services/crunch-run/crunchrun_test.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package main
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "context"
  11         "crypto/md5"
  12         "encoding/json"
  13         "errors"
  14         "fmt"
  15         "io"
  16         "io/ioutil"
  17         "net"
  18         "os"
  19         "os/exec"
  20         "path/filepath"
  21         "runtime/pprof"
  22         "sort"
  23         "strings"
  24         "sync"
  25         "syscall"
  26         "testing"
  27         "time"
  28
  29         "git.curoverse.com/arvados.git/sdk/go/arvados"
  30         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  31         "git.curoverse.com/arvados.git/sdk/go/manifest"
  32
  33         dockertypes "github.com/docker/docker/api/types"
  34         dockercontainer "github.com/docker/docker/api/types/container"
  35         dockernetwork "github.com/docker/docker/api/types/network"
  36         . "gopkg.in/check.v1"
  37 )
  38
  39 // Gocheck boilerplate
  40 func TestCrunchExec(t *testing.T) {
  41         TestingT(t)
  42 }
  43
  44 type TestSuite struct{}
  45
  46 // Gocheck boilerplate
  47 var _ = Suite(&TestSuite{})
  48
  49 type ArvTestClient struct {
  50         Total   int64
  51         Calls   int
  52         Content []arvadosclient.Dict
  53         arvados.Container
  54         Logs map[string]*bytes.Buffer
  55         sync.Mutex
  56         WasSetRunning bool
  57         callraw       bool
  58 }
  59
  60 type KeepTestClient struct {
  61         Called  bool
  62         Content []byte
  63 }
  64
  65 var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0@569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
  66 var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
  67 var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
  68
  69 var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
  70 var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
  71
  72 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
  73 ./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
  74 ./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
  75 `
  76
  77 var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
  78
  79 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"
  80 var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
  81
  82 var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
  83 var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
  84
  85 type TestDockerClient struct {
  86         imageLoaded string
  87         logReader   io.ReadCloser
  88         logWriter   io.WriteCloser
  89         fn          func(t *TestDockerClient)
  90         finish      int
  91         stop        chan bool
  92         cwd         string
  93         env         []string
  94         api         *ArvTestClient
  95         realTemp    string
  96 }
  97
  98 func NewTestDockerClient(exitCode int) *TestDockerClient {
  99         t := &TestDockerClient{}
 100         t.logReader, t.logWriter = io.Pipe()
 101         t.finish = exitCode
 102         t.stop = make(chan bool, 1)
 103         t.cwd = "/"
 104         return t
 105 }
 106
 107 type MockConn struct {
 108         net.Conn
 109 }
 110
 111 func (m *MockConn) Write(b []byte) (int, error) {
 112         return len(b), nil
 113 }
 114
 115 func NewMockConn() *MockConn {
 116         c := &MockConn{}
 117         return c
 118 }
 119
 120 func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
 121         return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
 122 }
 123
 124 func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
 125         if config.WorkingDir != "" {
 126                 t.cwd = config.WorkingDir
 127         }
 128         t.env = config.Env
 129         return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
 130 }
 131
 132 func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 133         if container == "abcde" {
 134                 // t.fn gets executed in ContainerWait
 135                 return nil
 136         } else {
 137                 return errors.New("Invalid container id")
 138         }
 139 }
 140
 141 func (t *TestDockerClient) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
 142         t.stop <- true
 143         return nil
 144 }
 145
 146 func (t *TestDockerClient) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
 147         body := make(chan dockercontainer.ContainerWaitOKBody)
 148         err := make(chan error)
 149         go func() {
 150                 t.fn(t)
 151                 body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.finish)}
 152                 close(body)
 153                 close(err)
 154         }()
 155         return body, err
 156 }
 157
 158 func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 159         if t.finish == 2 {
 160                 return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 161         }
 162
 163         if t.imageLoaded == image {
 164                 return dockertypes.ImageInspect{}, nil, nil
 165         } else {
 166                 return dockertypes.ImageInspect{}, nil, errors.New("")
 167         }
 168 }
 169
 170 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 171         if t.finish == 2 {
 172                 return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 173         }
 174         _, err := io.Copy(ioutil.Discard, input)
 175         if err != nil {
 176                 return dockertypes.ImageLoadResponse{}, err
 177         } else {
 178                 t.imageLoaded = hwImageId
 179                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 180         }
 181 }
 182
 183 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 184         return nil, nil
 185 }
 186
 187 func (client *ArvTestClient) Create(resourceType string,
 188         parameters arvadosclient.Dict,
 189         output interface{}) error {
 190
 191         client.Mutex.Lock()
 192         defer client.Mutex.Unlock()
 193
 194         client.Calls++
 195         client.Content = append(client.Content, parameters)
 196
 197         if resourceType == "logs" {
 198                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 199                 if client.Logs == nil {
 200                         client.Logs = make(map[string]*bytes.Buffer)
 201                 }
 202                 if client.Logs[et] == nil {
 203                         client.Logs[et] = &bytes.Buffer{}
 204                 }
 205                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 206         }
 207
 208         if resourceType == "collections" && output != nil {
 209                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 210                 outmap := output.(*arvados.Collection)
 211                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 212         }
 213
 214         return nil
 215 }
 216
 217 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 218         switch {
 219         case method == "GET" && resourceType == "containers" && action == "auth":
 220                 return json.Unmarshal([]byte(`{
 221                         "kind": "arvados#api_client_authorization",
 222                         "uuid": "`+fakeAuthUUID+`",
 223                         "api_token": "`+fakeAuthToken+`"
 224                         }`), output)
 225         default:
 226                 return fmt.Errorf("Not found")
 227         }
 228 }
 229
 230 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 231         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 232         var j []byte
 233         if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
 234                 j, err = json.Marshal(client.Container)
 235         } else {
 236                 j = []byte(`{
 237                         "command": ["sleep", "1"],
 238                         "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 239                         "cwd": ".",
 240                         "environment": {},
 241                         "mounts": {"/tmp": {"kind": "tmp"}, "/json": {"kind": "json", "content": {"number": 123456789123456789}}},
 242                         "output_path": "/tmp",
 243                         "priority": 1,
 244                         "runtime_constraints": {}
 245                 }`)
 246         }
 247         return ioutil.NopCloser(bytes.NewReader(j)), err
 248 }
 249
 250 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 251         if resourceType == "collections" {
 252                 if uuid == hwPDH {
 253                         output.(*arvados.Collection).ManifestText = hwManifest
 254                 } else if uuid == otherPDH {
 255                         output.(*arvados.Collection).ManifestText = otherManifest
 256                 } else if uuid == normalizedWithSubdirsPDH {
 257                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 258                 } else if uuid == denormalizedWithSubdirsPDH {
 259                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 260                 }
 261         }
 262         if resourceType == "containers" {
 263                 (*output.(*arvados.Container)) = client.Container
 264         }
 265         return nil
 266 }
 267
 268 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 269         client.Mutex.Lock()
 270         defer client.Mutex.Unlock()
 271         client.Calls++
 272         client.Content = append(client.Content, parameters)
 273         if resourceType == "containers" {
 274                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 275                         client.WasSetRunning = true
 276                 }
 277         }
 278         return nil
 279 }
 280
 281 var discoveryMap = map[string]interface{}{
 282         "defaultTrashLifetime":               float64(1209600),
 283         "crunchLimitLogBytesPerJob":          float64(67108864),
 284         "crunchLogThrottleBytes":             float64(65536),
 285         "crunchLogThrottlePeriod":            float64(60),
 286         "crunchLogThrottleLines":             float64(1024),
 287         "crunchLogPartialLineThrottlePeriod": float64(5),
 288         "crunchLogBytesPerEvent":             float64(4096),
 289         "crunchLogSecondsBetweenEvents":      float64(1),
 290 }
 291
 292 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 293         return discoveryMap[key], nil
 294 }
 295
 296 // CalledWith returns the parameters from the first API call whose
 297 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 298 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 299 // no call matches, it returns nil.
