"encoding/json"
"fmt"
"io"
+ "io/fs"
"io/ioutil"
"math"
"net"
"git.arvados.org/arvados.git/sdk/go/arvadostest"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/httpserver"
+ "git.arvados.org/arvados.git/sdk/go/keepclient"
check "gopkg.in/check.v1"
)
Insecure: true
SystemLogs:
Format: text
+ API:
+ MaxConcurrentRequests: 128
+ Containers:
+ CloudVMs:
+ Enable: true
+ Driver: loopback
+ BootProbeCommand: "rm -f /var/lock/crunch-run-broken"
+ ProbeInterval: 1s
+ PollInterval: 5s
+ SyncInterval: 10s
+ TimeoutIdle: 1s
+ TimeoutBooting: 2s
+ RuntimeEngine: singularity
+ CrunchRunArgumentsList: ["--broken-node-hook", "true"]
RemoteClusters:
z1111:
Host: ` + hostport["z1111"] + `
c.Assert(coll.StorageClassesDesired, check.DeepEquals, kc.DefaultStorageClasses)
}
+func (s *IntegrationSuite) createTestCollectionManifest(c *check.C, ac *arvados.Client, kc *keepclient.KeepClient, content string) string {
+ fs, err := (&arvados.Collection{}).FileSystem(ac, kc)
+ c.Assert(err, check.IsNil)
+ f, err := fs.OpenFile("test.txt", os.O_CREATE|os.O_RDWR, 0777)
+ c.Assert(err, check.IsNil)
+ _, err = io.WriteString(f, content)
+ c.Assert(err, check.IsNil)
+ err = f.Close()
+ c.Assert(err, check.IsNil)
+ mtxt, err := fs.MarshalManifest(".")
+ c.Assert(err, check.IsNil)
+ return mtxt
+}
+
func (s *IntegrationSuite) TestGetCollectionByPDH(c *check.C) {
conn1 := s.super.Conn("z1111")
rootctx1, _, _ := s.super.RootClients("z1111")
// Create the collection to find its PDH (but don't save it
// anywhere yet)
- var coll1 arvados.Collection
- fs1, err := coll1.FileSystem(ac1, kc1)
- c.Assert(err, check.IsNil)
- f, err := fs1.OpenFile("test.txt", os.O_CREATE|os.O_RDWR, 0777)
- c.Assert(err, check.IsNil)
- _, err = io.WriteString(f, "IntegrationSuite.TestGetCollectionByPDH")
- c.Assert(err, check.IsNil)
- err = f.Close()
- c.Assert(err, check.IsNil)
- mtxt, err := fs1.MarshalManifest(".")
- c.Assert(err, check.IsNil)
+ mtxt := s.createTestCollectionManifest(c, ac1, kc1, c.TestName())
pdh := arvados.PortableDataHash(mtxt)
// Looking up the PDH before saving returns 404 if cycle
// detection is working.
- _, err = conn1.CollectionGet(userctx1, arvados.GetOptions{UUID: pdh})
+ _, err := conn1.CollectionGet(userctx1, arvados.GetOptions{UUID: pdh})
c.Assert(err, check.ErrorMatches, `.*404 Not Found.*`)
// Save the collection on cluster z1111.
- coll1, err = conn1.CollectionCreate(userctx1, arvados.CreateOptions{Attrs: map[string]interface{}{
+ _, err = conn1.CollectionCreate(userctx1, arvados.CreateOptions{Attrs: map[string]interface{}{
"manifest_text": mtxt,
}})
c.Assert(err, check.IsNil)
// Retrieve the collection from cluster z3333.
