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 (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 406         if filename == hwImageId+".tar" {
 407                 rdr := ioutil.NopCloser(&bytes.Buffer{})
 408                 client.Called = true
 409                 return FileWrapper{rdr, 1321984}, nil
 410         } else if filename == "/file1_in_main.txt" {
 411                 rdr := ioutil.NopCloser(strings.NewReader("foo"))
 412                 client.Called = true
 413                 return FileWrapper{rdr, 3}, nil
 414         }
 415         return nil, nil
 416 }
 417
 418 func (s *TestSuite) TestLoadImage(c *C) {
 419         kc := &KeepTestClient{}
 420         defer kc.Close()
 421         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 422         c.Assert(err, IsNil)
 423
 424         _, err = cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 425         c.Check(err, IsNil)
 426
 427         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 428         c.Check(err, NotNil)
 429
 430         cr.Container.ContainerImage = hwPDH
 431
 432         // (1) Test loading image from keep
 433         c.Check(kc.Called, Equals, false)
 434         c.Check(cr.ContainerConfig.Image, Equals, "")
 435
 436         err = cr.LoadImage()
 437
 438         c.Check(err, IsNil)
 439         defer func() {
 440                 cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 441         }()
 442
 443         c.Check(kc.Called, Equals, true)
 444         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 445
 446         _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId)
 447         c.Check(err, IsNil)
 448
 449         // (2) Test using image that's already loaded
 450         kc.Called = false
 451         cr.ContainerConfig.Image = ""
 452
 453         err = cr.LoadImage()
 454         c.Check(err, IsNil)
 455         c.Check(kc.Called, Equals, false)
 456         c.Check(cr.ContainerConfig.Image, Equals, hwImageId)
 457
 458 }
 459
 460 type ArvErrorTestClient struct{}
 461
 462 func (ArvErrorTestClient) Create(resourceType string,
 463         parameters arvadosclient.Dict,
 464         output interface{}) error {
 465         return nil
 466 }
 467
 468 func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error {
 469         return errors.New("ArvError")
 470 }
 471
 472 func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string,
 473         parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
 474         return nil, errors.New("ArvError")
 475 }
 476
 477 func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error {
 478         return errors.New("ArvError")
 479 }
 480
 481 func (ArvErrorTestClient) Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) {
 482         return nil
 483 }
 484
 485 func (ArvErrorTestClient) Discovery(key string) (interface{}, error) {
 486         return discoveryMap[key], nil
 487 }
 488
 489 type KeepErrorTestClient struct {
 490         KeepTestClient
 491 }
 492
 493 func (*KeepErrorTestClient) ManifestFileReader(manifest.Manifest, string) (arvados.File, error) {
 494         return nil, errors.New("KeepError")
 495 }
 496
 497 func (*KeepErrorTestClient) PutB(buf []byte) (string, int, error) {
 498         return "", 0, errors.New("KeepError")
 499 }
 500
 501 type KeepReadErrorTestClient struct {
 502         KeepTestClient
 503 }
 504
 505 func (*KeepReadErrorTestClient) ReadAt(string, []byte, int) (int, error) {
 506         return 0, errors.New("KeepError")
 507 }
 508
 509 type ErrorReader struct {
 510         FileWrapper
 511 }
 512
 513 func (ErrorReader) Read(p []byte) (n int, err error) {
 514         return 0, errors.New("ErrorReader")
 515 }
 516
 517 func (ErrorReader) Seek(int64, int) (int64, error) {
 518         return 0, errors.New("ErrorReader")
 519 }
 520
 521 func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
 522         return ErrorReader{}, nil
 523 }
 524
 525 func (s *TestSuite) TestLoadImageArvError(c *C) {
 526         // (1) Arvados error
 527         kc := &KeepTestClient{}
 528         defer kc.Close()
 529         cr, err := NewContainerRunner(s.client, ArvErrorTestClient{}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 530         c.Assert(err, IsNil)
 531         cr.Container.ContainerImage = hwPDH
 532
 533         err = cr.LoadImage()
 534         c.Check(err.Error(), Equals, "While getting container image collection: ArvError")
 535 }
 536
 537 func (s *TestSuite) TestLoadImageKeepError(c *C) {
 538         // (2) Keep error
 539         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 540         c.Assert(err, IsNil)
 541         cr.Container.ContainerImage = hwPDH
 542
 543         err = cr.LoadImage()
 544         c.Assert(err, NotNil)
 545         c.Check(err.Error(), Equals, "While creating ManifestFileReader for container image: KeepError")
 546 }
 547
 548 func (s *TestSuite) TestLoadImageCollectionError(c *C) {
 549         // (3) Collection doesn't contain image
 550         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepReadErrorTestClient{}, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 551         c.Assert(err, IsNil)
 552         cr.Container.ContainerImage = otherPDH
 553
 554         err = cr.LoadImage()
 555         c.Check(err.Error(), Equals, "First file in the container image collection does not end in .tar")
 556 }
 557
 558 func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
 559         // (4) Collection doesn't contain image
 560         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, &KeepReadErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 561         c.Assert(err, IsNil)
 562         cr.Container.ContainerImage = hwPDH
 563
 564         err = cr.LoadImage()
 565         c.Check(err, NotNil)
 566 }
 567
 568 type ClosableBuffer struct {
 569         bytes.Buffer
 570 }
 571
 572 func (*ClosableBuffer) Close() error {
 573         return nil
 574 }
 575
 576 type TestLogs struct {
 577         Stdout ClosableBuffer
 578         Stderr ClosableBuffer
 579 }
 580
 581 func (tl *TestLogs) NewTestLoggingWriter(logstr string) (io.WriteCloser, error) {
 582         if logstr == "stdout" {
 583                 return &tl.Stdout, nil
 584         }
 585         if logstr == "stderr" {
 586                 return &tl.Stderr, nil
 587         }
 588         return nil, errors.New("???")
 589 }
 590
 591 func dockerLog(fd byte, msg string) []byte {
 592         by := []byte(msg)
 593         header := make([]byte, 8+len(by))
 594         header[0] = fd
 595         header[7] = byte(len(by))
 596         copy(header[8:], by)
 597         return header
 598 }
 599
 600 func (s *TestSuite) TestRunContainer(c *C) {
 601         s.docker.fn = func(t *TestDockerClient) {
 602                 t.logWriter.Write(dockerLog(1, "Hello world\n"))
 603                 t.logWriter.Close()
 604         }
 605         kc := &KeepTestClient{}
 606         defer kc.Close()
 607         cr, err := NewContainerRunner(s.client, &ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 608         c.Assert(err, IsNil)
 609
 610         var logs TestLogs
 611         cr.NewLogWriter = logs.NewTestLoggingWriter
 612         cr.Container.ContainerImage = hwPDH
 613         cr.Container.Command = []string{"./hw"}
 614         err = cr.LoadImage()
 615         c.Check(err, IsNil)
 616
 617         err = cr.CreateContainer()
 618         c.Check(err, IsNil)
 619
 620         err = cr.StartContainer()
 621         c.Check(err, IsNil)
 622
 623         err = cr.WaitFinish()
 624         c.Check(err, IsNil)
 625
 626         c.Check(strings.HasSuffix(logs.Stdout.String(), "Hello world\n"), Equals, true)
 627         c.Check(logs.Stderr.String(), Equals, "")
 628 }
 629
 630 func (s *TestSuite) TestCommitLogs(c *C) {
 631         api := &ArvTestClient{}
 632         kc := &KeepTestClient{}
 633         defer kc.Close()
 634         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 635         c.Assert(err, IsNil)
 636         cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
 637
 638         cr.CrunchLog.Print("Hello world!")