 300 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 301 call:
 302         for _, content := range client.Content {
 303                 var v interface{} = content
 304                 for _, k := range strings.Split(jpath, ".") {
 305                         if dict, ok := v.(arvadosclient.Dict); !ok {
 306                                 continue call
 307                         } else {
 308                                 v = dict[k]
 309                         }
 310                 }
 311                 if v == expect {
 312                         return content
 313                 }
 314         }
 315         return nil
 316 }
 317
 318 func (client *KeepTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 319         client.Content = buf
 320         return fmt.Sprintf("%s+%d", hash, len(buf)), len(buf), nil
 321 }
 322
 323 func (*KeepTestClient) ClearBlockCache() {
 324 }
 325
 326 type FileWrapper struct {
 327         io.ReadCloser
 328         len int64
 329 }
 330
 331 func (fw FileWrapper) Readdir(n int) ([]os.FileInfo, error) {
 332         return nil, errors.New("not implemented")
 333 }
 334
 335 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 336         return 0, errors.New("not implemented")
 337 }
 338
 339 func (fw FileWrapper) Size() int64 {
 340         return fw.len
 341 }
 342
 343 func (fw FileWrapper) Stat() (os.FileInfo, error) {
 344         return nil, errors.New("not implemented")
 345 }
 346
 347 func (fw FileWrapper) Truncate(int64) error {
 348         return errors.New("not implemented")
 349 }
 350
 351 func (fw FileWrapper) Write([]byte) (int, error) {
 352         return 0, errors.New("not implemented")
 353 }
 354
 355 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 356         if filename == hwImageId+".tar" {
 357                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 358                 client.Called = true
 359                 return FileWrapper{rdr, 1321984}, nil
 360         } else if filename == "/file1_in_main.txt" {
 361                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 362                 client.Called = true
 363                 return FileWrapper{rdr, 3}, nil
 364         }
 365         return nil, nil
 366 }
 367
 368 func (s *TestSuite) TestLoadImage(c *C) {
 369         kc := &KeepTestClient{}
 370         docker := NewTestDockerClient(0)
 371         cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 372
 373         _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 374
 375         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 376         c.Check(err, NotNil)
 377
 378         cr.Container.ContainerImage = hwPDH
 379
 380         // (1) Test loading image from keep
 381         c.Check(kc.Called, Equals, false)
 382         c.Check(cr.ContainerConfig.Image, Equals, "")
 383
 384         err = cr.LoadImage()
 385
 386         c.Check(err, IsNil)
 387         defer func() {
 388                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 389         }()
 390
 391         c.Check(kc.Called, Equals, true)
 392         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 393
 394         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 395         c.Check(err, IsNil)
 396
 397         // (2) Test using image that's already loaded
 398         kc.Called = false
 399         cr.ContainerConfig.Image = ""
 400
 401         err = cr.LoadImage()
 402         c.Check(err, IsNil)
 403         c.Check(kc.Called, Equals, false)
 404         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 405
 406 }
 407
 408 type ArvErrorTestClient struct{}
 409
 410 func (ArvErrorTestClient) Create(resourceType string,
 411         parameters arvadosclient.Dict,
 412         output interface{}) error {
 413         return nil
 414 }
 415
 416 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 417         return errors.New("ArvError")
 418 }
 419
 420 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 421         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 422         return nil, errors.New("ArvError")
 423 }
 424
 425 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 426         return errors.New("ArvError")
 427 }
 428
 429 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 430         return nil
 431 }
 432
 433 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 434         return discoveryMap[key], nil
 435 }
 436
 437 type KeepErrorTestClient struct{}
 438
 439 func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 440         return "", 0, errors.New("KeepError")
 441 }
 442
 443 func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 444         return nil, errors.New("KeepError")
 445 }
 446
 447 func (KeepErrorTestClient) ClearBlockCache() {
 448 }
 449
 450 type KeepReadErrorTestClient struct{}
 451
 452 func (KeepReadErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 453         return "", 0, nil
 454 }
 455
 456 func (KeepReadErrorTestClient) ClearBlockCache() {
 457 }
 458
 459 type ErrorReader struct {
 460         FileWrapper
 461 }
 462
 463 func (ErrorReader) Read(p []byte) (n int, err error) {
 464         return 0, errors.New("ErrorReader")
 465 }
 466
 467 func (ErrorReader) Seek(int64, int) (int64, error) {
 468         return 0, errors.New("ErrorReader")
 469 }
 470
 471 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 472         return ErrorReader{}, nil
 473 }
 474
 475 func (s *TestSuite) TestLoadImageArvError(c *C) {
 476         // (1) Arvados error
 477         cr := NewContainerRunner(ArvErrorTestClient{}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 478         cr.Container.ContainerImage = hwPDH
 479
 480         err := cr.LoadImage()
 481         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 482 }
 483
 484 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 485         // (2) Keep error
 486         docker := NewTestDockerClient(0)
 487         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 488         cr.Container.ContainerImage = hwPDH
 489
 490         err := cr.LoadImage()
 491         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 492 }
 493
 494 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 495         // (3) Collection doesn't contain image
 496         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 497         cr.Container.ContainerImage = otherPDH
 498
 499         err := cr.LoadImage()
 500         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 501 }
 502
 503 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 504         // (4) Collection doesn't contain image
 505         docker := NewTestDockerClient(0)
 506         cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 507         cr.Container.ContainerImage = hwPDH
 508
 509         err := cr.LoadImage()
 510         c.Check(err, NotNil)
 511 }
 512
 513 type ClosableBuffer struct {
 514         bytes.Buffer
 515 }
 516
 517 func (*ClosableBuffer) Close() error {
 518         return nil
 519 }
 520
 521 type TestLogs struct {
 522         Stdout ClosableBuffer
 523         Stderr ClosableBuffer
 524 }
 525
 526 func (tl *TestLogs) NewTestLoggingWriter(logstr string) io.WriteCloser {
 527         if logstr == "stdout" {
 528                 return &tl.Stdout
 529         }
 530         if logstr == "stderr" {
 531                 return &tl.Stderr
 532         }
 533         return nil
 534 }
 535
 536 func dockerLog(fd byte, msg string) []byte {
 537         by := []byte(msg)
