services/crunch-run/crunchrun_test.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "context"
   7         "crypto/md5"
   8         "encoding/json"
   9         "errors"
  10         "fmt"
  11         "io"
  12         "io/ioutil"
  13         "net"
  14         "os"
  15         "os/exec"
  16         "path/filepath"
  17         "runtime/pprof"
  18         "sort"
  19         "strings"
  20         "sync"
  21         "syscall"
  22         "testing"
  23         "time"
  24
  25         "git.curoverse.com/arvados.git/sdk/go/arvados"
  26         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  27         "git.curoverse.com/arvados.git/sdk/go/keepclient"
  28         "git.curoverse.com/arvados.git/sdk/go/manifest"
  29
  30         dockertypes "github.com/docker/docker/api/types"
  31         dockercontainer "github.com/docker/docker/api/types/container"
  32         dockernetwork "github.com/docker/docker/api/types/network"
  33         . "gopkg.in/check.v1"
  34 )
  35
  36 // Gocheck boilerplate
  37 func TestCrunchExec(t *testing.T) {
  38         TestingT(t)
  39 }
  40
  41 type TestSuite struct{}
  42
  43 // Gocheck boilerplate
  44 var _ = Suite(&TestSuite{})
  45
  46 type ArvTestClient struct {
  47         Total   int64
  48         Calls   int
  49         Content []arvadosclient.Dict
  50         arvados.Container
  51         Logs map[string]*bytes.Buffer
  52         sync.Mutex
  53         WasSetRunning bool
  54 }
  55
  56 type KeepTestClient struct {
  57         Called  bool
  58         Content []byte
  59 }
  60
  61 var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0@569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
  62 var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
  63 var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
  64
  65 var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
  66 var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
  67
  68 var normalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt\n"
  69 var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
  70
  71 var denormalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt 0:10:subdir1/file1_in_subdir1.txt 10:17:subdir1/file2_in_subdir1.txt\n"
  72 var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
  73
  74 var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
  75 var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
  76
  77 type TestDockerClient struct {
  78         imageLoaded string
  79         logReader   io.ReadCloser
  80         logWriter   io.WriteCloser
  81         fn          func(t *TestDockerClient)
  82         finish      int
  83         stop        chan bool
  84         cwd         string
  85         env         []string
  86         api         *ArvTestClient
  87 }
  88
  89 func NewTestDockerClient(exitCode int) *TestDockerClient {
  90         t := &TestDockerClient{}
  91         t.logReader, t.logWriter = io.Pipe()
  92         t.finish = exitCode
  93         t.stop = make(chan bool)
  94         t.cwd = "/"
  95         return t
  96 }
  97
  98 type MockConn struct {
  99         net.Conn
 100 }
 101
 102 func (m *MockConn) Write(b []byte) (int, error) {
 103         return len(b), nil
 104 }
 105
 106 func NewMockConn() *MockConn {
 107         c := &MockConn{}
 108         return c
 109 }
 110
 111 func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
 112         return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
 113 }
 114
 115 func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
 116         if config.WorkingDir != "" {
 117                 t.cwd = config.WorkingDir
 118         }
 119         t.env = config.Env
 120         return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
 121 }
 122
 123 func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 124         if container == "abcde" {
 125                 go t.fn(t)
 126                 return nil
 127         } else {
 128                 return errors.New("Invalid container id")
 129         }
 130 }
 131
 132 func (t *TestDockerClient) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
 133         t.stop <- true
 134         return nil
 135 }
 136
 137 func (t *TestDockerClient) ContainerWait(ctx context.Context, container string) (int64, error) {
 138         return int64(t.finish), nil
 139 }
 140
 141 func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 142         if t.imageLoaded == image {
 143                 return dockertypes.ImageInspect{}, nil, nil
 144         } else {
 145                 return dockertypes.ImageInspect{}, nil, errors.New("")
 146         }
 147 }
 148
 149 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 150         _, err := io.Copy(ioutil.Discard, input)
 151         if err != nil {
 152                 return dockertypes.ImageLoadResponse{}, err
 153         } else {
 154                 t.imageLoaded = hwImageId
 155                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 156         }
 157 }
 158
 159 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 160         return nil, nil
 161 }
 162
 163 func (client *ArvTestClient) Create(resourceType string,
 164         parameters arvadosclient.Dict,
 165         output interface{}) error {
 166
 167         client.Mutex.Lock()
 168         defer client.Mutex.Unlock()
 169
 170         client.Calls++
 171         client.Content = append(client.Content, parameters)
 172
 173         if resourceType == "logs" {
 174                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 175                 if client.Logs == nil {
 176                         client.Logs = make(map[string]*bytes.Buffer)
 177                 }
 178                 if client.Logs[et] == nil {
 179                         client.Logs[et] = &bytes.Buffer{}
 180                 }
 181                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 182         }
 183
 184         if resourceType == "collections" && output != nil {
 185                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 186                 outmap := output.(*arvados.Collection)
 187                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 188         }
 189
 190         return nil
 191 }
 192
 193 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 194         switch {
 195         case method == "GET" && resourceType == "containers" && action == "auth":
 196                 return json.Unmarshal([]byte(`{
 197                         "kind": "arvados#api_client_authorization",
 198                         "uuid": "`+fakeAuthUUID+`",
