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         "crypto/md5"
  11         "encoding/json"
  12         "errors"
  13         "fmt"
  14         "io"
  15         "io/ioutil"
  16         "net"
  17         "os"
  18         "os/exec"
  19         "runtime/pprof"
  20         "sort"
  21         "strings"
  22         "sync"
  23         "syscall"
  24         "testing"
  25         "time"
  26
  27         "git.curoverse.com/arvados.git/sdk/go/arvados"
  28         "git.curoverse.com/arvados.git/sdk/go/arvadosclient"
  29         "git.curoverse.com/arvados.git/sdk/go/arvadostest"
  30         "git.curoverse.com/arvados.git/sdk/go/manifest"
  31         "golang.org/x/net/context"
  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 // Gocheck boilerplate
  45 var _ = Suite(&TestSuite{})
  46
  47 type TestSuite struct {
  48         docker *TestDockerClient
  49 }
  50
  51 func (s *TestSuite) SetUpTest(c *C) {
  52         s.docker = NewTestDockerClient()
  53 }
  54
  55 type ArvTestClient struct {
  56         Total   int64
  57         Calls   int
  58         Content []arvadosclient.Dict
  59         arvados.Container
  60         Logs map[string]*bytes.Buffer
  61         sync.Mutex
  62         WasSetRunning bool
  63         callraw       bool
  64 }
  65
  66 type KeepTestClient struct {
  67         Called  bool
  68         Content []byte
  69 }
  70
  71 var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0@569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
  72 var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
  73 var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
  74
  75 var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
  76 var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
  77
  78 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
  79 ./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
  80 ./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
  81 `
  82
  83 var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
  84
  85 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"
  86 var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
  87
  88 var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
  89 var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
  90
  91 type TestDockerClient struct {
  92         imageLoaded string
  93         logReader   io.ReadCloser
  94         logWriter   io.WriteCloser
  95         fn          func(t *TestDockerClient)
  96         exitCode    int
  97         stop        chan bool
  98         cwd         string
  99         env         []string
 100         api         *ArvTestClient
 101         realTemp    string
 102         calledWait  bool
 103 }
 104
 105 func NewTestDockerClient() *TestDockerClient {
 106         t := &TestDockerClient{}
 107         t.logReader, t.logWriter = io.Pipe()
 108         t.stop = make(chan bool, 1)
 109         t.cwd = "/"
 110         return t
 111 }
 112
 113 type MockConn struct {
 114         net.Conn
 115 }
 116
 117 func (m *MockConn) Write(b []byte) (int, error) {
 118         return len(b), nil
 119 }
 120
 121 func NewMockConn() *MockConn {
 122         c := &MockConn{}
 123         return c
 124 }
 125
 126 func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
 127         return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
 128 }
 129
 130 func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
 131         if config.WorkingDir != "" {
 132                 t.cwd = config.WorkingDir
 133         }
 134         t.env = config.Env
 135         return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
 136 }
 137
 138 func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 139         if t.exitCode == 3 {
 140                 return errors.New(`Error response from daemon: oci runtime error: container_linux.go:247: starting container process caused "process_linux.go:359: container init caused \"rootfs_linux.go:54: mounting \\\"/tmp/keep453790790/by_id/99999999999999999999999999999999+99999/myGenome\\\" to rootfs \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged\\\" at \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged/keep/99999999999999999999999999999999+99999/myGenome\\\" caused \\\"no such file or directory\\\"\""`)
 141         }
 142         if t.exitCode == 4 {
 143                 return errors.New(`panic: standard_init_linux.go:175: exec user process caused "no such file or directory"`)
 144         }
 145         if t.exitCode == 5 {
 146                 return errors.New(`Error response from daemon: Cannot start container 41f26cbc43bcc1280f4323efb1830a394ba8660c9d1c2b564ba42bf7f7694845: [8] System error: no such file or directory`)
 147         }
 148         if t.exitCode == 6 {
 149                 return errors.New(`Error response from daemon: Cannot start container 58099cd76c834f3dc2a4fb76c8028f049ae6d4fdf0ec373e1f2cfea030670c2d: [8] System error: exec: "foobar": executable file not found in $PATH`)
 150         }
 151
 152         if container == "abcde" {
 153                 // t.fn gets executed in ContainerWait
 154                 return nil
 155         } else {
 156                 return errors.New("Invalid container id")
 157         }
 158 }
 159
 160 func (t *TestDockerClient) ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error {
 161         t.stop <- true
 162         return nil
 163 }
 164
 165 func (t *TestDockerClient) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
 166         t.calledWait = true
 167         body := make(chan dockercontainer.ContainerWaitOKBody, 1)
 168         err := make(chan error)
 169         go func() {
 170                 t.fn(t)
 171                 body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.exitCode)}
 172         }()
 173         return body, err
 174 }
 175
 176 func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 177         if t.exitCode == 2 {
 178                 return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 179         }
 180
 181         if t.imageLoaded == image {
 182                 return dockertypes.ImageInspect{}, nil, nil
 183         } else {
 184                 return dockertypes.ImageInspect{}, nil, errors.New("")
 185         }
 186 }
 187
 188 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 189         if t.exitCode == 2 {
 190                 return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 191         }
 192         _, err := io.Copy(ioutil.Discard, input)
 193         if err != nil {
 194                 return dockertypes.ImageLoadResponse{}, err
 195         } else {
 196                 t.imageLoaded = hwImageId
 197                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 198         }
 199 }
 200
 201 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 202         return nil, nil
 203 }
 204
 205 func (client *ArvTestClient) Create(resourceType string,
 206         parameters arvadosclient.Dict,
 207         output interface{}) error {
 208
 209         client.Mutex.Lock()
 210         defer client.Mutex.Unlock()
 211
 212         client.Calls++
 213         client.Content = append(client.Content, parameters)
 214
 215         if resourceType == "logs" {
 216                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 217                 if client.Logs == nil {
 218                         client.Logs = make(map[string]*bytes.Buffer)
 219                 }
 220                 if client.Logs[et] == nil {
 221                         client.Logs[et] = &bytes.Buffer{}
 222                 }
 223                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 224         }
 225
 226         if resourceType == "collections" && output != nil {
 227                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 228                 outmap := output.(*arvados.Collection)
 229                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 230         }
 231
 232         return nil
 233 }
 234
 235 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 236         switch {
 237         case method == "GET" && resourceType == "containers" && action == "auth":
 238                 return json.Unmarshal([]byte(`{
 239                         "kind": "arvados#api_client_authorization",
 240                         "uuid": "`+fakeAuthUUID+`",
 241                         "api_token": "`+fakeAuthToken+`"
 242                         }`), output)
 243         default:
 244                 return fmt.Errorf("Not found")
 245         }
 246 }
 247
 248 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 249         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 250         var j []byte
 251         if method == "GET" && resourceType == "nodes" && uuid == "" && action == "" {
 252                 j = []byte(`{
 253                         "kind": "arvados#nodeList",
 254                         "items": [{
 255                                 "uuid": "zzzzz-7ekkf-2z3mc76g2q73aio",
 256                                 "hostname": "compute2",
 257                                 "properties": {"total_cpu_cores": 16}
 258                         }]}`)
 259         } else if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
 260                 if uuid == "" {
 261                         j, err = json.Marshal(map[string]interface{}{
 262                                 "items": []interface{}{client.Container},
 263                                 "kind":  "arvados#nodeList",
 264                         })
 265                 } else {
 266                         j, err = json.Marshal(client.Container)
 267                 }
 268         } else {
 269                 j = []byte(`{
 270                         "command": ["sleep", "1"],
 271                         "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 272                         "cwd": ".",
 273                         "environment": {},
 274                         "mounts": {"/tmp": {"kind": "tmp"}, "/json": {"kind": "json", "content": {"number": 123456789123456789}}},
 275                         "output_path": "/tmp",
 276                         "priority": 1,
 277                         "runtime_constraints": {}
 278                 }`)
 279         }
 280         return ioutil.NopCloser(bytes.NewReader(j)), err
 281 }
 282
 283 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 284         if resourceType == "collections" {
 285                 if uuid == hwPDH {
 286                         output.(*arvados.Collection).ManifestText = hwManifest
 287                 } else if uuid == otherPDH {
 288                         output.(*arvados.Collection).ManifestText = otherManifest
 289                 } else if uuid == normalizedWithSubdirsPDH {
 290                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 291                 } else if uuid == denormalizedWithSubdirsPDH {
 292                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 293                 }
 294         }
 295         if resourceType == "containers" {
 296                 (*output.(*arvados.Container)) = client.Container
 297         }
 298         return nil
 299 }
 300
 301 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 302         client.Mutex.Lock()
 303         defer client.Mutex.Unlock()
 304         client.Calls++
 305         client.Content = append(client.Content, parameters)
 306         if resourceType == "containers" {
 307                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 308                         client.WasSetRunning = true
 309                 }
 310         }
 311         return nil
 312 }
 313
 314 var discoveryMap = map[string]interface{}{
 315         "defaultTrashLifetime":               float64(1209600),
 316         "crunchLimitLogBytesPerJob":          float64(67108864),
 317         "crunchLogThrottleBytes":             float64(65536),
 318         "crunchLogThrottlePeriod":            float64(60),
 319         "crunchLogThrottleLines":             float64(1024),
 320         "crunchLogPartialLineThrottlePeriod": float64(5),
 321         "crunchLogBytesPerEvent":             float64(4096),
 322         "crunchLogSecondsBetweenEvents":      float64(1),
 323 }
 324
 325 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 326         return discoveryMap[key], nil
 327 }
 328
 329 // CalledWith returns the parameters from the first API call whose
 330 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 331 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 332 // no call matches, it returns nil.
