services/crunch-run/crunchrun_test.go

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