 538         header := make([]byte, 8+len(by))
 539         header[0] = fd
 540         header[7] = byte(len(by))
 541         copy(header[8:], by)
 542         return header
 543 }
 544
 545 func (s *TestSuite) TestRunContainer(c *C) {
 546         docker := NewTestDockerClient(0)
 547         docker.fn = func(t *TestDockerClient) {
 548                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 549                 t.logWriter.Close()
 550         }
 551         cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 552
 553         var logs TestLogs
 554         cr.NewLogWriter = logs.NewTestLoggingWriter
 555         cr.Container.ContainerImage = hwPDH
 556         cr.Container.Command = []string{"./hw"}
 557         err := cr.LoadImage()
 558         c.Check(err, IsNil)
 559
 560         err = cr.CreateContainer()
 561         c.Check(err, IsNil)
 562
 563         err = cr.StartContainer()
 564         c.Check(err, IsNil)
 565
 566         err = cr.WaitFinish()
 567         c.Check(err, IsNil)
 568
 569         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 570         c.Check(logs.Stderr.String(), Equals, "")
 571 }
 572
 573 func (s *TestSuite) TestCommitLogs(c *C) {
 574         api := &ArvTestClient{}
 575         kc := &KeepTestClient{}
 576         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 577         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 578
 579         cr.CrunchLog.Print("Hello world!")
 580         cr.CrunchLog.Print("Goodbye")
 581         cr.finalState = "Complete"
 582
 583         err := cr.CommitLogs()
 584         c.Check(err, IsNil)
 585
 586         c.Check(api.Calls, Equals, 2)
 587         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 588         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 589         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 590         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 591 }
 592
 593 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 594         api := &ArvTestClient{}
 595         kc := &KeepTestClient{}
 596         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 597
 598         err := cr.UpdateContainerRunning()
 599         c.Check(err, IsNil)
 600
 601         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 602 }
 603
 604 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 605         api := &ArvTestClient{}
 606         kc := &KeepTestClient{}
 607         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 608
 609         cr.LogsPDH = new(string)
 610         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 611
 612         cr.ExitCode = new(int)
 613         *cr.ExitCode = 42
 614         cr.finalState = "Complete"
 615
 616         err := cr.UpdateContainerFinal()
 617         c.Check(err, IsNil)
 618
 619         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 620         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 621         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 622 }
 623
 624 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 625         api := &ArvTestClient{}
 626         kc := &KeepTestClient{}
 627         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 628         cr.cCancelled = true
 629         cr.finalState = "Cancelled"
 630
 631         err := cr.UpdateContainerFinal()
 632         c.Check(err, IsNil)
 633
 634         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 635         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 636         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 637 }
 638
 639 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 640 // dress rehearsal of the Run() function, starting from a JSON container record.
 641 func FullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 642         rec := arvados.Container{}
 643         err := json.Unmarshal([]byte(record), &rec)
 644         c.Check(err, IsNil)
 645
 646         docker := NewTestDockerClient(exitCode)
 647         docker.fn = fn
 648         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 649
 650         api = &ArvTestClient{Container: rec}
 651         docker.api = api
 652         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 653         cr.statInterval = 100 * time.Millisecond
 654         am := &ArvMountCmdLine{}
 655         cr.RunArvMount = am.ArvMountTest
 656
 657         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 658         c.Assert(err, IsNil)
 659         defer os.RemoveAll(realTemp)
 660
 661         docker.realTemp = realTemp
 662
 663         tempcount := 0
 664         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 665                 tempcount++
 666                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 667                 err := os.Mkdir(d, os.ModePerm)
 668                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 669                         // Test case must have pre-populated the tempdir
 670                         err = nil
 671                 }
 672                 return d, err
 673         }
 674
 675         if extraMounts != nil && len(extraMounts) > 0 {
 676                 err := cr.SetupArvMountPoint("keep")
 677                 c.Check(err, IsNil)
 678
 679                 for _, m := range extraMounts {
 680                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 681                 }
 682         }
 683
 684         err = cr.Run()
 685         if api.CalledWith("container.state", "Complete") != nil {
 686                 c.Check(err, IsNil)
 687         }
 688         if exitCode != 2 {
 689                 c.Check(api.WasSetRunning, Equals, true)
 690                 c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
 691         }
 692
 693         if err != nil {
 694                 for k, v := range api.Logs {
 695                         c.Log(k)
 696                         c.Log(v.String())
 697                 }
 698         }
 699
 700         return
 701 }
 702
 703 func (s *TestSuite) TestFullRunHello(c *C) {
 704         api, _, _ := FullRunHelper(c, `{
 705     "command": ["echo", "hello world"],
 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, func(t *TestDockerClient) {
 714                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 715                 t.logWriter.Close()
 716         })
 717
 718         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 719         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 720         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 721
 722 }
 723
 724 func (s *TestSuite) TestCrunchstat(c *C) {
 725         api, _, _ := FullRunHelper(c, `{
 726                 "command": ["sleep", "1"],
 727                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 728                 "cwd": ".",
 729                 "environment": {},
 730                 "mounts": {"/tmp": {"kind": "tmp"} },
 731                 "output_path": "/tmp",
 732                 "priority": 1,
 733                 "runtime_constraints": {}
 734         }`, nil, 0, func(t *TestDockerClient) {
 735                 time.Sleep(time.Second)
 736                 t.logWriter.Close()
 737         })
 738
 739         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 740         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 741
 742         // We didn't actually start a container, so crunchstat didn't
 743         // find accounting files and therefore didn't log any stats.