 333 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 334 call:
 335         for _, content := range client.Content {
 336                 var v interface{} = content
 337                 for _, k := range strings.Split(jpath, ".") {
 338                         if dict, ok := v.(arvadosclient.Dict); !ok {
 339                                 continue call
 340                         } else {
 341                                 v = dict[k]
 342                         }
 343                 }
 344                 if v == expect {
 345                         return content
 346                 }
 347         }
 348         return nil
 349 }
 350
 351 func (client *KeepTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 352         client.Content = buf
 353         return fmt.Sprintf("%s+%d", hash, len(buf)), len(buf), nil
 354 }
 355
 356 func (*KeepTestClient) ClearBlockCache() {
 357 }
 358
 359 type FileWrapper struct {
 360         io.ReadCloser
 361         len int64
 362 }
 363
 364 func (fw FileWrapper) Readdir(n int) ([]os.FileInfo, error) {
 365         return nil, errors.New("not implemented")
 366 }
 367
 368 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 369         return 0, errors.New("not implemented")
 370 }
 371
 372 func (fw FileWrapper) Size() int64 {
 373         return fw.len
 374 }
 375
 376 func (fw FileWrapper) Stat() (os.FileInfo, error) {
 377         return nil, errors.New("not implemented")
 378 }
 379
 380 func (fw FileWrapper) Truncate(int64) error {
 381         return errors.New("not implemented")
 382 }
 383
 384 func (fw FileWrapper) Write([]byte) (int, error) {
 385         return 0, errors.New("not implemented")
 386 }
 387
 388 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 389         if filename == hwImageId+".tar" {
 390                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 391                 client.Called = true
 392                 return FileWrapper{rdr, 1321984}, nil
 393         } else if filename == "/file1_in_main.txt" {
 394                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 395                 client.Called = true
 396                 return FileWrapper{rdr, 3}, nil
 397         }
 398         return nil, nil
 399 }
 400
 401 func (s *TestSuite) TestLoadImage(c *C) {
 402         kc := &KeepTestClient{}
 403         cr := NewContainerRunner(&ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 404
 405         _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 406
 407         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 408         c.Check(err, NotNil)
 409
 410         cr.Container.ContainerImage = hwPDH
 411
 412         // (1) Test loading image from keep
 413         c.Check(kc.Called, Equals, false)
 414         c.Check(cr.ContainerConfig.Image, Equals, "")
 415
 416         err = cr.LoadImage()
 417
 418         c.Check(err, IsNil)
 419         defer func() {
 420                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 421         }()
 422
 423         c.Check(kc.Called, Equals, true)
 424         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 425
 426         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 427         c.Check(err, IsNil)
 428
 429         // (2) Test using image that's already loaded
 430         kc.Called = false
 431         cr.ContainerConfig.Image = ""
 432
 433         err = cr.LoadImage()
 434         c.Check(err, IsNil)
 435         c.Check(kc.Called, Equals, false)
 436         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 437
 438 }
 439
 440 type ArvErrorTestClient struct{}
 441
 442 func (ArvErrorTestClient) Create(resourceType string,
 443         parameters arvadosclient.Dict,
 444         output interface{}) error {
 445         return nil
 446 }
 447
 448 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 449         return errors.New("ArvError")
 450 }
 451
 452 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 453         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 454         return nil, errors.New("ArvError")
 455 }
 456
 457 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 458         return errors.New("ArvError")
 459 }
 460
 461 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 462         return nil
 463 }
 464
 465 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 466         return discoveryMap[key], nil
 467 }
 468
 469 type KeepErrorTestClient struct{}
 470
 471 func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 472         return "", 0, errors.New("KeepError")
 473 }
 474
 475 func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 476         return nil, errors.New("KeepError")
 477 }
 478
 479 func (KeepErrorTestClient) ClearBlockCache() {
 480 }
 481
 482 type KeepReadErrorTestClient struct{}
 483
 484 func (KeepReadErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) {
 485         return "", 0, nil
 486 }
 487
 488 func (KeepReadErrorTestClient) ClearBlockCache() {
 489 }
 490
 491 type ErrorReader struct {
 492         FileWrapper
 493 }
 494
 495 func (ErrorReader) Read(p []byte) (n int, err error) {
 496         return 0, errors.New("ErrorReader")
 497 }
 498
 499 func (ErrorReader) Seek(int64, int) (int64, error) {
 500         return 0, errors.New("ErrorReader")
 501 }
 502
 503 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 504         return ErrorReader{}, nil
 505 }
 506
 507 func (s *TestSuite) TestLoadImageArvError(c *C) {
 508         // (1) Arvados error
 509         cr := NewContainerRunner(ArvErrorTestClient{}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 510         cr.Container.ContainerImage = hwPDH
 511
 512         err := cr.LoadImage()
 513         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 514 }
 515
 516 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 517         // (2) Keep error
 518         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 519         cr.Container.ContainerImage = hwPDH
 520
 521         err := cr.LoadImage()
 522         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 523 }
 524
 525 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 526         // (3) Collection doesn't contain image
 527         cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 528         cr.Container.ContainerImage = otherPDH
 529
 530         err := cr.LoadImage()
 531         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 532 }
 533
 534 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 535         // (4) Collection doesn't contain image
 536         cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 537         cr.Container.ContainerImage = hwPDH
 538
 539         err := cr.LoadImage()
 540         c.Check(err, NotNil)
 541 }
 542
 543 type ClosableBuffer struct {
 544         bytes.Buffer
 545 }
 546
 547 func (*ClosableBuffer) Close() error {
 548         return nil
 549 }
 550
 551 type TestLogs struct {
 552         Stdout ClosableBuffer
 553         Stderr ClosableBuffer
 554 }
 555
 556 func (tl *TestLogs) NewTestLoggingWriter(logstr string) io.WriteCloser {
 557         if logstr == "stdout" {
 558                 return &tl.Stdout
 559         }
 560         if logstr == "stderr" {
 561                 return &tl.Stderr
 562         }
 563         return nil
 564 }
 565
 566 func dockerLog(fd byte, msg string) []byte {
 567         by := []byte(msg)
 568         header := make([]byte, 8+len(by))
 569         header[0] = fd
 570         header[7] = byte(len(by))
 571         copy(header[8:], by)
 572         return header
 573 }
 574
 575 func (s *TestSuite) TestRunContainer(c *C) {
 576         s.docker.fn = func(t *TestDockerClient) {
 577                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 578                 t.logWriter.Close()
 579         }
 580         cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 581
 582         var logs TestLogs
 583         cr.NewLogWriter = logs.NewTestLoggingWriter
 584         cr.Container.ContainerImage = hwPDH
 585         cr.Container.Command = []string{"./hw"}
 586         err := cr.LoadImage()
 587         c.Check(err, IsNil)
 588
 589         err = cr.CreateContainer()
 590         c.Check(err, IsNil)
 591
 592         err = cr.StartContainer()
 593         c.Check(err, IsNil)
 594
 595         err = cr.WaitFinish()
 596         c.Check(err, IsNil)
 597
 598         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 599         c.Check(logs.Stderr.String(), Equals, "")
 600 }
 601
 602 func (s *TestSuite) TestCommitLogs(c *C) {
 603         api := &ArvTestClient{}
 604         kc := &KeepTestClient{}
 605         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 606         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 607
 608         cr.CrunchLog.Print("Hello world!")