- coll, err := conn3.CollectionGet(userctx1, arvados.GetOptions{UUID: pdh})
+ coll2, err := conn3.CollectionGet(userctx1, arvados.GetOptions{UUID: pdh})
c.Check(err, check.IsNil)
- c.Check(coll.PortableDataHash, check.Equals, pdh)
+ c.Check(coll2.PortableDataHash, check.Equals, pdh)
+}
+
+func (s *IntegrationSuite) TestFederation_Write1Read2(c *check.C) {
+ s.testFederationCollectionAccess(c, "z1111", "z2222")
+}
+
+func (s *IntegrationSuite) TestFederation_Write2Read1(c *check.C) {
+ s.testFederationCollectionAccess(c, "z2222", "z1111")
+}
+
+func (s *IntegrationSuite) TestFederation_Write2Read3(c *check.C) {
+ s.testFederationCollectionAccess(c, "z2222", "z3333")
+}
+
+func (s *IntegrationSuite) testFederationCollectionAccess(c *check.C, writeCluster, readCluster string) {
+ conn1 := s.super.Conn("z1111")
+ rootctx1, _, _ := s.super.RootClients("z1111")
+ _, ac1, _, _ := s.super.UserClients("z1111", rootctx1, c, conn1, s.oidcprovider.AuthEmail, true)
+
+ connW := s.super.Conn(writeCluster)
+ userctxW, acW, kcW := s.super.ClientsWithToken(writeCluster, ac1.AuthToken)
+ kcW.DiskCacheSize = keepclient.DiskCacheDisabled
+ connR := s.super.Conn(readCluster)
+ userctxR, acR, kcR := s.super.ClientsWithToken(readCluster, ac1.AuthToken)
+ kcR.DiskCacheSize = keepclient.DiskCacheDisabled
+
+ filedata := fmt.Sprintf("%s: write to %s, read from %s", c.TestName(), writeCluster, readCluster)
+ mtxt := s.createTestCollectionManifest(c, acW, kcW, filedata)
+ collW, err := connW.CollectionCreate(userctxW, arvados.CreateOptions{Attrs: map[string]interface{}{
+ "manifest_text": mtxt,
+ }})
+ c.Assert(err, check.IsNil)
+
+ collR, err := connR.CollectionGet(userctxR, arvados.GetOptions{UUID: collW.UUID})
+ if !c.Check(err, check.IsNil) {
+ return
+ }
+ fsR, err := collR.FileSystem(acR, kcR)
+ if !c.Check(err, check.IsNil) {
+ return
+ }
+ buf, err := fs.ReadFile(arvados.FS(fsR), "test.txt")
+ if !c.Check(err, check.IsNil) {
+ return
+ }
+ c.Check(string(buf), check.Equals, filedata)
}
// Tests bug #18004
req.Header.Set("Authorization", "OAuth2 "+ac2.AuthToken)
resp, err = arvados.InsecureHTTPClient.Do(req)
c.Assert(err, check.IsNil)
+ defer resp.Body.Close()
err = json.NewDecoder(resp.Body).Decode(&cr)
c.Check(err, check.IsNil)
c.Check(cr.UUID, check.Matches, "z2222-.*")
c.Assert(err, check.IsNil)
req.Header.Set("Content-Type", "application/json")
resp, err := ac1.Do(req)
- c.Assert(err, check.IsNil)
- c.Assert(resp.StatusCode, check.Equals, tt.expectedCode)
+ if c.Check(err, check.IsNil) {
+ c.Assert(resp.StatusCode, check.Equals, tt.expectedCode)
+ resp.Body.Close()
+ }
}
}
var jresp httpserver.ErrorResponse
err := json.NewDecoder(resp.Body).Decode(&jresp)
c.Check(err, check.IsNil)
- c.Assert(jresp.Errors, check.HasLen, 1)
- c.Check(jresp.Errors[0], check.Matches, `.*\(`+respHdr+`\).*`)
+ if c.Check(jresp.Errors, check.HasLen, 1) {
+ c.Check(jresp.Errors[0], check.Matches, `.*\(`+respHdr+`\).*`)
+ }
}
+ resp.Body.Close()
}
}
"hostname": "example",
},
})
+ c.Assert(err, check.IsNil)
c.Check(outVM.UUID[0:5], check.Equals, "z3333")
- c.Check(err, check.IsNil)
// Make sure z3333 user list is up to date
_, err = conn3.UserList(rootctx3, arvados.ListOptions{Limit: 1000})
c.Check(err, check.ErrorMatches, `request failed: .* 401 Unauthorized: cannot use a locally issued token to forward a request to our login cluster \(z1111\)`)
c.Check(err, check.Not(check.ErrorMatches), `(?ms).*127\.0\.0\.11.*`)
}
+
+func (s *IntegrationSuite) TestRunTrivialContainer(c *check.C) {
