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         client *arvados.Client
  49         docker *TestDockerClient
  50 }
  51
  52 func (s *TestSuite) SetUpTest(c *C) {
  53         s.client = arvados.NewClientFromEnv()
  54         s.docker = NewTestDockerClient()
  55 }
  56
  57 type ArvTestClient struct {
  58         Total   int64
  59         Calls   int
  60         Content []arvadosclient.Dict
  61         arvados.Container
  62         secretMounts []byte
  63         Logs         map[string]*bytes.Buffer
  64         sync.Mutex
  65         WasSetRunning bool
  66         callraw       bool
  67 }
  68
  69 type KeepTestClient struct {
  70         Called  bool
  71         Content []byte
  72 }
  73
  74 var hwManifest = ". 82ab40c24fc8df01798e57ba66795bb1+841216+Aa124ac75e5168396c73c0a18eda641a4f41791c0@569fa8c3 0:841216:9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7.tar\n"
  75 var hwPDH = "a45557269dcb65a6b78f9ac061c0850b+120"
  76 var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea7"
  77
  78 var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n"
  79 var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54"
  80
  81 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
  82 ./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
  83 ./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
  84 `
  85
  86 var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367"
  87
  88 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"
  89 var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367"
  90
  91 var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem"
  92 var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt"
  93
  94 type TestDockerClient struct {
  95         imageLoaded string
  96         logReader   io.ReadCloser
  97         logWriter   io.WriteCloser
  98         fn          func(t *TestDockerClient)
  99         exitCode    int
 100         stop        chan bool
 101         cwd         string
 102         env         []string
 103         api         *ArvTestClient
 104         realTemp    string
 105         calledWait  bool
 106 }
 107
 108 func NewTestDockerClient() *TestDockerClient {
 109         t := &TestDockerClient{}
 110         t.logReader, t.logWriter = io.Pipe()
 111         t.stop = make(chan bool, 1)
 112         t.cwd = "/"
 113         return t
 114 }
 115
 116 type MockConn struct {
 117         net.Conn
 118 }
 119
 120 func (m *MockConn) Write(b []byte) (int, error) {
 121         return len(b), nil
 122 }
 123
 124 func NewMockConn() *MockConn {
 125         c := &MockConn{}
 126         return c
 127 }
 128
 129 func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) {
 130         return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil
 131 }
 132
 133 func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) {
 134         if config.WorkingDir != "" {
 135                 t.cwd = config.WorkingDir
 136         }
 137         t.env = config.Env
 138         return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil
 139 }
 140
 141 func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
 142         if t.exitCode == 3 {
 143                 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\\\"\""`)
 144         }
 145         if t.exitCode == 4 {
 146                 return errors.New(`panic: standard_init_linux.go:175: exec user process caused "no such file or directory"`)
 147         }
 148         if t.exitCode == 5 {
 149                 return errors.New(`Error response from daemon: Cannot start container 41f26cbc43bcc1280f4323efb1830a394ba8660c9d1c2b564ba42bf7f7694845: [8] System error: no such file or directory`)
 150         }
 151         if t.exitCode == 6 {
 152                 return errors.New(`Error response from daemon: Cannot start container 58099cd76c834f3dc2a4fb76c8028f049ae6d4fdf0ec373e1f2cfea030670c2d: [8] System error: exec: "foobar": executable file not found in $PATH`)
 153         }
 154
 155         if container == "abcde" {
 156                 // t.fn gets executed in ContainerWait
 157                 return nil
 158         } else {
 159                 return errors.New("Invalid container id")
 160         }
 161 }
 162
 163 func (t *TestDockerClient) ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error {
 164         t.stop <- true
 165         return nil
 166 }
 167
 168 func (t *TestDockerClient) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
 169         t.calledWait = true
 170         body := make(chan dockercontainer.ContainerWaitOKBody, 1)
 171         err := make(chan error)
 172         go func() {
 173                 t.fn(t)
 174                 body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.exitCode)}
 175         }()
 176         return body, err
 177 }
 178
 179 func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
 180         if t.exitCode == 2 {
 181                 return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 182         }
 183
 184         if t.imageLoaded == image {
 185                 return dockertypes.ImageInspect{}, nil, nil
 186         } else {
 187                 return dockertypes.ImageInspect{}, nil, errors.New("")
 188         }
 189 }
 190
 191 func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
 192         if t.exitCode == 2 {
 193                 return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
 194         }
 195         _, err := io.Copy(ioutil.Discard, input)
 196         if err != nil {
 197                 return dockertypes.ImageLoadResponse{}, err
 198         } else {
 199                 t.imageLoaded = hwImageId
 200                 return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil
 201         }
 202 }
 203
 204 func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) {
 205         return nil, nil
 206 }
 207
 208 func (client *ArvTestClient) Create(resourceType string,
 209         parameters arvadosclient.Dict,
 210         output interface{}) error {
 211
 212         client.Mutex.Lock()
 213         defer client.Mutex.Unlock()
 214
 215         client.Calls++
 216         client.Content = append(client.Content, parameters)
 217
 218         if resourceType == "logs" {
 219                 et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
 220                 if client.Logs == nil {
 221                         client.Logs = make(map[string]*bytes.Buffer)
 222                 }
 223                 if client.Logs[et] == nil {
 224                         client.Logs[et] = &bytes.Buffer{}
 225                 }
 226                 client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
 227         }
 228
 229         if resourceType == "collections" && output != nil {
 230                 mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
 231                 outmap := output.(*arvados.Collection)
 232                 outmap.PortableDataHash = fmt.Sprintf("%x+%d", md5.Sum([]byte(mt)), len(mt))
 233         }
 234
 235         return nil
 236 }
 237
 238 func (client *ArvTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 239         switch {
 240         case method == "GET" && resourceType == "containers" && action == "auth":
 241                 return json.Unmarshal([]byte(`{
 242                         "kind": "arvados#api_client_authorization",
 243                         "uuid": "`+fakeAuthUUID+`",
 244                         "api_token": "`+fakeAuthToken+`"
 245                         }`), output)
 246         case method == "GET" && resourceType == "containers" && action == "secret_mounts":
 247                 if client.secretMounts != nil {
 248                         return json.Unmarshal(client.secretMounts, output)
 249                 } else {
 250                         return json.Unmarshal([]byte(`{"secret_mounts":{}}`), output)
 251                 }
 252         default:
 253                 return fmt.Errorf("Not found")
 254         }
 255 }
 256
 257 func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
 258         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 259         var j []byte
 260         if method == "GET" && resourceType == "nodes" && uuid == "" && action == "" {
 261                 j = []byte(`{
 262                         "kind": "arvados#nodeList",
 263                         "items": [{
 264                                 "uuid": "zzzzz-7ekkf-2z3mc76g2q73aio",
 265                                 "hostname": "compute2",
 266                                 "properties": {"total_cpu_cores": 16}
 267                         }]}`)
 268         } else if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
 269                 if uuid == "" {
 270                         j, err = json.Marshal(map[string]interface{}{
 271                                 "items": []interface{}{client.Container},
 272                                 "kind":  "arvados#nodeList",
 273                         })
 274                 } else {
 275                         j, err = json.Marshal(client.Container)
 276                 }
 277         } else {
 278                 j = []byte(`{
 279                         "command": ["sleep", "1"],
 280                         "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 281                         "cwd": ".",
 282                         "environment": {},
 283                         "mounts": {"/tmp": {"kind": "tmp"}, "/json": {"kind": "json", "content": {"number": 123456789123456789}}},
 284                         "output_path": "/tmp",
 285                         "priority": 1,
 286                         "runtime_constraints": {}
 287                 }`)
 288         }
 289         return ioutil.NopCloser(bytes.NewReader(j)), err
 290 }
 291
 292 func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 293         if resourceType == "collections" {
 294                 if uuid == hwPDH {
 295                         output.(*arvados.Collection).ManifestText = hwManifest
 296                 } else if uuid == otherPDH {
 297                         output.(*arvados.Collection).ManifestText = otherManifest
 298                 } else if uuid == normalizedWithSubdirsPDH {
 299                         output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs
 300                 } else if uuid == denormalizedWithSubdirsPDH {
 301                         output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs
 302                 }
 303         }
 304         if resourceType == "containers" {
 305                 (*output.(*arvados.Container)) = client.Container
 306         }
 307         return nil
 308 }
 309
 310 func (client *ArvTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 311         client.Mutex.Lock()
 312         defer client.Mutex.Unlock()
 313         client.Calls++
 314         client.Content = append(client.Content, parameters)
 315         if resourceType == "containers" {
 316                 if parameters["container"].(arvadosclient.Dict)["state"] == "Running" {
 317                         client.WasSetRunning = true
 318                 }
 319         }
 320         return nil
 321 }
 322
 323 var discoveryMap = map[string]interface{}{
 324         "defaultTrashLifetime":               float64(1209600),
 325         "crunchLimitLogBytesPerJob":          float64(67108864),
 326         "crunchLogThrottleBytes":             float64(65536),
 327         "crunchLogThrottlePeriod":            float64(60),
 328         "crunchLogThrottleLines":             float64(1024),
 329         "crunchLogPartialLineThrottlePeriod": float64(5),
 330         "crunchLogBytesPerEvent":             float64(4096),
 331         "crunchLogSecondsBetweenEvents":      float64(1),
 332 }
 333
 334 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
 335         return discoveryMap[key], nil
 336 }
 337
 338 // CalledWith returns the parameters from the first API call whose
 339 // parameters match jpath/string. E.g., CalledWith(c, "foo.bar",
 340 // "baz") returns parameters with parameters["foo"]["bar"]=="baz". If
 341 // no call matches, it returns nil.