 609         cr.CrunchLog.Print("Goodbye")
 610         cr.finalState = "Complete"
 611
 612         err := cr.CommitLogs()
 613         c.Check(err, IsNil)
 614
 615         c.Check(api.Calls, Equals, 2)
 616         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 617         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 618         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 619         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 620 }
 621
 622 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 623         api := &ArvTestClient{}
 624         kc := &KeepTestClient{}
 625         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 626
 627         err := cr.UpdateContainerRunning()
 628         c.Check(err, IsNil)
 629
 630         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 631 }
 632
 633 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 634         api := &ArvTestClient{}
 635         kc := &KeepTestClient{}
 636         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 637
 638         cr.LogsPDH = new(string)
 639         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 640
 641         cr.ExitCode = new(int)
 642         *cr.ExitCode = 42
 643         cr.finalState = "Complete"
 644
 645         err := cr.UpdateContainerFinal()
 646         c.Check(err, IsNil)
 647
 648         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 649         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 650         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 651 }
 652
 653 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 654         api := &ArvTestClient{}
 655         kc := &KeepTestClient{}
 656         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 657         cr.cCancelled = true
 658         cr.finalState = "Cancelled"
 659
 660         err := cr.UpdateContainerFinal()
 661         c.Check(err, IsNil)
 662
 663         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 664         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 665         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 666 }
 667
 668 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 669 // dress rehearsal of the Run() function, starting from a JSON container record.
 670 func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 671         rec := arvados.Container{}
 672         err := json.Unmarshal([]byte(record), &rec)
 673         c.Check(err, IsNil)
 674
 675         s.docker.exitCode = exitCode
 676         s.docker.fn = fn
 677         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 678
 679         api = &ArvTestClient{Container: rec}
 680         s.docker.api = api
 681         cr = NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 682         cr.statInterval = 100 * time.Millisecond
 683         am := &ArvMountCmdLine{}
 684         cr.RunArvMount = am.ArvMountTest
 685
 686         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 687         c.Assert(err, IsNil)
 688         defer os.RemoveAll(realTemp)
 689
 690         s.docker.realTemp = realTemp
 691
 692         tempcount := 0
 693         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 694                 tempcount++
 695                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 696                 err := os.Mkdir(d, os.ModePerm)
 697                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 698                         // Test case must have pre-populated the tempdir
 699                         err = nil
 700                 }
 701                 return d, err
 702         }
 703
 704         if extraMounts != nil && len(extraMounts) > 0 {
 705                 err := cr.SetupArvMountPoint("keep")
 706                 c.Check(err, IsNil)
 707
 708                 for _, m := range extraMounts {
 709                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 710                 }
 711         }
 712
 713         err = cr.Run()
 714         if api.CalledWith("container.state", "Complete") != nil {
 715                 c.Check(err, IsNil)
 716         }
 717         if exitCode != 2 {
 718                 c.Check(api.WasSetRunning, Equals, true)
 719                 c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
 720         }
 721
 722         if err != nil {
 723                 for k, v := range api.Logs {
 724                         c.Log(k)
 725                         c.Log(v.String())
 726                 }
 727         }
 728
 729         return
 730 }
 731
 732 func (s *TestSuite) TestFullRunHello(c *C) {
 733         api, _, _ := s.fullRunHelper(c, `{
 734     "command": ["echo", "hello world"],
 735     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 736     "cwd": ".",
 737     "environment": {},
 738     "mounts": {"/tmp": {"kind": "tmp"} },
 739     "output_path": "/tmp",
 740     "priority": 1,
 741     "runtime_constraints": {}
 742 }`, nil, 0, func(t *TestDockerClient) {
 743                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 744                 t.logWriter.Close()
 745         })
 746
 747         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 748         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 749         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 750
 751 }
 752
 753 func (s *TestSuite) TestCrunchstat(c *C) {
 754         api, _, _ := s.fullRunHelper(c, `{
 755                 "command": ["sleep", "1"],
 756                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 757                 "cwd": ".",
 758                 "environment": {},
 759                 "mounts": {"/tmp": {"kind": "tmp"} },
 760                 "output_path": "/tmp",
 761                 "priority": 1,
 762                 "runtime_constraints": {}
 763         }`, nil, 0, func(t *TestDockerClient) {
 764                 time.Sleep(time.Second)
 765                 t.logWriter.Close()
 766         })
 767
 768         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 769         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 770
 771         // We didn't actually start a container, so crunchstat didn't
 772         // find accounting files and therefore didn't log any stats.
