{% endcomment %}
<notextile>
-<pre><code># <span class="userinput">apt-get --no-install-recommends install curl gnupg2</span>
-# <span class="userinput">curl -s https://apt.arvados.org/pubkey.gpg -o /etc/apt/trusted.gpg.d/arvados.asc</span>
+<pre><code># <span class="userinput">apt-get --no-install-recommends install curl gnupg2 ca-certificates</span>
+# <span class="userinput">curl https://apt.arvados.org/pubkey.gpg -o /etc/apt/trusted.gpg.d/arvados.asc</span>
</code></pre>
</notextile>
# is older than the amount of seconds defined on PreserveVersionIfIdle,
# a snapshot of the collection's previous state is created and linked to
# the current collection.
- CollectionVersioning: false
+ CollectionVersioning: true
# This setting control the auto-save aspect of collection versioning, and can be set to:
# 0s = auto-create a new version on every update.
# -1s = never auto-create new versions.
# > 0s = auto-create a new version when older than the specified number of seconds.
- PreserveVersionIfIdle: -1s
+ PreserveVersionIfIdle: 10s
</pre>
Note that if you set @CollectionVersioning@ to @false@ after being enabled, old versions will still be accessible, but further changes will not be versioned.
h2(#check_collection_versioning). Consider collection versioning
-Arvados supports collection versioning. If it has been "enabled":{{ site.baseurl }}/admin/collection-versioning.html on your cluster, the deleted collection may be recoverable from an older version. See "Using collection versioning":{{ site.baseurl }}/user/topics/collection-versioning.html for details.
+Arvados supports collection versioning. If it has not been "disabled":{{ site.baseurl }}/admin/collection-versioning.html on your cluster, the deleted collection may be recoverable from an older version. See "Using collection versioning":{{ site.baseurl }}/user/topics/collection-versioning.html for details.
h2(#recover_collection). Recovering collections
"previous: Upgrading from 2.3.0":#v2_3_0
+h3. Default LSF arguments have changed
+
+If you use LSF and your configuration specifies @Containers.LSF.BsubArgumentsList@, you should update it to include the new arguments (@"-R", "select[mem>=%MMB]", ...@, see "configuration reference":{{site.baseurl}}/admin/config.html). Otherwise, containers that are too big to run on any LSF host will remain in the LSF queue instead of being cancelled.
+
+h3. Previously trashed role groups will be deleted
+
+Due to a bug in previous versions, the @DELETE@ operation on a role group caused the group to be flagged as trash in the database, but continue to grant permissions regardless. After upgrading, any role groups that had been trashed this way will be deleted. This might surprise some users if they were relying on permissions that were still in effect due to this bug. Future @DELETE@ operations on a role group will immediately delete the group and revoke the associated permissions.
+
h3. Users are visible to other users by default
When a new user is set up (either via @AutoSetupNewUsers@ config or via Workbench admin interface) the user immediately becomes visible to other users. To revert to the previous behavior, where the administrator must add two users to the same group using the Workbench admin interface in order for the users to see each other, change the new @Users.ActivatedUsersAreVisibleToOthers@ config to @false@.
# Storage provider region. For Google Cloud Storage, use ""
# or omit.
- Region: <span class="userinput">us-east-1a</span>
+ Region: <span class="userinput">us-east-1</span>
# Storage provider endpoint. For Amazon S3, use "" or
# omit. For Google Cloud Storage, use
require (
github.com/AdRoll/goamz v0.0.0-20170825154802-2731d20f46f4
github.com/Azure/azure-sdk-for-go v45.1.0+incompatible
- github.com/Azure/go-autorest/autorest v0.11.3
- github.com/Azure/go-autorest/autorest/azure/auth v0.5.1
+ github.com/Azure/go-autorest/autorest v0.11.22
+ github.com/Azure/go-autorest/autorest/adal v0.9.17 // indirect
+ github.com/Azure/go-autorest/autorest/azure/auth v0.5.9
+ github.com/Azure/go-autorest/autorest/azure/cli v0.4.4 // indirect
github.com/Azure/go-autorest/autorest/to v0.4.0
github.com/Azure/go-autorest/autorest/validation v0.3.0 // indirect
github.com/Microsoft/go-winio v0.4.5 // indirect
github.com/go-asn1-ber/asn1-ber v1.4.1 // indirect
github.com/go-ldap/ldap v3.0.3+incompatible
github.com/gogo/protobuf v1.1.1
+ github.com/golang-jwt/jwt/v4 v4.1.0 // indirect
github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510
github.com/gorilla/context v1.1.1 // indirect
github.com/gorilla/mux v1.6.1-0.20180107155708-5bbbb5b2b572
github.com/sirupsen/logrus v1.8.1
github.com/src-d/gcfg v1.3.0 // indirect
github.com/xanzy/ssh-agent v0.1.0 // indirect
- golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9
- golang.org/x/net v0.0.0-20210405180319-a5a99cb37ef4
+ golang.org/x/crypto v0.0.0-20211117183948-ae814b36b871
+ golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2
golang.org/x/oauth2 v0.0.0-20190604053449-0f29369cfe45
- golang.org/x/sys v0.0.0-20210603125802-9665404d3644
- golang.org/x/tools v0.1.2 // indirect
+ golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e
+ golang.org/x/tools v0.1.7 // indirect
google.golang.org/api v0.13.0
gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d // indirect
gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405
github.com/Azure/azure-sdk-for-go v45.1.0+incompatible/go.mod h1:9XXNKU+eRnpl9moKnB4QOLf1HestfXbmab5FXxiDBjc=
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golang.org/x/sync v0.0.0-20190227155943-e225da77a7e6/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
-golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9 h1:SQFwaSi55rU7vdNs9Yr0Z324VNlrF+0wMqRXT4St8ck=
-golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
-golang.org/x/sync v0.0.0-20210220032951-036812b2e83c h1:5KslGYwFpkhGh+Q16bwMP3cOontH8FOep7tGV86Y7SQ=
golang.org/x/sync v0.0.0-20210220032951-036812b2e83c/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20191010194322-b09406accb47/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20191026070338-33540a1f6037/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
-golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4 h1:myAQVi0cGEoqQVR5POX+8RR2mrocKqNN1hmeMqhX27k=
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golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1 h1:v+OssWQX+hTHEmOBgwxdZxK4zHq3yOs8F9J7mk0PY8E=
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
golang.org/x/text v0.3.1-0.20180807135948-17ff2d5776d2/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk=
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golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
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golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ=
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golang.org/x/tools v0.0.0-20190312170243-e65039ee4138/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
golang.org/x/tools v0.0.0-20190506145303-2d16b83fe98c/go.mod h1:RgjU9mgBXZiqYHBnxXauZ1Gv1EHHAz9KjViQ78xBX0Q=
golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo=
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-golang.org/x/tools v0.1.2 h1:kRBLX7v7Af8W7Gdbbc908OJcdgtK8bOz9Uaj8/F1ACA=
-golang.org/x/tools v0.1.2/go.mod h1:o0xws9oXOQQZyjljx8fwUC0k7L1pTE6eaCbjGeHmOkk=
+golang.org/x/tools v0.1.7 h1:6j8CgantCy3yc8JGBqkDLMKWqZ0RDU2g1HVgacojGWQ=
+golang.org/x/tools v0.1.7/go.mod h1:LGqMHiF4EqQNHR1JncWGqT5BVaXmza+X+BDGol+dOxo=
golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=
google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c=
google.golang.org/grpc v1.20.1 h1:Hz2g2wirWK7H0qIIhGIqRGTuMwTE8HEKFnDZZ7lm9NU=
google.golang.org/grpc v1.20.1/go.mod h1:10oTOabMzJvdu6/UiuZezV6QK5dSlG84ov/aaiqXj38=
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gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw=
gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d h1:TxyelI5cVkbREznMhfzycHdkp5cLA7DpE+GKjSslYhM=
gopkg.in/asn1-ber.v1 v1.0.0-20181015200546-f715ec2f112d/go.mod h1:cuepJuh7vyXfUyUwEgHQXw849cJrilpS5NeIjOWESAw=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405 h1:829vOVxxusYHC+IqBtkX5mbKtsY9fheQiQn0MZRVLfQ=
gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
-gopkg.in/mgo.v2 v2.0.0-20180705113604-9856a29383ce h1:xcEWjVhvbDy+nHP67nPDDpbYrY+ILlfndk4bRioVHaU=
gopkg.in/mgo.v2 v2.0.0-20180705113604-9856a29383ce/go.mod h1:yeKp02qBN3iKW1OzL3MGk2IdtZzaj7SFntXj72NppTA=
gopkg.in/square/go-jose.v2 v2.3.1 h1:SK5KegNXmKmqE342YYN2qPHEnUYeoMiXXl1poUlI+o4=
gopkg.in/square/go-jose.v2 v2.3.1/go.mod h1:M9dMgbHiYLoDGQrXy7OpJDJWiKiU//h+vD76mk0e1AI=
gopkg.in/warnings.v0 v0.1.2/go.mod h1:jksf8JmL6Qr/oQM2OXTHunEvvTAsrWBLb6OOjuVWRNI=
honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
honnef.co/go/tools v0.0.0-20190106161140-3f1c8253044a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
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honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4=
rsc.io/getopt v0.0.0-20170811000552-20be20937449 h1:UukjJOsjQH0DIuyyrcod6CXHS6cdaMMuJmrt+SN1j4A=
rsc.io/getopt v0.0.0-20170811000552-20be20937449/go.mod h1:dhCdeqAxkyt5u3/sKRkUXuHaMXUu1Pt13GTQAM2xnig=
# is older than the amount of seconds defined on PreserveVersionIfIdle,
# a snapshot of the collection's previous state is created and linked to
# the current collection.
- CollectionVersioning: false
+ CollectionVersioning: true
# 0s = auto-create a new version on every update.
# -1s = never auto-create new versions.
# > 0s = auto-create a new version when older than the specified number of seconds.
- PreserveVersionIfIdle: -1s
+ PreserveVersionIfIdle: 10s
# If non-empty, allow project and collection names to contain
# the "/" character (slash/stroke/solidus), and replace "/" with
# in /tmp on the compute node each time an Arvados container
# runs. Ensure you have something in place to delete old files
# from /tmp, or adjust the "-o" and "-e" arguments accordingly.
- BsubArgumentsList: ["-o", "/tmp/crunch-run.%%J.out", "-e", "/tmp/crunch-run.%%J.err", "-J", "%U", "-n", "%C", "-D", "%MMB", "-R", "rusage[mem=%MMB:tmp=%TMB] span[hosts=1]"]
+ BsubArgumentsList: ["-o", "/tmp/crunch-run.%%J.out", "-e", "/tmp/crunch-run.%%J.err", "-J", "%U", "-n", "%C", "-D", "%MMB", "-R", "rusage[mem=%MMB:tmp=%TMB] span[hosts=1]", "-R", "select[mem>=%MMB]", "-R", "select[tmp>=%TMB]", "-R", "select[ncpus>=%C]"]
# Use sudo to switch to this user account when submitting LSF
# jobs.
AccessKeyID: aaaaa
SecretAccessKey: aaaaa
Endpoint: ""
