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.imageLoaded == image {
 160                 return dockertypes.ImageInspect{}, nil, nil
 161         } else {
 162                 return dockertypes.ImageInspect{}, nil, errors.New("")
 163         }
 164 }
 165
 166 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 167         _, err := io.Copy(ioutil.Discard, input)
 168         if err != nil {
 169                 return dockertypes.ImageLoadResponse{}, err
 170         } else {
 171                 t.imageLoaded = hwImageId
 172                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 173         }
 174 }
 175
 176 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 177         return nil, nil
 178 }
 179
 180 func (client *ArvTestClient) Create(resourceType string,
 181         parameters arvadosclient.Dict,
 182         output interface{}) error {
 183
 184         client.Mutex.Lock()
 185         defer client.Mutex.Unlock()
 186
 187         client.Calls++
 188         client.Content = append(client.Content, parameters)
 189
 190         if resourceType == "logs" {
 191                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 192                 if client.Logs == nil {
 193                         client.Logs = make(map[string]*bytes.Buffer)
 194                 }
 195                 if client.Logs[et] == nil {
 196                         client.Logs[et] = &bytes.Buffer{}
 197                 }
 198                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 199         }
 200
 201         if resourceType == "collections" && output != nil {
 202                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 203                 outmap := output.(*arvados.Collection)
 204                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 205         }
 206
 207         return nil
 208 }
 209
 210 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 211         switch {
 212         case method == "GET" && resourceType == "containers" && action == "auth":
 213                 return json.Unmarshal([]byte(`{
 214                         "kind": "arvados#api_client_authorization",
 215                         "uuid": "`+fakeAuthUUID+`",
 216                         "api_token": "`+fakeAuthToken+`"
 217                         }`), output)
 218         default:
 219                 return fmt.Errorf("Not found")
 220         }
 221 }
 222
 223 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 224         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 225         var j []byte
 226         if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
 227                 j, err = json.Marshal(client.Container)
 228         } else {
 229                 j = []byte(`{
 230                         "command": ["sleep", "1"],
 231                         "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 232                         "cwd": ".",
 233                         "environment": {},
 234                         "mounts": {"/tmp": {"kind": "tmp"}, "/json": {"kind": "json", "content": {"number": 123456789123456789}}},
 235                         "output_path": "/tmp",
 236                         "priority": 1,
 237                         "runtime_constraints": {}
 238                 }`)
 239         }
 240         return ioutil.NopCloser(bytes.NewReader(j)), err
 241 }
 242
 243 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 244         if resourceType == "collections" {
 245                 if uuid == hwPDH {
 246                         output.(*arvados.Collection).ManifestText = hwManifest
 247                 } else if uuid == otherPDH {
 248                         output.(*arvados.Collection).ManifestText = otherManifest
 249                 } else if uuid == normalizedWithSubdirsPDH {
 250                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 251                 } else if uuid == denormalizedWithSubdirsPDH {
 252                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 253                 }
 254         }
 255         if resourceType == "containers" {
 256                 (*output.(*arvados.Container)) = client.Container
 257         }
 258         return nil
 259 }
 260
 261 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 262         client.Mutex.Lock()
 263         defer client.Mutex.Unlock()
 264         client.Calls++
 265         client.Content = append(client.Content, parameters)
 266         if resourceType == "containers" {
 267                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 268                         client.WasSetRunning = true
 269                 }
 270         }
 271         return nil
 272 }
 273
 274 var discoveryMap = map[string]interface{}{
 275         "defaultTrashLifetime":               float64(1209600),
 276         "crunchLimitLogBytesPerJob":          float64(67108864),
 277         "crunchLogThrottleBytes":             float64(65536),
 278         "crunchLogThrottlePeriod":            float64(60),
 279         "crunchLogThrottleLines":             float64(1024),
 280         "crunchLogPartialLineThrottlePeriod": float64(5),
 281         "crunchLogBytesPerEvent":             float64(4096),
 282         "crunchLogSecondsBetweenEvents":      float64(1),
 283 }
 284
 285 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 286         return discoveryMap[key], nil
 287 }
 288
 289 // CalledWith returns the parameters from the first API call whose
 290 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 291 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 292 // no call matches, it returns nil.