 639         cr.CrunchLog.Print("Goodbye")
 640         cr.finalState = "Complete"
 641
 642         err = cr.CommitLogs()
 643         c.Check(err, IsNil)
 644
 645         c.Check(api.Calls, Equals, 2)
 646         c.Check(api.Content[1]["ensure_unique_name"], Equals, true)
 647         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 648         c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
 649         c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 650 }
 651
 652 func (s *TestSuite) TestUpdateContainerRunning(c *C) {
 653         api := &ArvTestClient{}
 654         kc := &KeepTestClient{}
 655         defer kc.Close()
 656         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 657         c.Assert(err, IsNil)
 658
 659         err = cr.UpdateContainerRunning()
 660         c.Check(err, IsNil)
 661
 662         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Running")
 663 }
 664
 665 func (s *TestSuite) TestUpdateContainerComplete(c *C) {
 666         api := &ArvTestClient{}
 667         kc := &KeepTestClient{}
 668         defer kc.Close()
 669         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 670         c.Assert(err, IsNil)
 671
 672         cr.LogsPDH = new(string)
 673         *cr.LogsPDH = "d3a229d2fe3690c2c3e75a71a153c6a3+60"
 674
 675         cr.ExitCode = new(int)
 676         *cr.ExitCode = 42
 677         cr.finalState = "Complete"
 678
 679         err = cr.UpdateContainerFinal()
 680         c.Check(err, IsNil)
 681
 682         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], Equals, *cr.LogsPDH)
 683         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], Equals, *cr.ExitCode)
 684         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Complete")
 685 }
 686
 687 func (s *TestSuite) TestUpdateContainerCancelled(c *C) {
 688         api := &ArvTestClient{}
 689         kc := &KeepTestClient{}
 690         defer kc.Close()
 691         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 692         c.Assert(err, IsNil)
 693         cr.cCancelled = true
 694         cr.finalState = "Cancelled"
 695
 696         err = cr.UpdateContainerFinal()
 697         c.Check(err, IsNil)
 698
 699         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["log"], IsNil)
 700         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["exit_code"], IsNil)
 701         c.Check(api.Content[0]["container"].(arvadosclient.Dict)["state"], Equals, "Cancelled")
 702 }
 703
 704 // Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
 705 // dress rehearsal of the Run() function, starting from a JSON container record.
 706 func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
 707         rec := arvados.Container{}
 708         err := json.Unmarshal([]byte(record), &rec)
 709         c.Check(err, IsNil)
 710
 711         var sm struct {
 712                 SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
 713         }
 714         err = json.Unmarshal([]byte(record), &sm)
 715         c.Check(err, IsNil)
 716         secretMounts, err := json.Marshal(sm)
 717         c.Logf("%s %q", sm, secretMounts)
 718         c.Check(err, IsNil)
 719
 720         s.docker.exitCode = exitCode
 721         s.docker.fn = fn
 722         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
 723
 724         api = &ArvTestClient{Container: rec}
 725         s.docker.api = api
 726         kc := &KeepTestClient{}
 727         defer kc.Close()
 728         cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
 729         c.Assert(err, IsNil)
 730         cr.statInterval = 100 * time.Millisecond
 731         am := &ArvMountCmdLine{}
 732         cr.RunArvMount = am.ArvMountTest
 733
 734         realTemp, err = ioutil.TempDir("", "crunchrun_test1-")
 735         c.Assert(err, IsNil)
 736         defer os.RemoveAll(realTemp)
 737
 738         s.docker.realTemp = realTemp
 739
 740         tempcount := 0
 741         cr.MkTempDir = func(_ string, prefix string) (string, error) {
 742                 tempcount++
 743                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount)
 744                 err := os.Mkdir(d, os.ModePerm)
 745                 if err != nil && strings.Contains(err.Error(), ": file exists") {
 746                         // Test case must have pre-populated the tempdir
 747                         err = nil
 748                 }
 749                 return d, err
 750         }
 751         cr.MkArvClient = func(token string) (IArvadosClient, error) {
 752                 return &ArvTestClient{secretMounts: secretMounts}, nil
 753         }
 754
 755         if extraMounts != nil && len(extraMounts) > 0 {
 756                 err := cr.SetupArvMountPoint("keep")
 757                 c.Check(err, IsNil)
 758
 759                 for _, m := range extraMounts {
 760                         os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm)
 761                 }
 762         }
 763
 764         err = cr.Run()
 765         if api.CalledWith("container.state", "Complete") != nil {
 766                 c.Check(err, IsNil)
 767         }
 768         if exitCode != 2 {
 769                 c.Check(api.WasSetRunning, Equals, true)
 770                 c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
 771         }
 772
 773         if err != nil {
 774                 for k, v := range api.Logs {
 775                         c.Log(k)
 776                         c.Log(v.String())
 777                 }
 778         }
 779
 780         return
 781 }
 782
 783 func (s *TestSuite) TestFullRunHello(c *C) {
 784         api, _, _ := s.fullRunHelper(c, `{
 785     "command": ["echo", "hello world"],
 786     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 787     "cwd": ".",
 788     "environment": {},
 789     "mounts": {"/tmp": {"kind": "tmp"} },
 790     "output_path": "/tmp",
 791     "priority": 1,
 792     "runtime_constraints": {}
 793 }`, nil, 0, func(t *TestDockerClient) {
 794                 t.logWriter.Write(dockerLog(1, "hello world\n"))
 795                 t.logWriter.Close()
 796         })
 797
 798         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 799         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 800         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello world\n"), Equals, true)
 801
 802 }
 803
 804 func (s *TestSuite) TestCrunchstat(c *C) {
 805         api, _, _ := s.fullRunHelper(c, `{
 806                 "command": ["sleep", "1"],
 807                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 808                 "cwd": ".",
 809                 "environment": {},
 810                 "mounts": {"/tmp": {"kind": "tmp"} },
 811                 "output_path": "/tmp",
 812                 "priority": 1,
 813                 "runtime_constraints": {}
 814         }`, nil, 0, func(t *TestDockerClient) {
 815                 time.Sleep(time.Second)
 816                 t.logWriter.Close()
 817         })
 818
 819         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 820         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 821
 822         // We didn't actually start a container, so crunchstat didn't
 823         // find accounting files and therefore didn't log any stats.