 199                         "api_token": "`+fakeAuthToken+`"
 200                         }`), output)
 201         default:
 202                 return fmt.Errorf("Not found")
 203         }
 204 }
 205
 206 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 207         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 208         j := []byte(`{
 209                 "command": ["sleep", "1"],
 210                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 211                 "cwd": ".",
 212                 "environment": {},
 213                 "mounts": {"/tmp": {"kind": "tmp"} },
 214                 "output_path": "/tmp",
 215                 "priority": 1,
 216                 "runtime_constraints": {}
 217         }`)
 218         return ioutil.NopCloser(bytes.NewReader(j)), nil
 219 }
 220
 221 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 222         if resourceType == "collections" {
 223                 if uuid == hwPDH {
 224                         output.(*arvados.Collection).ManifestText = hwManifest
 225                 } else if uuid == otherPDH {
 226                         output.(*arvados.Collection).ManifestText = otherManifest
 227                 } else if uuid == normalizedWithSubdirsPDH {
 228                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 229                 } else if uuid == denormalizedWithSubdirsPDH {
 230                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 231                 }
 232         }
 233         if resourceType == "containers" {
 234                 (*output.(*arvados.Container)) = client.Container
 235         }
 236         return nil
 237 }
 238
 239 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 240         client.Mutex.Lock()
 241         defer client.Mutex.Unlock()
 242         client.Calls++
 243         client.Content = append(client.Content, parameters)
 244         if resourceType == "containers" {
 245                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 246                         client.WasSetRunning = true
 247                 }
 248         }
 249         return nil
 250 }
 251
 252 var discoveryMap = map[string]interface{}{"defaultTrashLifetime": float64(1209600)}
 253
 254 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 255         return discoveryMap[key], nil
 256 }
 257
 258 // CalledWith returns the parameters from the first API call whose
 259 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 260 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 261 // no call matches, it returns nil.
 262 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 263 call:
 264         for _, content := range client.Content {
 265                 var v interface{} = content
 266                 for _, k := range strings.Split(jpath, ".") {
 267                         if dict, ok := v.(arvadosclient.Dict); !ok {
 268                                 continue call
 269                         } else {
 270                                 v = dict[k]
 271                         }
 272                 }
 273                 if v == expect {
 274                         return content
 275                 }
 276         }
 277         return nil
 278 }
 279
 280 func (client *KeepTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 281         client.Content = buf
 282         return fmt.Sprintf("%s+%d", hash, len(buf)), len(buf), nil
 283 }
 284
 285 type FileWrapper struct {
 286         io.ReadCloser
 287         len uint64
 288 }
 289
 290 func (fw FileWrapper) Len() uint64 {
 291         return fw.len
 292 }
 293
 294 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 295         return 0, errors.New("not implemented")
 296 }
 297
 298 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 299         if filename == hwImageId+".tar" {
 300                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 301                 client.Called = true
 302                 return FileWrapper{rdr, 1321984}, nil
 303         } else if filename == "/file1_in_main.txt" {
 304                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 305                 client.Called = true
 306                 return FileWrapper{rdr, 3}, nil
 307         }
 308         return nil, nil
 309 }
 310
 311 func (s *TestSuite) TestLoadImage(c *C) {
 312         kc := &KeepTestClient{}
 313         docker := NewTestDockerClient(0)
 314         cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 315
 316         _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 317
 318         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 319         c.Check(err, NotNil)
 320
 321         cr.Container.ContainerImage = hwPDH
 322
 323         // (1) Test loading image from keep
 324         c.Check(kc.Called, Equals, false)
 325         c.Check(cr.ContainerConfig.Image, Equals, "")
 326
 327         err = cr.LoadImage()
 328
 329         c.Check(err, IsNil)
 330         defer func() {
 331                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 332         }()
 333
 334         c.Check(kc.Called, Equals, true)
 335         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 336
 337         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 338         c.Check(err, IsNil)
 339
 340         // (2) Test using image that's already loaded
 341         kc.Called = false
 342         cr.ContainerConfig.Image = ""
 343
 344         err = cr.LoadImage()
 345         c.Check(err, IsNil)
 346         c.Check(kc.Called, Equals, false)
 347         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 348
 349 }
 350
 351 type ArvErrorTestClient struct{}
 352
 353 func (ArvErrorTestClient) Create(resourceType string,
 354         parameters arvadosclient.Dict,
 355         output interface{}) error {
 356         return nil
 357 }
 358
 359 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 360         return errors.New("ArvError")
 361 }
 362
 363 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 364         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 365         return nil, errors.New("ArvError")
 366 }
 367
 368 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 369         return errors.New("ArvError")
 370 }
 371
 372 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 373         return nil
 374 }
 375
 376 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 377         return discoveryMap[key], nil
 378 }
 379
 380 type KeepErrorTestClient struct{}
 381
 382 func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 383         return "", 0, errors.New("KeepError")
 384 }
 385