 342 func (client *ArvTestClient) CalledWith(jpath string, expect interface{}) arvadosclient.Dict {
 343 call:
 344         for _, content := range client.Content {
 345                 var v interface{} = content
 346                 for _, k := range strings.Split(jpath, ".") {
 347                         if dict, ok := v.(arvadosclient.Dict); !ok {
 348                                 continue call
 349                         } else {
 350                                 v = dict[k]
 351                         }
 352                 }
 353                 if v == expect {
 354                         return content
 355                 }
 356         }
 357         return nil
 358 }
 359
 360 func (client *KeepTestClient) PutB(buf []byte) (string, int, error) {
 361         client.Content = buf
 362         return fmt.Sprintf("%x+%d", md5.Sum(buf), len(buf)), len(buf), nil
 363 }
 364
 365 func (client *KeepTestClient) ReadAt(string, []byte, int) (int, error) {
 366         return 0, errors.New("not implemented")
 367 }
 368
 369 func (client *KeepTestClient) ClearBlockCache() {
 370 }
 371
 372 func (client *KeepTestClient) Close() {
 373         client.Content = nil
 374 }
 375
 376 type FileWrapper struct {
 377         io.ReadCloser
 378         len int64
 379 }
 380
 381 func (fw FileWrapper) Readdir(n int) ([]os.FileInfo, error) {
 382         return nil, errors.New("not implemented")
 383 }
 384
 385 func (fw FileWrapper) Seek(int64, int) (int64, error) {
 386         return 0, errors.New("not implemented")
 387 }
 388
 389 func (fw FileWrapper) Size() int64 {
 390         return fw.len
 391 }
 392
 393 func (fw FileWrapper) Stat() (os.FileInfo, error) {
 394         return nil, errors.New("not implemented")
 395 }
 396
 397 func (fw FileWrapper) Truncate(int64) error {
 398         return errors.New("not implemented")
 399 }
 400
 401 func (fw FileWrapper) Write([]byte) (int, error) {
 402         return 0, errors.New("not implemented")
 403 }
 404
 405 func (fw FileWrapper) Sync() error {
 406         return errors.New("not implemented")
 407 }
 408
 409 func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 410         if filename == hwImageId+".tar" {
 411                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 412                 client.Called = true
 413                 return FileWrapper{rdr, 1321984}, nil
 414         } else if filename == "/file1_in_main.txt" {
 415                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 416                 client.Called = true
 417                 return FileWrapper{rdr, 3}, nil
 418         }
 419         return nil, nil
 420 }
 421
 422 func (s *TestSuite) TestLoadImage(c *C) {
 423         kc := &KeepTestClient{}
 424         defer kc.Close()
 425         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 426         c.Assert(err, IsNil)
 427
 428         _, err = cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 429         c.Check(err, IsNil)
 430
 431         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 432         c.Check(err, NotNil)
 433
 434         cr.Container.ContainerImage = hwPDH
 435
 436         // (1) Test loading image from keep
 437         c.Check(kc.Called, Equals, false)
 438         c.Check(cr.ContainerConfig.Image, Equals, "")
 439
 440         err = cr.LoadImage()
 441
 442         c.Check(err, IsNil)
 443         defer func() {
 444                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 445         }()
 446
 447         c.Check(kc.Called, Equals, true)
 448         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 449
 450         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 451         c.Check(err, IsNil)
 452
 453         // (2) Test using image that's already loaded
 454         kc.Called = false
 455         cr.ContainerConfig.Image = ""
 456
 457         err = cr.LoadImage()
 458         c.Check(err, IsNil)
 459         c.Check(kc.Called, Equals, false)
 460         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 461
 462 }
 463
 464 type ArvErrorTestClient struct{}
 465
 466 func (ArvErrorTestClient) Create(resourceType string,
 467         parameters arvadosclient.Dict,
 468         output interface{}) error {
 469         return nil
 470 }
 471
 472 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 473         return errors.New("ArvError")
 474 }
 475
 476 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 477         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 478         return nil, errors.New("ArvError")
 479 }
 480
 481 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 482         return errors.New("ArvError")
 483 }
 484
 485 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 486         return nil
 487 }
 488
 489 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 490         return discoveryMap[key], nil
 491 }
 492
 493 type KeepErrorTestClient struct {
 494         KeepTestClient
 495 }
 496
 497 func (*KeepErrorTestClient) ManifestFileReader(manifest.Manifest, string) (arvados.File, error) {
 498         return nil, errors.New("KeepError")
 499 }
 500
 501 func (*KeepErrorTestClient) PutB(buf []byte) (string, int, error) {
 502         return "", 0, errors.New("KeepError")
 503 }
 504
 505 type KeepReadErrorTestClient struct {
 506         KeepTestClient
 507 }
 508
 509 func (*KeepReadErrorTestClient) ReadAt(string, []byte, int) (int, error) {
 510         return 0, errors.New("KeepError")
 511 }
 512
 513 type ErrorReader struct {
 514         FileWrapper
 515 }
 516
 517 func (ErrorReader) Read(p []byte) (n int, err error) {
 518         return 0, errors.New("ErrorReader")
 519 }
 520
 521 func (ErrorReader) Seek(int64, int) (int64, error) {
 522         return 0, errors.New("ErrorReader")
 523 }
 524
 525 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 526         return ErrorReader{}, nil
 527 }
 528
 529 func (s *TestSuite) TestLoadImageArvError(c *C) {
 530         // (1) Arvados error
 531         kc := &KeepTestClient{}
 532         defer kc.Close()
 533         cr, err := NewContainerRunner(s.client, ArvErrorTestClient{}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 534         c.Assert(err, IsNil)
 535         cr.Container.ContainerImage = hwPDH
 536
 537         err = cr.LoadImage()
 538         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 539 }
 540
 541 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 542         // (2) Keep error
 543         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 544         c.Assert(err, IsNil)
 545         cr.Container.ContainerImage = hwPDH
 546
 547         err = cr.LoadImage()
 548         c.Assert(err, NotNil)
 549         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 550 }
 551
 552 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 553         // (3) Collection doesn't contain image
 554         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepReadErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 555         c.Assert(err, IsNil)
 556         cr.Container.ContainerImage = otherPDH
 557
 558         err = cr.LoadImage()
 559         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 560 }
 561
 562 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 563         // (4) Collection doesn't contain image
 564         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepReadErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 565         c.Assert(err, IsNil)
 566         cr.Container.ContainerImage = hwPDH
 567
 568         err = cr.LoadImage()
 569         c.Check(err, NotNil)
 570 }
 571
 572 type ClosableBuffer struct {
 573         bytes.Buffer
 574 }
 575
 576 func (*ClosableBuffer) Close() error {
 577         return nil
 578 }
 579
 580 type TestLogs struct {
 581         Stdout ClosableBuffer
 582         Stderr ClosableBuffer
 583 }
 584
 585 func (tl *TestLogs) NewTestLoggingWriter(logstr string) (io.WriteCloser, error) {
 586         if logstr == "stdout" {
 587                 return &tl.Stdout, nil
 588         }
 589         if logstr == "stderr" {
 590                 return &tl.Stderr, nil
 591         }
 592         return nil, errors.New("???")