 824         // It should have logged a "can't find accounting files"
 825         // message after one poll interval, though, so we can confirm
 826         // it's alive:
 827         c.Assert(api.Logs["crunchstat"], NotNil)
 828         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files have not appeared after 100ms.*`)
 829
 830         // The "files never appeared" log assures us that we called
 831         // (*crunchstat.Reporter)Stop(), and that we set it up with
 832         // the correct container ID "abcde":
 833         c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`)
 834 }
 835
 836 func (s *TestSuite) TestNodeInfoLog(c *C) {
 837         os.Setenv("SLURMD_NODENAME", "compute2")
 838         api, _, _ := s.fullRunHelper(c, `{
 839                 "command": ["sleep", "1"],
 840                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 841                 "cwd": ".",
 842                 "environment": {},
 843                 "mounts": {"/tmp": {"kind": "tmp"} },
 844                 "output_path": "/tmp",
 845                 "priority": 1,
 846                 "runtime_constraints": {}
 847         }`, nil, 0,
 848                 func(t *TestDockerClient) {
 849                         time.Sleep(time.Second)
 850                         t.logWriter.Close()
 851                 })
 852
 853         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 854         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 855
 856         c.Assert(api.Logs["node"], NotNil)
 857         json := api.Logs["node"].String()
 858         c.Check(json, Matches, `(?ms).*"uuid": *"zzzzz-7ekkf-2z3mc76g2q73aio".*`)
 859         c.Check(json, Matches, `(?ms).*"total_cpu_cores": *16.*`)
 860         c.Check(json, Not(Matches), `(?ms).*"info":.*`)
 861
 862         c.Assert(api.Logs["node-info"], NotNil)
 863         json = api.Logs["node-info"].String()
 864         c.Check(json, Matches, `(?ms).*Host Information.*`)
 865         c.Check(json, Matches, `(?ms).*CPU Information.*`)
 866         c.Check(json, Matches, `(?ms).*Memory Information.*`)
 867         c.Check(json, Matches, `(?ms).*Disk Space.*`)
 868         c.Check(json, Matches, `(?ms).*Disk INodes.*`)
 869 }
 870
 871 func (s *TestSuite) TestContainerRecordLog(c *C) {
 872         api, _, _ := s.fullRunHelper(c, `{
 873                 "command": ["sleep", "1"],
 874                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 875                 "cwd": ".",
 876                 "environment": {},
 877                 "mounts": {"/tmp": {"kind": "tmp"} },
 878                 "output_path": "/tmp",
 879                 "priority": 1,
 880                 "runtime_constraints": {}
 881         }`, nil, 0,
 882                 func(t *TestDockerClient) {
 883                         time.Sleep(time.Second)
 884                         t.logWriter.Close()
 885                 })
 886
 887         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 888         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 889
 890         c.Assert(api.Logs["container"], NotNil)
 891         c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
 892 }
 893
 894 func (s *TestSuite) TestFullRunStderr(c *C) {
 895         api, _, _ := s.fullRunHelper(c, `{
 896     "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
 897     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 898     "cwd": ".",
 899     "environment": {},
 900     "mounts": {"/tmp": {"kind": "tmp"} },
 901     "output_path": "/tmp",
 902     "priority": 1,
 903     "runtime_constraints": {}
 904 }`, nil, 1, func(t *TestDockerClient) {
 905                 t.logWriter.Write(dockerLog(1, "hello\n"))
 906                 t.logWriter.Write(dockerLog(2, "world\n"))
 907                 t.logWriter.Close()
 908         })
 909
 910         final := api.CalledWith("container.state", "Complete")
 911         c.Assert(final, NotNil)
 912         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
 913         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 914
 915         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "hello\n"), Equals, true)
 916         c.Check(strings.HasSuffix(api.Logs["stderr"].String(), "world\n"), Equals, true)
 917 }
 918
 919 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 920         api, _, _ := s.fullRunHelper(c, `{
 921     "command": ["pwd"],
 922     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 923     "cwd": ".",
 924     "environment": {},
 925     "mounts": {"/tmp": {"kind": "tmp"} },
 926     "output_path": "/tmp",
 927     "priority": 1,
 928     "runtime_constraints": {}
 929 }`, nil, 0, func(t *TestDockerClient) {
 930                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 931                 t.logWriter.Close()
 932         })
 933
 934         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 935         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 936         c.Log(api.Logs["stdout"])
 937         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/\n"), Equals, true)
 938 }
 939
 940 func (s *TestSuite) TestFullRunSetCwd(c *C) {
 941         api, _, _ := s.fullRunHelper(c, `{
 942     "command": ["pwd"],
 943     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 944     "cwd": "/bin",
 945     "environment": {},
 946     "mounts": {"/tmp": {"kind": "tmp"} },
 947     "output_path": "/tmp",
 948     "priority": 1,
 949     "runtime_constraints": {}
 950 }`, nil, 0, func(t *TestDockerClient) {
 951                 t.logWriter.Write(dockerLog(1, t.cwd+"\n"))
 952                 t.logWriter.Close()
 953         })
 954
 955         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
 956         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
 957         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true)
 958 }
 959
 960 func (s *TestSuite) TestStopOnSignal(c *C) {
 961         s.testStopContainer(c, func(cr *ContainerRunner) {
 962                 go func() {
 963                         for !s.docker.calledWait {
 964                                 time.Sleep(time.Millisecond)
 965                         }
 966                         cr.SigChan <- syscall.SIGINT
 967                 }()
 968         })
 969 }
 970
 971 func (s *TestSuite) TestStopOnArvMountDeath(c *C) {
 972         s.testStopContainer(c, func(cr *ContainerRunner) {
 973                 cr.ArvMountExit = make(chan error)
 974                 go func() {
 975                         cr.ArvMountExit <- exec.Command("true").Run()
 976                         close(cr.ArvMountExit)
 977                 }()
 978         })
 979 }
 980
 981 func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) {
 982         record := `{
 983     "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"],
 984     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
 985     "cwd": ".",
 986     "environment": {},
 987     "mounts": {"/tmp": {"kind": "tmp"} },
 988     "output_path": "/tmp",
 989     "priority": 1,
 990     "runtime_constraints": {}
 991 }`
 992
 993         rec := arvados.Container{}
 994         err := json.Unmarshal([]byte(record), &rec)
 995         c.Check(err, IsNil)
 996
 997         s.docker.fn = func(t *TestDockerClient) {
 998                 <-t.stop
 999                 t.logWriter.Write(dockerLog(1, "foo\n"))
1000                 t.logWriter.Close()
1001         }
1002         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1003
1004         api := &ArvTestClient{Container: rec}
1005         kc := &KeepTestClient{}
1006         defer kc.Close()
1007         cr, err := NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1008         c.Assert(err, IsNil)
1009         cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
1010         cr.MkArvClient = func(token string) (IArvadosClient, error) {
1011                 return &ArvTestClient{}, nil
1012         }
1013         setup(cr)
1014
1015         done := make(chan error)
1016         go func() {
1017                 done <- cr.Run()
1018         }()
1019         select {
1020         case <-time.After(20 * time.Second):
1021                 pprof.Lookup("goroutine").WriteTo(os.Stderr, 1)
1022                 c.Fatal("timed out")
1023         case err = <-done:
1024                 c.Check(err, IsNil)
1025         }
1026         for k, v := range api.Logs {
1027                 c.Log(k)
1028                 c.Log(v.String())
1029         }
1030
1031         c.Check(api.CalledWith("container.log", nil), NotNil)
1032         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1033         c.Check(api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
1034 }