 386 func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 387         return nil, errors.New("KeepError")
 388 }
 389
 390 type KeepReadErrorTestClient struct{}
 391
 392 func (KeepReadErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 393         return "", 0, nil
 394 }
 395
 396 type ErrorReader struct{}
 397
 398 func (ErrorReader) Read(p []byte) (n int, err error) {
 399         return 0, errors.New("ErrorReader")
 400 }
 401
 402 func (ErrorReader) Close() error {
 403         return nil
 404 }
 405
 406 func (ErrorReader) Len() uint64 {
 407         return 0
 408 }
 409
 410 func (ErrorReader) Seek(int64, int) (int64, error) {
 411         return 0, errors.New("ErrorReader")
 412 }
 413
 414 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) {
 415         return ErrorReader{}, nil
 416 }
 417
 418 func (s *TestSuite) TestLoadImageArvError(c *C) {
 419         // (1) Arvados error
 420         cr := NewContainerRunner(ArvErrorTestClient{}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 421         cr.Container.ContainerImage = hwPDH
 422
 423         err := cr.LoadImage()
 424         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 425 }
 426
 427 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 428         // (2) Keep error
 429         docker := NewTestDockerClient(0)
 430         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 431         cr.Container.ContainerImage = hwPDH
 432
 433         err := cr.LoadImage()
 434         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 435 }
 436
 437 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 438         // (3) Collection doesn't contain image
 439         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 440         cr.Container.ContainerImage = otherPDH
 441
 442         err := cr.LoadImage()
 443         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 444 }
 445
 446 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 447         // (4) Collection doesn't contain image
 448         docker := NewTestDockerClient(0)
 449         cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 450         cr.Container.ContainerImage = hwPDH
 451
 452         err := cr.LoadImage()
 453         c.Check(err, NotNil)
 454 }
 455
 456 type ClosableBuffer struct {
 457         bytes.Buffer
 458 }
 459
 460 func (*ClosableBuffer) Close() error {
 461         return nil
 462 }
 463
 464 type TestLogs struct {
 465         Stdout ClosableBuffer
 466         Stderr ClosableBuffer
 467 }
 468
 469 func (tl *TestLogs) NewTestLoggingWriter(logstr string) io.WriteCloser {
 470         if logstr == "stdout" {
 471                 return &tl.Stdout
 472         }
 473         if logstr == "stderr" {
 474                 return &tl.Stderr
 475         }
 476         return nil
 477 }
 478
 479 func dockerLog(fd byte, msg string) []byte {
 480         by := []byte(msg)
 481         header := make([]byte, 8+len(by))
 482         header[0] = fd
 483         header[7] = byte(len(by))
 484         copy(header[8:], by)
 485         return header
 486 }
 487
 488 func (s *TestSuite) TestRunContainer(c *C) {
 489         docker := NewTestDockerClient(0)
 490         docker.fn = func(t *TestDockerClient) {
 491                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 492                 t.logWriter.Close()
 493         }
 494         cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 495
 496         var logs TestLogs
 497         cr.NewLogWriter = logs.NewTestLoggingWriter
 498         cr.Container.ContainerImage = hwPDH
 499         cr.Container.Command = []string{"./hw"}
 500         err := cr.LoadImage()
 501         c.Check(err, IsNil)
 502
 503         err = cr.CreateContainer()
 504         c.Check(err, IsNil)
 505
 506         err = cr.StartContainer()
 507         c.Check(err, IsNil)
 508
 509         err = cr.WaitFinish()
 510         c.Check(err, IsNil)
 511
 512         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 513         c.Check(logs.Stderr.String(), Equals, "")
 514 }
 515
 516 func (s *TestSuite) TestCommitLogs(c *C) {
 517         api := &ArvTestClient{}
 518         kc := &KeepTestClient{}
 519         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 520         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 521
 522         cr.CrunchLog.Print("Hello world!")
 523         cr.CrunchLog.Print("Goodbye")
 524         cr.finalState = "Complete"
 525
 526         err := cr.CommitLogs()
 527         c.Check(err, IsNil)
 528
 529         c.Check(api.Calls, Equals, 2)
 530         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 531         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 532         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 533         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 534 }
 535
 536 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 537         api := &ArvTestClient{}
 538         kc := &KeepTestClient{}
 539         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 540
 541         err := cr.UpdateContainerRunning()
 542         c.Check(err, IsNil)
 543
 544         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 545 }
 546
 547 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 548         api := &ArvTestClient{}
 549         kc := &KeepTestClient{}
 550         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 551
 552         cr.LogsPDH = new(string)
 553         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 554
 555         cr.ExitCode = new(int)
 556         *cr.ExitCode = 42
 557         cr.finalState = "Complete"
 558
 559         err := cr.UpdateContainerFinal()
 560         c.Check(err, IsNil)
 561
 562         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 563         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 564         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 565 }
 566
 567 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 568         api := &ArvTestClient{}
 569         kc := &KeepTestClient{}
 570         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 571         cr.cCancelled = true
 572         cr.finalState = "Cancelled"
 573
 574         err := cr.UpdateContainerFinal()
 575         c.Check(err, IsNil)
 576
 577         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 578         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 579         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 580 }
 581
 582 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 583 // dress rehearsal of the Run() function, starting from a JSON container record.