 744         // It should have logged a "can't find accounting files"
 745         // message after one poll interval, though, so we can confirm
 746         // it's alive:
 747         c.Assert(api.Logs["crunchstat"], NotNil)
 748         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 749
 750         // The "files never appeared" log assures us that we called
 751         // (*crunchstat.Reporter)Stop(), and that we set it up with
 752         // the correct container ID "abcde":
 753         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 754 }
 755
 756 func (s *TestSuite) TestNodeInfoLog(c *C) {
 757         api, _, _ := FullRunHelper(c, `{
 758                 "command": ["sleep", "1"],
 759                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 760                 "cwd": ".",
 761                 "environment": {},
 762                 "mounts": {"/tmp": {"kind": "tmp"} },
 763                 "output_path": "/tmp",
 764                 "priority": 1,
 765                 "runtime_constraints": {}
 766         }`, nil, 0,
 767                 func(t *TestDockerClient) {
 768                         time.Sleep(time.Second)
 769                         t.logWriter.Close()
 770                 })
 771
 772         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 773         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 774
 775         c.Assert(api.Logs["node-info"], NotNil)
 776         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Host Information.*`)
 777         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*CPU Information.*`)
 778         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Memory Information.*`)
 779         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk Space.*`)
 780         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk INodes.*`)
 781 }
 782
 783 func (s *TestSuite) TestContainerRecordLog(c *C) {
 784         api, _, _ := FullRunHelper(c, `{
 785                 "command": ["sleep", "1"],
 786                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 787                 "cwd": ".",
 788                 "environment": {},
 789                 "mounts": {"/tmp": {"kind": "tmp"} },
 790                 "output_path": "/tmp",
 791                 "priority": 1,
 792                 "runtime_constraints": {}
 793         }`, nil, 0,
 794                 func(t *TestDockerClient) {
 795                         time.Sleep(time.Second)
 796                         t.logWriter.Close()
 797                 })
 798
 799         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 800         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 801
 802         c.Assert(api.Logs["container"], NotNil)
 803         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 804 }
 805
 806 func (s *TestSuite) TestFullRunStderr(c *C) {
 807         api, _, _ := FullRunHelper(c, `{
 808     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 809     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 810     "cwd": ".",
 811     "environment": {},
 812     "mounts": {"/tmp": {"kind": "tmp"} },
 813     "output_path": "/tmp",
 814     "priority": 1,
 815     "runtime_constraints": {}
 816 }`, nil, 1, func(t *TestDockerClient) {
 817                 t.logWriter.Write(dockerLog(1, "hello\n"))
 818                 t.logWriter.Write(dockerLog(2, "world\n"))
 819                 t.logWriter.Close()
 820         })
 821
 822         final := api.CalledWith("container.state", "Complete")
 823         c.Assert(final, NotNil)
 824         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 825         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 826
 827         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 828         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 829 }
 830
 831 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 832         api, _, _ := FullRunHelper(c, `{
 833     "command": ["pwd"],
 834     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 835     "cwd": ".",
 836     "environment": {},
 837     "mounts": {"/tmp": {"kind": "tmp"} },
 838     "output_path": "/tmp",
 839     "priority": 1,
 840     "runtime_constraints": {}
 841 }`, nil, 0, func(t *TestDockerClient) {
 842                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 843                 t.logWriter.Close()
 844         })
 845
 846         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 847         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 848         c.Log(api.Logs["stdout"])
 849         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 850 }
 851
 852 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 853         api, _, _ := FullRunHelper(c, `{
 854     "command": ["pwd"],
 855     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 856     "cwd": "/bin",
 857     "environment": {},
 858     "mounts": {"/tmp": {"kind": "tmp"} },
 859     "output_path": "/tmp",
 860     "priority": 1,
 861     "runtime_constraints": {}
 862 }`, nil, 0, func(t *TestDockerClient) {
 863                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 864                 t.logWriter.Close()
 865         })
 866
 867         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 868         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 869         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 870 }
 871
 872 func (s *TestSuite) TestStopOnSignal(c *C) {
 873         s.testStopContainer(c, func(cr *ContainerRunner) {
 874                 go func() {
 875                         for !cr.cStarted {
 876                                 time.Sleep(time.Millisecond)
 877                         }
 878                         cr.SigChan <- syscall.SIGINT
 879                 }()
 880         })
 881 }
 882
 883 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 884         s.testStopContainer(c, func(cr *ContainerRunner) {
 885                 cr.ArvMountExit = make(chan error)
 886                 go func() {
 887                         cr.ArvMountExit <- exec.Command("true").Run()
 888                         close(cr.ArvMountExit)
 889                 }()
 890         })
 891 }
 892
 893 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 894         record := `{
 895     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 896     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 897     "cwd": ".",
 898     "environment": {},
 899     "mounts": {"/tmp": {"kind": "tmp"} },
 900     "output_path": "/tmp",
 901     "priority": 1,
 902     "runtime_constraints": {}
 903 }`
 904
 905         rec := arvados.Container{}
 906         err := json.Unmarshal([]byte(record), &rec)
 907         c.Check(err, IsNil)
 908
 909         docker := NewTestDockerClient(0)
 910         docker.fn = func(t *TestDockerClient) {
 911                 <-t.stop
 912                 t.logWriter.Write(dockerLog(1, "foo\n"))
 913                 t.logWriter.Close()
 914         }
 915         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 916
 917         api := &ArvTestClient{Container: rec}
 918         cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 919         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
 920         setup(cr)
 921
 922         done := make(chan error)
 923         go func() {
 924                 done <- cr.Run()
 925         }()
 926         select {
 927         case <-time.After(20 * time.Second):
 928                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
 929                 c.Fatal("timed out")
 930         case err = <-done:
 931                 c.Check(err, IsNil)
 932         }
 933         for k, v := range api.Logs {
 934                 c.Log(k)
 935                 c.Log(v.String())
 936         }
 937
 938         c.Check(api.CalledWith("container.log", nil), NotNil)
 939         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
 940         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
 941 }
 942
 943 func (s *TestSuite) TestFullRunSetEnv(c *C) {
 944         api, _, _ := FullRunHelper(c, `{
 945     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
 946     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 947     "cwd": "/bin",
 948     "environment": {"FROBIZ": "bilbo"},
 949     "mounts": {"/tmp": {"kind": "tmp"} },
 950     "output_path": "/tmp",
 951     "priority": 1,
 952     "runtime_constraints": {}
 953 }`, nil, 0, func(t *TestDockerClient) {
 954                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
 955                 t.logWriter.Close()
 956         })
 957
 958         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 959         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 960         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
 961 }
 962
 963 type ArvMountCmdLine struct {
 964         Cmd   []string
 965         token string
 966 }
 967
 968 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
 969         am.Cmd = c
 970         am.token = token
 971         return nil, nil
 972 }
 973