 593 }
 594
 595 func dockerLog(fd byte, msg string) []byte {
 596         by := []byte(msg)
 597         header := make([]byte, 8+len(by))
 598         header[0] = fd
 599         header[7] = byte(len(by))
 600         copy(header[8:], by)
 601         return header
 602 }
 603
 604 func (s *TestSuite) TestRunContainer(c *C) {
 605         s.docker.fn = func(t *TestDockerClient) {
 606                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 607                 t.logWriter.Close()
 608         }
 609         kc := &KeepTestClient{}
 610         defer kc.Close()
 611         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 612         c.Assert(err, IsNil)
 613
 614         var logs TestLogs
 615         cr.NewLogWriter = logs.NewTestLoggingWriter
 616         cr.Container.ContainerImage = hwPDH
 617         cr.Container.Command = []string{"./hw"}
 618         err = cr.LoadImage()
 619         c.Check(err, IsNil)
 620
 621         err = cr.CreateContainer()
 622         c.Check(err, IsNil)
 623
 624         err = cr.StartContainer()
 625         c.Check(err, IsNil)
 626
 627         err = cr.WaitFinish()
 628         c.Check(err, IsNil)
 629
 630         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 631         c.Check(logs.Stderr.String(), Equals, "")
 632 }
 633
 634 func (s *TestSuite) TestCommitLogs(c *C) {
 635         api := &ArvTestClient{}
 636         kc := &KeepTestClient{}
 637         defer kc.Close()
 638         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 639         c.Assert(err, IsNil)
 640         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 641
 642         cr.CrunchLog.Print("Hello world!")
 643         cr.CrunchLog.Print("Goodbye")
 644         cr.finalState = "Complete"
 645
 646         err = cr.CommitLogs()
 647         c.Check(err, IsNil)
 648
 649         c.Check(api.Calls, Equals, 2)
 650         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 651         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 652         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 653         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 654 }
 655
 656 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 657         api := &ArvTestClient{}
 658         kc := &KeepTestClient{}
 659         defer kc.Close()
 660         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 661         c.Assert(err, IsNil)
 662
 663         err = cr.UpdateContainerRunning()
 664         c.Check(err, IsNil)
 665
 666         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 667 }
 668
 669 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 670         api := &ArvTestClient{}
 671         kc := &KeepTestClient{}
 672         defer kc.Close()
 673         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 674         c.Assert(err, IsNil)
 675
 676         cr.LogsPDH = new(string)
 677         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 678
 679         cr.ExitCode = new(int)
 680         *cr.ExitCode = 42
 681         cr.finalState = "Complete"
 682
 683         err = cr.UpdateContainerFinal()
 684         c.Check(err, IsNil)
 685
 686         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 687         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 688         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 689 }
 690
 691 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 692         api := &ArvTestClient{}
 693         kc := &KeepTestClient{}
 694         defer kc.Close()
 695         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 696         c.Assert(err, IsNil)
 697         cr.cCancelled = true
 698         cr.finalState = "Cancelled"
 699
 700         err = cr.UpdateContainerFinal()
 701         c.Check(err, IsNil)
 702
 703         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 704         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 705         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 706 }
 707
 708 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 709 // dress rehearsal of the Run() function, starting from a JSON container record.
 710 func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 711         rec := arvados.Container{}
 712         err := json.Unmarshal([]byte(record), &rec)
 713         c.Check(err, IsNil)
 714
 715         var sm struct {
 716                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
 717         }
 718         err = json.Unmarshal([]byte(record), &sm)
 719         c.Check(err, IsNil)
 720         secretMounts, err := json.Marshal(sm)
 721         c.Logf("%s %q", sm, secretMounts)
 722         c.Check(err, IsNil)
 723
 724         s.docker.exitCode = exitCode
 725         s.docker.fn = fn
 726         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 727
 728         api = &ArvTestClient{Container: rec}
 729         s.docker.api = api
 730         kc := &KeepTestClient{}
 731         defer kc.Close()
 732         cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 733         c.Assert(err, IsNil)
 734         cr.statInterval = 100 * time.Millisecond
 735         am := &ArvMountCmdLine{}
 736         cr.RunArvMount = am.ArvMountTest
 737
 738         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 739         c.Assert(err, IsNil)
 740         defer os.RemoveAll(realTemp)
 741
 742         s.docker.realTemp = realTemp
 743
 744         tempcount := 0
 745         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 746                 tempcount++
 747                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 748                 err := os.Mkdir(d, os.ModePerm)
 749                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 750                         // Test case must have pre-populated the tempdir
 751                         err = nil
 752                 }
 753                 return d, err
 754         }
 755         cr.MkArvClient = func(token string) (IArvadosClient, error) {
 756                 return &ArvTestClient{secretMounts: secretMounts}, nil
 757         }
 758
 759         if extraMounts != nil && len(extraMounts) > 0 {
 760                 err := cr.SetupArvMountPoint("keep")
 761                 c.Check(err, IsNil)
 762
 763                 for _, m := range extraMounts {
 764                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 765                 }
 766         }
 767
 768         err = cr.Run()
 769         if api.CalledWith("container.state", "Complete") != nil {
 770                 c.Check(err, IsNil)
 771         }
 772         if exitCode != 2 {
 773                 c.Check(api.WasSetRunning, Equals, true)
 774                 c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
 775         }
 776
 777         if err != nil {
 778                 for k, v := range api.Logs {
 779                         c.Log(k)
 780                         c.Log(v.String())
 781                 }
 782         }
 783
 784         return
 785 }
 786
 787 func (s *TestSuite) TestFullRunHello(c *C) {
 788         api, _, _ := s.fullRunHelper(c, `{
 789     "command": ["echo", "hello world"],
 790     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 791     "cwd": ".",
 792     "environment": {},
 793     "mounts": {"/tmp": {"kind": "tmp"} },
 794     "output_path": "/tmp",
 795     "priority": 1,
 796     "runtime_constraints": {}
 797 }`, nil, 0, func(t *TestDockerClient) {
 798                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 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         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 805
 806 }
 807
 808 func (s *TestSuite) TestCrunchstat(c *C) {
 809         api, _, _ := s.fullRunHelper(c, `{
 810                 "command": ["sleep", "1"],
 811                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 812                 "cwd": ".",
 813                 "environment": {},
 814                 "mounts": {"/tmp": {"kind": "tmp"} },
 815                 "output_path": "/tmp",
 816                 "priority": 1,
 817                 "runtime_constraints": {}
 818         }`, nil, 0, func(t *TestDockerClient) {
 819                 time.Sleep(time.Second)
 820                 t.logWriter.Close()
 821         })
 822
 823         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 824         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 825
 826         // We didn't actually start a container, so crunchstat didn't
 827         // find accounting files and therefore didn't log any stats.