 293 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 294 call:
 295         for _, content := range client.Content {
 296                 var v interface{} = content
 297                 for _, k := range strings.Split(jpath, ".") {
 298                         if dict, ok := v.(arvadosclient.Dict); !ok {
 299                                 continue call
 300                         } else {
 301                                 v = dict[k]
 302                         }
 303                 }
 304                 if v == expect {
 305                         return content
 306                 }
 307         }
 308         return nil
 309 }
 310
 311 func (client *KeepTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 312         client.Content = buf
 313         return fmt.Sprintf("%s+%d", hash, len(buf)), len(buf), nil
 314 }
 315
 316 func (*KeepTestClient) ClearBlockCache() {
 317 }
 318
 319 type FileWrapper struct {
 320         io.ReadCloser
 321         len int64
 322 }
 323
 324 func (fw FileWrapper) Size() int64 {
 325         return fw.len
 326 }
 327
 328 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 329         return 0, errors.New("not implemented")
 330 }
 331
 332 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 333         if filename == hwImageId+".tar" {
 334                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 335                 client.Called = true
 336                 return FileWrapper{rdr, 1321984}, nil
 337         } else if filename == "/file1_in_main.txt" {
 338                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 339                 client.Called = true
 340                 return FileWrapper{rdr, 3}, nil
 341         }
 342         return nil, nil
 343 }
 344
 345 func (s *TestSuite) TestLoadImage(c *C) {
 346         kc := &KeepTestClient{}
 347         docker := NewTestDockerClient(0)
 348         cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 349
 350         _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 351
 352         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 353         c.Check(err, NotNil)
 354
 355         cr.Container.ContainerImage = hwPDH
 356
 357         // (1) Test loading image from keep
 358         c.Check(kc.Called, Equals, false)
 359         c.Check(cr.ContainerConfig.Image, Equals, "")
 360
 361         err = cr.LoadImage()
 362
 363         c.Check(err, IsNil)
 364         defer func() {
 365                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 366         }()
 367
 368         c.Check(kc.Called, Equals, true)
 369         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 370
 371         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 372         c.Check(err, IsNil)
 373
 374         // (2) Test using image that's already loaded
 375         kc.Called = false
 376         cr.ContainerConfig.Image = ""
 377
 378         err = cr.LoadImage()
 379         c.Check(err, IsNil)
 380         c.Check(kc.Called, Equals, false)
 381         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 382
 383 }
 384
 385 type ArvErrorTestClient struct{}
 386
 387 func (ArvErrorTestClient) Create(resourceType string,
 388         parameters arvadosclient.Dict,
 389         output interface{}) error {
 390         return nil
 391 }
 392
 393 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 394         return errors.New("ArvError")
 395 }
 396
 397 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 398         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 399         return nil, errors.New("ArvError")
 400 }
 401
 402 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 403         return errors.New("ArvError")
 404 }
 405
 406 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 407         return nil
 408 }
 409
 410 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 411         return discoveryMap[key], nil
 412 }
 413
 414 type KeepErrorTestClient struct{}
 415
 416 func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 417         return "", 0, errors.New("KeepError")
 418 }
 419
 420 func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 421         return nil, errors.New("KeepError")
 422 }
 423
 424 func (KeepErrorTestClient) ClearBlockCache() {
 425 }
 426
 427 type KeepReadErrorTestClient struct{}
 428
 429 func (KeepReadErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 430         return "", 0, nil
 431 }
 432
 433 func (KeepReadErrorTestClient) ClearBlockCache() {
 434 }
 435
 436 type ErrorReader struct{}
 437
 438 func (ErrorReader) Read(p []byte) (n int, err error) {
 439         return 0, errors.New("ErrorReader")
 440 }
 441
 442 func (ErrorReader) Close() error {
 443         return nil
 444 }
 445
 446 func (ErrorReader) Size() int64 {
 447         return 0
 448 }
 449
 450 func (ErrorReader) Seek(int64, int) (int64, error) {
 451         return 0, errors.New("ErrorReader")
 452 }
 453
 454 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 455         return ErrorReader{}, nil
 456 }
 457
 458 func (s *TestSuite) TestLoadImageArvError(c *C) {
 459         // (1) Arvados error
 460         cr := NewContainerRunner(ArvErrorTestClient{}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 461         cr.Container.ContainerImage = hwPDH
 462
 463         err := cr.LoadImage()
 464         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 465 }
 466
 467 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 468         // (2) Keep error
 469         docker := NewTestDockerClient(0)
 470         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 471         cr.Container.ContainerImage = hwPDH
 472
 473         err := cr.LoadImage()
 474         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 475 }
 476
 477 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 478         // (3) Collection doesn't contain image
 479         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 480         cr.Container.ContainerImage = otherPDH
 481
 482         err := cr.LoadImage()
 483         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 484 }
 485
 486 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 487         // (4) Collection doesn't contain image
 488         docker := NewTestDockerClient(0)
 489         cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 490         cr.Container.ContainerImage = hwPDH
 491
 492         err := cr.LoadImage()
 493         c.Check(err, NotNil)
 494 }
 495
 496 type ClosableBuffer struct {
 497         bytes.Buffer
 498 }
 499
 500 func (*ClosableBuffer) Close() error {
 501         return nil
 502 }
 503
 504 type TestLogs struct {
 505         Stdout ClosableBuffer
 506         Stderr ClosableBuffer
 507 }
 508
 509 func (tl *TestLogs) NewTestLoggingWriter(logstr string) io.WriteCloser {
 510         if logstr == "stdout" {
 511                 return &tl.Stdout
 512         }
 513         if logstr == "stderr" {
 514                 return &tl.Stderr
 515         }
 516         return nil
 517 }
 518
 519 func dockerLog(fd byte, msg string) []byte {
 520         by := []byte(msg)
 521         header := make([]byte, 8+len(by))
 522         header[0] = fd
 523         header[7] = byte(len(by))
 524         copy(header[8:], by)
 525         return header
 526 }
 527
 528 func (s *TestSuite) TestRunContainer(c *C) {
 529         docker := NewTestDockerClient(0)
 530         docker.fn = func(t *TestDockerClient) {
 531                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 532                 t.logWriter.Close()
 533         }
 534         cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 535
 536         var logs TestLogs
 537         cr.NewLogWriter = logs.NewTestLoggingWriter
 538         cr.Container.ContainerImage = hwPDH
 539         cr.Container.Command = []string{"./hw"}
 540         err := cr.LoadImage()
 541         c.Check(err, IsNil)
 542
 543         err = cr.CreateContainer()
 544         c.Check(err, IsNil)
 545
 546         err = cr.StartContainer()
 547         c.Check(err, IsNil)
 548
 549         err = cr.WaitFinish()
 550         c.Check(err, IsNil)
 551
 552         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 553         c.Check(logs.Stderr.String(), Equals, "")
 554 }
 555
 556 func (s *TestSuite) TestCommitLogs(c *C) {
 557         api := &ArvTestClient{}
 558         kc := &KeepTestClient{}
 559         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 560         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 561
 562         cr.CrunchLog.Print("Hello world!")