- Region: us-east-1a
+ Region: us-east-1
Bucket: aaaaa
LocationConstraint: false
V2Signature: false
# is older than the amount of seconds defined on PreserveVersionIfIdle,
# a snapshot of the collection's previous state is created and linked to
# the current collection.
- CollectionVersioning: false
+ CollectionVersioning: true
# 0s = auto-create a new version on every update.
# -1s = never auto-create new versions.
# > 0s = auto-create a new version when older than the specified number of seconds.
- PreserveVersionIfIdle: -1s
+ PreserveVersionIfIdle: 10s
# If non-empty, allow project and collection names to contain
# the "/" character (slash/stroke/solidus), and replace "/" with
# in /tmp on the compute node each time an Arvados container
# runs. Ensure you have something in place to delete old files
# from /tmp, or adjust the "-o" and "-e" arguments accordingly.
- BsubArgumentsList: ["-o", "/tmp/crunch-run.%%J.out", "-e", "/tmp/crunch-run.%%J.err", "-J", "%U", "-n", "%C", "-D", "%MMB", "-R", "rusage[mem=%MMB:tmp=%TMB] span[hosts=1]"]
+ BsubArgumentsList: ["-o", "/tmp/crunch-run.%%J.out", "-e", "/tmp/crunch-run.%%J.err", "-J", "%U", "-n", "%C", "-D", "%MMB", "-R", "rusage[mem=%MMB:tmp=%TMB] span[hosts=1]", "-R", "select[mem>=%MMB]", "-R", "select[tmp>=%TMB]", "-R", "select[ncpus>=%C]"]
# Use sudo to switch to this user account when submitting LSF
# jobs.
AccessKeyID: aaaaa
SecretAccessKey: aaaaa
Endpoint: ""
- Region: us-east-1a
+ Region: us-east-1
Bucket: aaaaa
LocationConstraint: false
V2Signature: false
cluster.Login.OpenIDConnect.AcceptAccessToken = true
cluster.Login.OpenIDConnect.AcceptAccessTokenScope = ""
- s.testHandler = &Handler{Cluster: cluster}
+ s.testHandler = &Handler{Cluster: cluster, BackgroundContext: ctxlog.Context(context.Background(), s.log)}
s.testServer = newServerFromIntegrationTestEnv(c)
s.testServer.Server.BaseContext = func(net.Listener) context.Context {
return ctxlog.Context(context.Background(), s.log)
// Command starts a controller service. See cmd/arvados-server/cmd.go
var Command cmd.Handler = service.Command(arvados.ServiceNameController, newHandler)
-func newHandler(_ context.Context, cluster *arvados.Cluster, _ string, _ *prometheus.Registry) service.Handler {
- return &Handler{Cluster: cluster}
+func newHandler(ctx context.Context, cluster *arvados.Cluster, _ string, _ *prometheus.Registry) service.Handler {
+ return &Handler{Cluster: cluster, BackgroundContext: ctx}
}
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package dblock
+
+import (
+ "context"
+ "database/sql"
+ "sync"
+ "time"
+
+ "git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "github.com/jmoiron/sqlx"
+)
+
+var (
+ TrashSweep = &DBLocker{key: 10001}
+ retryDelay = 5 * time.Second
+)
+
+// DBLocker uses pg_advisory_lock to maintain a cluster-wide lock for
+// a long-running task like "do X every N seconds".
+type DBLocker struct {
+ key int
+ mtx sync.Mutex
+ ctx context.Context
+ getdb func(context.Context) (*sqlx.DB, error)
+ conn *sql.Conn // != nil if advisory lock has been acquired
+}
+
+// Lock acquires the advisory lock, waiting/reconnecting if needed.
+func (dbl *DBLocker) Lock(ctx context.Context, getdb func(context.Context) (*sqlx.DB, error)) {
+ logger := ctxlog.FromContext(ctx)
+ for ; ; time.Sleep(retryDelay) {
+ dbl.mtx.Lock()
+ if dbl.conn != nil {
+ // Another goroutine is already locked/waiting
+ // on this lock. Wait for them to release.
+ dbl.mtx.Unlock()
+ continue
+ }
+ db, err := getdb(ctx)
+ if err != nil {
+ logger.WithError(err).Infof("error getting database pool")
+ dbl.mtx.Unlock()
+ continue
+ }
+ conn, err := db.Conn(ctx)
+ if err != nil {
+ logger.WithError(err).Info("error getting database connection")
+ dbl.mtx.Unlock()
+ continue
+ }
+ var locked bool
+ err = conn.QueryRowContext(ctx, `SELECT pg_try_advisory_lock($1)`, dbl.key).Scan(&locked)
+ if err != nil {
+ logger.WithError(err).Infof("error getting pg_try_advisory_lock %d", dbl.key)
+ conn.Close()
+ dbl.mtx.Unlock()
+ continue
+ }
+ if !locked {
+ conn.Close()
+ dbl.mtx.Unlock()
+ continue
+ }
+ logger.Debugf("acquired pg_advisory_lock %d", dbl.key)
+ dbl.ctx, dbl.getdb, dbl.conn = ctx, getdb, conn
+ dbl.mtx.Unlock()
+ return
+ }
+}
+
+// Check confirms that the lock is still active (i.e., the session is
+// still alive), and re-acquires if needed. Panics if Lock is not
+// acquired first.