 828         // It should have logged a "can't find accounting files"
 829         // message after one poll interval, though, so we can confirm
 830         // it's alive:
 831         c.Assert(api.Logs["crunchstat"], NotNil)
 832         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 833
 834         // The "files never appeared" log assures us that we called
 835         // (*crunchstat.Reporter)Stop(), and that we set it up with
 836         // the correct container ID "abcde":
 837         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 838 }
 839
 840 func (s *TestSuite) TestNodeInfoLog(c *C) {
 841         os.Setenv("SLURMD_NODENAME", "compute2")
 842         api, _, _ := s.fullRunHelper(c, `{
 843                 "command": ["sleep", "1"],
 844                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 845                 "cwd": ".",
 846                 "environment": {},
 847                 "mounts": {"/tmp": {"kind": "tmp"} },
 848                 "output_path": "/tmp",
 849                 "priority": 1,
 850                 "runtime_constraints": {}
 851         }`, nil, 0,
 852                 func(t *TestDockerClient) {
 853                         time.Sleep(time.Second)
 854                         t.logWriter.Close()
 855                 })
 856
 857         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 858         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 859
 860         c.Assert(api.Logs["node"], NotNil)
 861         json := api.Logs["node"].String()
 862         c.Check(json, Matches, `(?ms).*"uuid": *"zzzzz-7ekkf-2z3mc76g2q73aio".*`)
 863         c.Check(json, Matches, `(?ms).*"total_cpu_cores": *16.*`)
 864         c.Check(json, Not(Matches), `(?ms).*"info":.*`)
 865
 866         c.Assert(api.Logs["node-info"], NotNil)
 867         json = api.Logs["node-info"].String()
 868         c.Check(json, Matches, `(?ms).*Host Information.*`)
 869         c.Check(json, Matches, `(?ms).*CPU Information.*`)
 870         c.Check(json, Matches, `(?ms).*Memory Information.*`)
 871         c.Check(json, Matches, `(?ms).*Disk Space.*`)
 872         c.Check(json, Matches, `(?ms).*Disk INodes.*`)
 873 }
 874
 875 func (s *TestSuite) TestContainerRecordLog(c *C) {
 876         api, _, _ := s.fullRunHelper(c, `{
 877                 "command": ["sleep", "1"],
 878                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 879                 "cwd": ".",
 880                 "environment": {},
 881                 "mounts": {"/tmp": {"kind": "tmp"} },
 882                 "output_path": "/tmp",
 883                 "priority": 1,
 884                 "runtime_constraints": {}
 885         }`, nil, 0,
 886                 func(t *TestDockerClient) {
 887                         time.Sleep(time.Second)
 888                         t.logWriter.Close()
 889                 })
 890
 891         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 892         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 893
 894         c.Assert(api.Logs["container"], NotNil)
 895         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 896 }
 897
 898 func (s *TestSuite) TestFullRunStderr(c *C) {
 899         api, _, _ := s.fullRunHelper(c, `{
 900     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 901     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 902     "cwd": ".",
 903     "environment": {},
 904     "mounts": {"/tmp": {"kind": "tmp"} },
 905     "output_path": "/tmp",
 906     "priority": 1,
 907     "runtime_constraints": {}
 908 }`, nil, 1, func(t *TestDockerClient) {
 909                 t.logWriter.Write(dockerLog(1, "hello\n"))
 910                 t.logWriter.Write(dockerLog(2, "world\n"))
 911                 t.logWriter.Close()
 912         })
 913
 914         final := api.CalledWith("container.state", "Complete")
 915         c.Assert(final, NotNil)
 916         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 917         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 918
 919         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 920         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 921 }
 922
 923 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 924         api, _, _ := s.fullRunHelper(c, `{
 925     "command": ["pwd"],
 926     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 927     "cwd": ".",
 928     "environment": {},
 929     "mounts": {"/tmp": {"kind": "tmp"} },
 930     "output_path": "/tmp",
 931     "priority": 1,
 932     "runtime_constraints": {}
 933 }`, nil, 0, func(t *TestDockerClient) {
 934                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 935                 t.logWriter.Close()
 936         })
 937
 938         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 939         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 940         c.Log(api.Logs["stdout"])
 941         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 942 }
 943
 944 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 945         api, _, _ := s.fullRunHelper(c, `{
 946     "command": ["pwd"],
 947     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 948     "cwd": "/bin",
 949     "environment": {},
 950     "mounts": {"/tmp": {"kind": "tmp"} },
 951     "output_path": "/tmp",
 952     "priority": 1,
 953     "runtime_constraints": {}
 954 }`, nil, 0, func(t *TestDockerClient) {
 955                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 956                 t.logWriter.Close()
 957         })
 958
 959         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 960         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 961         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 962 }
 963
 964 func (s *TestSuite) TestStopOnSignal(c *C) {
 965         s.testStopContainer(c, func(cr *ContainerRunner) {
 966                 go func() {
 967                         for !s.docker.calledWait {
 968                                 time.Sleep(time.Millisecond)
 969                         }
 970                         cr.SigChan <- syscall.SIGINT
 971                 }()
 972         })
 973 }
 974
 975 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 976         s.testStopContainer(c, func(cr *ContainerRunner) {
 977                 cr.ArvMountExit = make(chan error)
 978                 go func() {
 979                         cr.ArvMountExit <- exec.Command("true").Run()
 980                         close(cr.ArvMountExit)
 981                 }()
 982         })
 983 }
 984
 985 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 986         record := `{
 987     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 988     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 989     "cwd": ".",
 990     "environment": {},
 991     "mounts": {"/tmp": {"kind": "tmp"} },
 992     "output_path": "/tmp",
 993     "priority": 1,
 994     "runtime_constraints": {}
 995 }`
 996
 997         rec := arvados.Container{}
 998         err := json.Unmarshal([]byte(record), &rec)
 999         c.Check(err, IsNil)
1000
1001         s.docker.fn = func(t *TestDockerClient) {
1002                 <-t.stop
1003                 t.logWriter.Write(dockerLog(1, "foo\n"))
1004                 t.logWriter.Close()
1005         }
1006         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1007
1008         api := &ArvTestClient{Container: rec}
1009         kc := &KeepTestClient{}
1010         defer kc.Close()
1011         cr, err := NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1012         c.Assert(err, IsNil)
1013         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
1014         cr.MkArvClient = func(token string) (IArvadosClient, error) {
1015                 return &ArvTestClient{}, nil
1016         }
1017         setup(cr)
1018
1019         done := make(chan error)
1020         go func() {
1021                 done <- cr.Run()
1022         }()
1023         select {
1024         case <-time.After(20 * time.Second):
1025                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
1026                 c.Fatal("timed out")
1027         case err = <-done:
1028                 c.Check(err, IsNil)
1029         }
1030         for k, v := range api.Logs {
1031                 c.Log(k)
1032                 c.Log(v.String())
1033         }
1034
1035         c.Check(api.CalledWith("container.log", nil), NotNil)
1036         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1037         c.Check(api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
1038 }
1039
1040 func (s *TestSuite) TestFullRunSetEnv(c *C) {
1041         api, _, _ := s.fullRunHelper(c, `{
1042     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1043     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1044     "cwd": "/bin",
1045     "environment": {"FROBIZ": "bilbo"},
1046     "mounts": {"/tmp": {"kind": "tmp"} },
1047     "output_path": "/tmp",
1048     "priority": 1,
1049     "runtime_constraints": {}
1050 }`, nil, 0, func(t *TestDockerClient) {
1051                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1052                 t.logWriter.Close()
1053         })
1054
1055         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1056         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1057         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
1058 }
1059
1060 type ArvMountCmdLine struct {
1061         Cmd   []string
1062         token string
1063 }
1064
1065 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
1066         am.Cmd = c
1067         am.token = token
1068         return nil, nil
1069 }
1070
1071 func stubCert(temp string) string {
1072         path := temp + "/ca-certificates.crt"
1073         crt, _ := os.Create(path)
1074         crt.Close()
1075         arvadosclient.CertFiles = []string{path}
1076         return path
1077 }
1078
1079 func (s *TestSuite) TestSetupMounts(c *C) {
1080         api := &ArvTestClient{}
1081         kc := &KeepTestClient{}
1082         defer kc.Close()
1083         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1084         c.Assert(err, IsNil)