 563         cr.CrunchLog.Print("Goodbye")
 564         cr.finalState = "Complete"
 565
 566         err := cr.CommitLogs()
 567         c.Check(err, IsNil)
 568
 569         c.Check(api.Calls, Equals, 2)
 570         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 571         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 572         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 573         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 574 }
 575
 576 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 577         api := &ArvTestClient{}
 578         kc := &KeepTestClient{}
 579         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 580
 581         err := cr.UpdateContainerRunning()
 582         c.Check(err, IsNil)
 583
 584         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 585 }
 586
 587 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 588         api := &ArvTestClient{}
 589         kc := &KeepTestClient{}
 590         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 591
 592         cr.LogsPDH = new(string)
 593         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 594
 595         cr.ExitCode = new(int)
 596         *cr.ExitCode = 42
 597         cr.finalState = "Complete"
 598
 599         err := cr.UpdateContainerFinal()
 600         c.Check(err, IsNil)
 601
 602         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 603         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 604         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 605 }
 606
 607 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 608         api := &ArvTestClient{}
 609         kc := &KeepTestClient{}
 610         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 611         cr.cCancelled = true
 612         cr.finalState = "Cancelled"
 613
 614         err := cr.UpdateContainerFinal()
 615         c.Check(err, IsNil)
 616
 617         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 618         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 619         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 620 }
 621
 622 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 623 // dress rehearsal of the Run() function, starting from a JSON container record.
 624 func FullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 625         rec := arvados.Container{}
 626         err := json.Unmarshal([]byte(record), &rec)
 627         c.Check(err, IsNil)
 628
 629         docker := NewTestDockerClient(exitCode)
 630         docker.fn = fn
 631         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 632
 633         api = &ArvTestClient{Container: rec}
 634         docker.api = api
 635         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 636         cr.statInterval = 100 * time.Millisecond
 637         am := &ArvMountCmdLine{}
 638         cr.RunArvMount = am.ArvMountTest
 639
 640         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 641         c.Assert(err, IsNil)
 642         defer os.RemoveAll(realTemp)
 643
 644         docker.realTemp = realTemp
 645
 646         tempcount := 0
 647         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 648                 tempcount++
 649                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 650                 err := os.Mkdir(d, os.ModePerm)
 651                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 652                         // Test case must have pre-populated the tempdir
 653                         err = nil
 654                 }
 655                 return d, err
 656         }
 657
 658         if extraMounts != nil && len(extraMounts) > 0 {
 659                 err := cr.SetupArvMountPoint("keep")
 660                 c.Check(err, IsNil)
 661
 662                 for _, m := range extraMounts {
 663                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 664                 }
 665         }
 666
 667         err = cr.Run()
 668         if api.CalledWith("container.state", "Complete") != nil {
 669                 c.Check(err, IsNil)
 670         }
 671         c.Check(api.WasSetRunning, Equals, true)
 672
 673         c.Check(api.Content[api.Calls-1]["container"].(arvadosclient.Dict)["log"], NotNil)
 674
 675         if err != nil {
 676                 for k, v := range api.Logs {
 677                         c.Log(k)
 678                         c.Log(v.String())
 679                 }
 680         }
 681
 682         return
 683 }
 684
 685 func (s *TestSuite) TestFullRunHello(c *C) {
 686         api, _, _ := FullRunHelper(c, `{
 687     "command": ["echo", "hello world"],
 688     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 689     "cwd": ".",
 690     "environment": {},
 691     "mounts": {"/tmp": {"kind": "tmp"} },
 692     "output_path": "/tmp",
 693     "priority": 1,
 694     "runtime_constraints": {}
 695 }`, nil, 0, func(t *TestDockerClient) {
 696                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 697                 t.logWriter.Close()
 698         })
 699
 700         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 701         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 702         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 703
 704 }
 705
 706 func (s *TestSuite) TestCrunchstat(c *C) {
 707         api, _, _ := FullRunHelper(c, `{
 708                 "command": ["sleep", "1"],
 709                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 710                 "cwd": ".",
 711                 "environment": {},
 712                 "mounts": {"/tmp": {"kind": "tmp"} },
 713                 "output_path": "/tmp",
 714                 "priority": 1,
 715                 "runtime_constraints": {}
 716         }`, nil, 0, func(t *TestDockerClient) {
 717                 time.Sleep(time.Second)
 718                 t.logWriter.Close()
 719         })
 720
 721         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 722         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 723
 724         // We didn't actually start a container, so crunchstat didn't
 725         // find accounting files and therefore didn't log any stats.