1035
1036 func (s *TestSuite) TestFullRunSetEnv(c *C) {
1037         api, _, _ := s.fullRunHelper(c, `{
1038     "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1039     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1040     "cwd": "/bin",
1041     "environment": {"FROBIZ": "bilbo"},
1042     "mounts": {"/tmp": {"kind": "tmp"} },
1043     "output_path": "/tmp",
1044     "priority": 1,
1045     "runtime_constraints": {}
1046 }`, nil, 0, func(t *TestDockerClient) {
1047                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1048                 t.logWriter.Close()
1049         })
1050
1051         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1052         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1053         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "bilbo\n"), Equals, true)
1054 }
1055
1056 type ArvMountCmdLine struct {
1057         Cmd   []string
1058         token string
1059 }
1060
1061 func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, error) {
1062         am.Cmd = c
1063         am.token = token
1064         return nil, nil
1065 }
1066
1067 func stubCert(temp string) string {
1068         path := temp + "/ca-certificates.crt"
1069         crt, _ := os.Create(path)
1070         crt.Close()
1071         arvadosclient.CertFiles = []string{path}
1072         return path
1073 }
1074
1075 func (s *TestSuite) TestSetupMounts(c *C) {
1076         api := &ArvTestClient{}
1077         kc := &KeepTestClient{}
1078         defer kc.Close()
1079         cr, err := NewContainerRunner(s.client, api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1080         c.Assert(err, IsNil)
1081         am := &ArvMountCmdLine{}
1082         cr.RunArvMount = am.ArvMountTest
1083
1084         realTemp, err := ioutil.TempDir("", "crunchrun_test1-")
1085         c.Assert(err, IsNil)
1086         certTemp, err := ioutil.TempDir("", "crunchrun_test2-")
1087         c.Assert(err, IsNil)
1088         stubCertPath := stubCert(certTemp)
1089
1090         cr.parentTemp = realTemp
1091
1092         defer os.RemoveAll(realTemp)
1093         defer os.RemoveAll(certTemp)
1094
1095         i := 0
1096         cr.MkTempDir = func(_ string, prefix string) (string, error) {
1097                 i++
1098                 d := fmt.Sprintf("%s/%s%d", realTemp, prefix, i)
1099                 err := os.Mkdir(d, os.ModePerm)
1100                 if err != nil && strings.Contains(err.Error(), ": file exists") {
1101                         // Test case must have pre-populated the tempdir
1102                         err = nil
1103                 }
1104                 return d, err
1105         }
1106
1107         checkEmpty := func() {
1108                 // Should be deleted.
1109                 _, err := os.Stat(realTemp)
1110                 c.Assert(os.IsNotExist(err), Equals, true)
1111
1112                 // Now recreate it for the next test.
1113                 c.Assert(os.Mkdir(realTemp, 0777), IsNil)
1114         }
1115
1116         {
1117                 i = 0
1118                 cr.ArvMountPoint = ""
1119                 cr.Container.Mounts = make(map[string]arvados.Mount)
1120                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1121                 cr.OutputPath = "/tmp"
1122                 cr.statInterval = 5 * time.Second
1123                 err := cr.SetupMounts()
1124                 c.Check(err, IsNil)
1125                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1126                         "--read-write", "--crunchstat-interval=5",
1127                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1128                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
1129                 os.RemoveAll(cr.ArvMountPoint)
1130                 cr.CleanupDirs()
1131                 checkEmpty()
1132         }
1133
1134         {
1135                 i = 0
1136                 cr.ArvMountPoint = ""
1137                 cr.Container.Mounts = make(map[string]arvados.Mount)
1138                 cr.Container.Mounts["/out"] = arvados.Mount{Kind: "tmp"}
1139                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1140                 cr.OutputPath = "/out"
1141
1142                 err := cr.SetupMounts()
1143                 c.Check(err, IsNil)
1144                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1145                         "--read-write", "--crunchstat-interval=5",
1146                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1147                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
1148                 os.RemoveAll(cr.ArvMountPoint)
1149                 cr.CleanupDirs()
1150                 checkEmpty()
1151         }
1152
1153         {
1154                 i = 0
1155                 cr.ArvMountPoint = ""
1156                 cr.Container.Mounts = make(map[string]arvados.Mount)
1157                 cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
1158                 cr.OutputPath = "/tmp"
1159
1160                 apiflag := true
1161                 cr.Container.RuntimeConstraints.API = &apiflag
1162
1163                 err := cr.SetupMounts()
1164                 c.Check(err, IsNil)
1165                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1166                         "--read-write", "--crunchstat-interval=5",
1167                         "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1168                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
1169                 os.RemoveAll(cr.ArvMountPoint)
1170                 cr.CleanupDirs()
1171                 checkEmpty()
1172
1173                 apiflag = false
1174         }
1175
1176         {
1177                 i = 0
1178                 cr.ArvMountPoint = ""
1179                 cr.Container.Mounts = map[string]arvados.Mount{
1180                         "/keeptmp": {Kind: "collection", Writable: true},
1181                 }
1182                 cr.OutputPath = "/keeptmp"
1183
1184                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1185
1186                 err := cr.SetupMounts()
1187                 c.Check(err, IsNil)
1188                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1189                         "--read-write", "--crunchstat-interval=5",
1190                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1191                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
1192                 os.RemoveAll(cr.ArvMountPoint)
1193                 cr.CleanupDirs()
1194                 checkEmpty()
1195         }
1196
1197         {
1198                 i = 0
1199                 cr.ArvMountPoint = ""
1200                 cr.Container.Mounts = map[string]arvados.Mount{
1201                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1202                         "/keepout": {Kind: "collection", Writable: true},
1203                 }
1204                 cr.OutputPath = "/keepout"
1205
1206                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1207                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1208
1209                 err := cr.SetupMounts()
1210                 c.Check(err, IsNil)
1211                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1212                         "--read-write", "--crunchstat-interval=5",
1213                         "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1214                 sort.StringSlice(cr.Binds).Sort()
1215                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1216                         realTemp + "/keep1/tmp0:/keepout"})
1217                 os.RemoveAll(cr.ArvMountPoint)
1218                 cr.CleanupDirs()
1219                 checkEmpty()
1220         }
1221
1222         {
1223                 i = 0
1224                 cr.ArvMountPoint = ""
1225                 cr.Container.RuntimeConstraints.KeepCacheRAM = 512
1226                 cr.Container.Mounts = map[string]arvados.Mount{
1227                         "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"},
1228                         "/keepout": {Kind: "collection", Writable: true},
1229                 }
1230                 cr.OutputPath = "/keepout"
1231
1232                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1233                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1234
1235                 err := cr.SetupMounts()
1236                 c.Check(err, IsNil)
1237                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1238                         "--read-write", "--crunchstat-interval=5",
1239                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1240                 sort.StringSlice(cr.Binds).Sort()