1085         am := &ArvMountCmdLine{}
1086         cr.RunArvMount = am.ArvMountTest
1087
1088         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
1089         c.Assert(err, IsNil)
1090         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
1091         c.Assert(err, IsNil)
1092         stubCertPath := stubCert(certTemp)
1093
1094         cr.parentTemp = realTemp
1095
1096         defer os.RemoveAll(realTemp)
1097         defer os.RemoveAll(certTemp)
1098
1099         i := 0
1100         cr.MkTempDir = func(_ string, prefix string) (string, error) {
1101                 i++
1102                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
1103                 err := os.Mkdir(d, os.ModePerm)
1104                 if err != nil && strings.Contains(err.Error(), ": file exists") {
1105                         // Test case must have pre-populated the tempdir
1106                         err = nil
1107                 }
1108                 return d, err
1109         }
1110
1111         checkEmpty := func() {
1112                 // Should be deleted.
1113                 _, err := os.Stat(realTemp)
1114                 c.Assert(os.IsNotExist(err), Equals, true)
1115
1116                 // Now recreate it for the next test.
1117                 c.Assert(os.Mkdir(realTemp, 0777), IsNil)
1118         }
1119
1120         {
1121                 i = 0
1122                 cr.ArvMountPoint = ""
1123                 cr.Container.Mounts = make(map[string]arvados.Mount)
1124                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1125                 cr.OutputPath = "/tmp"
1126                 cr.statInterval = 5 * time.Second
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-by-pdh", "by_id", realTemp + "/keep1"})
1132                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
1133                 os.RemoveAll(cr.ArvMountPoint)
1134                 cr.CleanupDirs()
1135                 checkEmpty()
1136         }
1137
1138         {
1139                 i = 0
1140                 cr.ArvMountPoint = ""
1141                 cr.Container.Mounts = make(map[string]arvados.Mount)
1142                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
1143                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1144                 cr.OutputPath = "/out"
1145
1146                 err := cr.SetupMounts()
1147                 c.Check(err, IsNil)
1148                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1149                         "--read-write", "--crunchstat-interval=5",
1150                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1151                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
1152                 os.RemoveAll(cr.ArvMountPoint)
1153                 cr.CleanupDirs()
1154                 checkEmpty()
1155         }
1156
1157         {
1158                 i = 0
1159                 cr.ArvMountPoint = ""
1160                 cr.Container.Mounts = make(map[string]arvados.Mount)
1161                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1162                 cr.OutputPath = "/tmp"
1163
1164                 apiflag := true
1165                 cr.Container.RuntimeConstraints.API = &apiflag
1166
1167                 err := cr.SetupMounts()
1168                 c.Check(err, IsNil)
1169                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1170                         "--read-write", "--crunchstat-interval=5",
1171                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1172                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1173                 os.RemoveAll(cr.ArvMountPoint)
1174                 cr.CleanupDirs()
1175                 checkEmpty()
1176
1177                 apiflag = false
1178         }
1179
1180         {
1181                 i = 0
1182                 cr.ArvMountPoint = ""
1183                 cr.Container.Mounts = map[string]arvados.Mount{
1184                         "/keeptmp": {Kind: "collection", Writable: true},
1185                 }
1186                 cr.OutputPath = "/keeptmp"
1187
1188                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1189
1190                 err := cr.SetupMounts()
1191                 c.Check(err, IsNil)
1192                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1193                         "--read-write", "--crunchstat-interval=5",
1194                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1195                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1196                 os.RemoveAll(cr.ArvMountPoint)
1197                 cr.CleanupDirs()
1198                 checkEmpty()
1199         }
1200
1201         {
1202                 i = 0
1203                 cr.ArvMountPoint = ""
1204                 cr.Container.Mounts = map[string]arvados.Mount{
1205                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1206                         "/keepout": {Kind: "collection", Writable: true},
1207                 }
1208                 cr.OutputPath = "/keepout"
1209
1210                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1211                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1212
1213                 err := cr.SetupMounts()
1214                 c.Check(err, IsNil)
1215                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1216                         "--read-write", "--crunchstat-interval=5",
1217                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1218                 sort.StringSlice(cr.Binds).Sort()
1219                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1220                         realTemp + "/keep1/tmp0:/keepout"})
1221                 os.RemoveAll(cr.ArvMountPoint)
1222                 cr.CleanupDirs()
1223                 checkEmpty()
1224         }
1225
1226         {
1227                 i = 0
1228                 cr.ArvMountPoint = ""
1229                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1230                 cr.Container.Mounts = map[string]arvados.Mount{
1231                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1232                         "/keepout": {Kind: "collection", Writable: true},
1233                 }
1234                 cr.OutputPath = "/keepout"
1235
1236                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1237                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1238
1239                 err := cr.SetupMounts()
1240                 c.Check(err, IsNil)
1241                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1242                         "--read-write", "--crunchstat-interval=5",
1243                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1244                 sort.StringSlice(cr.Binds).Sort()
1245                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1246                         realTemp + "/keep1/tmp0:/keepout"})
1247                 os.RemoveAll(cr.ArvMountPoint)
1248                 cr.CleanupDirs()
1249                 checkEmpty()
1250         }
1251
1252         for _, test := range []struct {
1253                 in  interface{}
1254                 out string
1255         }{
1256                 {in: "foo", out: `"foo"`},
1257                 {in: nil, out: `null`},
1258                 {in: map[string]int64{"foo": 123456789123456789}, out: `{"foo":123456789123456789}`},
1259         } {
1260                 i = 0
1261                 cr.ArvMountPoint = ""
1262                 cr.Container.Mounts = map[string]arvados.Mount{
1263                         "/mnt/test.json": {Kind: "json", Content: test.in},
1264                 }
1265                 err := cr.SetupMounts()
1266                 c.Check(err, IsNil)
1267                 sort.StringSlice(cr.Binds).Sort()
1268                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
1269                 content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
1270                 c.Check(err, IsNil)
1271                 c.Check(content, DeepEquals, []byte(test.out))
1272                 os.RemoveAll(cr.ArvMountPoint)
1273                 cr.CleanupDirs()
1274                 checkEmpty()
1275         }
1276
1277         for _, test := range []struct {
1278                 in  interface{}
1279                 out string
1280         }{
1281                 {in: "foo", out: `foo`},
1282                 {in: nil, out: "error"},
1283                 {in: map[string]int64{"foo": 123456789123456789}, out: "error"},
1284         } {
1285                 i = 0
1286                 cr.ArvMountPoint = ""
1287                 cr.Container.Mounts = map[string]arvados.Mount{
1288                         "/mnt/test.txt": {Kind: "text", Content: test.in},
1289                 }
1290                 err := cr.SetupMounts()
1291                 if test.out == "error" {
1292                         c.Check(err.Error(), Equals, "content for mount \"/mnt/test.txt\" must be a string")
1293                 } else {
1294                         c.Check(err, IsNil)
1295                         sort.StringSlice(cr.Binds).Sort()
1296                         c.Check(cr.Binds, DeepEquals, []string{realTemp + "/text2/mountdata.text:/mnt/test.txt:ro"})
1297                         content, err := ioutil.ReadFile(realTemp + "/text2/mountdata.text")
1298                         c.Check(err, IsNil)
1299                         c.Check(content, DeepEquals, []byte(test.out))
1300                 }
1301                 os.RemoveAll(cr.ArvMountPoint)
1302                 cr.CleanupDirs()
1303                 checkEmpty()
1304         }
1305
1306         // Read-only mount points are allowed underneath output_dir mount point
1307         {
1308                 i = 0
1309                 cr.ArvMountPoint = ""
1310                 cr.Container.Mounts = make(map[string]arvados.Mount)
1311                 cr.Container.Mounts = map[string]arvados.Mount{
1312                         "/tmp":     {Kind: "tmp"},
1313                         "/tmp/foo": {Kind: "collection"},
1314                 }