 974 func stubCert(temp string) string {
 975         path := temp + "/ca-certificates.crt"
 976         crt, _ := os.Create(path)
 977         crt.Close()
 978         arvadosclient.CertFiles = []string{path}
 979         return path
 980 }
 981
 982 func (s *TestSuite) TestSetupMounts(c *C) {
 983         api := &ArvTestClient{}
 984         kc := &KeepTestClient{}
 985         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 986         am := &ArvMountCmdLine{}
 987         cr.RunArvMount = am.ArvMountTest
 988
 989         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
 990         c.Assert(err, IsNil)
 991         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
 992         c.Assert(err, IsNil)
 993         stubCertPath := stubCert(certTemp)
 994
 995         defer os.RemoveAll(realTemp)
 996         defer os.RemoveAll(certTemp)
 997
 998         i := 0
 999         cr.MkTempDir = func(_ string, prefix string) (string, error) {
1000                 i++
1001                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
1002                 err := os.Mkdir(d, os.ModePerm)
1003                 if err != nil && strings.Contains(err.Error(), ": file exists") {
1004                         // Test case must have pre-populated the tempdir
1005                         err = nil
1006                 }
1007                 return d, err
1008         }
1009
1010         checkEmpty := func() {
1011                 filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
1012                         c.Check(path, Equals, realTemp)
1013                         c.Check(err, IsNil)
1014                         return nil
1015                 })
1016         }
1017
1018         {
1019                 i = 0
1020                 cr.ArvMountPoint = ""
1021                 cr.Container.Mounts = make(map[string]arvados.Mount)
1022                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1023                 cr.OutputPath = "/tmp"
1024                 cr.statInterval = 5 * time.Second
1025                 err := cr.SetupMounts()
1026                 c.Check(err, IsNil)
1027                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1028                         "--read-write", "--crunchstat-interval=5",
1029                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1030                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
1031                 os.RemoveAll(cr.ArvMountPoint)
1032                 cr.CleanupDirs()
1033                 checkEmpty()
1034         }
1035
1036         {
1037                 i = 0
1038                 cr.ArvMountPoint = ""
1039                 cr.Container.Mounts = make(map[string]arvados.Mount)
1040                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
1041                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1042                 cr.OutputPath = "/out"
1043
1044                 err := cr.SetupMounts()
1045                 c.Check(err, IsNil)
1046                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1047                         "--read-write", "--crunchstat-interval=5",
1048                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1049                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/out", realTemp + "/3:/tmp"})
1050                 os.RemoveAll(cr.ArvMountPoint)
1051                 cr.CleanupDirs()
1052                 checkEmpty()
1053         }
1054
1055         {
1056                 i = 0
1057                 cr.ArvMountPoint = ""
1058                 cr.Container.Mounts = make(map[string]arvados.Mount)
1059                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1060                 cr.OutputPath = "/tmp"
1061
1062                 apiflag := true
1063                 cr.Container.RuntimeConstraints.API = &apiflag
1064
1065                 err := cr.SetupMounts()
1066                 c.Check(err, IsNil)
1067                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1068                         "--read-write", "--crunchstat-interval=5",
1069                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1070                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1071                 os.RemoveAll(cr.ArvMountPoint)
1072                 cr.CleanupDirs()
1073                 checkEmpty()
1074
1075                 apiflag = false
1076         }
1077
1078         {
1079                 i = 0
1080                 cr.ArvMountPoint = ""
1081                 cr.Container.Mounts = map[string]arvados.Mount{
1082                         "/keeptmp": {Kind: "collection", Writable: true},
1083                 }
1084                 cr.OutputPath = "/keeptmp"
1085
1086                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1087
1088                 err := cr.SetupMounts()
1089                 c.Check(err, IsNil)
1090                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1091                         "--read-write", "--crunchstat-interval=5",
1092                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1093                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1094                 os.RemoveAll(cr.ArvMountPoint)
1095                 cr.CleanupDirs()
1096                 checkEmpty()
1097         }
1098
1099         {
1100                 i = 0
1101                 cr.ArvMountPoint = ""
1102                 cr.Container.Mounts = map[string]arvados.Mount{
1103                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1104                         "/keepout": {Kind: "collection", Writable: true},
1105                 }
1106                 cr.OutputPath = "/keepout"
1107
1108                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1109                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1110
1111                 err := cr.SetupMounts()
1112                 c.Check(err, IsNil)
1113                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1114                         "--read-write", "--crunchstat-interval=5",
1115                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1116                 sort.StringSlice(cr.Binds).Sort()
1117                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1118                         realTemp + "/keep1/tmp0:/keepout"})
1119                 os.RemoveAll(cr.ArvMountPoint)
1120                 cr.CleanupDirs()
1121                 checkEmpty()
1122         }
1123
1124         {
1125                 i = 0
1126                 cr.ArvMountPoint = ""
1127                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1128                 cr.Container.Mounts = map[string]arvados.Mount{
1129                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1130                         "/keepout": {Kind: "collection", Writable: true},
1131                 }
1132                 cr.OutputPath = "/keepout"
1133
1134                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1135                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1136
1137                 err := cr.SetupMounts()
1138                 c.Check(err, IsNil)
1139                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1140                         "--read-write", "--crunchstat-interval=5",
1141                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1142                 sort.StringSlice(cr.Binds).Sort()
1143                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1144                         realTemp + "/keep1/tmp0:/keepout"})
1145                 os.RemoveAll(cr.ArvMountPoint)
1146                 cr.CleanupDirs()
1147                 checkEmpty()
1148         }
1149
1150         for _, test := range []struct {
1151                 in  interface{}
1152                 out string
1153         }{
1154                 {in: "foo", out: `"foo"`},
1155                 {in: nil, out: `null`},
1156                 {in: map[string]int64{"foo": 123456789123456789}, out: `{"foo":123456789123456789}`},
1157         } {
1158                 i = 0
1159                 cr.ArvMountPoint = ""
1160                 cr.Container.Mounts = map[string]arvados.Mount{
1161                         "/mnt/test.json": {Kind: "json", Content: test.in},
1162                 }
1163                 err := cr.SetupMounts()
1164                 c.Check(err, IsNil)
1165                 sort.StringSlice(cr.Binds).Sort()
1166                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
1167                 content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
1168                 c.Check(err, IsNil)
1169                 c.Check(content, DeepEquals, []byte(test.out))
1170                 os.RemoveAll(cr.ArvMountPoint)
1171                 cr.CleanupDirs()
1172                 checkEmpty()
1173         }
1174
1175         // Read-only mount points are allowed underneath output_dir mount point
1176         {
1177                 i = 0
1178                 cr.ArvMountPoint = ""
1179                 cr.Container.Mounts = make(map[string]arvados.Mount)