+func (dbl *DBLocker) Check() {
+ dbl.mtx.Lock()
+ err := dbl.conn.PingContext(dbl.ctx)
+ if err == nil {
+ ctxlog.FromContext(dbl.ctx).Debugf("pg_advisory_lock %d connection still alive", dbl.key)
+ dbl.mtx.Unlock()
+ return
+ }
+ ctxlog.FromContext(dbl.ctx).WithError(err).Info("database connection ping failed")
+ dbl.conn.Close()
+ dbl.conn = nil
+ ctx, getdb := dbl.ctx, dbl.getdb
+ dbl.mtx.Unlock()
+ dbl.Lock(ctx, getdb)
+}
+
+func (dbl *DBLocker) Unlock() {
+ dbl.mtx.Lock()
+ defer dbl.mtx.Unlock()
+ if dbl.conn != nil {
+ _, err := dbl.conn.ExecContext(context.Background(), `SELECT pg_advisory_unlock($1)`, dbl.key)
+ if err != nil {
+ ctxlog.FromContext(dbl.ctx).WithError(err).Infof("error releasing pg_advisory_lock %d", dbl.key)
+ } else {
+ ctxlog.FromContext(dbl.ctx).Debugf("released pg_advisory_lock %d", dbl.key)
+ }
+ dbl.conn.Close()
+ dbl.conn = nil
+ }
+}
}
return &arvados.APIClientAuthorization{
- UUID: uuid,
- APIToken: token,
- ExpiresAt: "",
- Scopes: scopes}, nil
+ UUID: uuid,
+ APIToken: token,
+ Scopes: scopes}, nil
}
// Extract the auth token supplied in req, and replace it with a
return conn.chooseBackend(options.UUID).SpecimenDelete(ctx, options)
}
+func (conn *Conn) SysTrashSweep(ctx context.Context, options struct{}) (struct{}, error) {
+ return conn.local.SysTrashSweep(ctx, options)
+}
+
var userAttrsCachedFromLoginCluster = map[string]bool{
"created_at": true,
"email": true,
return conn.chooseBackend(options.UUID).APIClientAuthorizationCurrent(ctx, options)
}
+func (conn *Conn) APIClientAuthorizationCreate(ctx context.Context, options arvados.CreateOptions) (arvados.APIClientAuthorization, error) {
+ if conn.cluster.Login.LoginCluster != "" {
+ return conn.chooseBackend(conn.cluster.Login.LoginCluster).APIClientAuthorizationCreate(ctx, options)
+ }
+ ownerUUID, ok := options.Attrs["owner_uuid"].(string)
+ if ok && ownerUUID != "" {
+ return conn.chooseBackend(ownerUUID).APIClientAuthorizationCreate(ctx, options)
+ }
+ return conn.local.APIClientAuthorizationCreate(ctx, options)
+}
+
+func (conn *Conn) APIClientAuthorizationUpdate(ctx context.Context, options arvados.UpdateOptions) (arvados.APIClientAuthorization, error) {
+ return conn.chooseBackend(options.UUID).APIClientAuthorizationUpdate(ctx, options)
+}
+
+func (conn *Conn) APIClientAuthorizationDelete(ctx context.Context, options arvados.DeleteOptions) (arvados.APIClientAuthorization, error) {
+ return conn.chooseBackend(options.UUID).APIClientAuthorizationDelete(ctx, options)
+}
+
+func (conn *Conn) APIClientAuthorizationList(ctx context.Context, options arvados.ListOptions) (arvados.APIClientAuthorizationList, error) {
+ return conn.local.APIClientAuthorizationList(ctx, options)
+}
+
+func (conn *Conn) APIClientAuthorizationGet(ctx context.Context, options arvados.GetOptions) (arvados.APIClientAuthorization, error) {
+ return conn.chooseBackend(options.UUID).APIClientAuthorizationGet(ctx, options)
+}
+
type backend interface {
arvados.API
BaseURL() url.URL
cluster.Collections.BlobSigningTTL = arvados.Duration(time.Hour * 24 * 14)
arvadostest.SetServiceURL(&cluster.Services.RailsAPI, "http://localhost:1/")
arvadostest.SetServiceURL(&cluster.Services.Controller, "http://localhost:/")
- s.testHandler = &Handler{Cluster: cluster}
+ s.testHandler = &Handler{Cluster: cluster, BackgroundContext: ctxlog.Context(context.Background(), s.log)}
s.testServer = newServerFromIntegrationTestEnv(c)
s.testServer.Server.BaseContext = func(net.Listener) context.Context {
return ctxlog.Context(context.Background(), s.log)
var aca arvados.APIClientAuthorization
c.Check(json.NewDecoder(resp.Body).Decode(&aca), check.IsNil)
c.Check(aca.ExpiresAt, check.NotNil) // Time.Now()+BlobSigningTTL
- t, _ := time.Parse(time.RFC3339Nano, aca.ExpiresAt)
+ t := aca.ExpiresAt
c.Check(t.After(time.Now().Add(s.testHandler.Cluster.API.MaxTokenLifetime.Duration())), check.Equals, true)
c.Check(t.Before(time.Now().Add(s.testHandler.Cluster.Collections.BlobSigningTTL.Duration())), check.Equals, true)
}
)
type Handler struct {
- Cluster *arvados.Cluster
+ Cluster *arvados.Cluster
+ BackgroundContext context.Context
setupOnce sync.Once
+ federation *federation.Conn
handlerStack http.Handler
proxy *proxy
secureClient *http.Client
healthFuncs := make(map[string]health.Func)
oidcAuthorizer := localdb.OIDCAccessTokenAuthorizer(h.Cluster, h.db)
- rtr := router.New(federation.New(h.Cluster, &healthFuncs), router.Config{
+ h.federation = federation.New(h.Cluster, &healthFuncs)
+ rtr := router.New(h.federation, router.Config{