1241                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
1242                         realTemp + "/keep1/tmp0:/keepout"})
1243                 os.RemoveAll(cr.ArvMountPoint)
1244                 cr.CleanupDirs()
1245                 checkEmpty()
1246         }
1247
1248         for _, test := range []struct {
1249                 in  interface{}
1250                 out string
1251         }{
1252                 {in: "foo", out: `"foo"`},
1253                 {in: nil, out: `null`},
1254                 {in: map[string]int64{"foo": 123456789123456789}, out: `{"foo":123456789123456789}`},
1255         } {
1256                 i = 0
1257                 cr.ArvMountPoint = ""
1258                 cr.Container.Mounts = map[string]arvados.Mount{
1259                         "/mnt/test.json": {Kind: "json", Content: test.in},
1260                 }
1261                 err := cr.SetupMounts()
1262                 c.Check(err, IsNil)
1263                 sort.StringSlice(cr.Binds).Sort()
1264                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
1265                 content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
1266                 c.Check(err, IsNil)
1267                 c.Check(content, DeepEquals, []byte(test.out))
1268                 os.RemoveAll(cr.ArvMountPoint)
1269                 cr.CleanupDirs()
1270                 checkEmpty()
1271         }
1272
1273         for _, test := range []struct {
1274                 in  interface{}
1275                 out string
1276         }{
1277                 {in: "foo", out: `foo`},
1278                 {in: nil, out: "error"},
1279                 {in: map[string]int64{"foo": 123456789123456789}, out: "error"},
1280         } {
1281                 i = 0
1282                 cr.ArvMountPoint = ""
1283                 cr.Container.Mounts = map[string]arvados.Mount{
1284                         "/mnt/test.txt": {Kind: "text", Content: test.in},
1285                 }
1286                 err := cr.SetupMounts()
1287                 if test.out == "error" {
1288                         c.Check(err.Error(), Equals, "content for mount \"/mnt/test.txt\" must be a string")
1289                 } else {
1290                         c.Check(err, IsNil)
1291                         sort.StringSlice(cr.Binds).Sort()
1292                         c.Check(cr.Binds, DeepEquals, []string{realTemp + "/text2/mountdata.text:/mnt/test.txt:ro"})
1293                         content, err := ioutil.ReadFile(realTemp + "/text2/mountdata.text")
1294                         c.Check(err, IsNil)
1295                         c.Check(content, DeepEquals, []byte(test.out))
1296                 }
1297                 os.RemoveAll(cr.ArvMountPoint)
1298                 cr.CleanupDirs()
1299                 checkEmpty()
1300         }
1301
1302         // Read-only mount points are allowed underneath output_dir mount point
1303         {
1304                 i = 0
1305                 cr.ArvMountPoint = ""
1306                 cr.Container.Mounts = make(map[string]arvados.Mount)
1307                 cr.Container.Mounts = map[string]arvados.Mount{
1308                         "/tmp":     {Kind: "tmp"},
1309                         "/tmp/foo": {Kind: "collection"},
1310                 }
1311                 cr.OutputPath = "/tmp"
1312
1313                 os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm)
1314
1315                 err := cr.SetupMounts()
1316                 c.Check(err, IsNil)
1317                 c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
1318                         "--read-write", "--crunchstat-interval=5",
1319                         "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
1320                 c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
1321                 os.RemoveAll(cr.ArvMountPoint)
1322                 cr.CleanupDirs()
1323                 checkEmpty()
1324         }
1325
1326         // Writable mount points copied to output_dir mount point
1327         {
1328                 i = 0
1329                 cr.ArvMountPoint = ""
1330                 cr.Container.Mounts = make(map[string]arvados.Mount)
1331                 cr.Container.Mounts = map[string]arvados.Mount{
1332                         "/tmp": {Kind: "tmp"},
1333                         "/tmp/foo": {Kind: "collection",
1334                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53",
1335                                 Writable:         true},
1336                         "/tmp/bar": {Kind: "collection",
1337                                 PortableDataHash: "59389a8f9ee9d399be35462a0f92541d+53",
1338                                 Path:             "baz",
1339                                 Writable:         true},
1340                 }
1341                 cr.OutputPath = "/tmp"
1342
1343                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
1344                 os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz", os.ModePerm)
1345
1346                 rf, _ := os.Create(realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz/quux")
1347                 rf.Write([]byte("bar"))
1348                 rf.Close()
1349
1350                 err := cr.SetupMounts()
1351                 c.Check(err, IsNil)
1352                 _, err = os.Stat(cr.HostOutputDir + "/foo")
1353                 c.Check(err, IsNil)
1354                 _, err = os.Stat(cr.HostOutputDir + "/bar/quux")
1355                 c.Check(err, IsNil)
1356                 os.RemoveAll(cr.ArvMountPoint)
1357                 cr.CleanupDirs()
1358                 checkEmpty()
1359         }
1360
1361         // Only mount points of kind 'collection' are allowed underneath output_dir mount point
1362         {
1363                 i = 0
1364                 cr.ArvMountPoint = ""
1365                 cr.Container.Mounts = make(map[string]arvados.Mount)
1366                 cr.Container.Mounts = map[string]arvados.Mount{
1367                         "/tmp":     {Kind: "tmp"},
1368                         "/tmp/foo": {Kind: "tmp"},
1369                 }
1370                 cr.OutputPath = "/tmp"
1371
1372                 err := cr.SetupMounts()
1373                 c.Check(err, NotNil)
1374                 c.Check(err, ErrorMatches, `Only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path.*`)
1375                 os.RemoveAll(cr.ArvMountPoint)
1376                 cr.CleanupDirs()
1377                 checkEmpty()
1378         }
1379
1380         // Only mount point of kind 'collection' is allowed for stdin
1381         {
1382                 i = 0
1383                 cr.ArvMountPoint = ""
1384                 cr.Container.Mounts = make(map[string]arvados.Mount)
1385                 cr.Container.Mounts = map[string]arvados.Mount{
1386                         "stdin": {Kind: "tmp"},
1387                 }
1388
1389                 err := cr.SetupMounts()
1390                 c.Check(err, NotNil)
1391                 c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
1392                 os.RemoveAll(cr.ArvMountPoint)
1393                 cr.CleanupDirs()
1394                 checkEmpty()
1395         }
1396
1397         // git_tree mounts
1398         {
1399                 i = 0
1400                 cr.ArvMountPoint = ""
1401                 (*GitMountSuite)(nil).useTestGitServer(c)
1402                 cr.token = arvadostest.ActiveToken
1403                 cr.Container.Mounts = make(map[string]arvados.Mount)
1404                 cr.Container.Mounts = map[string]arvados.Mount{
1405                         "/tip": {
1406                                 Kind:   "git_tree",
1407                                 UUID:   arvadostest.Repository2UUID,
1408                                 Commit: "fd3531f42995344f36c30b79f55f27b502f3d344",
1409                                 Path:   "/",
1410                         },
1411                         "/non-tip": {
1412                                 Kind:   "git_tree",
1413                                 UUID:   arvadostest.Repository2UUID,
1414                                 Commit: "5ebfab0522851df01fec11ec55a6d0f4877b542e",
1415                                 Path:   "/",
1416                         },
1417                 }
1418                 cr.OutputPath = "/tmp"
1419
1420                 err := cr.SetupMounts()
1421                 c.Check(err, IsNil)
1422
1423                 // dirMap[mountpoint] == tmpdir
1424                 dirMap := make(map[string]string)
1425                 for _, bind := range cr.Binds {
1426                         tokens := strings.Split(bind, ":")