1180                 cr.Container.Mounts = map[string]arvados.Mount{
1181                         "/tmp":     {Kind: "tmp"},
1182                         "/tmp/foo": {Kind: "collection"},
1183                 }
1184                 cr.OutputPath = "/tmp"
1185
1186                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1187
1188                 err := cr.SetupMounts()
1189                 c.Check(err, IsNil)
1190                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1191                         "--read-write", "--crunchstat-interval=5",
1192                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1193                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1194                 os.RemoveAll(cr.ArvMountPoint)
1195                 cr.CleanupDirs()
1196                 checkEmpty()
1197         }
1198
1199         // Writable mount points are not allowed underneath output_dir mount point
1200         {
1201                 i = 0
1202                 cr.ArvMountPoint = ""
1203                 cr.Container.Mounts = make(map[string]arvados.Mount)
1204                 cr.Container.Mounts = map[string]arvados.Mount{
1205                         "/tmp":     {Kind: "tmp"},
1206                         "/tmp/foo": {Kind: "collection", Writable: true},
1207                 }
1208                 cr.OutputPath = "/tmp"
1209
1210                 err := cr.SetupMounts()
1211                 c.Check(err, NotNil)
1212                 c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
1213                 os.RemoveAll(cr.ArvMountPoint)
1214                 cr.CleanupDirs()
1215                 checkEmpty()
1216         }
1217
1218         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1219         {
1220                 i = 0
1221                 cr.ArvMountPoint = ""
1222                 cr.Container.Mounts = make(map[string]arvados.Mount)
1223                 cr.Container.Mounts = map[string]arvados.Mount{
1224                         "/tmp":     {Kind: "tmp"},
1225                         "/tmp/foo": {Kind: "json"},
1226                 }
1227                 cr.OutputPath = "/tmp"
1228
1229                 err := cr.SetupMounts()
1230                 c.Check(err, NotNil)
1231                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
1232                 os.RemoveAll(cr.ArvMountPoint)
1233                 cr.CleanupDirs()
1234                 checkEmpty()
1235         }
1236
1237         // Only mount point of kind 'collection' is allowed for stdin
1238         {
1239                 i = 0
1240                 cr.ArvMountPoint = ""
1241                 cr.Container.Mounts = make(map[string]arvados.Mount)
1242                 cr.Container.Mounts = map[string]arvados.Mount{
1243                         "stdin": {Kind: "tmp"},
1244                 }
1245
1246                 err := cr.SetupMounts()
1247                 c.Check(err, NotNil)
1248                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1249                 os.RemoveAll(cr.ArvMountPoint)
1250                 cr.CleanupDirs()
1251                 checkEmpty()
1252         }
1253 }
1254
1255 func (s *TestSuite) TestStdout(c *C) {
1256         helperRecord := `{
1257                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1258                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1259                 "cwd": "/bin",
1260                 "environment": {"FROBIZ": "bilbo"},
1261                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1262                 "output_path": "/tmp",
1263                 "priority": 1,
1264                 "runtime_constraints": {}
1265         }`
1266
1267         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1268                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
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("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1275 }
1276
1277 // Used by the TestStdoutWithWrongPath*()
1278 func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1279         rec := arvados.Container{}
1280         err = json.Unmarshal([]byte(record), &rec)
1281         c.Check(err, IsNil)
1282
1283         docker := NewTestDockerClient(0)
1284         docker.fn = fn
1285         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1286
1287         api = &ArvTestClient{Container: rec}
1288         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1289         am := &ArvMountCmdLine{}
1290         cr.RunArvMount = am.ArvMountTest
1291
1292         err = cr.Run()
1293         return
1294 }
1295
1296 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1297         _, _, err := StdoutErrorRunHelper(c, `{
1298     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1299     "output_path": "/tmp"
1300 }`, func(t *TestDockerClient) {})
1301
1302         c.Check(err, NotNil)
1303         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1304 }
1305
1306 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1307         _, _, err := StdoutErrorRunHelper(c, `{
1308     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1309     "output_path": "/tmp"
1310 }`, func(t *TestDockerClient) {})
1311
1312         c.Check(err, NotNil)
1313         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1314 }
1315
1316 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1317         _, _, err := StdoutErrorRunHelper(c, `{
1318     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1319     "output_path": "/tmp"
1320 }`, func(t *TestDockerClient) {})
1321
1322         c.Check(err, NotNil)
1323         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1324 }
1325
1326 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1327         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1328         defer os.Unsetenv("ARVADOS_API_HOST")
1329         api, _, _ := FullRunHelper(c, `{
1330     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1331     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1332     "cwd": "/bin",
1333     "environment": {},
1334     "mounts": {"/tmp": {"kind": "tmp"} },
1335     "output_path": "/tmp",
1336     "priority": 1,
1337     "runtime_constraints": {"API": true}
1338 }`, nil, 0, func(t *TestDockerClient) {
1339                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1340                 t.logWriter.Close()
1341         })
1342
1343         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1344         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1345         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1346         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1347 }
1348
1349 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1350         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1351         defer os.Unsetenv("ARVADOS_API_HOST")
1352         api, _, _ := FullRunHelper(c, `{
1353     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1354     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1355     "cwd": "/bin",
1356     "environment": {},
1357     "mounts": {"/tmp": {"kind": "tmp"} },
1358     "output_path": "/tmp",
1359     "priority": 1,
1360     "runtime_constraints": {"API": true}
1361 }`, nil, 0, func(t *TestDockerClient) {
1362                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1363                 t.logWriter.Close()
1364         })
1365
1366         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1367         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1368         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1369 }
1370
1371 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1372         helperRecord := `{
1373                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1374                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1375                 "cwd": "/bin",
1376                 "environment": {"FROBIZ": "bilbo"},
1377                 "mounts": {
1378         "/tmp": {"kind": "tmp"},
1379         "/tmp/foo": {"kind": "collection",
1380                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1381                      "exclude_from_output": true
1382         },
1383         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1384     },
1385                 "output_path": "/tmp",
1386                 "priority": 1,
1387                 "runtime_constraints": {}
1388         }`
1389
1390         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1391
1392         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1393                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1394                 t.logWriter.Close()
1395         })
1396
1397         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1398         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1399         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1400 }
1401
1402 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1403         helperRecord := `{
1404                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1405                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1406                 "cwd": "/bin",