 773         // It should have logged a "can't find accounting files"
 774         // message after one poll interval, though, so we can confirm
 775         // it's alive:
 776         c.Assert(api.Logs["crunchstat"], NotNil)
 777         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 778
 779         // The "files never appeared" log assures us that we called
 780         // (*crunchstat.Reporter)Stop(), and that we set it up with
 781         // the correct container ID "abcde":
 782         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 783 }
 784
 785 func (s *TestSuite) TestNodeInfoLog(c *C) {
 786         os.Setenv("SLURMD_NODENAME", "compute2")
 787         api, _, _ := s.fullRunHelper(c, `{
 788                 "command": ["sleep", "1"],
 789                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 790                 "cwd": ".",
 791                 "environment": {},
 792                 "mounts": {"/tmp": {"kind": "tmp"} },
 793                 "output_path": "/tmp",
 794                 "priority": 1,
 795                 "runtime_constraints": {}
 796         }`, nil, 0,
 797                 func(t *TestDockerClient) {
 798                         time.Sleep(time.Second)
 799                         t.logWriter.Close()
 800                 })
 801
 802         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 803         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 804
 805         c.Assert(api.Logs["node"], NotNil)
 806         json := api.Logs["node"].String()
 807         c.Check(json, Matches, `(?ms).*"uuid": *"zzzzz-7ekkf-2z3mc76g2q73aio".*`)
 808         c.Check(json, Matches, `(?ms).*"total_cpu_cores": *16.*`)
 809         c.Check(json, Not(Matches), `(?ms).*"info":.*`)
 810
 811         c.Assert(api.Logs["node-info"], NotNil)
 812         json = api.Logs["node-info"].String()
 813         c.Check(json, Matches, `(?ms).*Host Information.*`)
 814         c.Check(json, Matches, `(?ms).*CPU Information.*`)
 815         c.Check(json, Matches, `(?ms).*Memory Information.*`)
 816         c.Check(json, Matches, `(?ms).*Disk Space.*`)
 817         c.Check(json, Matches, `(?ms).*Disk INodes.*`)
 818 }
 819
 820 func (s *TestSuite) TestContainerRecordLog(c *C) {
 821         api, _, _ := s.fullRunHelper(c, `{
 822                 "command": ["sleep", "1"],
 823                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 824                 "cwd": ".",
 825                 "environment": {},
 826                 "mounts": {"/tmp": {"kind": "tmp"} },
 827                 "output_path": "/tmp",
 828                 "priority": 1,
 829                 "runtime_constraints": {}
 830         }`, nil, 0,
 831                 func(t *TestDockerClient) {
 832                         time.Sleep(time.Second)
 833                         t.logWriter.Close()
 834                 })
 835
 836         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 837         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 838
 839         c.Assert(api.Logs["container"], NotNil)
 840         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 841 }
 842
 843 func (s *TestSuite) TestFullRunStderr(c *C) {
 844         api, _, _ := s.fullRunHelper(c, `{
 845     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 846     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 847     "cwd": ".",
 848     "environment": {},
 849     "mounts": {"/tmp": {"kind": "tmp"} },
 850     "output_path": "/tmp",
 851     "priority": 1,
 852     "runtime_constraints": {}
 853 }`, nil, 1, func(t *TestDockerClient) {
 854                 t.logWriter.Write(dockerLog(1, "hello\n"))
 855                 t.logWriter.Write(dockerLog(2, "world\n"))
 856                 t.logWriter.Close()
 857         })
 858
 859         final := api.CalledWith("container.state", "Complete")
 860         c.Assert(final, NotNil)
 861         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 862         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 863
 864         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 865         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 866 }
 867
 868 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 869         api, _, _ := s.fullRunHelper(c, `{
 870     "command": ["pwd"],
 871     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 872     "cwd": ".",
 873     "environment": {},
 874     "mounts": {"/tmp": {"kind": "tmp"} },
 875     "output_path": "/tmp",
 876     "priority": 1,
 877     "runtime_constraints": {}
 878 }`, nil, 0, func(t *TestDockerClient) {
 879                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 880                 t.logWriter.Close()
 881         })
 882
 883         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 884         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 885         c.Log(api.Logs["stdout"])
 886         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 887 }
 888
 889 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 890         api, _, _ := s.fullRunHelper(c, `{
 891     "command": ["pwd"],
 892     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 893     "cwd": "/bin",
 894     "environment": {},
 895     "mounts": {"/tmp": {"kind": "tmp"} },
 896     "output_path": "/tmp",
 897     "priority": 1,
 898     "runtime_constraints": {}
 899 }`, nil, 0, func(t *TestDockerClient) {
 900                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 901                 t.logWriter.Close()
 902         })
 903
 904         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 905         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 906         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 907 }
 908
 909 func (s *TestSuite) TestStopOnSignal(c *C) {
 910         s.testStopContainer(c, func(cr *ContainerRunner) {
 911                 go func() {
 912                         for !s.docker.calledWait {
 913                                 time.Sleep(time.Millisecond)
 914                         }
 915                         cr.SigChan <- syscall.SIGINT
 916                 }()
 917         })
 918 }
 919
 920 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 921         s.testStopContainer(c, func(cr *ContainerRunner) {
 922                 cr.ArvMountExit = make(chan error)
 923                 go func() {
 924                         cr.ArvMountExit <- exec.Command("true").Run()
 925                         close(cr.ArvMountExit)
 926                 }()
 927         })
 928 }
 929
 930 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 931         record := `{
 932     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 933     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 934     "cwd": ".",
 935     "environment": {},
 936     "mounts": {"/tmp": {"kind": "tmp"} },
 937     "output_path": "/tmp",
 938     "priority": 1,
 939     "runtime_constraints": {}
 940 }`
 941
 942         rec := arvados.Container{}
 943         err := json.Unmarshal([]byte(record), &rec)
 944         c.Check(err, IsNil)
 945
 946         s.docker.fn = func(t *TestDockerClient) {
 947                 <-t.stop
 948                 t.logWriter.Write(dockerLog(1, "foo\n"))
 949                 t.logWriter.Close()
 950         }
 951         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 952
 953         api := &ArvTestClient{Container: rec}
 954         cr := NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 955         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
 956         setup(cr)
 957
 958         done := make(chan error)
 959         go func() {
 960                 done <- cr.Run()
 961         }()
 962         select {
 963         case <-time.After(20 * time.Second):
 964                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
 965                 c.Fatal("timed out")
 966         case err = <-done:
 967                 c.Check(err, IsNil)
 968         }
 969         for k, v := range api.Logs {
 970                 c.Log(k)
 971                 c.Log(v.String())
 972         }
 973
 974         c.Check(api.CalledWith("container.log", nil), NotNil)
 975         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
 976         c.Check(api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
 977 }
 978
 979 func (s *TestSuite) TestFullRunSetEnv(c *C) {
 980         api, _, _ := s.fullRunHelper(c, `{
 981     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
 982     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 983     "cwd": "/bin",
 984     "environment": {"FROBIZ": "bilbo"},
 985     "mounts": {"/tmp": {"kind": "tmp"} },
 986     "output_path": "/tmp",
 987     "priority": 1,
 988     "runtime_constraints": {}
 989 }`, nil, 0, func(t *TestDockerClient) {
 990                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
 991                 t.logWriter.Close()
 992         })
 993
 994         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 995         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 996         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
 997 }
 998
 999 type ArvMountCmdLine struct {
1000         Cmd   []string
1001         token string
1002 }
1003
1004 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
1005         am.Cmd = c
1006         am.token = token
1007         return nil, nil
1008 }
1009
1010 func stubCert(temp string) string {
1011         path := temp + "/ca-certificates.crt"
1012         crt, _ := os.Create(path)
1013         crt.Close()
1014         arvadosclient.CertFiles = []string{path}
1015         return path
1016 }
1017
1018 func (s *TestSuite) TestSetupMounts(c *C) {
1019         api := &ArvTestClient{}
1020         kc := &KeepTestClient{}
1021         cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1022         am := &ArvMountCmdLine{}
1023         cr.RunArvMount = am.ArvMountTest
1024
1025         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
1026         c.Assert(err, IsNil)
1027         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
1028         c.Assert(err, IsNil)
1029         stubCertPath := stubCert(certTemp)
1030
1031         cr.parentTemp = realTemp
1032
1033         defer os.RemoveAll(realTemp)
1034         defer os.RemoveAll(certTemp)
1035
1036         i := 0
1037         cr.MkTempDir = func(_ string, prefix string) (string, error) {
1038                 i++
1039                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
1040                 err := os.Mkdir(d, os.ModePerm)
1041                 if err != nil && strings.Contains(err.Error(), ": file exists") {
1042                         // Test case must have pre-populated the tempdir
1043                         err = nil
1044                 }
1045                 return d, err
1046         }
1047
1048         checkEmpty := func() {
1049                 // Should be deleted.
1050                 _, err := os.Stat(realTemp)
1051                 c.Assert(os.IsNotExist(err), Equals, true)
1052
1053                 // Now recreate it for the next test.