MaxRequestSize: h.Cluster.API.MaxRequestSize,
WrapCalls: api.ComposeWrappers(ctrlctx.WrapCallsInTransactions(h.db), oidcAuthorizer.WrapCalls),
})
mux.Handle("/arvados/v1/links/", rtr)
mux.Handle("/login", rtr)
mux.Handle("/logout", rtr)
+ mux.Handle("/arvados/v1/api_client_authorizations", rtr)
+ mux.Handle("/arvados/v1/api_client_authorizations/", rtr)
hs := http.NotFoundHandler()
hs = prepend(hs, h.proxyRailsAPI)
h.proxy = &proxy{
Name: "arvados-controller",
}
+
+ go h.trashSweepWorker()
}
var errDBConnection = errors.New("database connection error")
type HandlerSuite struct {
cluster *arvados.Cluster
- handler http.Handler
+ handler *Handler
ctx context.Context
cancel context.CancelFunc
}
s.cluster.TLS.Insecure = true
arvadostest.SetServiceURL(&s.cluster.Services.RailsAPI, "https://"+os.Getenv("ARVADOS_TEST_API_HOST"))
arvadostest.SetServiceURL(&s.cluster.Services.Controller, "http://localhost:/")
- s.handler = newHandler(s.ctx, s.cluster, "", prometheus.NewRegistry())
+ s.handler = newHandler(s.ctx, s.cluster, "", prometheus.NewRegistry()).(*Handler)
}
func (s *HandlerSuite) TearDownTest(c *check.C) {
func (s *HandlerSuite) TestValidateV1APIToken(c *check.C) {
req := httptest.NewRequest("GET", "/arvados/v1/users/current", nil)
- user, ok, err := s.handler.(*Handler).validateAPItoken(req, arvadostest.ActiveToken)
+ user, ok, err := s.handler.validateAPItoken(req, arvadostest.ActiveToken)
c.Assert(err, check.IsNil)
c.Check(ok, check.Equals, true)
c.Check(user.Authorization.UUID, check.Equals, arvadostest.ActiveTokenUUID)
func (s *HandlerSuite) TestValidateV2APIToken(c *check.C) {
req := httptest.NewRequest("GET", "/arvados/v1/users/current", nil)
- user, ok, err := s.handler.(*Handler).validateAPItoken(req, arvadostest.ActiveTokenV2)
+ user, ok, err := s.handler.validateAPItoken(req, arvadostest.ActiveTokenV2)
c.Assert(err, check.IsNil)
c.Check(ok, check.Equals, true)
c.Check(user.Authorization.UUID, check.Equals, arvadostest.ActiveTokenUUID)
func (s *HandlerSuite) TestCreateAPIToken(c *check.C) {
req := httptest.NewRequest("GET", "/arvados/v1/users/current", nil)
- auth, err := s.handler.(*Handler).createAPItoken(req, arvadostest.ActiveUserUUID, nil)
+ auth, err := s.handler.createAPItoken(req, arvadostest.ActiveUserUUID, nil)
c.Assert(err, check.IsNil)
c.Check(auth.Scopes, check.DeepEquals, []string{"all"})
- user, ok, err := s.handler.(*Handler).validateAPItoken(req, auth.TokenV2())
+ user, ok, err := s.handler.validateAPItoken(req, auth.TokenV2())
c.Assert(err, check.IsNil)
c.Check(ok, check.Equals, true)
c.Check(user.Authorization.UUID, check.Equals, auth.UUID)
json.Unmarshal(resp.Body.Bytes(), &ksList)
c.Assert(len(ksList.Items), check.Not(check.Equals), 0)
ksUUID := ksList.Items[0].UUID
+ // Create a new token for the test user so that we're not comparing
+ // the ones from the fixtures.
+ req = httptest.NewRequest("POST", "/arvados/v1/api_client_authorizations",
+ strings.NewReader(`{
+ "api_client_authorization": {
+ "owner_uuid": "`+arvadostest.AdminUserUUID+`",
+ "created_by_ip_address": "::1",
+ "last_used_by_ip_address": "::1",
+ "default_owner_uuid": "`+arvadostest.AdminUserUUID+`"
+ }
+ }`))
+ req.Header.Set("Authorization", "Bearer "+arvadostest.SystemRootToken)
+ req.Header.Set("Content-type", "application/json")
+ resp = httptest.NewRecorder()
+ s.handler.ServeHTTP(resp, req)
+ c.Assert(resp.Code, check.Equals, http.StatusOK,
+ check.Commentf("%s", resp.Body.String()))
+ var auth arvados.APIClientAuthorization
+ json.Unmarshal(resp.Body.Bytes(), &auth)
+ c.Assert(auth.UUID, check.Not(check.Equals), "")
testCases := map[string]map[string]bool{
"api_clients/" + arvadostest.TrustedWorkbenchAPIClientUUID: nil,
- "api_client_authorizations/" + arvadostest.AdminTokenUUID: nil,
+ "api_client_authorizations/" + auth.UUID: {"href": true, "modified_by_client_uuid": true, "modified_by_user_uuid": true},
"authorized_keys/" + arvadostest.AdminAuthorizedKeysUUID: nil,
"collections/" + arvadostest.CollectionWithUniqueWordsUUID: {"href": true},
"containers/" + arvadostest.RunningContainerUUID: nil,
"workflows/" + arvadostest.WorkflowWithDefinitionYAMLUUID: nil,
}
for url, skippedFields := range testCases {
- s.CheckObjectType(c, "/arvados/v1/"+url, arvadostest.AdminToken, skippedFields)
+ c.Logf("Testing %q", url)
+ s.CheckObjectType(c, "/arvados/v1/"+url, auth.TokenV2(), skippedFields)
}
}
c.Check(jresp.Errors[0], check.Matches, `.*//railsapi\.internal/arvados/v1/collections/.*: 404 Not Found.*`)
c.Check(jresp.Errors[0], check.Not(check.Matches), `(?ms).*127.0.0.1.*`)
}
+