1407                 "environment": {"FROBIZ": "bilbo"},
1408                 "mounts": {
1409         "/tmp": {"kind": "tmp"},
1410         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1411         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1412         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1413         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1414         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1415     },
1416                 "output_path": "/tmp",
1417                 "priority": 1,
1418                 "runtime_constraints": {}
1419         }`
1420
1421         extraMounts := []string{
1422                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1423                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1424                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1425         }
1426
1427         api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1428                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1429                 t.logWriter.Close()
1430         })
1431
1432         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
1433                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1434                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1435                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1436                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1437         })
1438
1439         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1440         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1441         for _, v := range api.Content {
1442                 if v["collection"] != nil {
1443                         c.Check(v["ensure_unique_name"], Equals, true)
1444                         collection := v["collection"].(arvadosclient.Dict)
1445                         if strings.Index(collection["name"].(string), "output") == 0 {
1446                                 manifest := collection["manifest_text"].(string)
1447
1448                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1449 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
1450 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1451 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1452 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1453 `)
1454                         }
1455                 }
1456         }
1457 }
1458
1459 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1460         helperRecord := `{
1461                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1462                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1463                 "cwd": "/bin",
1464                 "environment": {"FROBIZ": "bilbo"},
1465                 "mounts": {
1466         "/tmp": {"kind": "tmp"},
1467         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
1468         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1469     },
1470                 "output_path": "/tmp",
1471                 "priority": 1,
1472                 "runtime_constraints": {}
1473         }`
1474
1475         extraMounts := []string{
1476                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1477         }
1478
1479         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1480                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1481                 t.logWriter.Close()
1482         })
1483
1484         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1485         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1486         for _, v := range api.Content {
1487                 if v["collection"] != nil {
1488                         collection := v["collection"].(arvadosclient.Dict)
1489                         if strings.Index(collection["name"].(string), "output") == 0 {
1490                                 manifest := collection["manifest_text"].(string)
1491
1492                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1493 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1494 `)
1495                         }
1496                 }
1497         }
1498 }
1499
1500 func (s *TestSuite) TestOutputSymlinkToInput(c *C) {
1501         helperRecord := `{
1502                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1503                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1504                 "cwd": "/bin",
1505                 "environment": {"FROBIZ": "bilbo"},
1506                 "mounts": {
1507         "/tmp": {"kind": "tmp"},
1508         "/keep/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
1509         "/keep/foo2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"}
1510     },
1511                 "output_path": "/tmp",
1512                 "priority": 1,
1513                 "runtime_constraints": {}
1514         }`
1515
1516         extraMounts := []string{
1517                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1518         }
1519
1520         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1521                 os.Symlink("/keep/foo/sub1file2", t.realTemp+"/2/baz")
1522                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz2")
1523                 os.Symlink("/keep/foo2/subdir1", t.realTemp+"/2/baz3")
1524                 os.Mkdir(t.realTemp+"/2/baz4", 0700)
1525                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz4/baz5")
1526                 t.logWriter.Close()
1527         })
1528
1529         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1530         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1531         for _, v := range api.Content {
1532                 if v["collection"] != nil {
1533                         collection := v["collection"].(arvadosclient.Dict)
1534                         if strings.Index(collection["name"].(string), "output") == 0 {
1535                                 manifest := collection["manifest_text"].(string)
1536                                 c.Check(manifest, Equals, `. 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz 9:18:baz2
1537 ./baz3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1538 ./baz3/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1539 ./baz4 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz5
1540 `)
1541                         }
1542                 }
1543         }
1544 }
1545
1546 func (s *TestSuite) TestOutputError(c *C) {
1547         helperRecord := `{
1548                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1549                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1550                 "cwd": "/bin",
1551                 "environment": {"FROBIZ": "bilbo"},
1552                 "mounts": {
1553         "/tmp": {"kind": "tmp"}
1554     },
1555                 "output_path": "/tmp",
1556                 "priority": 1,
1557                 "runtime_constraints": {}
1558         }`
1559
1560         extraMounts := []string{}
1561
1562         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1563                 os.Symlink("/etc/hosts", t.realTemp+"/2/baz")
1564                 t.logWriter.Close()
1565         })
1566
1567         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1568 }
1569
1570 func (s *TestSuite) TestOutputSymlinkToOutput(c *C) {
1571         helperRecord := `{
1572                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1573                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1574                 "cwd": "/bin",
1575                 "environment": {"FROBIZ": "bilbo"},
1576                 "mounts": {
1577         "/tmp": {"kind": "tmp"}
1578     },
1579                 "output_path": "/tmp",
1580                 "priority": 1,
1581                 "runtime_constraints": {}
1582         }`
1583
1584         extraMounts := []string{}
1585
1586         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1587                 rf, _ := os.Create(t.realTemp + "/2/realfile")
1588                 rf.Write([]byte("foo"))
1589                 rf.Close()
1590
1591                 os.Mkdir(t.realTemp+"/2/realdir", 0700)
1592                 rf, _ = os.Create(t.realTemp + "/2/realdir/subfile")
1593                 rf.Write([]byte("bar"))
1594                 rf.Close()
1595
1596                 os.Symlink("/tmp/realfile", t.realTemp+"/2/file1")
1597                 os.Symlink("realfile", t.realTemp+"/2/file2")
1598                 os.Symlink("/tmp/file1", t.realTemp+"/2/file3")
1599                 os.Symlink("file2", t.realTemp+"/2/file4")
1600                 os.Symlink("realdir", t.realTemp+"/2/dir1")
1601                 os.Symlink("/tmp/realdir", t.realTemp+"/2/dir2")
1602                 t.logWriter.Close()
1603         })
1604
1605         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1606         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1607         for _, v := range api.Content {
1608                 if v["collection"] != nil {