1315                 cr.OutputPath = "/tmp"
1316
1317                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1318
1319                 err := cr.SetupMounts()
1320                 c.Check(err, IsNil)
1321                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1322                         "--read-write", "--crunchstat-interval=5",
1323                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1324                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1325                 os.RemoveAll(cr.ArvMountPoint)
1326                 cr.CleanupDirs()
1327                 checkEmpty()
1328         }
1329
1330         // Writable mount points copied to output_dir mount point
1331         {
1332                 i = 0
1333                 cr.ArvMountPoint = ""
1334                 cr.Container.Mounts = make(map[string]arvados.Mount)
1335                 cr.Container.Mounts = map[string]arvados.Mount{
1336                         "/tmp": {Kind: "tmp"},
1337                         "/tmp/foo": {Kind: "collection",
1338                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53",
1339                                 Writable:         true},
1340                         "/tmp/bar": {Kind: "collection",
1341                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541d+53",
1342                                 Path:             "baz",
1343                                 Writable:         true},
1344                 }
1345                 cr.OutputPath = "/tmp"
1346
1347                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1348                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz", os.ModePerm)
1349
1350                 rf, _ := os.Create(realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz/quux")
1351                 rf.Write([]byte("bar"))
1352                 rf.Close()
1353
1354                 err := cr.SetupMounts()
1355                 c.Check(err, IsNil)
1356                 _, err = os.Stat(cr.HostOutputDir + "/foo")
1357                 c.Check(err, IsNil)
1358                 _, err = os.Stat(cr.HostOutputDir + "/bar/quux")
1359                 c.Check(err, IsNil)
1360                 os.RemoveAll(cr.ArvMountPoint)
1361                 cr.CleanupDirs()
1362                 checkEmpty()
1363         }
1364
1365         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1366         {
1367                 i = 0
1368                 cr.ArvMountPoint = ""
1369                 cr.Container.Mounts = make(map[string]arvados.Mount)
1370                 cr.Container.Mounts = map[string]arvados.Mount{
1371                         "/tmp":     {Kind: "tmp"},
1372                         "/tmp/foo": {Kind: "tmp"},
1373                 }
1374                 cr.OutputPath = "/tmp"
1375
1376                 err := cr.SetupMounts()
1377                 c.Check(err, NotNil)
1378                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path.*`)
1379                 os.RemoveAll(cr.ArvMountPoint)
1380                 cr.CleanupDirs()
1381                 checkEmpty()
1382         }
1383
1384         // Only mount point of kind 'collection' is allowed for stdin
1385         {
1386                 i = 0
1387                 cr.ArvMountPoint = ""
1388                 cr.Container.Mounts = make(map[string]arvados.Mount)
1389                 cr.Container.Mounts = map[string]arvados.Mount{
1390                         "stdin": {Kind: "tmp"},
1391                 }
1392
1393                 err := cr.SetupMounts()
1394                 c.Check(err, NotNil)
1395                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1396                 os.RemoveAll(cr.ArvMountPoint)
1397                 cr.CleanupDirs()
1398                 checkEmpty()
1399         }
1400
1401         // git_tree mounts
1402         {
1403                 i = 0
1404                 cr.ArvMountPoint = ""
1405                 (*GitMountSuite)(nil).useTestGitServer(c)
1406                 cr.token = arvadostest.ActiveToken
1407                 cr.Container.Mounts = make(map[string]arvados.Mount)
1408                 cr.Container.Mounts = map[string]arvados.Mount{
1409                         "/tip": {
1410                                 Kind:   "git_tree",
1411                                 UUID:   arvadostest.Repository2UUID,
1412                                 Commit: "fd3531f42995344f36c30b79f55f27b502f3d344",
1413                                 Path:   "/",
1414                         },
1415                         "/non-tip": {
1416                                 Kind:   "git_tree",
1417                                 UUID:   arvadostest.Repository2UUID,
1418                                 Commit: "5ebfab0522851df01fec11ec55a6d0f4877b542e",
1419                                 Path:   "/",
1420                         },
1421                 }
1422                 cr.OutputPath = "/tmp"
1423
1424                 err := cr.SetupMounts()
1425                 c.Check(err, IsNil)
1426
1427                 // dirMap[mountpoint] == tmpdir
1428                 dirMap := make(map[string]string)
1429                 for _, bind := range cr.Binds {
1430                         tokens := strings.Split(bind, ":")
1431                         dirMap[tokens[1]] = tokens[0]
1432
1433                         if cr.Container.Mounts[tokens[1]].Writable {
1434                                 c.Check(len(tokens), Equals, 2)
1435                         } else {
1436                                 c.Check(len(tokens), Equals, 3)
1437                                 c.Check(tokens[2], Equals, "ro")
1438                         }
1439                 }
1440
1441                 data, err := ioutil.ReadFile(dirMap["/tip"] + "/dir1/dir2/file with mode 0644")
1442                 c.Check(err, IsNil)
1443                 c.Check(string(data), Equals, "\000\001\002\003")
1444                 _, err = ioutil.ReadFile(dirMap["/tip"] + "/file only on testbranch")
1445                 c.Check(err, FitsTypeOf, &os.PathError{})
1446                 c.Check(os.IsNotExist(err), Equals, true)
1447
1448                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/dir1/dir2/file with mode 0644")
1449                 c.Check(err, IsNil)
1450                 c.Check(string(data), Equals, "\000\001\002\003")
1451                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/file only on testbranch")
1452                 c.Check(err, IsNil)
1453                 c.Check(string(data), Equals, "testfile\n")
1454
1455                 cr.CleanupDirs()
1456                 checkEmpty()
1457         }
1458 }
1459
1460 func (s *TestSuite) TestStdout(c *C) {
1461         helperRecord := `{
1462                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1463                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1464                 "cwd": "/bin",
1465                 "environment": {"FROBIZ": "bilbo"},
1466                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1467                 "output_path": "/tmp",
1468                 "priority": 1,
1469                 "runtime_constraints": {}
1470         }`
1471
1472         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1473                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1474                 t.logWriter.Close()
1475         })
1476
1477         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1478         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1479         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1480 }
1481
1482 // Used by the TestStdoutWithWrongPath*()
1483 func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1484         rec := arvados.Container{}
1485         err = json.Unmarshal([]byte(record), &rec)
1486         c.Check(err, IsNil)
1487
1488         s.docker.fn = fn
1489         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1490
1491         api = &ArvTestClient{Container: rec}
1492         kc := &KeepTestClient{}
1493         defer kc.Close()
1494         cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1495         c.Assert(err, IsNil)
1496         am := &ArvMountCmdLine{}
1497         cr.RunArvMount = am.ArvMountTest
1498         cr.MkArvClient = func(token string) (IArvadosClient, error) {
1499                 return &ArvTestClient{}, nil
1500         }
1501
1502         err = cr.Run()
1503         return
1504 }
1505
1506 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1507         _, _, err := s.stdoutErrorRunHelper(c, `{
1508     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1509     "output_path": "/tmp"
1510 }`, func(t *TestDockerClient) {})
1511
1512         c.Check(err, NotNil)
1513         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1514 }
1515
1516 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1517         _, _, err := s.stdoutErrorRunHelper(c, `{
1518     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1519     "output_path": "/tmp"
1520 }`, func(t *TestDockerClient) {})
1521
1522         c.Check(err, NotNil)
1523         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1524 }
1525
1526 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1527         _, _, err := s.stdoutErrorRunHelper(c, `{
1528     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1529     "output_path": "/tmp"
1530 }`, func(t *TestDockerClient) {})
1531
1532         c.Check(err, NotNil)
1533         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1534 }
1535
1536 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1537         defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
1538         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1539         api, _, _ := s.fullRunHelper(c, `{
1540     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1541     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1542     "cwd": "/bin",
1543     "environment": {},
1544     "mounts": {"/tmp": {"kind": "tmp"} },
1545     "output_path": "/tmp",
1546     "priority": 1,
1547     "runtime_constraints": {"API": true}
1548 }`, nil, 0, func(t *TestDockerClient) {