1054                 c.Assert(os.Mkdir(realTemp, 0777), IsNil)
1055         }
1056
1057         {
1058                 i = 0
1059                 cr.ArvMountPoint = ""
1060                 cr.Container.Mounts = make(map[string]arvados.Mount)
1061                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1062                 cr.OutputPath = "/tmp"
1063                 cr.statInterval = 5 * time.Second
1064                 err := cr.SetupMounts()
1065                 c.Check(err, IsNil)
1066                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1067                         "--read-write", "--crunchstat-interval=5",
1068                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1069                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
1070                 os.RemoveAll(cr.ArvMountPoint)
1071                 cr.CleanupDirs()
1072                 checkEmpty()
1073         }
1074
1075         {
1076                 i = 0
1077                 cr.ArvMountPoint = ""
1078                 cr.Container.Mounts = make(map[string]arvados.Mount)
1079                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
1080                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1081                 cr.OutputPath = "/out"
1082
1083                 err := cr.SetupMounts()
1084                 c.Check(err, IsNil)
1085                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1086                         "--read-write", "--crunchstat-interval=5",
1087                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1088                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
1089                 os.RemoveAll(cr.ArvMountPoint)
1090                 cr.CleanupDirs()
1091                 checkEmpty()
1092         }
1093
1094         {
1095                 i = 0
1096                 cr.ArvMountPoint = ""
1097                 cr.Container.Mounts = make(map[string]arvados.Mount)
1098                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1099                 cr.OutputPath = "/tmp"
1100
1101                 apiflag := true
1102                 cr.Container.RuntimeConstraints.API = &apiflag
1103
1104                 err := cr.SetupMounts()
1105                 c.Check(err, IsNil)
1106                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1107                         "--read-write", "--crunchstat-interval=5",
1108                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1109                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1110                 os.RemoveAll(cr.ArvMountPoint)
1111                 cr.CleanupDirs()
1112                 checkEmpty()
1113
1114                 apiflag = false
1115         }
1116
1117         {
1118                 i = 0
1119                 cr.ArvMountPoint = ""
1120                 cr.Container.Mounts = map[string]arvados.Mount{
1121                         "/keeptmp": {Kind: "collection", Writable: true},
1122                 }
1123                 cr.OutputPath = "/keeptmp"
1124
1125                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1126
1127                 err := cr.SetupMounts()
1128                 c.Check(err, IsNil)
1129                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1130                         "--read-write", "--crunchstat-interval=5",
1131                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1132                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1133                 os.RemoveAll(cr.ArvMountPoint)
1134                 cr.CleanupDirs()
1135                 checkEmpty()
1136         }
1137
1138         {
1139                 i = 0
1140                 cr.ArvMountPoint = ""
1141                 cr.Container.Mounts = map[string]arvados.Mount{
1142                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1143                         "/keepout": {Kind: "collection", Writable: true},
1144                 }
1145                 cr.OutputPath = "/keepout"
1146
1147                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1148                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1149
1150                 err := cr.SetupMounts()
1151                 c.Check(err, IsNil)
1152                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1153                         "--read-write", "--crunchstat-interval=5",
1154                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1155                 sort.StringSlice(cr.Binds).Sort()
1156                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1157                         realTemp + "/keep1/tmp0:/keepout"})
1158                 os.RemoveAll(cr.ArvMountPoint)
1159                 cr.CleanupDirs()
1160                 checkEmpty()
1161         }
1162
1163         {
1164                 i = 0
1165                 cr.ArvMountPoint = ""
1166                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1167                 cr.Container.Mounts = map[string]arvados.Mount{
1168                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1169                         "/keepout": {Kind: "collection", Writable: true},
1170                 }
1171                 cr.OutputPath = "/keepout"
1172
1173                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1174                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1175
1176                 err := cr.SetupMounts()
1177                 c.Check(err, IsNil)
1178                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1179                         "--read-write", "--crunchstat-interval=5",
1180                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1181                 sort.StringSlice(cr.Binds).Sort()
1182                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1183                         realTemp + "/keep1/tmp0:/keepout"})
1184                 os.RemoveAll(cr.ArvMountPoint)
1185                 cr.CleanupDirs()
1186                 checkEmpty()
1187         }
1188
1189         for _, test := range []struct {
1190                 in  interface{}
1191                 out string
1192         }{
1193                 {in: "foo", out: `"foo"`},
1194                 {in: nil, out: `null`},
1195                 {in: map[string]int64{"foo": 123456789123456789}, out: `{"foo":123456789123456789}`},
1196         } {
1197                 i = 0
1198                 cr.ArvMountPoint = ""
1199                 cr.Container.Mounts = map[string]arvados.Mount{
1200                         "/mnt/test.json": {Kind: "json", Content: test.in},
1201                 }
1202                 err := cr.SetupMounts()
1203                 c.Check(err, IsNil)
1204                 sort.StringSlice(cr.Binds).Sort()
1205                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
1206                 content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
1207                 c.Check(err, IsNil)
1208                 c.Check(content, DeepEquals, []byte(test.out))
1209                 os.RemoveAll(cr.ArvMountPoint)
1210                 cr.CleanupDirs()
1211                 checkEmpty()
1212         }
1213
1214         // Read-only mount points are allowed underneath output_dir mount point
1215         {
1216                 i = 0
1217                 cr.ArvMountPoint = ""
1218                 cr.Container.Mounts = make(map[string]arvados.Mount)
1219                 cr.Container.Mounts = map[string]arvados.Mount{
1220                         "/tmp":     {Kind: "tmp"},
1221                         "/tmp/foo": {Kind: "collection"},
1222                 }
1223                 cr.OutputPath = "/tmp"
1224
1225                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1226
1227                 err := cr.SetupMounts()
1228                 c.Check(err, IsNil)
1229                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1230                         "--read-write", "--crunchstat-interval=5",
1231                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1232                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1233                 os.RemoveAll(cr.ArvMountPoint)
1234                 cr.CleanupDirs()
1235                 checkEmpty()
1236         }
1237
1238         // Writable mount points copied to output_dir mount point
1239         {
1240                 i = 0
1241                 cr.ArvMountPoint = ""
1242                 cr.Container.Mounts = make(map[string]arvados.Mount)
1243                 cr.Container.Mounts = map[string]arvados.Mount{
1244                         "/tmp": {Kind: "tmp"},
1245                         "/tmp/foo": {Kind: "collection",
1246                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53",
1247                                 Writable:         true},
1248                         "/tmp/bar": {Kind: "collection",
1249                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541d+53",
1250                                 Path:             "baz",
1251                                 Writable:         true},
1252                 }
1253                 cr.OutputPath = "/tmp"
1254
1255                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1256                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz", os.ModePerm)
1257
1258                 rf, _ := os.Create(realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz/quux")
1259                 rf.Write([]byte("bar"))
1260                 rf.Close()
1261
1262                 err := cr.SetupMounts()
1263                 c.Check(err, IsNil)
1264                 _, err = os.Stat(cr.HostOutputDir + "/foo")
1265                 c.Check(err, IsNil)
1266                 _, err = os.Stat(cr.HostOutputDir + "/bar/quux")
1267                 c.Check(err, IsNil)
1268                 os.RemoveAll(cr.ArvMountPoint)
1269                 cr.CleanupDirs()
1270                 checkEmpty()
1271         }
1272
1273         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1274         {
1275                 i = 0
1276                 cr.ArvMountPoint = ""
1277                 cr.Container.Mounts = make(map[string]arvados.Mount)
1278                 cr.Container.Mounts = map[string]arvados.Mount{
1279                         "/tmp":     {Kind: "tmp"},
1280                         "/tmp/foo": {Kind: "json"},
1281                 }