1609                         collection := v["collection"].(arvadosclient.Dict)
1610                         if strings.Index(collection["name"].(string), "output") == 0 {
1611                                 manifest := collection["manifest_text"].(string)
1612                                 c.Check(manifest, Equals,
1613                                         `. 7a2c86e102dcc231bd232aad99686dfa+15 0:3:file1 3:3:file2 6:3:file3 9:3:file4 12:3:realfile
1614 ./dir1 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1615 ./dir2 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1616 ./realdir 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1617 `)
1618                         }
1619                 }
1620         }
1621 }
1622
1623 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1624         helperRecord := `{
1625                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1626                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1627                 "cwd": "/bin",
1628                 "environment": {"FROBIZ": "bilbo"},
1629                 "mounts": {
1630         "/tmp": {"kind": "tmp"},
1631         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1632         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1633     },
1634                 "output_path": "/tmp",
1635                 "priority": 1,
1636                 "runtime_constraints": {}
1637         }`
1638
1639         extraMounts := []string{
1640                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1641         }
1642
1643         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1644                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1645                 t.logWriter.Close()
1646         })
1647
1648         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1649         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1650         for _, v := range api.Content {
1651                 if v["collection"] != nil {
1652                         collection := v["collection"].(arvadosclient.Dict)
1653                         if strings.Index(collection["name"].(string), "output") == 0 {
1654                                 manifest := collection["manifest_text"].(string)
1655                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1656 `)
1657                         }
1658                 }
1659         }
1660 }
1661
1662 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1663         helperRecord := `{
1664                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1665                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1666                 "cwd": "/bin",
1667                 "environment": {"FROBIZ": "bilbo"},
1668                 "mounts": {
1669         "/tmp": {"kind": "tmp"},
1670         "stdin": {"kind": "json", "content": "foo"},
1671         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1672     },
1673                 "output_path": "/tmp",
1674                 "priority": 1,
1675                 "runtime_constraints": {}
1676         }`
1677
1678         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1679                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1680                 t.logWriter.Close()
1681         })
1682
1683         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1684         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1685         for _, v := range api.Content {
1686                 if v["collection"] != nil {
1687                         collection := v["collection"].(arvadosclient.Dict)
1688                         if strings.Index(collection["name"].(string), "output") == 0 {
1689                                 manifest := collection["manifest_text"].(string)
1690                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1691 `)
1692                         }
1693                 }
1694         }
1695 }
1696
1697 func (s *TestSuite) TestStderrMount(c *C) {
1698         api, _, _ := FullRunHelper(c, `{
1699     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1700     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1701     "cwd": ".",
1702     "environment": {},
1703     "mounts": {"/tmp": {"kind": "tmp"},
1704                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1705                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1706     "output_path": "/tmp",
1707     "priority": 1,
1708     "runtime_constraints": {}
1709 }`, nil, 1, func(t *TestDockerClient) {
1710                 t.logWriter.Write(dockerLog(1, "hello\n"))
1711                 t.logWriter.Write(dockerLog(2, "oops\n"))
1712                 t.logWriter.Close()
1713         })
1714
1715         final := api.CalledWith("container.state", "Complete")
1716         c.Assert(final, NotNil)
1717         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1718         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1719
1720         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1721 }
1722
1723 func (s *TestSuite) TestNumberRoundTrip(c *C) {
1724         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1725         cr.fetchContainerRecord()
1726
1727         jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
1728
1729         c.Check(err, IsNil)
1730         c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
1731 }
1732
1733 func (s *TestSuite) TestEvalSymlinks(c *C) {
1734         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1735
1736         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1737         c.Assert(err, IsNil)
1738         defer os.RemoveAll(realTemp)
1739
1740         cr.HostOutputDir = realTemp
1741
1742         // Absolute path outside output dir
1743         os.Symlink("/etc/passwd", realTemp+"/p1")
1744
1745         // Relative outside output dir
1746         os.Symlink("../zip", realTemp+"/p2")
1747
1748         // Circular references
1749         os.Symlink("p4", realTemp+"/p3")
1750         os.Symlink("p5", realTemp+"/p4")
1751         os.Symlink("p3", realTemp+"/p5")
1752
1753         // Target doesn't exist
1754         os.Symlink("p99", realTemp+"/p6")
1755
1756         for _, v := range []string{"p1", "p2", "p3", "p4", "p5"} {
1757                 info, err := os.Lstat(realTemp + "/" + v)
1758                 _, _, _, err = cr.derefOutputSymlink(realTemp+"/"+v, info)
1759                 c.Assert(err, NotNil)
1760         }
1761 }
1762
1763 func (s *TestSuite) TestEvalSymlinkDir(c *C) {
1764         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1765
1766         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1767         c.Assert(err, IsNil)
1768         defer os.RemoveAll(realTemp)
1769
1770         cr.HostOutputDir = realTemp
1771
1772         // Absolute path outside output dir
1773         os.Symlink(".", realTemp+"/loop")
1774
1775         v := "loop"
1776         info, err := os.Lstat(realTemp + "/" + v)
1777         _, err = cr.UploadOutputFile(realTemp+"/"+v, info, err, []string{}, nil, "", "", 0)
1778         c.Assert(err, NotNil)
1779 }
1780
1781 func (s *TestSuite) TestFullBrokenDocker1(c *C) {
1782         tf, err := ioutil.TempFile("", "brokenNodeHook-")
1783         c.Assert(err, IsNil)
1784         defer os.Remove(tf.Name())
1785
1786         tf.Write([]byte(`#!/bin/sh
1787 exec echo killme
1788 `))
1789         tf.Close()
1790         os.Chmod(tf.Name(), 0700)
1791
1792         ech := tf.Name()
1793         brokenNodeHook = &ech
1794
1795         api, _, _ := FullRunHelper(c, `{
1796     "command": ["echo", "hello world"],
1797     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1798     "cwd": ".",
1799     "environment": {},
1800     "mounts": {"/tmp": {"kind": "tmp"} },
1801     "output_path": "/tmp",
1802     "priority": 1,
1803     "runtime_constraints": {}
1804 }`, nil, 2, func(t *TestDockerClient) {
1805                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1806                 t.logWriter.Close()
1807         })
1808
1809         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1810         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1811         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
1812         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
1813
1814 }
1815
1816 func (s *TestSuite) TestFullBrokenDocker2(c *C) {
1817         ech := ""
1818         brokenNodeHook = &ech
1819
1820         api, _, _ := FullRunHelper(c, `{
1821     "command": ["echo", "hello world"],
1822     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1823     "cwd": ".",
1824     "environment": {},
1825     "mounts": {"/tmp": {"kind": "tmp"} },
1826     "output_path": "/tmp",
1827     "priority": 1,
1828     "runtime_constraints": {}
1829 }`, nil, 2, func(t *TestDockerClient) {
1830                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1831                 t.logWriter.Close()
1832         })
1833
1834         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1835         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1836         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
1837 }