+func (s *HandlerSuite) TestTrashSweep(c *check.C) {
+ s.cluster.SystemRootToken = arvadostest.SystemRootToken
+ s.cluster.Collections.TrashSweepInterval = arvados.Duration(time.Second / 10)
+ s.handler.CheckHealth()
+ ctx := auth.NewContext(s.ctx, &auth.Credentials{Tokens: []string{arvadostest.ActiveTokenV2}})
+ coll, err := s.handler.federation.CollectionCreate(ctx, arvados.CreateOptions{Attrs: map[string]interface{}{"name": "test trash sweep"}, EnsureUniqueName: true})
+ c.Assert(err, check.IsNil)
+ defer s.handler.federation.CollectionDelete(ctx, arvados.DeleteOptions{UUID: coll.UUID})
+ db, err := s.handler.db(s.ctx)
+ c.Assert(err, check.IsNil)
+ _, err = db.ExecContext(s.ctx, `update collections set trash_at = $1, delete_at = $2 where uuid = $3`, time.Now().UTC().Add(time.Second/10), time.Now().UTC().Add(time.Hour), coll.UUID)
+ c.Assert(err, check.IsNil)
+ deadline := time.Now().Add(5 * time.Second)
+ for {
+ if time.Now().After(deadline) {
+ c.Log("timed out")
+ c.FailNow()
+ }
+ updated, err := s.handler.federation.CollectionGet(ctx, arvados.GetOptions{UUID: coll.UUID, IncludeTrash: true})
+ c.Assert(err, check.IsNil)
+ if updated.IsTrashed {
+ break
+ }
+ time.Sleep(time.Second / 10)
+ }
+}
}
}
+// Test for #17785
+func (s *IntegrationSuite) TestFederatedApiClientAuthHandling(c *check.C) {
+ rootctx1, rootclnt1, _ := s.testClusters["z1111"].RootClients()
+ conn1 := s.testClusters["z1111"].Conn()
+
+ // Make sure LoginCluster is properly configured
+ for _, cls := range []string{"z1111", "z3333"} {
+ c.Check(
+ s.testClusters[cls].Config.Clusters[cls].Login.LoginCluster,
+ check.Equals, "z1111",
+ check.Commentf("incorrect LoginCluster config on cluster %q", cls))
+ }
+ // Get user's UUID & attempt to create a token for it on the remote cluster
+ _, _, _, user := s.testClusters["z1111"].UserClients(rootctx1, c, conn1,
+ "user@example.com", true)
+ _, rootclnt3, _ := s.testClusters["z3333"].ClientsWithToken(rootclnt1.AuthToken)
+ var resp arvados.APIClientAuthorization
+ err := rootclnt3.RequestAndDecode(
+ &resp, "POST", "arvados/v1/api_client_authorizations", nil,
+ map[string]interface{}{
+ "api_client_authorization": map[string]string{
+ "owner_uuid": user.UUID,
+ },
+ },
+ )
+ c.Assert(err, check.IsNil)
+ newTok := resp.TokenV2()
+ c.Assert(newTok, check.Not(check.Equals), "")
+
+ // Confirm the token is from z1111
+ c.Assert(strings.HasPrefix(newTok, "v2/z1111-gj3su-"), check.Equals, true)
+
+ // Confirm the token works and is from the correct user
+ _, rootclnt3bis, _ := s.testClusters["z3333"].ClientsWithToken(newTok)
+ var curUser arvados.User
+ err = rootclnt3bis.RequestAndDecode(
+ &curUser, "GET", "arvados/v1/users/current", nil, nil,
+ )
+ c.Assert(err, check.IsNil)
+ c.Assert(curUser.UUID, check.Equals, user.UUID)
+}
+
// Test for bug #18076
func (s *IntegrationSuite) TestStaleCachedUserRecord(c *check.C) {
rootctx1, _, _ := s.testClusters["z1111"].RootClients()
conn3 := s.testClusters["z3333"].Conn()
// Make sure LoginCluster is properly configured
- for cls := range s.testClusters {
- if cls == "z1111" || cls == "z3333" {
- c.Check(
- s.testClusters[cls].Config.Clusters[cls].Login.LoginCluster,
- check.Equals, "z1111",
- check.Commentf("incorrect LoginCluster config on cluster %q", cls))
- }
+ for _, cls := range []string{"z1111", "z3333"} {
+ c.Check(
+ s.testClusters[cls].Config.Clusters[cls].Login.LoginCluster,
+ check.Equals, "z1111",
+ check.Commentf("incorrect LoginCluster config on cluster %q", cls))
}
for testCaseNr, testCase := range []struct {
// Receive binary
_, err = io.ReadFull(sshconn.Conn, buf[:4])
c.Check(err, check.IsNil)
- c.Check(buf[:4], check.DeepEquals, []byte{0, 0, 1, 0xfc})
// If we can get this far into an SSH handshake...
- c.Log("success, tunnel is working")
+ c.Logf("was able to read %x -- success, tunnel is working", buf[:4])
}()
select {
case <-done:
tokensecret = tokenparts[2]
}
}
- var exp sql.NullString
+ var exp sql.NullTime
var scopes []byte
err = tx.QueryRowxContext(ctx, "select uuid, api_token, expires_at, scopes from api_client_authorizations where api_token=$1", tokensecret).Scan(&resp.UUID, &resp.APIToken, &exp, &scopes)
if err != nil {
return
}
- resp.ExpiresAt = exp.String
+ resp.ExpiresAt = exp.Time
if len(scopes) > 0 {
err = json.Unmarshal(scopes, &resp.Scopes)
if err != nil {
// cached positive result
aca := cached.(arvados.APIClientAuthorization)
var expiring bool
- if aca.ExpiresAt != "" {
- t, err := time.Parse(time.RFC3339Nano, aca.ExpiresAt)
- if err != nil {
- return fmt.Errorf("error parsing expires_at value: %w", err)