1427                         dirMap[tokens[1]] = tokens[0]
1428
1429                         if cr.Container.Mounts[tokens[1]].Writable {
1430                                 c.Check(len(tokens), Equals, 2)
1431                         } else {
1432                                 c.Check(len(tokens), Equals, 3)
1433                                 c.Check(tokens[2], Equals, "ro")
1434                         }
1435                 }
1436
1437                 data, err := ioutil.ReadFile(dirMap["/tip"] + "/dir1/dir2/file with mode 0644")
1438                 c.Check(err, IsNil)
1439                 c.Check(string(data), Equals, "\000\001\002\003")
1440                 _, err = ioutil.ReadFile(dirMap["/tip"] + "/file only on testbranch")
1441                 c.Check(err, FitsTypeOf, &os.PathError{})
1442                 c.Check(os.IsNotExist(err), Equals, true)
1443
1444                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/dir1/dir2/file with mode 0644")
1445                 c.Check(err, IsNil)
1446                 c.Check(string(data), Equals, "\000\001\002\003")
1447                 data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/file only on testbranch")
1448                 c.Check(err, IsNil)
1449                 c.Check(string(data), Equals, "testfile\n")
1450
1451                 cr.CleanupDirs()
1452                 checkEmpty()
1453         }
1454 }
1455
1456 func (s *TestSuite) TestStdout(c *C) {
1457         helperRecord := `{
1458                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1459                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1460                 "cwd": "/bin",
1461                 "environment": {"FROBIZ": "bilbo"},
1462                 "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} },
1463                 "output_path": "/tmp",
1464                 "priority": 1,
1465                 "runtime_constraints": {}
1466         }`
1467
1468         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1469                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1470                 t.logWriter.Close()
1471         })
1472
1473         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1474         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1475         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1476 }
1477
1478 // Used by the TestStdoutWithWrongPath*()
1479 func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
1480         rec := arvados.Container{}
1481         err = json.Unmarshal([]byte(record), &rec)
1482         c.Check(err, IsNil)
1483
1484         s.docker.fn = fn
1485         s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
1486
1487         api = &ArvTestClient{Container: rec}
1488         kc := &KeepTestClient{}
1489         defer kc.Close()
1490         cr, err = NewContainerRunner(s.client, api, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1491         c.Assert(err, IsNil)
1492         am := &ArvMountCmdLine{}
1493         cr.RunArvMount = am.ArvMountTest
1494         cr.MkArvClient = func(token string) (IArvadosClient, error) {
1495                 return &ArvTestClient{}, nil
1496         }
1497
1498         err = cr.Run()
1499         return
1500 }
1501
1502 func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
1503         _, _, err := s.stdoutErrorRunHelper(c, `{
1504     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
1505     "output_path": "/tmp"
1506 }`, func(t *TestDockerClient) {})
1507
1508         c.Check(err, NotNil)
1509         c.Check(strings.Contains(err.Error(), "Stdout path does not start with OutputPath"), Equals, true)
1510 }
1511
1512 func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
1513         _, _, err := s.stdoutErrorRunHelper(c, `{
1514     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
1515     "output_path": "/tmp"
1516 }`, func(t *TestDockerClient) {})
1517
1518         c.Check(err, NotNil)
1519         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'tmp' for stdout"), Equals, true)
1520 }
1521
1522 func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
1523         _, _, err := s.stdoutErrorRunHelper(c, `{
1524     "mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
1525     "output_path": "/tmp"
1526 }`, func(t *TestDockerClient) {})
1527
1528         c.Check(err, NotNil)
1529         c.Check(strings.Contains(err.Error(), "Unsupported mount kind 'collection' for stdout"), Equals, true)
1530 }
1531
1532 func (s *TestSuite) TestFullRunWithAPI(c *C) {
1533         defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
1534         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1535         api, _, _ := s.fullRunHelper(c, `{
1536     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1537     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1538     "cwd": "/bin",
1539     "environment": {},
1540     "mounts": {"/tmp": {"kind": "tmp"} },
1541     "output_path": "/tmp",
1542     "priority": 1,
1543     "runtime_constraints": {"API": true}
1544 }`, nil, 0, func(t *TestDockerClient) {
1545                 t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n"))
1546                 t.logWriter.Close()
1547         })
1548
1549         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1550         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1551         c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "test.arvados.org\n"), Equals, true)
1552         c.Check(api.CalledWith("container.output", "d41d8cd98f00b204e9800998ecf8427e+0"), NotNil)
1553 }
1554
1555 func (s *TestSuite) TestFullRunSetOutput(c *C) {
1556         defer os.Setenv("ARVADOS_API_HOST", os.Getenv("ARVADOS_API_HOST"))
1557         os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
1558         api, _, _ := s.fullRunHelper(c, `{
1559     "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
1560     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1561     "cwd": "/bin",
1562     "environment": {},
1563     "mounts": {"/tmp": {"kind": "tmp"} },
1564     "output_path": "/tmp",
1565     "priority": 1,
1566     "runtime_constraints": {"API": true}
1567 }`, nil, 0, func(t *TestDockerClient) {
1568                 t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122"
1569                 t.logWriter.Close()
1570         })
1571
1572         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1573         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1574         c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil)
1575 }
1576
1577 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
1578         helperRecord := `{
1579                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1580                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1581                 "cwd": "/bin",
1582                 "environment": {"FROBIZ": "bilbo"},
1583                 "mounts": {
1584         "/tmp": {"kind": "tmp"},
1585         "/tmp/foo": {"kind": "collection",
1586                      "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54",
1587                      "exclude_from_output": true
1588         },
1589         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1590     },
1591                 "output_path": "/tmp",
1592                 "priority": 1,
1593                 "runtime_constraints": {}
1594         }`
1595
1596         extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
1597
1598         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1599                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1600                 t.logWriter.Close()
1601         })
1602
1603         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1604         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1605         c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil)
1606 }
1607
1608 func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) {
1609         helperRecord := `{
1610                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1611                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1612                 "cwd": "/bin",
1613                 "environment": {"FROBIZ": "bilbo"},
1614                 "mounts": {
1615         "/tmp": {"kind": "tmp"},
1616         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"},
1617         "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"},
1618         "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"},
1619         "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"},
1620         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1621     },
1622                 "output_path": "/tmp",