+ outcoll, _ := s.runContainer(c, "z1111", "", map[string]interface{}{
+ "command": []string{"sh", "-c", "touch \"/out/hello world\" /out/ohai"},
+ "container_image": "busybox:uclibc",
+ "cwd": "/tmp",
+ "environment": map[string]string{},
+ "mounts": map[string]arvados.Mount{"/out": {Kind: "tmp", Capacity: 10000}},
+ "output_path": "/out",
+ "runtime_constraints": arvados.RuntimeConstraints{RAM: 100000000, VCPUs: 1, KeepCacheRAM: 1 << 26},
+ "priority": 1,
+ "state": arvados.ContainerRequestStateCommitted,
+ }, 0)
+ c.Check(outcoll.ManifestText, check.Matches, `\. d41d8.* 0:0:hello\\040world 0:0:ohai\n`)
+ c.Check(outcoll.PortableDataHash, check.Equals, "8fa5dee9231a724d7cf377c5a2f4907c+65")
+}
+
+func (s *IntegrationSuite) TestContainerInputOnDifferentCluster(c *check.C) {
+ conn := s.super.Conn("z1111")
+ rootctx, _, _ := s.super.RootClients("z1111")
+ userctx, ac, _, _ := s.super.UserClients("z1111", rootctx, c, conn, s.oidcprovider.AuthEmail, true)
+ z1coll, err := conn.CollectionCreate(userctx, arvados.CreateOptions{Attrs: map[string]interface{}{
+ "manifest_text": ". d41d8cd98f00b204e9800998ecf8427e+0 0:0:ocelot\n",
+ }})
+ c.Assert(err, check.IsNil)
+
+ outcoll, logcfs := s.runContainer(c, "z2222", ac.AuthToken, map[string]interface{}{
+ "command": []string{"ls", "/in"},
+ "container_image": "busybox:uclibc",
+ "cwd": "/tmp",
+ "environment": map[string]string{},
+ "mounts": map[string]arvados.Mount{
+ "/in": {Kind: "collection", PortableDataHash: z1coll.PortableDataHash},
+ "/out": {Kind: "tmp", Capacity: 10000},
+ },
+ "output_path": "/out",
+ "runtime_constraints": arvados.RuntimeConstraints{RAM: 100000000, VCPUs: 1, KeepCacheRAM: 1 << 26},
+ "priority": 1,
+ "state": arvados.ContainerRequestStateCommitted,
+ "container_count_max": 1,
+ }, -1)
+ if outcoll.UUID == "" {
+ arvmountlog, err := fs.ReadFile(arvados.FS(logcfs), "/arv-mount.txt")
+ c.Check(err, check.IsNil)
+ c.Check(string(arvmountlog), check.Matches, `(?ms).*cannot use a locally issued token to forward a request to our login cluster \(z1111\).*`)
+ c.Skip("this use case is not supported yet")
+ }
+ stdout, err := fs.ReadFile(arvados.FS(logcfs), "/stdout.txt")
+ c.Check(err, check.IsNil)
+ c.Check(string(stdout), check.Equals, "ocelot\n")
+}
+
+func (s *IntegrationSuite) runContainer(c *check.C, clusterID string, token string, ctrSpec map[string]interface{}, expectExitCode int) (outcoll arvados.Collection, logcfs arvados.CollectionFileSystem) {
+ conn := s.super.Conn(clusterID)
+ rootctx, _, _ := s.super.RootClients(clusterID)
+ if token == "" {
+ _, ac, _, _ := s.super.UserClients(clusterID, rootctx, c, conn, s.oidcprovider.AuthEmail, true)
+ token = ac.AuthToken
+ }
+ _, ac, kc := s.super.ClientsWithToken(clusterID, token)
+
+ c.Log("[docker load]")
+ out, err := exec.Command("docker", "load", "--input", arvadostest.BusyboxDockerImage(c)).CombinedOutput()
+ c.Logf("[docker load output] %s", out)
+ c.Check(err, check.IsNil)
+
+ c.Log("[arv-keepdocker]")
+ akd := exec.Command("arv-keepdocker", "--no-resume", "busybox:uclibc")
+ akd.Env = append(os.Environ(), "ARVADOS_API_HOST="+ac.APIHost, "ARVADOS_API_HOST_INSECURE=1", "ARVADOS_API_TOKEN="+ac.AuthToken)
+ out, err = akd.CombinedOutput()
+ c.Logf("[arv-keepdocker output]\n%s", out)
+ c.Check(err, check.IsNil)
+
+ var cr arvados.ContainerRequest
+ err = ac.RequestAndDecode(&cr, "POST", "/arvados/v1/container_requests", nil, map[string]interface{}{
+ "container_request": ctrSpec,
+ })