 726         // It should have logged a "can't find accounting files"
 727         // message after one poll interval, though, so we can confirm
 728         // it's alive:
 729         c.Assert(api.Logs["crunchstat"], NotNil)
 730         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 731
 732         // The "files never appeared" log assures us that we called
 733         // (*crunchstat.Reporter)Stop(), and that we set it up with
 734         // the correct container ID "abcde":
 735         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 736 }
 737
 738 func (s *TestSuite) TestNodeInfoLog(c *C) {
 739         api, _, _ := FullRunHelper(c, `{
 740                 "command": ["sleep", "1"],
 741                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 742                 "cwd": ".",
 743                 "environment": {},
 744                 "mounts": {"/tmp": {"kind": "tmp"} },
 745                 "output_path": "/tmp",
 746                 "priority": 1,
 747                 "runtime_constraints": {}
 748         }`, nil, 0,
 749                 func(t *TestDockerClient) {
 750                         time.Sleep(time.Second)
 751                         t.logWriter.Close()
 752                 })
 753
 754         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 755         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 756
 757         c.Assert(api.Logs["node-info"], NotNil)
 758         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Host Information.*`)
 759         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*CPU Information.*`)
 760         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Memory Information.*`)
 761         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk Space.*`)
 762         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk INodes.*`)
 763 }
 764
 765 func (s *TestSuite) TestContainerRecordLog(c *C) {
 766         api, _, _ := FullRunHelper(c, `{
 767                 "command": ["sleep", "1"],
 768                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 769                 "cwd": ".",
 770                 "environment": {},
 771                 "mounts": {"/tmp": {"kind": "tmp"} },
 772                 "output_path": "/tmp",
 773                 "priority": 1,
 774                 "runtime_constraints": {}
 775         }`, nil, 0,
 776                 func(t *TestDockerClient) {
 777                         time.Sleep(time.Second)
 778                         t.logWriter.Close()
 779                 })
 780
 781         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 782         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 783
 784         c.Assert(api.Logs["container"], NotNil)
 785         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 786 }
 787
 788 func (s *TestSuite) TestFullRunStderr(c *C) {
 789         api, _, _ := FullRunHelper(c, `{
 790     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 791     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 792     "cwd": ".",
 793     "environment": {},
 794     "mounts": {"/tmp": {"kind": "tmp"} },
 795     "output_path": "/tmp",
 796     "priority": 1,
 797     "runtime_constraints": {}
 798 }`, nil, 1, func(t *TestDockerClient) {
 799                 t.logWriter.Write(dockerLog(1, "hello\n"))
 800                 t.logWriter.Write(dockerLog(2, "world\n"))
 801                 t.logWriter.Close()
 802         })
 803
 804         final := api.CalledWith("container.state", "Complete")
 805         c.Assert(final, NotNil)
 806         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 807         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 808
 809         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 810         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 811 }
 812
 813 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 814         api, _, _ := FullRunHelper(c, `{
 815     "command": ["pwd"],
 816     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 817     "cwd": ".",
 818     "environment": {},
 819     "mounts": {"/tmp": {"kind": "tmp"} },
 820     "output_path": "/tmp",
 821     "priority": 1,
 822     "runtime_constraints": {}
 823 }`, nil, 0, func(t *TestDockerClient) {
 824                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 825                 t.logWriter.Close()
 826         })
 827
 828         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 829         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 830         c.Log(api.Logs["stdout"])
 831         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 832 }
 833
 834 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 835         api, _, _ := FullRunHelper(c, `{
 836     "command": ["pwd"],
 837     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 838     "cwd": "/bin",
 839     "environment": {},
 840     "mounts": {"/tmp": {"kind": "tmp"} },
 841     "output_path": "/tmp",
 842     "priority": 1,
 843     "runtime_constraints": {}
 844 }`, nil, 0, func(t *TestDockerClient) {
 845                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 846                 t.logWriter.Close()
 847         })
 848
 849         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 850         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 851         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 852 }
 853
 854 func (s *TestSuite) TestStopOnSignal(c *C) {
 855         s.testStopContainer(c, func(cr *ContainerRunner) {
 856                 go func() {
 857                         for !cr.cStarted {
 858                                 time.Sleep(time.Millisecond)
 859                         }
 860                         cr.SigChan <- syscall.SIGINT
 861                 }()
 862         })
 863 }
 864
 865 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 866         s.testStopContainer(c, func(cr *ContainerRunner) {
 867                 cr.ArvMountExit = make(chan error)
 868                 go func() {
 869                         cr.ArvMountExit <- exec.Command("true").Run()
 870                         close(cr.ArvMountExit)
 871                 }()
 872         })
 873 }
 874
 875 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 876         record := `{
 877     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 878     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 879     "cwd": ".",
 880     "environment": {},
 881     "mounts": {"/tmp": {"kind": "tmp"} },
 882     "output_path": "/tmp",
 883     "priority": 1,
 884     "runtime_constraints": {}
 885 }`
 886
 887         rec := arvados.Container{}
 888         err := json.Unmarshal([]byte(record), &rec)
 889         c.Check(err, IsNil)
 890
 891         docker := NewTestDockerClient(0)
 892         docker.fn = func(t *TestDockerClient) {
 893                 <-t.stop
 894                 t.logWriter.Write(dockerLog(1, "foo\n"))
 895                 t.logWriter.Close()
 896         }
 897         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 898
 899         api := &ArvTestClient{Container: rec}
 900         cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 901         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
 902         setup(cr)
 903
 904         done := make(chan error)
 905         go func() {
 906                 done <- cr.Run()
 907         }()
 908         select {
 909         case <-time.After(20 * time.Second):
 910                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
 911                 c.Fatal("timed out")
 912         case err = <-done:
 913                 c.Check(err, IsNil)
 914         }
 915         for k, v := range api.Logs {
 916                 c.Log(k)
 917                 c.Log(v.String())
 918         }
 919
 920         c.Check(api.CalledWith("container.log", nil), NotNil)
 921         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
 922         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
 923 }
 924
 925 func (s *TestSuite) TestFullRunSetEnv(c *C) {
 926         api, _, _ := FullRunHelper(c, `{
 927     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
 928     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 929     "cwd": "/bin",
 930     "environment": {"FROBIZ": "bilbo"},
 931     "mounts": {"/tmp": {"kind": "tmp"} },
 932     "output_path": "/tmp",
 933     "priority": 1,
 934     "runtime_constraints": {}
 935 }`, nil, 0, func(t *TestDockerClient) {
 936                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