1282                 cr.OutputPath = "/tmp"
1283
1284                 err := cr.SetupMounts()
1285                 c.Check(err, NotNil)
1286                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
1287                 os.RemoveAll(cr.ArvMountPoint)
1288                 cr.CleanupDirs()
1289                 checkEmpty()
1290         }
1291
1292         // Only mount point of kind 'collection' is allowed for stdin
1293         {
1294                 i = 0
1295                 cr.ArvMountPoint = ""
1296                 cr.Container.Mounts = make(map[string]arvados.Mount)
1297                 cr.Container.Mounts = map[string]arvados.Mount{
1298                         "stdin": {Kind: "tmp"},
1299                 }
1300
1301                 err := cr.SetupMounts()
1302                 c.Check(err, NotNil)
1303                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1304                 os.RemoveAll(cr.ArvMountPoint)
1305                 cr.CleanupDirs()
1306                 checkEmpty()
1307         }
1308
1309         // git_tree mounts
1310         {
1311                 i = 0
1312                 cr.ArvMountPoint = ""
1313                 (*GitMountSuite)(nil).useTestGitServer(c)
1314                 cr.token = arvadostest.ActiveToken
1315                 cr.Container.Mounts = make(map[string]arvados.Mount)
1316                 cr.Container.Mounts = map[string]arvados.Mount{
1317                         "/tip": {
1318                                 Kind:   "git_tree",
1319                                 UUID:   arvadostest.Repository2UUID,
1320                                 Commit: "fd3531f42995344f36c30b79f55f27b502f3d344",
1321                                 Path:   "/",
1322                         },
1323                         "/non-tip": {
1324                                 Kind:   "git_tree",
1325                                 UUID:   arvadostest.Repository2UUID,
1326                                 Commit: "5ebfab0522851df01fec11ec55a6d0f4877b542e",
1327                                 Path:   "/",
1328                         },
1329                 }
1330                 cr.OutputPath = "/tmp"
1331
1332                 err := cr.SetupMounts()
1333                 c.Check(err, IsNil)
1334
1335                 // dirMap[mountpoint] == tmpdir
1336                 dirMap := make(map[string]string)
1337                 for _, bind := range cr.Binds {
1338                         tokens := strings.Split(bind, ":")
1339                         dirMap[tokens[1]] = tokens[0]
1340
1341                         if cr.Container.Mounts[tokens[1]].Writable {
1342                                 c.Check(len(tokens), Equals, 2)
1343                         } else {
1344                                 c.Check(len(tokens), Equals, 3)
1345                                 c.Check(tokens[2], Equals, "ro")
1346                         }
1347                 }
1348
1349                 data, err := ioutil.ReadFile(dirMap["/tip"] + "/dir1/dir2/file with mode 0644")
1350                 c.Check(err, IsNil)
1351                 c.Check(string(data), Equals, "\000\001\002\003")
1352                 _, err = ioutil.ReadFile(dirMap["/tip"] + "/file only on testbranch")
1353                 c.Check(err, FitsTypeOf, &os.PathError{})
1354                 c.Check(os.IsNotExist(err), Equals, true)
1355
1356                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/dir1/dir2/file with mode 0644")
1357                 c.Check(err, IsNil)
1358                 c.Check(string(data), Equals, "\000\001\002\003")
1359                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/file only on testbranch")
1360                 c.Check(err, IsNil)
1361                 c.Check(string(data), Equals, "testfile\n")
1362
1363                 cr.CleanupDirs()
1364                 checkEmpty()
1365         }
1366 }
1367
1368 func (s *TestSuite) TestStdout(c *C) {
1369         helperRecord := `{
1370                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1371                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1372                 "cwd": "/bin",
1373                 "environment": {"FROBIZ": "bilbo"},
1374                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1375                 "output_path": "/tmp",
1376                 "priority": 1,
1377                 "runtime_constraints": {}
1378         }`
1379
1380         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1381                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1382                 t.logWriter.Close()
1383         })
1384
1385         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1386         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1387         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1388 }
1389
1390 // Used by the TestStdoutWithWrongPath*()
1391 func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1392         rec := arvados.Container{}
1393         err = json.Unmarshal([]byte(record), &rec)
1394         c.Check(err, IsNil)
1395
1396         s.docker.fn = fn
1397         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1398
1399         api = &ArvTestClient{Container: rec}
1400         cr = NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1401         am := &ArvMountCmdLine{}
1402         cr.RunArvMount = am.ArvMountTest
1403
1404         err = cr.Run()
1405         return
1406 }
1407
1408 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1409         _, _, err := s.stdoutErrorRunHelper(c, `{
1410     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1411     "output_path": "/tmp"
1412 }`, func(t *TestDockerClient) {})
1413
1414         c.Check(err, NotNil)
1415         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1416 }
1417
1418 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1419         _, _, err := s.stdoutErrorRunHelper(c, `{
1420     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1421     "output_path": "/tmp"
1422 }`, func(t *TestDockerClient) {})
1423
1424         c.Check(err, NotNil)
1425         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1426 }
1427
1428 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1429         _, _, err := s.stdoutErrorRunHelper(c, `{
1430     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1431     "output_path": "/tmp"
1432 }`, func(t *TestDockerClient) {})
1433
1434         c.Check(err, NotNil)
1435         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1436 }
1437
1438 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1439         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1440         defer os.Unsetenv("ARVADOS_API_HOST")
1441         api, _, _ := s.fullRunHelper(c, `{
1442     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1443     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1444     "cwd": "/bin",
1445     "environment": {},
1446     "mounts": {"/tmp": {"kind": "tmp"} },
1447     "output_path": "/tmp",
1448     "priority": 1,
1449     "runtime_constraints": {"API": true}
1450 }`, nil, 0, func(t *TestDockerClient) {
1451                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\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         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1458         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1459 }
1460
1461 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1462         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1463         defer os.Unsetenv("ARVADOS_API_HOST")
1464         api, _, _ := s.fullRunHelper(c, `{
1465     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1466     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1467     "cwd": "/bin",
1468     "environment": {},
1469     "mounts": {"/tmp": {"kind": "tmp"} },
1470     "output_path": "/tmp",
1471     "priority": 1,
1472     "runtime_constraints": {"API": true}
1473 }`, nil, 0, func(t *TestDockerClient) {
1474                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1475                 t.logWriter.Close()
1476         })
1477
1478         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1479         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1480         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1481 }
1482
1483 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1484         helperRecord := `{
1485                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1486                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1487                 "cwd": "/bin",
1488                 "environment": {"FROBIZ": "bilbo"},
1489                 "mounts": {
1490         "/tmp": {"kind": "tmp"},
1491         "/tmp/foo": {"kind": "collection",
1492                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1493                      "exclude_from_output": true
1494         },
1495         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1496     },
1497                 "output_path": "/tmp",
1498                 "priority": 1,
1499                 "runtime_constraints": {}
1500         }`
1501
1502         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1503
1504         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1505                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1506                 t.logWriter.Close()
1507         })
1508
1509         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1510         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1511         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1512 }
1513
1514 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1515         helperRecord := `{
1516                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1517                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1518                 "cwd": "/bin",
1519                 "environment": {"FROBIZ": "bilbo"},
1520                 "mounts": {
1521         "/tmp": {"kind": "tmp"},
1522         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1523         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1524         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1525         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1526         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1527     },
1528                 "output_path": "/tmp",