- }
+ if !aca.ExpiresAt.IsZero() {
+ t := aca.ExpiresAt
expiring = t.Before(time.Now().Add(time.Minute))
}
if !expiring {
if err != nil {
return err
}
- aca.ExpiresAt = exp.Format(time.RFC3339Nano)
+ aca.ExpiresAt = exp
ta.cache.Add(tok, aca)
return nil
}
}
var infixMap = map[string]interface{}{
+ "gj3su": arvados.APIClientAuthorization{},
"4zz18": arvados.Collection{},
"xvhdp": arvados.ContainerRequest{},
"dz642": arvados.Container{},
"7fd4e": arvados.Workflow{},
}
+var specialKindTransforms = map[string]string{
+ "arvados.APIClientAuthorization": "arvados#apiClientAuthorization",
+ "arvados.APIClientAuthorizationList": "arvados#apiClientAuthorizationList",
+}
+
var mungeKind = regexp.MustCompile(`\..`)
func kind(resp interface{}) string {
if !strings.HasPrefix(t, "arvados.") {
return ""
}
+ if k, ok := specialKindTransforms[t]; ok {
+ return k
+ }
return mungeKind.ReplaceAllStringFunc(t, func(s string) string {
// "arvados.CollectionList" => "arvados#collectionList"
return "#" + strings.ToLower(s[1:])
return rtr.backend.SpecimenDelete(ctx, *opts.(*arvados.DeleteOptions))
},
},
+ {
+ arvados.EndpointAPIClientAuthorizationCreate,
+ func() interface{} { return &arvados.CreateOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationCreate(ctx, *opts.(*arvados.CreateOptions))
+ },
+ },
+ {
+ arvados.EndpointAPIClientAuthorizationUpdate,
+ func() interface{} { return &arvados.UpdateOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationUpdate(ctx, *opts.(*arvados.UpdateOptions))
+ },
+ },
+ {
+ arvados.EndpointAPIClientAuthorizationDelete,
+ func() interface{} { return &arvados.DeleteOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationDelete(ctx, *opts.(*arvados.DeleteOptions))
+ },
+ },
+ {
+ arvados.EndpointAPIClientAuthorizationList,
+ func() interface{} { return &arvados.ListOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationList(ctx, *opts.(*arvados.ListOptions))
+ },
+ },
+ {
+ arvados.EndpointAPIClientAuthorizationCurrent,
+ func() interface{} { return &arvados.GetOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationCurrent(ctx, *opts.(*arvados.GetOptions))
+ },
+ },
+ {
+ arvados.EndpointAPIClientAuthorizationGet,
+ func() interface{} { return &arvados.GetOptions{} },
+ func(ctx context.Context, opts interface{}) (interface{}, error) {
+ return rtr.backend.APIClientAuthorizationGet(ctx, *opts.(*arvados.GetOptions))
+ },
+ },
{
arvados.EndpointUserCreate,
func() interface{} { return &arvados.CreateOptions{} },
return resp, err
}
+func (conn *Conn) SysTrashSweep(ctx context.Context, options struct{}) (struct{}, error) {
+ ep := arvados.EndpointSysTrashSweep
+ var resp struct{}
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
+
func (conn *Conn) UserCreate(ctx context.Context, options arvados.CreateOptions) (arvados.User, error) {
ep := arvados.EndpointUserCreate
var resp arvados.User
err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
return resp, err
}
+func (conn *Conn) APIClientAuthorizationCreate(ctx context.Context, options arvados.CreateOptions) (arvados.APIClientAuthorization, error) {
+ ep := arvados.EndpointAPIClientAuthorizationCreate
+ var resp arvados.APIClientAuthorization
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
+func (conn *Conn) APIClientAuthorizationUpdate(ctx context.Context, options arvados.UpdateOptions) (arvados.APIClientAuthorization, error) {
+ ep := arvados.EndpointAPIClientAuthorizationUpdate
+ var resp arvados.APIClientAuthorization
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
+func (conn *Conn) APIClientAuthorizationDelete(ctx context.Context, options arvados.DeleteOptions) (arvados.APIClientAuthorization, error) {
+ ep := arvados.EndpointAPIClientAuthorizationDelete
+ var resp arvados.APIClientAuthorization
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
+func (conn *Conn) APIClientAuthorizationList(ctx context.Context, options arvados.ListOptions) (arvados.APIClientAuthorizationList, error) {
+ ep := arvados.EndpointAPIClientAuthorizationList
+ var resp arvados.APIClientAuthorizationList
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
+func (conn *Conn) APIClientAuthorizationGet(ctx context.Context, options arvados.GetOptions) (arvados.APIClientAuthorization, error) {
+ ep := arvados.EndpointAPIClientAuthorizationGet
+ var resp arvados.APIClientAuthorization
+ err := conn.requestAndDecode(ctx, &resp, ep, nil, options)
+ return resp, err
+}
type UserSessionAuthInfo struct {
UserUUID string `json:"user_uuid"`
// provided by the integration-testing environment.