 937                 t.logWriter.Close()
 938         })
 939
 940         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 941         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 942         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
 943 }
 944
 945 type ArvMountCmdLine struct {
 946         Cmd   []string
 947         token string
 948 }
 949
 950 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
 951         am.Cmd = c
 952         am.token = token
 953         return nil, nil
 954 }
 955
 956 func stubCert(temp string) string {
 957         path := temp + "/ca-certificates.crt"
 958         crt, _ := os.Create(path)
 959         crt.Close()
 960         arvadosclient.CertFiles = []string{path}
 961         return path
 962 }
 963
 964 func (s *TestSuite) TestSetupMounts(c *C) {
 965         api := &ArvTestClient{}
 966         kc := &KeepTestClient{}
 967         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 968         am := &ArvMountCmdLine{}
 969         cr.RunArvMount = am.ArvMountTest
 970
 971         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
 972         c.Assert(err, IsNil)
 973         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
 974         c.Assert(err, IsNil)
 975         stubCertPath := stubCert(certTemp)
 976
 977         defer os.RemoveAll(realTemp)
 978         defer os.RemoveAll(certTemp)
 979
 980         i := 0
 981         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 982                 i++
 983                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
 984                 err := os.Mkdir(d, os.ModePerm)
 985                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 986                         // Test case must have pre-populated the tempdir
 987                         err = nil
 988                 }
 989                 return d, err
 990         }
 991
 992         checkEmpty := func() {
 993                 filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
 994                         c.Check(path, Equals, realTemp)
 995                         c.Check(err, IsNil)
 996                         return nil
 997                 })
 998         }
 999
1000         {
1001                 i = 0
1002                 cr.ArvMountPoint = ""
1003                 cr.Container.Mounts = make(map[string]arvados.Mount)
1004                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1005                 cr.OutputPath = "/tmp"
1006                 cr.statInterval = 5 * time.Second
1007                 err := cr.SetupMounts()
1008                 c.Check(err, IsNil)
1009                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1010                         "--read-write", "--crunchstat-interval=5",
1011                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1012                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
1013                 cr.CleanupDirs()
1014                 checkEmpty()
1015         }
1016
1017         {
1018                 i = 0
1019                 cr.ArvMountPoint = ""
1020                 cr.Container.Mounts = make(map[string]arvados.Mount)
1021                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
1022                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1023                 cr.OutputPath = "/out"
1024
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:/out", realTemp + "/3:/tmp"})
1031                 cr.CleanupDirs()
1032                 checkEmpty()
1033         }
1034
1035         {
1036                 i = 0
1037                 cr.ArvMountPoint = ""
1038                 cr.Container.Mounts = make(map[string]arvados.Mount)
1039                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1040                 cr.OutputPath = "/tmp"
1041
1042                 apiflag := true
1043                 cr.Container.RuntimeConstraints.API = &apiflag
1044
1045                 err := cr.SetupMounts()
1046                 c.Check(err, IsNil)
1047                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1048                         "--read-write", "--crunchstat-interval=5",
1049                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1050                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1051                 cr.CleanupDirs()
1052                 checkEmpty()
1053
1054                 apiflag = false
1055         }
1056
1057         {
1058                 i = 0
1059                 cr.ArvMountPoint = ""
1060                 cr.Container.Mounts = map[string]arvados.Mount{
1061                         "/keeptmp": {Kind: "collection", Writable: true},
1062                 }
1063                 cr.OutputPath = "/keeptmp"
1064
1065                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1066
1067                 err := cr.SetupMounts()
1068                 c.Check(err, IsNil)
1069                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1070                         "--read-write", "--crunchstat-interval=5",
1071                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1072                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1073                 cr.CleanupDirs()
1074                 checkEmpty()
1075         }
1076
1077         {
1078                 i = 0
1079                 cr.ArvMountPoint = ""
1080                 cr.Container.Mounts = map[string]arvados.Mount{
1081                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1082                         "/keepout": {Kind: "collection", Writable: true},
1083                 }
1084                 cr.OutputPath = "/keepout"
1085
1086                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1087                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1088
1089                 err := cr.SetupMounts()
1090                 c.Check(err, IsNil)
1091                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1092                         "--read-write", "--crunchstat-interval=5",
1093                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1094                 sort.StringSlice(cr.Binds).Sort()
1095                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1096                         realTemp + "/keep1/tmp0:/keepout"})
1097                 cr.CleanupDirs()
1098                 checkEmpty()
1099         }
1100
1101         {
1102                 i = 0
1103                 cr.ArvMountPoint = ""
1104                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1105                 cr.Container.Mounts = map[string]arvados.Mount{
1106                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1107                         "/keepout": {Kind: "collection", Writable: true},
1108                 }
1109                 cr.OutputPath = "/keepout"
1110
1111                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1112                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1113
1114                 err := cr.SetupMounts()
1115                 c.Check(err, IsNil)
1116                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1117                         "--read-write", "--crunchstat-interval=5",
1118                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1119                 sort.StringSlice(cr.Binds).Sort()
1120                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1121                         realTemp + "/keep1/tmp0:/keepout"})
1122                 cr.CleanupDirs()
1123                 checkEmpty()
1124         }
1125
1126         for _, test := range []struct {
1127                 in  interface{}
1128                 out string
1129         }{
1130                 {in: "foo", out: `"foo"`},
1131                 {in: nil, out: `null`},
1132                 {in: map[string]int64{"foo": 123456789123456789}, out: `{"foo":123456789123456789}`},
1133         } {
1134                 i = 0
1135                 cr.ArvMountPoint = ""
1136                 cr.Container.Mounts = map[string]arvados.Mount{
1137                         "/mnt/test.json": {Kind: "json", Content: test.in},
1138                 }
1139                 err := cr.SetupMounts()
1140                 c.Check(err, IsNil)
1141                 sort.StringSlice(cr.Binds).Sort()
1142                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
1143                 content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
1144                 c.Check(err, IsNil)