+ c.Assert(err, check.IsNil)
+
+ showlogs := func(collectionID string) arvados.CollectionFileSystem {
+ var logcoll arvados.Collection
+ err = ac.RequestAndDecode(&logcoll, "GET", "/arvados/v1/collections/"+collectionID, nil, nil)
+ c.Assert(err, check.IsNil)
+ cfs, err := logcoll.FileSystem(ac, kc)
+ c.Assert(err, check.IsNil)
+ fs.WalkDir(arvados.FS(cfs), "/", func(path string, d fs.DirEntry, err error) error {
+ if d.IsDir() || strings.HasPrefix(path, "/log for container") {
+ return nil
+ }
+ f, err := cfs.Open(path)
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ buf, err := ioutil.ReadAll(f)
+ c.Assert(err, check.IsNil)
+ c.Logf("=== %s\n%s\n", path, buf)
+ return nil
+ })
+ return cfs
+ }
+
+ checkwebdavlogs := func(cr arvados.ContainerRequest) {
+ req, err := http.NewRequest("OPTIONS", "https://"+ac.APIHost+"/arvados/v1/container_requests/"+cr.UUID+"/log/"+cr.ContainerUUID+"/", nil)
+ c.Assert(err, check.IsNil)
+ req.Header.Set("Origin", "http://example.example")
+ resp, err := ac.Do(req)
+ c.Assert(err, check.IsNil)
+ c.Check(resp.StatusCode, check.Equals, http.StatusOK)
+ // Check for duplicate headers -- must use Header[], not Header.Get()
+ c.Check(resp.Header["Access-Control-Allow-Origin"], check.DeepEquals, []string{"*"})
+ }
+
+ var ctr arvados.Container
+ var lastState arvados.ContainerState
+ var status, lastStatus arvados.ContainerStatus
+ var allStatus string
+ checkstatus := func() {
+ err := ac.RequestAndDecode(&status, "GET", "/arvados/v1/container_requests/"+cr.UUID+"/container_status", nil, nil)
+ c.Assert(err, check.IsNil)
+ if status != lastStatus {
+ c.Logf("container status: %s, %s", status.State, status.SchedulingStatus)
+ allStatus += fmt.Sprintf("%s, %s\n", status.State, status.SchedulingStatus)
+ lastStatus = status
+ }
+ }
+ deadline := time.Now().Add(time.Minute)
+ for cr.State != arvados.ContainerRequestStateFinal || (lastStatus.State != arvados.ContainerStateComplete && lastStatus.State != arvados.ContainerStateCancelled) {
+ err = ac.RequestAndDecode(&cr, "GET", "/arvados/v1/container_requests/"+cr.UUID, nil, nil)
+ c.Assert(err, check.IsNil)
+ checkstatus()
+ err = ac.RequestAndDecode(&ctr, "GET", "/arvados/v1/containers/"+cr.ContainerUUID, nil, nil)
+ if err != nil {
+ c.Logf("error getting container state: %s", err)
+ } else if ctr.State != lastState {
+ c.Logf("container state changed to %q", ctr.State)
+ lastState = ctr.State
+ } else {
+ if time.Now().After(deadline) {
+ c.Errorf("timed out, container state is %q", cr.State)
+ if ctr.Log == "" {
+ c.Logf("=== NO LOG COLLECTION saved for container")
+ } else {
+ showlogs(ctr.Log)
+ }
+ c.FailNow()
+ }
+ time.Sleep(time.Second / 2)
+ }
+ }
+ checkstatus()
+ c.Logf("cr.CumulativeCost == %f", cr.CumulativeCost)
+ c.Check(cr.CumulativeCost, check.Not(check.Equals), 0.0)
+ if expectExitCode >= 0 {
+ c.Check(ctr.State, check.Equals, arvados.ContainerStateComplete)
+ c.Check(ctr.ExitCode, check.Equals, expectExitCode)
+ err = ac.RequestAndDecode(&outcoll, "GET", "/arvados/v1/collections/"+cr.OutputUUID, nil, nil)
+ c.Assert(err, check.IsNil)
+ c.Check(allStatus, check.Matches, `Queued, waiting for dispatch\n`+
+ `(Queued, waiting.*\n)*`+
+ `(Locked, waiting for dispatch\n)?`+
+ `(Locked, waiting for new instance to be ready\n)?`+
+ `(Locked, preparing runtime environment\n)?`+
+ `(Running, \n)?`+
+ `Complete, \n`)
+ }
+ logcfs = showlogs(cr.LogUUID)
+ checkwebdavlogs(cr)
+ return outcoll, logcfs
+}
projects / arvados.git / blobdiff