 584 func FullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 585         rec := arvados.Container{}
 586         err := json.Unmarshal([]byte(record), &rec)
 587         c.Check(err, IsNil)
 588
 589         docker := NewTestDockerClient(exitCode)
 590         docker.fn = fn
 591         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 592
 593         api = &ArvTestClient{Container: rec}
 594         docker.api = api
 595         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 596         cr.statInterval = 100 * time.Millisecond
 597         am := &ArvMountCmdLine{}
 598         cr.RunArvMount = am.ArvMountTest
 599
 600         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 601         c.Assert(err, IsNil)
 602         defer os.RemoveAll(realTemp)
 603
 604         tempcount := 0
 605         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 606                 tempcount++
 607                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 608                 err := os.Mkdir(d, os.ModePerm)
 609                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 610                         // Test case must have pre-populated the tempdir
 611                         err = nil
 612                 }
 613                 return d, err
 614         }
 615
 616         if extraMounts != nil && len(extraMounts) > 0 {
 617                 err := cr.SetupArvMountPoint("keep")
 618                 c.Check(err, IsNil)
 619
 620                 for _, m := range extraMounts {
 621                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 622                 }
 623         }
 624
 625         err = cr.Run()
 626         c.Check(err, IsNil)
 627         c.Check(api.WasSetRunning, Equals, true)
 628
 629         c.Check(api.Content[api.Calls-1]["container"].(arvadosclient.Dict)["log"], NotNil)
 630
 631         if err != nil {
 632                 for k, v := range api.Logs {
 633                         c.Log(k)
 634                         c.Log(v.String())
 635                 }
 636         }
 637
 638         return
 639 }
 640
 641 func (s *TestSuite) TestFullRunHello(c *C) {
 642         api, _, _ := FullRunHelper(c, `{
 643     "command": ["echo", "hello world"],
 644     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 645     "cwd": ".",
 646     "environment": {},
 647     "mounts": {"/tmp": {"kind": "tmp"} },
 648     "output_path": "/tmp",
 649     "priority": 1,
 650     "runtime_constraints": {}
 651 }`, nil, 0, func(t *TestDockerClient) {
 652                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 653                 t.logWriter.Close()
 654         })
 655
 656         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 657         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 658         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 659
 660 }
 661
 662 func (s *TestSuite) TestCrunchstat(c *C) {
 663         api, _, _ := FullRunHelper(c, `{
 664                 "command": ["sleep", "1"],
 665                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 666                 "cwd": ".",
 667                 "environment": {},
 668                 "mounts": {"/tmp": {"kind": "tmp"} },
 669                 "output_path": "/tmp",
 670                 "priority": 1,
 671                 "runtime_constraints": {}
 672         }`, nil, 0, func(t *TestDockerClient) {
 673                 time.Sleep(time.Second)
 674                 t.logWriter.Close()
 675         })
 676
 677         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 678         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 679
 680         // We didn't actually start a container, so crunchstat didn't
 681         // find accounting files and therefore didn't log any stats.
 682         // It should have logged a "can't find accounting files"
 683         // message after one poll interval, though, so we can confirm
 684         // it's alive:
 685         c.Assert(api.Logs["crunchstat"], NotNil)
 686         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 687
 688         // The "files never appeared" log assures us that we called
 689         // (*crunchstat.Reporter)Stop(), and that we set it up with
 690         // the correct container ID "abcde":
 691         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 692 }
 693
 694 func (s *TestSuite) TestNodeInfoLog(c *C) {
 695         api, _, _ := FullRunHelper(c, `{
 696                 "command": ["sleep", "1"],
 697                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 698                 "cwd": ".",
 699                 "environment": {},
 700                 "mounts": {"/tmp": {"kind": "tmp"} },
 701                 "output_path": "/tmp",
 702                 "priority": 1,
 703                 "runtime_constraints": {}
 704         }`, nil, 0,
 705                 func(t *TestDockerClient) {
 706                         time.Sleep(time.Second)
 707                         t.logWriter.Close()
 708                 })
 709
 710         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 711         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 712
 713         c.Assert(api.Logs["node-info"], NotNil)
 714         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Host Information.*`)
 715         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*CPU Information.*`)
 716         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Memory Information.*`)
 717         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk Space.*`)
 718         c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk INodes.*`)
 719 }
 720
 721 func (s *TestSuite) TestContainerRecordLog(c *C) {
 722         api, _, _ := FullRunHelper(c, `{
 723                 "command": ["sleep", "1"],
 724                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 725                 "cwd": ".",
 726                 "environment": {},
 727                 "mounts": {"/tmp": {"kind": "tmp"} },
 728                 "output_path": "/tmp",
 729                 "priority": 1,
 730                 "runtime_constraints": {}
 731         }`, nil, 0,
 732                 func(t *TestDockerClient) {
 733                         time.Sleep(time.Second)
 734                         t.logWriter.Close()
 735                 })
 736
 737         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 738         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 739
 740         c.Assert(api.Logs["container"], NotNil)
 741         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 742 }
 743
 744 func (s *TestSuite) TestFullRunStderr(c *C) {
 745         api, _, _ := FullRunHelper(c, `{
 746     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 747     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 748     "cwd": ".",
 749     "environment": {},
 750     "mounts": {"/tmp": {"kind": "tmp"} },
 751     "output_path": "/tmp",
 752     "priority": 1,
 753     "runtime_constraints": {}
 754 }`, nil, 1, func(t *TestDockerClient) {
 755                 t.logWriter.Write(dockerLog(1, "hello\n"))
 756                 t.logWriter.Write(dockerLog(2, "world\n"))
 757                 t.logWriter.Close()
 758         })
 759
 760         final := api.CalledWith("container.state", "Complete")
 761         c.Assert(final, NotNil)
 762         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 763         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 764