1549                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1550                 t.logWriter.Close()
1551         })
1552
1553         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1554         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1555         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1556         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1557 }
1558
1559 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1560         defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
1561         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1562         api, _, _ := s.fullRunHelper(c, `{
1563     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1564     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1565     "cwd": "/bin",
1566     "environment": {},
1567     "mounts": {"/tmp": {"kind": "tmp"} },
1568     "output_path": "/tmp",
1569     "priority": 1,
1570     "runtime_constraints": {"API": true}
1571 }`, nil, 0, func(t *TestDockerClient) {
1572                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1573                 t.logWriter.Close()
1574         })
1575
1576         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1577         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1578         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1579 }
1580
1581 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1582         helperRecord := `{
1583                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1584                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1585                 "cwd": "/bin",
1586                 "environment": {"FROBIZ": "bilbo"},
1587                 "mounts": {
1588         "/tmp": {"kind": "tmp"},
1589         "/tmp/foo": {"kind": "collection",
1590                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1591                      "exclude_from_output": true
1592         },
1593         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1594     },
1595                 "output_path": "/tmp",
1596                 "priority": 1,
1597                 "runtime_constraints": {}
1598         }`
1599
1600         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1601
1602         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1603                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1604                 t.logWriter.Close()
1605         })
1606
1607         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1608         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1609         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1610 }
1611
1612 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(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         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1621         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1622         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1623         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1624         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1625     },
1626                 "output_path": "/tmp",
1627                 "priority": 1,
1628                 "runtime_constraints": {}
1629         }`
1630
1631         extraMounts := []string{
1632                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1633                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1634                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1635         }
1636
1637         api, runner, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1638                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1639                 t.logWriter.Close()
1640         })
1641
1642         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
1643                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1644                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1645                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1646                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1647         })
1648
1649         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1650         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1651         for _, v := range api.Content {
1652                 if v["collection"] != nil {
1653                         c.Check(v["ensure_unique_name"], Equals, true)
1654                         collection := v["collection"].(arvadosclient.Dict)
1655                         if strings.Index(collection["name"].(string), "output") == 0 {
1656                                 manifest := collection["manifest_text"].(string)
1657
1658                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1659 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:bar 36:18:sub1file2
1660 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1661 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1662 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1663 `)
1664                         }
1665                 }
1666         }
1667 }
1668
1669 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1670         helperRecord := `{
1671                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1672                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1673                 "cwd": "/bin",
1674                 "environment": {"FROBIZ": "bilbo"},
1675                 "mounts": {
1676         "/tmp": {"kind": "tmp"},
1677         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
1678         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1679     },
1680                 "output_path": "/tmp",
1681                 "priority": 1,
1682                 "runtime_constraints": {}
1683         }`
1684
1685         extraMounts := []string{
1686                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1687         }
1688
1689         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1690                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1691                 t.logWriter.Close()
1692         })
1693
1694         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1695         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1696         for _, v := range api.Content {
1697                 if v["collection"] != nil {
1698                         collection := v["collection"].(arvadosclient.Dict)
1699                         if strings.Index(collection["name"].(string), "output") == 0 {
1700                                 manifest := collection["manifest_text"].(string)
1701
1702                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1703 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1704 `)
1705                         }
1706                 }
1707         }
1708 }
1709
1710 func (s *TestSuite) TestOutputError(c *C) {
1711         helperRecord := `{
1712                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1713                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1714                 "cwd": "/bin",
1715                 "environment": {"FROBIZ": "bilbo"},
1716                 "mounts": {
1717         "/tmp": {"kind": "tmp"}
1718     },
1719                 "output_path": "/tmp",
1720                 "priority": 1,
1721                 "runtime_constraints": {}
1722         }`
1723
1724         extraMounts := []string{}
1725
1726         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1727                 os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
1728                 t.logWriter.Close()
1729         })
1730
1731         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1732 }
1733
1734 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1735         helperRecord := `{
1736                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1737                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1738                 "cwd": "/bin",
1739                 "environment": {"FROBIZ": "bilbo"},
1740                 "mounts": {
1741         "/tmp": {"kind": "tmp"},
1742         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1743         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1744     },
1745                 "output_path": "/tmp",
1746                 "priority": 1,
1747                 "runtime_constraints": {}
1748         }`
1749
1750         extraMounts := []string{
1751                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1752         }
1753
1754         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1755                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1756                 t.logWriter.Close()
1757         })
1758
1759         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1760         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1761         for _, v := range api.Content {
1762                 if v["collection"] != nil {
1763                         collection := v["collection"].(arvadosclient.Dict)
1764                         if strings.Index(collection["name"].(string), "output") == 0 {
1765                                 manifest := collection["manifest_text"].(string)
1766                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1767 `)
1768                         }
1769                 }
1770         }
1771 }
1772
1773 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1774         helperRecord := `{
1775                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1776                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1777                 "cwd": "/bin",
1778                 "environment": {"FROBIZ": "bilbo"},
1779                 "mounts": {
1780         "/tmp": {"kind": "tmp"},
1781         "stdin": {"kind": "json", "content": "foo"},
1782         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1783     },
1784                 "output_path": "/tmp",
1785                 "priority": 1,
1786                 "runtime_constraints": {}
1787         }`
1788
1789         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1790                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1791                 t.logWriter.Close()