1145                 c.Check(content, DeepEquals, []byte(test.out))
1146                 cr.CleanupDirs()
1147                 checkEmpty()
1148         }
1149
1150         // Read-only mount points are allowed underneath output_dir mount point
1151         {
1152                 i = 0
1153                 cr.ArvMountPoint = ""
1154                 cr.Container.Mounts = make(map[string]arvados.Mount)
1155                 cr.Container.Mounts = map[string]arvados.Mount{
1156                         "/tmp":     {Kind: "tmp"},
1157                         "/tmp/foo": {Kind: "collection"},
1158                 }
1159                 cr.OutputPath = "/tmp"
1160
1161                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1162
1163                 err := cr.SetupMounts()
1164                 c.Check(err, IsNil)
1165                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1166                         "--read-write", "--crunchstat-interval=5",
1167                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1168                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1169                 cr.CleanupDirs()
1170                 checkEmpty()
1171         }
1172
1173         // Writable mount points are not allowed underneath output_dir mount point
1174         {
1175                 i = 0
1176                 cr.ArvMountPoint = ""
1177                 cr.Container.Mounts = make(map[string]arvados.Mount)
1178                 cr.Container.Mounts = map[string]arvados.Mount{
1179                         "/tmp":     {Kind: "tmp"},
1180                         "/tmp/foo": {Kind: "collection", Writable: true},
1181                 }
1182                 cr.OutputPath = "/tmp"
1183
1184                 err := cr.SetupMounts()
1185                 c.Check(err, NotNil)
1186                 c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
1187                 cr.CleanupDirs()
1188                 checkEmpty()
1189         }
1190
1191         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1192         {
1193                 i = 0
1194                 cr.ArvMountPoint = ""
1195                 cr.Container.Mounts = make(map[string]arvados.Mount)
1196                 cr.Container.Mounts = map[string]arvados.Mount{
1197                         "/tmp":     {Kind: "tmp"},
1198                         "/tmp/foo": {Kind: "json"},
1199                 }
1200                 cr.OutputPath = "/tmp"
1201
1202                 err := cr.SetupMounts()
1203                 c.Check(err, NotNil)
1204                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
1205                 cr.CleanupDirs()
1206                 checkEmpty()
1207         }
1208
1209         // Only mount point of kind 'collection' is allowed for stdin
1210         {
1211                 i = 0
1212                 cr.ArvMountPoint = ""
1213                 cr.Container.Mounts = make(map[string]arvados.Mount)
1214                 cr.Container.Mounts = map[string]arvados.Mount{
1215                         "stdin": {Kind: "tmp"},
1216                 }
1217
1218                 err := cr.SetupMounts()
1219                 c.Check(err, NotNil)
1220                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1221                 cr.CleanupDirs()
1222                 checkEmpty()
1223         }
1224 }
1225
1226 func (s *TestSuite) TestStdout(c *C) {
1227         helperRecord := `{
1228                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1229                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1230                 "cwd": "/bin",
1231                 "environment": {"FROBIZ": "bilbo"},
1232                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1233                 "output_path": "/tmp",
1234                 "priority": 1,
1235                 "runtime_constraints": {}
1236         }`
1237
1238         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1239                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1240                 t.logWriter.Close()
1241         })
1242
1243         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1244         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1245         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1246 }
1247
1248 // Used by the TestStdoutWithWrongPath*()
1249 func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1250         rec := arvados.Container{}
1251         err = json.Unmarshal([]byte(record), &rec)
1252         c.Check(err, IsNil)
1253
1254         docker := NewTestDockerClient(0)
1255         docker.fn = fn
1256         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1257
1258         api = &ArvTestClient{Container: rec}
1259         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1260         am := &ArvMountCmdLine{}
1261         cr.RunArvMount = am.ArvMountTest
1262
1263         err = cr.Run()
1264         return
1265 }
1266
1267 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1268         _, _, err := StdoutErrorRunHelper(c, `{
1269     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1270     "output_path": "/tmp"
1271 }`, func(t *TestDockerClient) {})
1272
1273         c.Check(err, NotNil)
1274         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1275 }
1276
1277 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1278         _, _, err := StdoutErrorRunHelper(c, `{
1279     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1280     "output_path": "/tmp"
1281 }`, func(t *TestDockerClient) {})
1282
1283         c.Check(err, NotNil)
1284         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1285 }
1286
1287 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1288         _, _, err := StdoutErrorRunHelper(c, `{
1289     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1290     "output_path": "/tmp"
1291 }`, func(t *TestDockerClient) {})
1292
1293         c.Check(err, NotNil)
1294         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1295 }
1296
1297 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1298         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1299         defer os.Unsetenv("ARVADOS_API_HOST")
1300         api, _, _ := FullRunHelper(c, `{
1301     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1302     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1303     "cwd": "/bin",
1304     "environment": {},
1305     "mounts": {"/tmp": {"kind": "tmp"} },
1306     "output_path": "/tmp",
1307     "priority": 1,
1308     "runtime_constraints": {"API": true}
1309 }`, nil, 0, func(t *TestDockerClient) {
1310                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1311                 t.logWriter.Close()
1312         })
1313
1314         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1315         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1316         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1317         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1318 }
1319
1320 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1321         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1322         defer os.Unsetenv("ARVADOS_API_HOST")
1323         api, _, _ := FullRunHelper(c, `{
1324     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1325     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1326     "cwd": "/bin",
1327     "environment": {},
1328     "mounts": {"/tmp": {"kind": "tmp"} },
1329     "output_path": "/tmp",
1330     "priority": 1,
1331     "runtime_constraints": {"API": true}
1332 }`, nil, 0, func(t *TestDockerClient) {
1333                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1334                 t.logWriter.Close()
1335         })
1336
1337         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1338         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1339         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1340 }
1341
1342 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1343         helperRecord := `{
1344                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1345                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1346                 "cwd": "/bin",
1347                 "environment": {"FROBIZ": "bilbo"},
1348                 "mounts": {
1349         "/tmp": {"kind": "tmp"},
1350         "/tmp/foo": {"kind": "collection",
1351                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1352                      "exclude_from_output": true
