr.Binds).Sort()
1079                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
1080                 content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
1081                 c.Check(err, IsNil)
1082                 c.Check(content, DeepEquals, []byte(test.out))
1083                 cr.CleanupDirs()
1084                 checkEmpty()
1085         }
1086
1087         // Read-only mount points are allowed underneath output_dir mount point
1088         {
1089                 i = 0
1090                 cr.ArvMountPoint = ""
1091                 cr.Container.Mounts = make(map[string]arvados.Mount)
1092                 cr.Container.Mounts = map[string]arvados.Mount{
1093                         "/tmp":     {Kind: "tmp"},
1094                         "/tmp/foo": {Kind: "collection"},
1095                 }
1096                 cr.OutputPath = "/tmp"
1097
1098                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1099
1100                 err := cr.SetupMounts()
1101                 c.Check(err, IsNil)
1102                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1103                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1104                 cr.CleanupDirs()
1105                 checkEmpty()
1106         }
1107
1108         // Writable mount points are not allowed underneath output_dir mount point
1109         {
1110                 i = 0
1111                 cr.ArvMountPoint = ""
1112                 cr.Container.Mounts = make(map[string]arvados.Mount)
1113                 cr.Container.Mounts = map[string]arvados.Mount{
1114                         "/tmp":     {Kind: "tmp"},
1115                         "/tmp/foo": {Kind: "collection", Writable: true},
1116                 }
1117                 cr.OutputPath = "/tmp"
1118
1119                 err := cr.SetupMounts()
1120                 c.Check(err, NotNil)
1121                 c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
1122                 cr.CleanupDirs()
1123                 checkEmpty()
1124         }
1125
1126         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1127         {
1128                 i = 0
1129                 cr.ArvMountPoint = ""
1130                 cr.Container.Mounts = make(map[string]arvados.Mount)
1131                 cr.Container.Mounts = map[string]arvados.Mount{
1132                         "/tmp":     {Kind: "tmp"},
1133                         "/tmp/foo": {Kind: "json"},
1134                 }
1135                 cr.OutputPath = "/tmp"
1136
1137                 err := cr.SetupMounts()
1138                 c.Check(err, NotNil)
1139                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
1140                 cr.CleanupDirs()
1141                 checkEmpty()
1142         }
1143
1144         // Only mount point of kind 'collection' is allowed for stdin
1145         {
1146                 i = 0
1147                 cr.ArvMountPoint = ""
1148                 cr.Container.Mounts = make(map[string]arvados.Mount)
1149                 cr.Container.Mounts = map[string]arvados.Mount{
1150                         "stdin": {Kind: "tmp"},
1151                 }
1152
1153                 err := cr.SetupMounts()
1154                 c.Check(err, NotNil)
1155                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1156                 cr.CleanupDirs()
1157                 checkEmpty()
1158         }
1159 }
1160
1161 func (s *TestSuite) TestStdout(c *C) {
1162         helperRecord := `{
1163                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1164                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1165                 "cwd": "/bin",
1166                 "environment": {"FROBIZ": "bilbo"},
1167                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1168                 "output_path": "/tmp",
1169                 "priority": 1,
1170                 "runtime_constraints": {}
1171         }`
1172
1173         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1174                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1175                 t.logWriter.Close()
1176         })
1177
1178         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1179         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1180         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1181 }
1182
1183 // Used by the TestStdoutWithWrongPath*()
1184 func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1185         rec := arvados.Container{}
1186         err = json.Unmarshal([]byte(record), &rec)
1187         c.Check(err, IsNil)
1188
1189         docker := NewTestDockerClient(0)
1190         docker.fn = fn
1191         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1192
1193         api = &ArvTestClient{Container: rec}
1194         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1195         am := &ArvMountCmdLine{}
1196         cr.RunArvMount = am.ArvMountTest
1197
1198         err = cr.Run()
1199         return
1200 }
1201
1202 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1203         _, _, err := StdoutErrorRunHelper(c, `{
1204     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1205     "output_path": "/tmp"
1206 }`, func(t *TestDockerClient) {})
1207
1208         c.Check(err, NotNil)
1209         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1210 }
1211
1212 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1213         _, _, err := StdoutErrorRunHelper(c, `{
1214     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1215     "output_path": "/tmp"
1216 }`, func(t *TestDockerClient) {})
1217
1218         c.Check(err, NotNil)
1219         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1220 }
1221
1222 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1223         _, _, err := StdoutErrorRunHelper(c, `{
1224     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1225     "output_path": "/tmp"
1226 }`, func(t *TestDockerClient) {})
1227
1228         c.Check(err, NotNil)
1229         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1230 }
1231
1232 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1233         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1234         defer os.Unsetenv("ARVADOS_API_HOST")
1235         api, _, _ := FullRunHelper(c, `{
1236     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1237     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1238     "cwd": "/bin",
1239     "environment": {},
1240     "mounts": {"/tmp": {"kind": "tmp"} },
1241     "output_path": "/tmp",
1242     "priority": 1,
1243     "runtime_constraints": {"API": true}
1244 }`, nil, 0, func(t *TestDockerClient) {
1245                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1246                 t.logWriter.Close()
1247         })
1248
1249         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1250         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1251         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1252         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1253 }
1254
1255 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1256         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1257         defer os.Unsetenv("ARVADOS_API_HOST")
1258         api, _, _ := FullRunHelper(c, `{
1259     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1260     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1261     "cwd": "/bin",
1262     "environment": {},
1263     "mounts": {"/tmp": {"kind": "tmp"} },
1264     "output_path": "/tmp",
1265     "priority": 1,
1266     "runtime_constraints": {"API": true}
1267 }`, nil, 0, func(t *TestDockerClient) {
1268                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1269                 t.logWriter.Close()
1270         })
1271
1272         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1273         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1274         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1275 }
1276
1277 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1278         helperRecord := `{
1279                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1280                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1281                 "cwd": "/bin",
1282                 "environment": {"FROBIZ": "bilbo"},
1283                 "mounts": {
1284         "/tmp": {"kind": "tmp"},
1285         "/tmp/foo": {"kind": "collection",
1286                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1287                      "exclude_from_output": true
1288         },
1289         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1290     },
1291                 "output_path": "/tmp",
1292                 "priority": 1,
1293                 "runtime_constraints": {}
1294         }`
1295
1296         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1297
1298         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1299                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1300                 t.logWriter.Close()