 765         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 766         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 767 }
 768
 769 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 770         api, _, _ := FullRunHelper(c, `{
 771     "command": ["pwd"],
 772     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 773     "cwd": ".",
 774     "environment": {},
 775     "mounts": {"/tmp": {"kind": "tmp"} },
 776     "output_path": "/tmp",
 777     "priority": 1,
 778     "runtime_constraints": {}
 779 }`, nil, 0, func(t *TestDockerClient) {
 780                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 781                 t.logWriter.Close()
 782         })
 783
 784         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 785         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 786         c.Log(api.Logs["stdout"])
 787         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 788 }
 789
 790 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 791         api, _, _ := FullRunHelper(c, `{
 792     "command": ["pwd"],
 793     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 794     "cwd": "/bin",
 795     "environment": {},
 796     "mounts": {"/tmp": {"kind": "tmp"} },
 797     "output_path": "/tmp",
 798     "priority": 1,
 799     "runtime_constraints": {}
 800 }`, nil, 0, func(t *TestDockerClient) {
 801                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 802                 t.logWriter.Close()
 803         })
 804
 805         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 806         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 807         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 808 }
 809
 810 func (s *TestSuite) TestStopOnSignal(c *C) {
 811         s.testStopContainer(c, func(cr *ContainerRunner) {
 812                 go func() {
 813                         for !cr.cStarted {
 814                                 time.Sleep(time.Millisecond)
 815                         }
 816                         cr.SigChan <- syscall.SIGINT
 817                 }()
 818         })
 819 }
 820
 821 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 822         s.testStopContainer(c, func(cr *ContainerRunner) {
 823                 cr.ArvMountExit = make(chan error)
 824                 go func() {
 825                         cr.ArvMountExit <- exec.Command("true").Run()
 826                         close(cr.ArvMountExit)
 827                 }()
 828         })
 829 }
 830
 831 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 832         record := `{
 833     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 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 }`
 842
 843         rec := arvados.Container{}
 844         err := json.Unmarshal([]byte(record), &rec)
 845         c.Check(err, IsNil)
 846
 847         docker := NewTestDockerClient(0)
 848         docker.fn = func(t *TestDockerClient) {
 849                 <-t.stop
 850                 t.logWriter.Write(dockerLog(1, "foo\n"))
 851                 t.logWriter.Close()
 852         }
 853         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 854
 855         api := &ArvTestClient{Container: rec}
 856         cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 857         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
 858         setup(cr)
 859
 860         done := make(chan error)
 861         go func() {
 862                 done <- cr.Run()
 863         }()
 864         select {
 865         case <-time.After(20 * time.Second):
 866                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
 867                 c.Fatal("timed out")
 868         case err = <-done:
 869                 c.Check(err, IsNil)
 870         }
 871         for k, v := range api.Logs {
 872                 c.Log(k)
 873                 c.Log(v.String())
 874         }
 875
 876         c.Check(api.CalledWith("container.log", nil), NotNil)
 877         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
 878         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
 879 }
 880
 881 func (s *TestSuite) TestFullRunSetEnv(c *C) {
 882         api, _, _ := FullRunHelper(c, `{
 883     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
 884     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 885     "cwd": "/bin",
 886     "environment": {"FROBIZ": "bilbo"},
 887     "mounts": {"/tmp": {"kind": "tmp"} },
 888     "output_path": "/tmp",
 889     "priority": 1,
 890     "runtime_constraints": {}
 891 }`, nil, 0, func(t *TestDockerClient) {
 892                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
 893                 t.logWriter.Close()
 894         })
 895
 896         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 897         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 898         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
 899 }
 900
 901 type ArvMountCmdLine struct {
 902         Cmd   []string
 903         token string
 904 }
 905
 906 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
 907         am.Cmd = c
 908         am.token = token
 909         return nil, nil
 910 }
 911
 912 func stubCert(temp string) string {
 913         path := temp + "/ca-certificates.crt"
 914         crt, _ := os.Create(path)
 915         crt.Close()
 916         arvadosclient.CertFiles = []string{path}
 917         return path
 918 }
 919
 920 func (s *TestSuite) TestSetupMounts(c *C) {
 921         api := &ArvTestClient{}
 922         kc := &KeepTestClient{}
 923         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 924         am := &ArvMountCmdLine{}
 925         cr.RunArvMount = am.ArvMountTest
 926
 927         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
 928         c.Assert(err, IsNil)
 929         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
 930         c.Assert(err, IsNil)
 931         stubCertPath := stubCert(certTemp)
 932
 933         defer os.RemoveAll(realTemp)
 934         defer os.RemoveAll(certTemp)
 935
 936         i := 0
 937         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 938                 i++
 939                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
 940                 err := os.Mkdir(d, os.ModePerm)
 941                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 942                         // Test case must have pre-populated the tempdir
 943                         err = nil
 944                 }
 945                 return d, err
 946         }
 947
 948         checkEmpty := func() {
 949                 filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
 950                         c.Check(path, Equals, realTemp)
 951                         c.Check(err, IsNil)
 952                         return nil
 953                 })
 954         }
 955
 956         {
 957                 i = 0
 958                 cr.ArvMountPoint = ""
 959                 cr.Container.Mounts = make(map[string]arvados.Mount)
 960                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
 961                 cr.OutputPath = "/tmp"
 962
 963                 err := cr.SetupMounts()
 964                 c.Check(err, IsNil)
 965                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
 966                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
 967                 cr.CleanupDirs()
 968                 checkEmpty()
 969         }
 970
 971         {
 972                 i = 0
 973                 cr.ArvMountPoint = ""