1792         })
1793
1794         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1795         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1796         for _, v := range api.Content {
1797                 if v["collection"] != nil {
1798                         collection := v["collection"].(arvadosclient.Dict)
1799                         if strings.Index(collection["name"].(string), "output") == 0 {
1800                                 manifest := collection["manifest_text"].(string)
1801                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1802 `)
1803                         }
1804                 }
1805         }
1806 }
1807
1808 func (s *TestSuite) TestStderrMount(c *C) {
1809         api, _, _ := s.fullRunHelper(c, `{
1810     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1811     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1812     "cwd": ".",
1813     "environment": {},
1814     "mounts": {"/tmp": {"kind": "tmp"},
1815                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1816                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1817     "output_path": "/tmp",
1818     "priority": 1,
1819     "runtime_constraints": {}
1820 }`, nil, 1, func(t *TestDockerClient) {
1821                 t.logWriter.Write(dockerLog(1, "hello\n"))
1822                 t.logWriter.Write(dockerLog(2, "oops\n"))
1823                 t.logWriter.Close()
1824         })
1825
1826         final := api.CalledWith("container.state", "Complete")
1827         c.Assert(final, NotNil)
1828         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1829         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1830
1831         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1832 }
1833
1834 func (s *TestSuite) TestNumberRoundTrip(c *C) {
1835         kc := &KeepTestClient{}
1836         defer kc.Close()
1837         cr, err := NewContainerRunner(s.client, &ArvTestClient{callraw: true}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1838         c.Assert(err, IsNil)
1839         cr.fetchContainerRecord()
1840
1841         jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
1842
1843         c.Check(err, IsNil)
1844         c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
1845 }
1846
1847 func (s *TestSuite) TestFullBrokenDocker1(c *C) {
1848         tf, err := ioutil.TempFile("", "brokenNodeHook-")
1849         c.Assert(err, IsNil)
1850         defer os.Remove(tf.Name())
1851
1852         tf.Write([]byte(`#!/bin/sh
1853 exec echo killme
1854 `))
1855         tf.Close()
1856         os.Chmod(tf.Name(), 0700)
1857
1858         ech := tf.Name()
1859         brokenNodeHook = &ech
1860
1861         api, _, _ := s.fullRunHelper(c, `{
1862     "command": ["echo", "hello world"],
1863     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1864     "cwd": ".",
1865     "environment": {},
1866     "mounts": {"/tmp": {"kind": "tmp"} },
1867     "output_path": "/tmp",
1868     "priority": 1,
1869     "runtime_constraints": {}
1870 }`, nil, 2, func(t *TestDockerClient) {
1871                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1872                 t.logWriter.Close()
1873         })
1874
1875         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1876         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1877         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
1878         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
1879
1880 }
1881
1882 func (s *TestSuite) TestFullBrokenDocker2(c *C) {
1883         ech := ""
1884         brokenNodeHook = &ech
1885
1886         api, _, _ := s.fullRunHelper(c, `{
1887     "command": ["echo", "hello world"],
1888     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1889     "cwd": ".",
1890     "environment": {},
1891     "mounts": {"/tmp": {"kind": "tmp"} },
1892     "output_path": "/tmp",
1893     "priority": 1,
1894     "runtime_constraints": {}
1895 }`, nil, 2, func(t *TestDockerClient) {
1896                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1897                 t.logWriter.Close()
1898         })
1899
1900         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1901         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1902         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
1903 }
1904
1905 func (s *TestSuite) TestFullBrokenDocker3(c *C) {
1906         ech := ""
1907         brokenNodeHook = &ech
1908
1909         api, _, _ := s.fullRunHelper(c, `{
1910     "command": ["echo", "hello world"],
1911     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1912     "cwd": ".",
1913     "environment": {},
1914     "mounts": {"/tmp": {"kind": "tmp"} },
1915     "output_path": "/tmp",
1916     "priority": 1,
1917     "runtime_constraints": {}
1918 }`, nil, 3, func(t *TestDockerClient) {
1919                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1920                 t.logWriter.Close()
1921         })
1922
1923         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1924         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1925 }
1926
1927 func (s *TestSuite) TestBadCommand1(c *C) {
1928         ech := ""
1929         brokenNodeHook = &ech
1930
1931         api, _, _ := s.fullRunHelper(c, `{
1932     "command": ["echo", "hello world"],
1933     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1934     "cwd": ".",
1935     "environment": {},
1936     "mounts": {"/tmp": {"kind": "tmp"} },
1937     "output_path": "/tmp",
1938     "priority": 1,
1939     "runtime_constraints": {}
1940 }`, nil, 4, func(t *TestDockerClient) {
1941                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1942                 t.logWriter.Close()
1943         })
1944
1945         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1946         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1947 }
1948
1949 func (s *TestSuite) TestBadCommand2(c *C) {
1950         ech := ""
1951         brokenNodeHook = &ech
1952
1953         api, _, _ := s.fullRunHelper(c, `{
1954     "command": ["echo", "hello world"],
1955     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1956     "cwd": ".",
1957     "environment": {},
1958     "mounts": {"/tmp": {"kind": "tmp"} },
1959     "output_path": "/tmp",
1960     "priority": 1,
1961     "runtime_constraints": {}
1962 }`, nil, 5, func(t *TestDockerClient) {
1963                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1964                 t.logWriter.Close()
1965         })
1966
1967         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1968         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1969 }
1970
1971 func (s *TestSuite) TestBadCommand3(c *C) {
1972         ech := ""
1973         brokenNodeHook = &ech
1974
1975         api, _, _ := s.fullRunHelper(c, `{
1976     "command": ["echo", "hello world"],
1977     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1978     "cwd": ".",
1979     "environment": {},
1980     "mounts": {"/tmp": {"kind": "tmp"} },
1981     "output_path": "/tmp",
1982     "priority": 1,
1983     "runtime_constraints": {}
1984 }`, nil, 6, func(t *TestDockerClient) {
1985                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1986                 t.logWriter.Close()
1987         })
1988
1989         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1990         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1991 }
1992
1993 func (s *TestSuite) TestSecretTextMountPoint(c *C) {
1994         // under normal mounts, gets captured in output, oops
1995         helperRecord := `{
1996                 "command": ["true"],
1997                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1998                 "cwd": "/bin",
1999                 "mounts": {
2000                     "/tmp": {"kind": "tmp"},
2001                     "/tmp/secret.conf": {"kind": "text", "content": "mypassword"}
2002                 },
2003                 "secret_mounts": {
2004                 },
2005                 "output_path": "/tmp",
2006                 "priority": 1,
2007                 "runtime_constraints": {}
2008         }`
2009
2010         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
2011                 content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
2012                 c.Check(err, IsNil)
2013                 c.Check(content, DeepEquals, []byte("mypassword"))
2014                 t.logWriter.Close()
2015         })
2016
2017         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
2018         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
2019         c.Check(api.CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), NotNil)
2020         c.Check(api.CalledWith("collection.manifest_text", ""), IsNil)
2021
2022         // under secret mounts, not captured in output
2023         helperRecord = `{
2024                 "command": ["true"],
2025                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
2026                 "cwd": "/bin",
2027                 "mounts": {
2028                     "/tmp": {"kind": "tmp"}
2029                 },
2030                 "secret_mounts": {
2031                     "/tmp/secret.conf": {"kind": "text", "content": "mypassword"}
2032                 },
2033                 "output_path": "/tmp",
2034                 "priority": 1,
2035                 "runtime_constraints": {}
2036         }`
2037
2038         api, _, _ = s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
2039                 content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
2040                 c.Check(err, IsNil)
2041                 c.Check(content, DeepEquals, []byte("mypassword"))
2042                 t.logWriter.Close()
2043         })
2044
2045         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
2046         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
2047         c.Check(api.CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), IsNil)
2048         c.Check(api.CalledWith("collection.manifest_text", ""), NotNil)
2049 }