1623                 "priority": 1,
1624                 "runtime_constraints": {}
1625         }`
1626
1627         extraMounts := []string{
1628                 "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt",
1629                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1630                 "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
1631         }
1632
1633         api, runner, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1634                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1635                 t.logWriter.Close()
1636         })
1637
1638         c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
1639                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
1640                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
1641                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
1642                 realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro",
1643         })
1644
1645         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1646         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1647         for _, v := range api.Content {
1648                 if v["collection"] != nil {
1649                         c.Check(v["ensure_unique_name"], Equals, true)
1650                         collection := v["collection"].(arvadosclient.Dict)
1651                         if strings.Index(collection["name"].(string), "output") == 0 {
1652                                 manifest := collection["manifest_text"].(string)
1653
1654                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1655 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 9:18:bar 36:18:sub1file2
1656 ./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2
1657 ./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt
1658 ./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt
1659 `)
1660                         }
1661                 }
1662         }
1663 }
1664
1665 func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) {
1666         helperRecord := `{
1667                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1668                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1669                 "cwd": "/bin",
1670                 "environment": {"FROBIZ": "bilbo"},
1671                 "mounts": {
1672         "/tmp": {"kind": "tmp"},
1673         "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/subdir1/file2_in_subdir1.txt"},
1674         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1675     },
1676                 "output_path": "/tmp",
1677                 "priority": 1,
1678                 "runtime_constraints": {}
1679         }`
1680
1681         extraMounts := []string{
1682                 "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
1683         }
1684
1685         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1686                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1687                 t.logWriter.Close()
1688         })
1689
1690         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1691         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1692         for _, v := range api.Content {
1693                 if v["collection"] != nil {
1694                         collection := v["collection"].(arvadosclient.Dict)
1695                         if strings.Index(collection["name"].(string), "output") == 0 {
1696                                 manifest := collection["manifest_text"].(string)
1697
1698                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1699 ./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar
1700 `)
1701                         }
1702                 }
1703         }
1704 }
1705
1706 func (s *TestSuite) TestOutputError(c *C) {
1707         helperRecord := `{
1708                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1709                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1710                 "cwd": "/bin",
1711                 "environment": {"FROBIZ": "bilbo"},
1712                 "mounts": {
1713         "/tmp": {"kind": "tmp"}
1714     },
1715                 "output_path": "/tmp",
1716                 "priority": 1,
1717                 "runtime_constraints": {}
1718         }`
1719
1720         extraMounts := []string{}
1721
1722         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1723                 os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
1724                 t.logWriter.Close()
1725         })
1726
1727         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1728 }
1729
1730 func (s *TestSuite) TestStdinCollectionMountPoint(c *C) {
1731         helperRecord := `{
1732                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1733                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1734                 "cwd": "/bin",
1735                 "environment": {"FROBIZ": "bilbo"},
1736                 "mounts": {
1737         "/tmp": {"kind": "tmp"},
1738         "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"},
1739         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1740     },
1741                 "output_path": "/tmp",
1742                 "priority": 1,
1743                 "runtime_constraints": {}
1744         }`
1745
1746         extraMounts := []string{
1747                 "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
1748         }
1749
1750         api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
1751                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1752                 t.logWriter.Close()
1753         })
1754
1755         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1756         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1757         for _, v := range api.Content {
1758                 if v["collection"] != nil {
1759                         collection := v["collection"].(arvadosclient.Dict)
1760                         if strings.Index(collection["name"].(string), "output") == 0 {
1761                                 manifest := collection["manifest_text"].(string)
1762                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1763 `)
1764                         }
1765                 }
1766         }
1767 }
1768
1769 func (s *TestSuite) TestStdinJsonMountPoint(c *C) {
1770         helperRecord := `{
1771                 "command": ["/bin/sh", "-c", "echo $FROBIZ"],
1772                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1773                 "cwd": "/bin",
1774                 "environment": {"FROBIZ": "bilbo"},
1775                 "mounts": {
1776         "/tmp": {"kind": "tmp"},
1777         "stdin": {"kind": "json", "content": "foo"},
1778         "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"}
1779     },
1780                 "output_path": "/tmp",
1781                 "priority": 1,
1782                 "runtime_constraints": {}
1783         }`
1784
1785         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
1786                 t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
1787                 t.logWriter.Close()
1788         })
1789
1790         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
1791         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
1792         for _, v := range api.Content {
1793                 if v["collection"] != nil {
1794                         collection := v["collection"].(arvadosclient.Dict)
1795                         if strings.Index(collection["name"].(string), "output") == 0 {
1796                                 manifest := collection["manifest_text"].(string)
1797                                 c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out
1798 `)
1799                         }
1800                 }
1801         }
1802 }
1803
1804 func (s *TestSuite) TestStderrMount(c *C) {
1805         api, _, _ := s.fullRunHelper(c, `{
1806     "command": ["/bin/sh", "-c", "echo hello;exit 1"],
1807     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1808     "cwd": ".",
1809     "environment": {},
1810     "mounts": {"/tmp": {"kind": "tmp"},
1811                "stdout": {"kind": "file", "path": "/tmp/a/out.txt"},
1812                "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}},
1813     "output_path": "/tmp",
1814     "priority": 1,
1815     "runtime_constraints": {}
1816 }`, nil, 1, func(t *TestDockerClient) {
1817                 t.logWriter.Write(dockerLog(1, "hello\n"))
1818                 t.logWriter.Write(dockerLog(2, "oops\n"))
1819                 t.logWriter.Close()
1820         })
1821
1822         final := api.CalledWith("container.state", "Complete")