 974                 cr.Container.Mounts = make(map[string]arvados.Mount)
 975                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
 976                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
 977                 cr.OutputPath = "/out"
 978
 979                 err := cr.SetupMounts()
 980                 c.Check(err, IsNil)
 981                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
 982                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/out", realTemp + "/3:/tmp"})
 983                 cr.CleanupDirs()
 984                 checkEmpty()
 985         }
 986
 987         {
 988                 i = 0
 989                 cr.ArvMountPoint = ""
 990                 cr.Container.Mounts = make(map[string]arvados.Mount)
 991                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
 992                 cr.OutputPath = "/tmp"
 993
 994                 apiflag := true
 995                 cr.Container.RuntimeConstraints.API = &apiflag
 996
 997                 err := cr.SetupMounts()
 998                 c.Check(err, IsNil)
 999                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1000                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1001                 cr.CleanupDirs()
1002                 checkEmpty()
1003
1004                 apiflag = false
1005         }
1006
1007         {
1008                 i = 0
1009                 cr.ArvMountPoint = ""
1010                 cr.Container.Mounts = map[string]arvados.Mount{
1011                         "/keeptmp": {Kind: "collection", Writable: true},
1012                 }
1013                 cr.OutputPath = "/keeptmp"
1014
1015                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1016
1017                 err := cr.SetupMounts()
1018                 c.Check(err, IsNil)
1019                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1020                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1021                 cr.CleanupDirs()
1022                 checkEmpty()
1023         }
1024
1025         {
1026                 i = 0
1027                 cr.ArvMountPoint = ""
1028                 cr.Container.Mounts = map[string]arvados.Mount{
1029                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1030                         "/keepout": {Kind: "collection", Writable: true},
1031                 }
1032                 cr.OutputPath = "/keepout"
1033
1034                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1035                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1036
1037                 err := cr.SetupMounts()
1038                 c.Check(err, IsNil)
1039                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1040                 sort.StringSlice(cr.Binds).Sort()
1041                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1042                         realTemp + "/keep1/tmp0:/keepout"})
1043                 cr.CleanupDirs()
1044                 checkEmpty()
1045         }
1046
1047         {
1048                 i = 0
1049                 cr.ArvMountPoint = ""
1050                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1051                 cr.Container.Mounts = map[string]arvados.Mount{
1052                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1053                         "/keepout": {Kind: "collection", Writable: true},
1054                 }
1055                 cr.OutputPath = "/keepout"
1056
1057                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1058                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1059
1060                 err := cr.SetupMounts()
1061                 c.Check(err, IsNil)
1062                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1063                 sort.StringSlice(cr.Binds).Sort()
1064                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1065                         realTemp + "/keep1/tmp0:/keepout"})
1066                 cr.CleanupDirs()
1067                 checkEmpty()
1068         }
1069
1070         for _, test := range []struct {
1071                 in  interface{}
1072                 out string
1073         }{
1074                 {in: "foo", out: `"foo"`},
1075                 {in: nil, out: `null`},
1076                 {in: map[string]int{"foo": 123}, out: `{"foo":123}`},
1077         } {
1078                 i = 0
1079                 cr.ArvMountPoint = ""
1080                 cr.Container.Mounts = map[string]arvados.Mount{
1081                         "/mnt/test.json": {Kind: "json", Content: test.in},
1082                 }
1083                 err := cr.SetupMounts()
1084                 c.Check(err, IsNil)
1085                 sort.StringSlice(cr.Binds).Sort()
1086                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
1087                 content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
1088                 c.Check(err, IsNil)
1089                 c.Check(content, DeepEquals, []byte(test.out))
1090                 cr.CleanupDirs()
1091                 checkEmpty()
1092         }
1093
1094         // Read-only mount points are allowed underneath output_dir mount point
1095         {
1096                 i = 0
1097                 cr.ArvMountPoint = ""
1098                 cr.Container.Mounts = make(map[string]arvados.Mount)
1099                 cr.Container.Mounts = map[string]arvados.Mount{
1100                         "/tmp":     {Kind: "tmp"},
1101                         "/tmp/foo": {Kind: "collection"},
1102                 }
1103                 cr.OutputPath = "/tmp"
1104
1105                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1106
1107                 err := cr.SetupMounts()
1108                 c.Check(err, IsNil)
1109                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1110                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1111                 cr.CleanupDirs()
1112                 checkEmpty()
1113         }
1114
1115         // Writable mount points are not allowed underneath output_dir mount point
1116         {
1117                 i = 0
1118                 cr.ArvMountPoint = ""
1119                 cr.Container.Mounts = make(map[string]arvados.Mount)
1120                 cr.Container.Mounts = map[string]arvados.Mount{
1121                         "/tmp":     {Kind: "tmp"},
1122                         "/tmp/foo": {Kind: "collection", Writable: true},
1123                 }
1124                 cr.OutputPath = "/tmp"
1125
1126                 err := cr.SetupMounts()
1127                 c.Check(err, NotNil)
1128                 c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
1129                 cr.CleanupDirs()
1130                 checkEmpty()
1131         }
1132
1133         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1134         {
1135                 i = 0
1136                 cr.ArvMountPoint = ""
1137                 cr.Container.Mounts = make(map[string]arvados.Mount)
1138                 cr.Container.Mounts = map[string]arvados.Mount{
1139                         "/tmp":     {Kind: "tmp"},
1140                         "/tmp/foo": {Kind: "json"},
1141                 }
1142                 cr.OutputPath = "/tmp"
1143
1144                 err := cr.SetupMounts()
1145                 c.Check(err, NotNil)
1146                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
1147                 cr.CleanupDirs()