1529                 "priority": 1,
1530                 "runtime_constraints": {}
1531         }`
1532
1533         extraMounts := []string{
1534                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1535                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1536                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1537         }
1538
1539         api, runner, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1540                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1541                 t.logWriter.Close()
1542         })
1543
1544         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
1545                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1546                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1547                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1548                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1549         })
1550
1551         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1552         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1553         for _, v := range api.Content {
1554                 if v["collection"] != nil {
1555                         c.Check(v["ensure_unique_name"], Equals, true)
1556                         collection := v["collection"].(arvadosclient.Dict)
1557                         if strings.Index(collection["name"].(string), "output") == 0 {
1558                                 manifest := collection["manifest_text"].(string)
1559
1560                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1561 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2
1562 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1563 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1564 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1565 `)
1566                         }
1567                 }
1568         }
1569 }
1570
1571 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1572         helperRecord := `{
1573                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1574                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1575                 "cwd": "/bin",
1576                 "environment": {"FROBIZ": "bilbo"},
1577                 "mounts": {
1578         "/tmp": {"kind": "tmp"},
1579         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"},
1580         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1581     },
1582                 "output_path": "/tmp",
1583                 "priority": 1,
1584                 "runtime_constraints": {}
1585         }`
1586
1587         extraMounts := []string{
1588                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1589         }
1590
1591         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1592                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1593                 t.logWriter.Close()
1594         })
1595
1596         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1597         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1598         for _, v := range api.Content {
1599                 if v["collection"] != nil {
1600                         collection := v["collection"].(arvadosclient.Dict)
1601                         if strings.Index(collection["name"].(string), "output") == 0 {
1602                                 manifest := collection["manifest_text"].(string)
1603
1604                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1605 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1606 `)
1607                         }
1608                 }
1609         }
1610 }
1611
1612 func (s *TestSuite) TestOutputSymlinkToInput(c *C) {
1613         helperRecord := `{
1614                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1615                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1616                 "cwd": "/bin",
1617                 "environment": {"FROBIZ": "bilbo"},
1618                 "mounts": {
1619         "/tmp": {"kind": "tmp"},
1620         "/keep/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
1621         "/keep/foo2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367"}
1622     },
1623                 "output_path": "/tmp",
1624                 "priority": 1,
1625                 "runtime_constraints": {}
1626         }`
1627
1628         extraMounts := []string{
1629                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1630         }
1631
1632         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1633                 os.Symlink("/keep/foo/sub1file2", t.realTemp+"/tmp2/baz")
1634                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz2")
1635                 os.Symlink("/keep/foo2/subdir1", t.realTemp+"/tmp2/baz3")
1636                 os.Mkdir(t.realTemp+"/tmp2/baz4", 0700)
1637                 os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz4/baz5")
1638                 t.logWriter.Close()
1639         })
1640
1641         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1642         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1643         for _, v := range api.Content {
1644                 if v["collection"] != nil {
1645                         collection := v["collection"].(arvadosclient.Dict)
1646                         if strings.Index(collection["name"].(string), "output") == 0 {
1647                                 manifest := collection["manifest_text"].(string)
1648                                 c.Check(manifest, Equals, `. 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz 9:18:baz2
1649 ./baz3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1650 ./baz3/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1651 ./baz4 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:baz5
1652 `)
1653                         }
1654                 }
1655         }
1656 }
1657
1658 func (s *TestSuite) TestOutputError(c *C) {
1659         helperRecord := `{
1660                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1661                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1662                 "cwd": "/bin",
1663                 "environment": {"FROBIZ": "bilbo"},
1664                 "mounts": {
1665         "/tmp": {"kind": "tmp"}
1666     },
1667                 "output_path": "/tmp",
1668                 "priority": 1,
1669                 "runtime_constraints": {}
1670         }`
1671
1672         extraMounts := []string{}
1673
1674         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1675                 os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
1676                 t.logWriter.Close()
1677         })
1678
1679         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1680 }
1681
1682 func (s *TestSuite) TestOutputSymlinkToOutput(c *C) {
1683         helperRecord := `{
1684                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1685                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1686                 "cwd": "/bin",
1687                 "environment": {"FROBIZ": "bilbo"},
1688                 "mounts": {
1689         "/tmp": {"kind": "tmp"}
1690     },
1691                 "output_path": "/tmp",
1692                 "priority": 1,
1693                 "runtime_constraints": {}
1694         }`
1695
1696         extraMounts := []string{}
1697
1698         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1699                 rf, _ := os.Create(t.realTemp + "/tmp2/realfile")
1700                 rf.Write([]byte("foo"))
1701                 rf.Close()
1702
1703                 os.Mkdir(t.realTemp+"/tmp2/realdir", 0700)
1704                 rf, _ = os.Create(t.realTemp + "/tmp2/realdir/subfile")
1705                 rf.Write([]byte("bar"))
1706                 rf.Close()
1707
1708                 os.Symlink("/tmp/realfile", t.realTemp+"/tmp2/file1")
1709                 os.Symlink("realfile", t.realTemp+"/tmp2/file2")
1710                 os.Symlink("/tmp/file1", t.realTemp+"/tmp2/file3")
1711                 os.Symlink("file2", t.realTemp+"/tmp2/file4")
1712                 os.Symlink("realdir", t.realTemp+"/tmp2/dir1")
1713                 os.Symlink("/tmp/realdir", t.realTemp+"/tmp2/dir2")
1714                 t.logWriter.Close()
1715         })
1716
1717         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1718         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1719         for _, v := range api.Content {
1720                 if v["collection"] != nil {
1721                         collection := v["collection"].(arvadosclient.Dict)
1722                         if strings.Index(collection["name"].(string), "output") == 0 {
1723                                 manifest := collection["manifest_text"].(string)
1724                                 c.Check(manifest, Equals,
1725                                         `. 7a2c86e102dcc231bd232aad99686dfa+15 0:3:file1 3:3:file2 6:3:file3 9:3:file4 12:3:realfile
1726 ./dir1 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1727 ./dir2 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1728 ./realdir 37b51d194a7513e45b56f6524f2d51f2+3 0:3:subfile
1729 `)
1730                         }
1731                 }
1732         }
1733 }
1734
1735 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1736         helperRecord := `{
1737                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1738                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1739                 "cwd": "/bin",
1740                 "environment": {"FROBIZ": "bilbo"},
1741                 "mounts": {
1742         "/tmp": {"kind": "tmp"},
1743         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1744         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1745     },
1746                 "output_path": "/tmp",
1747                 "priority": 1,
1748                 "runtime_constraints": {}
1749         }`
1750
1751         extraMounts := []string{
1752                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1753         }
1754
1755         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1756                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1757                 t.logWriter.Close()
1758         })
1759
1760         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1761         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1762         for _, v := range api.Content {