1353         },
1354         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1355     },
1356                 "output_path": "/tmp",
1357                 "priority": 1,
1358                 "runtime_constraints": {}
1359         }`
1360
1361         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1362
1363         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1364                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1365                 t.logWriter.Close()
1366         })
1367
1368         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1369         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1370         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1371 }
1372
1373 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1374         helperRecord := `{
1375                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1376                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1377                 "cwd": "/bin",
1378                 "environment": {"FROBIZ": "bilbo"},
1379                 "mounts": {
1380         "/tmp": {"kind": "tmp"},
1381         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1382         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1383         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1384         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1385         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1386     },
1387                 "output_path": "/tmp",
1388                 "priority": 1,
1389                 "runtime_constraints": {}
1390         }`
1391
1392         extraMounts := []string{
1393                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1394                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1395                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1396         }
1397
1398         api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1399                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1400                 t.logWriter.Close()
1401         })
1402
1403         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
1404                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1405                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1406                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1407                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1408         })
1409
1410         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1411         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1412         for _, v := range api.Content {
1413                 if v["collection"] != nil {
1414                         c.Check(v["ensure_unique_name"], Equals, true)
1415                         collection := v["collection"].(arvadosclient.Dict)
1416                         if strings.Index(collection["name"].(string), "output") == 0 {
1417                                 manifest := collection["manifest_text"].(string)
1418
1419                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1420 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
1421 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1422 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1423 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1424 `)
1425                         }
1426                 }
1427         }
1428 }
1429
1430 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1431         helperRecord := `{
1432                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1433                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1434                 "cwd": "/bin",
1435                 "environment": {"FROBIZ": "bilbo"},
1436                 "mounts": {
1437         "/tmp": {"kind": "tmp"},
1438         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
1439         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1440     },
1441                 "output_path": "/tmp",
1442                 "priority": 1,
1443                 "runtime_constraints": {}
1444         }`
1445
1446         extraMounts := []string{
1447                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1448         }
1449
1450         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1451                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1452                 t.logWriter.Close()
1453         })
1454
1455         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1456         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1457         for _, v := range api.Content {
1458                 if v["collection"] != nil {
1459                         collection := v["collection"].(arvadosclient.Dict)
1460                         if strings.Index(collection["name"].(string), "output") == 0 {
1461                                 manifest := collection["manifest_text"].(string)
1462
1463                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1464 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1465 `)
1466                         }
1467                 }
1468         }
1469 }
1470
1471 func (s *TestSuite) TestOutputSymlinkToInput(c *C) {
1472         helperRecord := `{
1473                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1474                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1475                 "cwd": "/bin",
1476                 "environment": {"FROBIZ": "bilbo"},
1477                 "mounts": {
1478         "/tmp": {"kind": "tmp"},
1479         "/keep/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
1480         "/keep/foo2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"}
1481     },
1482                 "output_path": "/tmp",
1483                 "priority": 1,
1484                 "runtime_constraints": {}
1485         }`
1486
1487         extraMounts := []string{
1488                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1489         }
1490
1491         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1492                 os.Symlink("/keep/foo/sub1file2", t.realTemp+"/2/baz")
1493                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz2")
1494                 os.Symlink("/keep/foo2/subdir1", t.realTemp+"/2/baz3")
1495                 os.Mkdir(t.realTemp+"/2/baz4", 0700)
1496                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz4/baz5")
1497                 t.logWriter.Close()
1498         })
1499
1500         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1501         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1502         for _, v := range api.Content {
1503                 if v["collection"] != nil {
1504                         collection := v["collection"].(arvadosclient.Dict)
1505                         if strings.Index(collection["name"].(string), "output") == 0 {
1506                                 manifest := collection["manifest_text"].(string)
1507                                 c.Check(manifest, Equals, `. 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz 9:18:baz2
1508 ./baz3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1509 ./baz3/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1510 ./baz4 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz5
1511 `)
1512                         }
1513                 }
1514         }
1515 }
1516
1517 func (s *TestSuite) TestOutputError(c *C) {
1518         helperRecord := `{
1519                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1520                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1521                 "cwd": "/bin",
1522                 "environment": {"FROBIZ": "bilbo"},
1523                 "mounts": {
1524         "/tmp": {"kind": "tmp"}
1525     },
1526                 "output_path": "/tmp",
1527                 "priority": 1,
1528                 "runtime_constraints": {}
1529         }`
1530
1531         extraMounts := []string{}
1532
1533         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1534                 os.Symlink("/etc/hosts", t.realTemp+"/2/baz")
1535                 t.logWriter.Close()
1536         })
1537
1538         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1539 }
1540
1541 func (s *TestSuite) TestOutputSymlinkToOutput(c *C) {
1542         helperRecord := `{
1543                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1544                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1545                 "cwd": "/bin",