1148                 checkEmpty()
1149         }
1150
1151         // Only mount point of kind 'collection' is allowed for stdin
1152         {
1153                 i = 0
1154                 cr.ArvMountPoint = ""
1155                 cr.Container.Mounts = make(map[string]arvados.Mount)
1156                 cr.Container.Mounts = map[string]arvados.Mount{
1157                         "stdin": {Kind: "tmp"},
1158                 }
1159
1160                 err := cr.SetupMounts()
1161                 c.Check(err, NotNil)
1162                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1163                 cr.CleanupDirs()
1164                 checkEmpty()
1165         }
1166 }
1167
1168 func (s *TestSuite) TestStdout(c *C) {
1169         helperRecord := `{
1170                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1171                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1172                 "cwd": "/bin",
1173                 "environment": {"FROBIZ": "bilbo"},
1174                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1175                 "output_path": "/tmp",
1176                 "priority": 1,
1177                 "runtime_constraints": {}
1178         }`
1179
1180         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1181                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1182                 t.logWriter.Close()
1183         })
1184
1185         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1186         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1187         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1188 }
1189
1190 // Used by the TestStdoutWithWrongPath*()
1191 func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1192         rec := arvados.Container{}
1193         err = json.Unmarshal([]byte(record), &rec)
1194         c.Check(err, IsNil)
1195
1196         docker := NewTestDockerClient(0)
1197         docker.fn = fn
1198         docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1199
1200         api = &ArvTestClient{Container: rec}
1201         cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1202         am := &ArvMountCmdLine{}
1203         cr.RunArvMount = am.ArvMountTest
1204
1205         err = cr.Run()
1206         return
1207 }
1208
1209 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1210         _, _, err := StdoutErrorRunHelper(c, `{
1211     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1212     "output_path": "/tmp"
1213 }`, func(t *TestDockerClient) {})
1214
1215         c.Check(err, NotNil)
1216         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1217 }
1218
1219 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1220         _, _, err := StdoutErrorRunHelper(c, `{
1221     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1222     "output_path": "/tmp"
1223 }`, func(t *TestDockerClient) {})
1224
1225         c.Check(err, NotNil)
1226         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1227 }
1228
1229 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1230         _, _, err := StdoutErrorRunHelper(c, `{
1231     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1232     "output_path": "/tmp"
1233 }`, func(t *TestDockerClient) {})
1234
1235         c.Check(err, NotNil)
1236         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1237 }
1238
1239 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1240         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1241         defer os.Unsetenv("ARVADOS_API_HOST")
1242         api, _, _ := FullRunHelper(c, `{
1243     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1244     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1245     "cwd": "/bin",
1246     "environment": {},
1247     "mounts": {"/tmp": {"kind": "tmp"} },
1248     "output_path": "/tmp",
1249     "priority": 1,
1250     "runtime_constraints": {"API": true}
1251 }`, nil, 0, func(t *TestDockerClient) {
1252                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1253                 t.logWriter.Close()
1254         })
1255
1256         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1257         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1258         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1259         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1260 }
1261
1262 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1263         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1264         defer os.Unsetenv("ARVADOS_API_HOST")
1265         api, _, _ := FullRunHelper(c, `{
1266     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1267     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1268     "cwd": "/bin",
1269     "environment": {},
1270     "mounts": {"/tmp": {"kind": "tmp"} },
1271     "output_path": "/tmp",
1272     "priority": 1,
1273     "runtime_constraints": {"API": true}
1274 }`, nil, 0, func(t *TestDockerClient) {
1275                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1276                 t.logWriter.Close()
1277         })
1278
1279         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1280         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1281         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1282 }
1283
1284 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1285         helperRecord := `{
1286                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1287                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1288                 "cwd": "/bin",
1289                 "environment": {"FROBIZ": "bilbo"},
1290                 "mounts": {
1291         "/tmp": {"kind": "tmp"},
1292         "/tmp/foo": {"kind": "collection",
1293                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1294                      "exclude_from_output": true
1295         },
1296         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1297     },
1298                 "output_path": "/tmp",
1299                 "priority": 1,
1300                 "runtime_constraints": {}
1301         }`
1302
1303         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1304
1305         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1306                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1307                 t.logWriter.Close()
1308         })
1309
1310         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1311         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1312         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1313 }
1314
1315 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1316         helperRecord := `{
1317                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1318                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1319                 "cwd": "/bin",
1320                 "environment": {"FROBIZ": "bilbo"},
1321                 "mounts": {
1322         "/tmp": {"kind": "tmp"},
1323         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1324         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1325         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1326         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1327         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1328     },
1329                 "output_path": "/tmp",
1330                 "priority": 1,
1331                 "runtime_constraints": {}
1332         }`
1333
1334         extraMounts := []string{