1301         })
1302
1303         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1304         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1305         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1306 }
1307
1308 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1309         helperRecord := `{
1310                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1311                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1312                 "cwd": "/bin",
1313                 "environment": {"FROBIZ": "bilbo"},
1314                 "mounts": {
1315         "/tmp": {"kind": "tmp"},
1316         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1317         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1318         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1319         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1320         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1321     },
1322                 "output_path": "/tmp",
1323                 "priority": 1,
1324                 "runtime_constraints": {}
1325         }`
1326
1327         extraMounts := []string{
1328                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1329                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1330                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1331         }
1332
1333         api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1334                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1335                 t.logWriter.Close()
1336         })
1337
1338         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
1339                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1340                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1341                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1342                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1343         })
1344
1345         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1346         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1347         for _, v := range api.Content {
1348                 if v["collection"] != nil {
1349                         c.Check(v["ensure_unique_name"], Equals, true)
1350                         collection := v["collection"].(arvadosclient.Dict)
1351                         if strings.Index(collection["name"].(string), "output") == 0 {
1352                                 manifest := collection["manifest_text"].(string)
1353
1354                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1355 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
1356 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1357 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1358 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1359 `)
1360                         }
1361                 }
1362         }
1363 }
1364
1365 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1366         helperRecord := `{
1367                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1368                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1369                 "cwd": "/bin",
1370                 "environment": {"FROBIZ": "bilbo"},
1371                 "mounts": {
1372         "/tmp": {"kind": "tmp"},
1373         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
1374         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1375     },
1376                 "output_path": "/tmp",
1377                 "priority": 1,
1378                 "runtime_constraints": {}
1379         }`
1380
1381         extraMounts := []string{
1382                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1383         }
1384
1385         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1386                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1387                 t.logWriter.Close()
1388         })
1389
1390         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1391         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1392         for _, v := range api.Content {
1393                 if v["collection"] != nil {
1394                         collection := v["collection"].(arvadosclient.Dict)
1395                         if strings.Index(collection["name"].(string), "output") == 0 {
1396                                 manifest := collection["manifest_text"].(string)
1397
1398                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1399 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1400 `)
1401                         }
1402                 }
1403         }
1404 }
1405
1406 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1407         helperRecord := `{
1408                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1409                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1410                 "cwd": "/bin",
1411                 "environment": {"FROBIZ": "bilbo"},
1412                 "mounts": {
1413         "/tmp": {"kind": "tmp"},
1414         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1415         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1416     },
1417                 "output_path": "/tmp",
1418                 "priority": 1,
1419                 "runtime_constraints": {}
1420         }`
1421
1422         extraMounts := []string{
1423                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1424         }
1425
1426         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1427                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1428                 t.logWriter.Close()
1429         })
1430
1431         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1432         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1433         for _, v := range api.Content {
1434                 if v["collection"] != nil {
1435                         collection := v["collection"].(arvadosclient.Dict)
1436                         if strings.Index(collection["name"].(string), "output") == 0 {
1437                                 manifest := collection["manifest_text"].(string)
1438                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1439 `)
1440                         }
1441                 }
1442         }
1443 }
1444
1445 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1446         helperRecord := `{
1447                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1448                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1449                 "cwd": "/bin",
1450                 "environment": {"FROBIZ": "bilbo"},
1451                 "mounts": {
1452         "/tmp": {"kind": "tmp"},
1453         "stdin": {"kind": "json", "content": "foo"},
1454         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1455     },
1456                 "output_path": "/tmp",
1457                 "priority": 1,
1458                 "runtime_constraints": {}
1459         }`
1460
1461         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1462                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1463                 t.logWriter.Close()
1464         })
1465
1466         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1467         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1468         for _, v := range api.Content {
1469                 if v["collection"] != nil {
1470                         collection := v["collection"].(arvadosclient.Dict)
1471                         if strings.Index(collection["name"].(string), "output") == 0 {
1472                                 manifest := collection["manifest_text"].(string)
1473                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1474 `)
1475                         }
1476                 }
1477         }
1478 }
1479
1480 func (s *TestSuite) TestStderrMount(c *C) {
1481         api, _, _ := FullRunHelper(c, `{
1482     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1483     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1484     "cwd": ".",
1485     "environment": {},
1486     "mounts": {"/tmp": {"kind": "tmp"},
1487                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1488                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1489     "output_path": "/tmp",
1490     "priority": 1,
1491     "runtime_constraints": {}
1492 }`, nil, 1, func(t *TestDockerClient) {
1493                 t.logWriter.Write(dockerLog(1, "hello\n"))
1494                 t.logWriter.Write(dockerLog(2, "oops\n"))
1495                 t.logWriter.Close()
1496         })
1497
1498         final := api.CalledWith("container.state", "Complete")
1499         c.Assert(final, NotNil)
1500         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1501         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1502
1503         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1504 }