1763                 if v["collection"] != nil {
1764                         collection := v["collection"].(arvadosclient.Dict)
1765                         if strings.Index(collection["name"].(string), "output") == 0 {
1766                                 manifest := collection["manifest_text"].(string)
1767                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1768 `)
1769                         }
1770                 }
1771         }
1772 }
1773
1774 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1775         helperRecord := `{
1776                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1777                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1778                 "cwd": "/bin",
1779                 "environment": {"FROBIZ": "bilbo"},
1780                 "mounts": {
1781         "/tmp": {"kind": "tmp"},
1782         "stdin": {"kind": "json", "content": "foo"},
1783         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1784     },
1785                 "output_path": "/tmp",
1786                 "priority": 1,
1787                 "runtime_constraints": {}
1788         }`
1789
1790         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1791                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1792                 t.logWriter.Close()
1793         })
1794
1795         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1796         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1797         for _, v := range api.Content {
1798                 if v["collection"] != nil {
1799                         collection := v["collection"].(arvadosclient.Dict)
1800                         if strings.Index(collection["name"].(string), "output") == 0 {
1801                                 manifest := collection["manifest_text"].(string)
1802                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1803 `)
1804                         }
1805                 }
1806         }
1807 }
1808
1809 func (s *TestSuite) TestStderrMount(c *C) {
1810         api, _, _ := s.fullRunHelper(c, `{
1811     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1812     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1813     "cwd": ".",
1814     "environment": {},
1815     "mounts": {"/tmp": {"kind": "tmp"},
1816                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1817                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1818     "output_path": "/tmp",
1819     "priority": 1,
1820     "runtime_constraints": {}
1821 }`, nil, 1, func(t *TestDockerClient) {
1822                 t.logWriter.Write(dockerLog(1, "hello\n"))
1823                 t.logWriter.Write(dockerLog(2, "oops\n"))
1824                 t.logWriter.Close()
1825         })
1826
1827         final := api.CalledWith("container.state", "Complete")
1828         c.Assert(final, NotNil)
1829         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1830         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1831
1832         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1833 }
1834
1835 func (s *TestSuite) TestNumberRoundTrip(c *C) {
1836         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1837         cr.fetchContainerRecord()
1838
1839         jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
1840
1841         c.Check(err, IsNil)
1842         c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
1843 }
1844
1845 func (s *TestSuite) TestEvalSymlinks(c *C) {
1846         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1847
1848         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1849         c.Assert(err, IsNil)
1850         defer os.RemoveAll(realTemp)
1851
1852         cr.HostOutputDir = realTemp
1853
1854         // Absolute path outside output dir
1855         os.Symlink("/etc/passwd", realTemp+"/p1")
1856
1857         // Relative outside output dir
1858         os.Symlink("../zip", realTemp+"/p2")
1859
1860         // Circular references
1861         os.Symlink("p4", realTemp+"/p3")
1862         os.Symlink("p5", realTemp+"/p4")
1863         os.Symlink("p3", realTemp+"/p5")
1864
1865         // Target doesn't exist
1866         os.Symlink("p99", realTemp+"/p6")
1867
1868         for _, v := range []string{"p1", "p2", "p3", "p4", "p5"} {
1869                 info, err := os.Lstat(realTemp + "/" + v)
1870                 _, _, _, err = cr.derefOutputSymlink(realTemp+"/"+v, info)
1871                 c.Assert(err, NotNil)
1872         }
1873 }
1874
1875 func (s *TestSuite) TestEvalSymlinkDir(c *C) {
1876         cr := NewContainerRunner(&ArvTestClient{callraw: true}, &KeepTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1877
1878         realTemp, err := ioutil.TempDir("", "crunchrun_test-")
1879         c.Assert(err, IsNil)
1880         defer os.RemoveAll(realTemp)
1881
1882         cr.HostOutputDir = realTemp
1883
1884         // Absolute path outside output dir
1885         os.Symlink(".", realTemp+"/loop")
1886
1887         v := "loop"
1888         info, err := os.Lstat(realTemp + "/" + v)
1889         _, err = cr.UploadOutputFile(realTemp+"/"+v, info, err, []string{}, nil, "", "", 0)
1890         c.Assert(err, NotNil)
1891 }
1892
1893 func (s *TestSuite) TestFullBrokenDocker1(c *C) {
1894         tf, err := ioutil.TempFile("", "brokenNodeHook-")
1895         c.Assert(err, IsNil)
1896         defer os.Remove(tf.Name())
1897
1898         tf.Write([]byte(`#!/bin/sh
1899 exec echo killme
1900 `))
1901         tf.Close()
1902         os.Chmod(tf.Name(), 0700)
1903
1904         ech := tf.Name()
1905         brokenNodeHook = &ech
1906
1907         api, _, _ := s.fullRunHelper(c, `{
1908     "command": ["echo", "hello world"],
1909     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1910     "cwd": ".",
1911     "environment": {},
1912     "mounts": {"/tmp": {"kind": "tmp"} },
1913     "output_path": "/tmp",
1914     "priority": 1,
1915     "runtime_constraints": {}
1916 }`, nil, 2, func(t *TestDockerClient) {
1917                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1918                 t.logWriter.Close()
1919         })
1920
1921         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1922         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1923         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
1924         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
1925
1926 }
1927
1928 func (s *TestSuite) TestFullBrokenDocker2(c *C) {
1929         ech := ""
1930         brokenNodeHook = &ech
1931
1932         api, _, _ := s.fullRunHelper(c, `{
1933     "command": ["echo", "hello world"],
1934     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1935     "cwd": ".",
1936     "environment": {},
1937     "mounts": {"/tmp": {"kind": "tmp"} },
1938     "output_path": "/tmp",
1939     "priority": 1,
1940     "runtime_constraints": {}
1941 }`, nil, 2, func(t *TestDockerClient) {
1942                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1943                 t.logWriter.Close()
1944         })
1945
1946         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1947         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1948         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
1949 }
1950
1951 func (s *TestSuite) TestFullBrokenDocker3(c *C) {
1952         ech := ""
1953         brokenNodeHook = &ech
1954
1955         api, _, _ := s.fullRunHelper(c, `{
1956     "command": ["echo", "hello world"],
1957     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1958     "cwd": ".",
1959     "environment": {},
1960     "mounts": {"/tmp": {"kind": "tmp"} },
1961     "output_path": "/tmp",
1962     "priority": 1,
1963     "runtime_constraints": {}
1964 }`, nil, 3, func(t *TestDockerClient) {
1965                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1966                 t.logWriter.Close()
1967         })
1968
1969         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1970         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1971 }
1972
1973 func (s *TestSuite) TestBadCommand1(c *C) {
1974         ech := ""
1975         brokenNodeHook = &ech
1976
1977         api, _, _ := s.fullRunHelper(c, `{
1978     "command": ["echo", "hello world"],
1979     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1980     "cwd": ".",
1981     "environment": {},
1982     "mounts": {"/tmp": {"kind": "tmp"} },
1983     "output_path": "/tmp",
1984     "priority": 1,
1985     "runtime_constraints": {}
1986 }`, nil, 4, func(t *TestDockerClient) {
1987                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1988                 t.logWriter.Close()
1989         })
1990
1991         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1992         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1993 }
1994
1995 func (s *TestSuite) TestBadCommand2(c *C) {
1996         ech := ""
1997         brokenNodeHook = &ech
1998
1999         api, _, _ := s.fullRunHelper(c, `{
2000     "command": ["echo", "hello world"],
2001     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
2002     "cwd": ".",
2003     "environment": {},
2004     "mounts": {"/tmp": {"kind": "tmp"} },
2005     "output_path": "/tmp",
2006     "priority": 1,
2007     "runtime_constraints": {}
2008 }`, nil, 5, func(t *TestDockerClient) {
2009                 t.logWriter.Write(dockerLog(1, "hello world\n"))
2010                 t.logWriter.Close()
2011         })
2012
2013         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
2014         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
2015 }
2016
2017 func (s *TestSuite) TestBadCommand3(c *C) {
2018         ech := ""
2019         brokenNodeHook = &ech
2020
2021         api, _, _ := s.fullRunHelper(c, `{
2022     "command": ["echo", "hello world"],
2023     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
2024     "cwd": ".",
2025     "environment": {},
2026     "mounts": {"/tmp": {"kind": "tmp"} },
2027     "output_path": "/tmp",
2028     "priority": 1,
2029     "runtime_constraints": {}
2030 }`, nil, 6, func(t *TestDockerClient) {
2031                 t.logWriter.Write(dockerLog(1, "hello world\n"))
2032                 t.logWriter.Close()
2033         })
2034
2035         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
2036         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
2037 }