1823         c.Assert(final, NotNil)
1824         c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
1825         c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
1826
1827         c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil)
1828 }
1829
1830 func (s *TestSuite) TestNumberRoundTrip(c *C) {
1831         kc := &KeepTestClient{}
1832         defer kc.Close()
1833         cr, err := NewContainerRunner(s.client, &ArvTestClient{callraw: true}, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
1834         c.Assert(err, IsNil)
1835         cr.fetchContainerRecord()
1836
1837         jsondata, err := json.Marshal(cr.Container.Mounts["/json"].Content)
1838
1839         c.Check(err, IsNil)
1840         c.Check(string(jsondata), Equals, `{"number":123456789123456789}`)
1841 }
1842
1843 func (s *TestSuite) TestFullBrokenDocker1(c *C) {
1844         tf, err := ioutil.TempFile("", "brokenNodeHook-")
1845         c.Assert(err, IsNil)
1846         defer os.Remove(tf.Name())
1847
1848         tf.Write([]byte(`#!/bin/sh
1849 exec echo killme
1850 `))
1851         tf.Close()
1852         os.Chmod(tf.Name(), 0700)
1853
1854         ech := tf.Name()
1855         brokenNodeHook = &ech
1856
1857         api, _, _ := s.fullRunHelper(c, `{
1858     "command": ["echo", "hello world"],
1859     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1860     "cwd": ".",
1861     "environment": {},
1862     "mounts": {"/tmp": {"kind": "tmp"} },
1863     "output_path": "/tmp",
1864     "priority": 1,
1865     "runtime_constraints": {}
1866 }`, nil, 2, func(t *TestDockerClient) {
1867                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1868                 t.logWriter.Close()
1869         })
1870
1871         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1872         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1873         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
1874         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
1875
1876 }
1877
1878 func (s *TestSuite) TestFullBrokenDocker2(c *C) {
1879         ech := ""
1880         brokenNodeHook = &ech
1881
1882         api, _, _ := s.fullRunHelper(c, `{
1883     "command": ["echo", "hello world"],
1884     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1885     "cwd": ".",
1886     "environment": {},
1887     "mounts": {"/tmp": {"kind": "tmp"} },
1888     "output_path": "/tmp",
1889     "priority": 1,
1890     "runtime_constraints": {}
1891 }`, nil, 2, func(t *TestDockerClient) {
1892                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1893                 t.logWriter.Close()
1894         })
1895
1896         c.Check(api.CalledWith("container.state", "Queued"), NotNil)
1897         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1898         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
1899 }
1900
1901 func (s *TestSuite) TestFullBrokenDocker3(c *C) {
1902         ech := ""
1903         brokenNodeHook = &ech
1904
1905         api, _, _ := s.fullRunHelper(c, `{
1906     "command": ["echo", "hello world"],
1907     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1908     "cwd": ".",
1909     "environment": {},
1910     "mounts": {"/tmp": {"kind": "tmp"} },
1911     "output_path": "/tmp",
1912     "priority": 1,
1913     "runtime_constraints": {}
1914 }`, nil, 3, func(t *TestDockerClient) {
1915                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1916                 t.logWriter.Close()
1917         })
1918
1919         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1920         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
1921 }
1922
1923 func (s *TestSuite) TestBadCommand1(c *C) {
1924         ech := ""
1925         brokenNodeHook = &ech
1926
1927         api, _, _ := s.fullRunHelper(c, `{
1928     "command": ["echo", "hello world"],
1929     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1930     "cwd": ".",
1931     "environment": {},
1932     "mounts": {"/tmp": {"kind": "tmp"} },
1933     "output_path": "/tmp",
1934     "priority": 1,
1935     "runtime_constraints": {}
1936 }`, nil, 4, func(t *TestDockerClient) {
1937                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1938                 t.logWriter.Close()
1939         })
1940
1941         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1942         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1943 }
1944
1945 func (s *TestSuite) TestBadCommand2(c *C) {
1946         ech := ""
1947         brokenNodeHook = &ech
1948
1949         api, _, _ := s.fullRunHelper(c, `{
1950     "command": ["echo", "hello world"],
1951     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1952     "cwd": ".",
1953     "environment": {},
1954     "mounts": {"/tmp": {"kind": "tmp"} },
1955     "output_path": "/tmp",
1956     "priority": 1,
1957     "runtime_constraints": {}
1958 }`, nil, 5, func(t *TestDockerClient) {
1959                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1960                 t.logWriter.Close()
1961         })
1962
1963         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1964         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1965 }
1966
1967 func (s *TestSuite) TestBadCommand3(c *C) {
1968         ech := ""
1969         brokenNodeHook = &ech
1970
1971         api, _, _ := s.fullRunHelper(c, `{
1972     "command": ["echo", "hello world"],
1973     "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1974     "cwd": ".",
1975     "environment": {},
1976     "mounts": {"/tmp": {"kind": "tmp"} },
1977     "output_path": "/tmp",
1978     "priority": 1,
1979     "runtime_constraints": {}
1980 }`, nil, 6, func(t *TestDockerClient) {
1981                 t.logWriter.Write(dockerLog(1, "hello world\n"))
1982                 t.logWriter.Close()
1983         })
1984
1985         c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
1986         c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
1987 }
1988
1989 func (s *TestSuite) TestSecretTextMountPoint(c *C) {
1990         // under normal mounts, gets captured in output, oops
1991         helperRecord := `{
1992                 "command": ["true"],
1993                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
1994                 "cwd": "/bin",
1995                 "mounts": {
1996                     "/tmp": {"kind": "tmp"},
1997                     "/tmp/secret.conf": {"kind": "text", "content": "mypassword"}
1998                 },
1999                 "secret_mounts": {
2000                 },
2001                 "output_path": "/tmp",
2002                 "priority": 1,
2003                 "runtime_constraints": {}
2004         }`
2005
2006         api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
2007                 content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
2008                 c.Check(err, IsNil)
2009                 c.Check(content, DeepEquals, []byte("mypassword"))
2010                 t.logWriter.Close()
2011         })
2012
2013         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
2014         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
2015         c.Check(api.CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), NotNil)
2016         c.Check(api.CalledWith("collection.manifest_text", ""), IsNil)
2017
2018         // under secret mounts, not captured in output
2019         helperRecord = `{
2020                 "command": ["true"],
2021                 "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
2022                 "cwd": "/bin",
2023                 "mounts": {
2024                     "/tmp": {"kind": "tmp"}
2025                 },
2026                 "secret_mounts": {
2027                     "/tmp/secret.conf": {"kind": "text", "content": "mypassword"}
2028                 },
2029                 "output_path": "/tmp",
2030                 "priority": 1,
2031                 "runtime_constraints": {}
2032         }`
2033
2034         api, _, _ = s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
2035                 content, err := ioutil.ReadFile(t.realTemp + "/tmp2/secret.conf")
2036                 c.Check(err, IsNil)
2037                 c.Check(content, DeepEquals, []byte("mypassword"))
2038                 t.logWriter.Close()
2039         })
2040
2041         c.Check(api.CalledWith("container.exit_code", 0), NotNil)
2042         c.Check(api.CalledWith("container.state", "Complete"), NotNil)
2043         c.Check(api.CalledWith("collection.manifest_text", ". 34819d7beeabb9260a5c854bc85b3e44+10 0:10:secret.conf\n"), IsNil)
2044         c.Check(api.CalledWith("collection.manifest_text", ""), NotNil)
2045 }