1546                 "environment": {"FROBIZ": "bilbo"},
1547                 "mounts": {
1548         "/tmp": {"kind": "tmp"}
1549     },
1550                 "output_path": "/tmp",
1551                 "priority": 1,
1552                 "runtime_constraints": {}
1553         }`
1554
1555         extraMounts := []string{}
1556
1557         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1558                 rf, _ := os.Create(t.realTemp + "/2/realfile")
1559                 rf.Write([]byte("foo"))
1560                 rf.Close()
1561
1562                 os.Mkdir(t.realTemp+"/2/realdir", 0700)
1563                 rf, _ = os.Create(t.realTemp + "/2/realdir/subfile")
1564                 rf.Write([]byte("bar"))
1565                 rf.Close()
1566
1567                 os.Symlink("/tmp/realfile", t.realTemp+"/2/file1")
1568                 os.Symlink("realfile", t.realTemp+"/2/file2")
1569                 os.Symlink("/tmp/file1", t.realTemp+"/2/file3")
1570                 os.Symlink("file2", t.realTemp+"/2/file4")
1571                 os.Symlink("realdir", t.realTemp+"/2/dir1")
1572                 os.Symlink("/tmp/realdir", t.realTemp+"/2/dir2")
1573                 t.logWriter.Close()
1574         })
1575
1576         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1577         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1578         for _, v := range api.Content {
1579                 if v["collection"] != nil {
1580                         collection := v["collection"].(arvadosclient.Dict)
1581                         if strings.Index(collection["name"].(string), "output") == 0 {
1582                                 manifest := collection["manifest_text"].(string)
1583                                 c.Check(manifest, Equals,
1584                                         `. 7a2c86e102dcc231bd232aad99686dfa+15 0:3:file1 3:3:file2 6:3:file3 9:3:file4 12:3:realfile
1585 ./dir1 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1586 ./dir2 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1587 ./realdir 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1588 `)
1589                         }
1590                 }
1591         }
1592 }
1593
1594 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1595         helperRecord := `{
1596                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1597                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1598                 "cwd": "/bin",
1599                 "environment": {"FROBIZ": "bilbo"},
1600                 "mounts": {
1601         "/tmp": {"kind": "tmp"},
1602         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1603         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1604     },
1605                 "output_path": "/tmp",
1606                 "priority": 1,
1607                 "runtime_constraints": {}
1608         }`
1609
1610         extraMounts := []string{
1611                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1612         }
1613
1614         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1615                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1616                 t.logWriter.Close()
1617         })
1618
1619         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1620         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1621         for _, v := range api.Content {
1622                 if v["collection"] != nil {
1623                         collection := v["collection"].(arvadosclient.Dict)
1624                         if strings.Index(collection["name"].(string), "output") == 0 {
1625                                 manifest := collection["manifest_text"].(string)
1626                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1627 `)
1628                         }
1629                 }
1630         }
1631 }
1632
1633 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1634         helperRecord := `{
1635                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1636                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1637                 "cwd": "/bin",
1638                 "environment": {"FROBIZ": "bilbo"},
1639                 "mounts": {
1640         "/tmp": {"kind": "tmp"},
1641         "stdin": {"kind": "json", "content": "foo"},
1642         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1643     },
1644                 "output_path": "/tmp",
1645                 "priority": 1,
1646                 "runtime_constraints": {}
1647         }`
1648
1649         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1650                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1651                 t.logWriter.Close()
1652         })
1653
1654         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1655         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1656         for _, v := range api.Content {
1657                 if v["collection"] != nil {
1658                         collection := v["collection"].(arvadosclient.Dict)
1659                         if strings.Index(collection["name"].(string), "output") == 0 {
1660                                 manifest := collection["manifest_text"].(string)
1661                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1662 `)
1663                         }
1664                 }
1665         }
1666 }
1667
1668 func (s *TestSuite) TestStderrMount(c *C) {
1669         api, _, _ := FullRunHelper(c, `{
1670     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1671     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1672     "cwd": ".",
1673     "environment": {},
1674     "mounts": {"/tmp": {"kind": "tmp"},
1675                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1676                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1677     "output_path": "/tmp",
1678     "priority": 1,
1679     "runtime_constraints": {}
1680 }`, nil, 1, func(t *TestDockerClient) {
1681                 t.logWriter.Write(dockerLog(1, "hello\n"))
1682                 t.logWriter.Write(dockerLog(2, "oops\n"))
1683                 t.logWriter.Close()
1684         })
1685
1686         final := api.CalledWith("container.state", "Complete")
1687         c.Assert(final, NotNil)
1688         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1689         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1690
1691         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1692 }
1693
1694 func (s *TestSuite) TestNumberRoundTrip(c *C) {
1695         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1696         cr.fetchContainerRecord()
1697
1698         jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
1699
1700         c.Check(err, IsNil)
1701         c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
1702 }
1703
1704 func (s *TestSuite) TestEvalSymlinks(c *C) {
1705         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1706
1707         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1708         c.Assert(err, IsNil)
1709         defer os.RemoveAll(realTemp)
1710
1711         cr.HostOutputDir = realTemp
1712
1713         // Absolute path outside output dir
1714         os.Symlink("/etc/passwd", realTemp+"/p1")
1715
1716         // Relative outside output dir
1717         os.Symlink("../zip", realTemp+"/p2")
1718
1719         // Circular references
1720         os.Symlink("p4", realTemp+"/p3")
1721         os.Symlink("p5", realTemp+"/p4")
1722         os.Symlink("p3", realTemp+"/p5")
1723
1724         // Target doesn't exist
1725         os.Symlink("p99", realTemp+"/p6")
1726
1727         for _, v := range []string{"p1", "p2", "p3", "p4", "p5"} {
1728                 info, err := os.Lstat(realTemp + "/" + v)
1729                 _, _, _, err = cr.derefOutputSymlink(realTemp+"/"+v, info)
1730                 c.Assert(err, NotNil)
1731         }
1732 }
1733
1734 func (s *TestSuite) TestEvalSymlinkDir(c *C) {
1735         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1736
1737         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1738         c.Assert(err, IsNil)
1739         defer os.RemoveAll(realTemp)
1740
1741         cr.HostOutputDir = realTemp
1742
1743         // Absolute path outside output dir
1744         os.Symlink(".", realTemp+"/loop")
1745
1746         v := "loop"
1747         info, err := os.Lstat(realTemp + "/" + v)
1748         _, err = cr.UploadOutputFile(realTemp+"/"+v, info, err, []string{}, nil, "", "", 0)
1749         c.Assert(err, NotNil)
1750 }