1335                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1336                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1337                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1338         }
1339
1340         api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1341                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1342                 t.logWriter.Close()
1343         })
1344
1345         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
1346                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1347                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1348                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1349                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1350         })
1351
1352         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1353         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1354         for _, v := range api.Content {
1355                 if v["collection"] != nil {
1356                         c.Check(v["ensure_unique_name"], Equals, true)
1357                         collection := v["collection"].(arvadosclient.Dict)
1358                         if strings.Index(collection["name"].(string), "output") == 0 {
1359                                 manifest := collection["manifest_text"].(string)
1360
1361                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1362 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
1363 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1364 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1365 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1366 `)
1367                         }
1368                 }
1369         }
1370 }
1371
1372 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1373         helperRecord := `{
1374                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1375                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1376                 "cwd": "/bin",
1377                 "environment": {"FROBIZ": "bilbo"},
1378                 "mounts": {
1379         "/tmp": {"kind": "tmp"},
1380         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
1381         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1382     },
1383                 "output_path": "/tmp",
1384                 "priority": 1,
1385                 "runtime_constraints": {}
1386         }`
1387
1388         extraMounts := []string{
1389                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1390         }
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         for _, v := range api.Content {
1400                 if v["collection"] != nil {
1401                         collection := v["collection"].(arvadosclient.Dict)
1402                         if strings.Index(collection["name"].(string), "output") == 0 {
1403                                 manifest := collection["manifest_text"].(string)
1404
1405                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1406 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1407 `)
1408                         }
1409                 }
1410         }
1411 }
1412
1413 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1414         helperRecord := `{
1415                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1416                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1417                 "cwd": "/bin",
1418                 "environment": {"FROBIZ": "bilbo"},
1419                 "mounts": {
1420         "/tmp": {"kind": "tmp"},
1421         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1422         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1423     },
1424                 "output_path": "/tmp",
1425                 "priority": 1,
1426                 "runtime_constraints": {}
1427         }`
1428
1429         extraMounts := []string{
1430                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1431         }
1432
1433         api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1434                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1435                 t.logWriter.Close()
1436         })
1437
1438         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1439         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1440         for _, v := range api.Content {
1441                 if v["collection"] != nil {
1442                         collection := v["collection"].(arvadosclient.Dict)
1443                         if strings.Index(collection["name"].(string), "output") == 0 {
1444                                 manifest := collection["manifest_text"].(string)
1445                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1446 `)
1447                         }
1448                 }
1449         }
1450 }
1451
1452 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1453         helperRecord := `{
1454                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1455                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1456                 "cwd": "/bin",
1457                 "environment": {"FROBIZ": "bilbo"},
1458                 "mounts": {
1459         "/tmp": {"kind": "tmp"},
1460         "stdin": {"kind": "json", "content": "foo"},
1461         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1462     },
1463                 "output_path": "/tmp",
1464                 "priority": 1,
1465                 "runtime_constraints": {}
1466         }`
1467
1468         api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1469                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1470                 t.logWriter.Close()
1471         })
1472
1473         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1474         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1475         for _, v := range api.Content {
1476                 if v["collection"] != nil {
1477                         collection := v["collection"].(arvadosclient.Dict)
1478                         if strings.Index(collection["name"].(string), "output") == 0 {
1479                                 manifest := collection["manifest_text"].(string)
1480                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1481 `)
1482                         }
1483                 }
1484         }
1485 }
1486
1487 func (s *TestSuite) TestStderrMount(c *C) {
1488         api, _, _ := FullRunHelper(c, `{
1489     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1490     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1491     "cwd": ".",
1492     "environment": {},
1493     "mounts": {"/tmp": {"kind": "tmp"},
1494                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1495                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1496     "output_path": "/tmp",
1497     "priority": 1,
1498     "runtime_constraints": {}
1499 }`, nil, 1, func(t *TestDockerClient) {
1500                 t.logWriter.Write(dockerLog(1, "hello\n"))
1501                 t.logWriter.Write(dockerLog(2, "oops\n"))
1502                 t.logWriter.Close()
1503         })
1504
1505         final := api.CalledWith("container.state", "Complete")
1506         c.Assert(final, NotNil)
1507         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1508         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1509
1510         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1511 }