func newServerFromIntegrationTestEnv(c *check.C) *httpserver.Server {
log := ctxlog.TestLogger(c)
-
- handler := &Handler{Cluster: &arvados.Cluster{
- ClusterID: "zzzzz",
- PostgreSQL: integrationTestCluster().PostgreSQL,
- }}
+ ctx := ctxlog.Context(context.Background(), log)
+ handler := &Handler{
+ Cluster: &arvados.Cluster{
+ ClusterID: "zzzzz",
+ PostgreSQL: integrationTestCluster().PostgreSQL,
+ },
+ BackgroundContext: ctx,
+ }
handler.Cluster.TLS.Insecure = true
handler.Cluster.Collections.BlobSigning = true
handler.Cluster.Collections.BlobSigningKey = arvadostest.BlobSigningKey
srv := &httpserver.Server{
Server: http.Server{
- BaseContext: func(net.Listener) context.Context {
- return ctxlog.Context(context.Background(), log)
- },
- Handler: httpserver.AddRequestIDs(httpserver.LogRequests(handler)),
+ BaseContext: func(net.Listener) context.Context { return ctx },
+ Handler: httpserver.AddRequestIDs(httpserver.LogRequests(handler)),
},
Addr: ":",
}
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package controller
+
+import (
+ "time"
+
+ "git.arvados.org/arvados.git/lib/controller/dblock"
+ "git.arvados.org/arvados.git/sdk/go/auth"
+ "git.arvados.org/arvados.git/sdk/go/ctxlog"
+)
+
+func (h *Handler) trashSweepWorker() {
+ sleep := h.Cluster.Collections.TrashSweepInterval.Duration()
+ logger := ctxlog.FromContext(h.BackgroundContext).WithField("worker", "trash sweep")
+ ctx := ctxlog.Context(h.BackgroundContext, logger)
+ if sleep <= 0 {
+ logger.Debugf("Collections.TrashSweepInterval is %v, not running worker", sleep)
+ return
+ }
+ dblock.TrashSweep.Lock(ctx, h.db)
+ defer dblock.TrashSweep.Unlock()
+ for time.Sleep(sleep); ctx.Err() == nil; time.Sleep(sleep) {
+ dblock.TrashSweep.Check()
+ ctx := auth.NewContext(ctx, &auth.Credentials{Tokens: []string{h.Cluster.SystemRootToken}})
+ _, err := h.federation.SysTrashSweep(ctx, struct{}{})
+ if err != nil {
+ logger.WithError(err).Info("trash sweep failed")
+ }
+ }
+}
if ok, code := cmd.ParseFlags(flags, prog, args, "container-uuid", stderr); !ok {
return code
- } else if flags.NArg() != 1 {
+ } else if !*list && flags.NArg() != 1 {
fmt.Fprintf(stderr, "missing required argument: container-uuid (try -help)\n")
return 2
}
if ctr.State != dispatch.Locked {
// already started by prior invocation
- } else if _, ok := disp.lsfqueue.JobID(ctr.UUID); !ok {
+ } else if _, ok := disp.lsfqueue.Lookup(ctr.UUID); !ok {
disp.logger.Printf("Submitting container %s to LSF", ctr.UUID)
cmd := []string{disp.Cluster.Containers.CrunchRunCommand}
cmd = append(cmd, "--runtime-engine="+disp.Cluster.Containers.RuntimeEngine)
disp.logger.Printf("Start monitoring container %v in state %q", ctr.UUID, ctr.State)
defer disp.logger.Printf("Done monitoring container %s", ctr.UUID)
- // If the container disappears from the lsf queue, there is
- // no point in waiting for further dispatch updates: just
- // clean up and return.
go func(uuid string) {
+ cancelled := false
for ctx.Err() == nil {
- if _, ok := disp.lsfqueue.JobID(uuid); !ok {
+ qent, ok := disp.lsfqueue.Lookup(uuid)
+ if !ok {
+ // If the container disappears from
+ // the lsf queue, there is no point in
+ // waiting for further dispatch
+ // updates: just clean up and return.
disp.logger.Printf("container %s job disappeared from LSF queue", uuid)
cancel()
return
}
+ if !cancelled && qent.Stat == "PEND" && strings.Contains(qent.PendReason, "There are no suitable hosts for the job") {
+ disp.logger.Printf("container %s: %s", uuid, qent.PendReason)
+ err := disp.arvDispatcher.Arv.Update("containers", uuid, arvadosclient.Dict{
+ "container": map[string]interface{}{
+ "runtime_status": map[string]string{
+ "error": qent.PendReason,
+ },
+ },
+ }, nil)
+ if err != nil {
+ disp.logger.Printf("error setting runtime_status on %s: %s", uuid, err)
+ continue // retry
+ }
+ err = disp.arvDispatcher.UpdateState(uuid, dispatch.Cancelled)
+ if err != nil {
+ continue // retry (UpdateState() already logged the error)
+ }
+ cancelled = true
+ }
}
}(ctr.UUID)
// from the queue.
ticker := time.NewTicker(5 * time.Second)
defer ticker.Stop()
- for jobid, ok := disp.lsfqueue.JobID(ctr.UUID); ok; _, ok = disp.lsfqueue.JobID(ctr.UUID) {
- err := disp.lsfcli.Bkill(jobid)
+ for qent, ok := disp.lsfqueue.Lookup(ctr.UUID); ok; _, ok = disp.lsfqueue.Lookup(ctr.UUID) {
+ err := disp.lsfcli.Bkill(qent.ID)
if err != nil {
- disp.logger.Warnf("%s: bkill(%d): %s", ctr.UUID, jobid, err)
+ disp.logger.Warnf("%s: bkill(%s): %s", ctr.UUID, qent.ID, err)
}
<-ticker.C
}
}
func (disp *dispatcher) bkill(ctr arvados.Container) {
- if jobid, ok := disp.lsfqueue.JobID(ctr.UUID); !ok {
+ if qent, ok := disp.lsfqueue.Lookup(ctr.UUID); !ok {
disp.logger.Debugf("bkill(%s): redundant, job not in queue", ctr.UUID)
- } else if err := disp.lsfcli.Bkill(jobid); err != nil {
- disp.logger.Warnf("%s: bkill(%d): %s", ctr.UUID, jobid, err)
+ } else if err := disp.lsfcli.Bkill(qent.ID); err != nil {
+ disp.logger.Warnf("%s: bkill(%s): %s", ctr.UUID, qent.ID, err)
}
}
import (
"context"
+ "encoding/json"
"fmt"
"math/rand"
"os/exec"
var _ = check.Suite(&suite{})
type suite struct {
- disp *dispatcher
+ disp *dispatcher
+ crTooBig arvados.ContainerRequest
}
func (s *suite) TearDownTest(c *check.C) {
s.disp.lsfcli.stubCommand = func(string, ...string) *exec.Cmd {
return exec.Command("bash", "-c", "echo >&2 unimplemented stub; false")
}
+ err = arvados.NewClientFromEnv().RequestAndDecode(&s.crTooBig, "POST", "arvados/v1/container_requests", nil, map[string]interface{}{
+ "container_request": map[string]interface{}{
+ "runtime_constraints": arvados.RuntimeConstraints{
+ RAM: 1000000000000,
+ VCPUs: 1,
+ },
+ "container_image": arvadostest.DockerImage112PDH,
+ "command": []string{"sleep", "1"},
+ "mounts": map[string]arvados.Mount{"/mnt/out": {Kind: "tmp", Capacity: 1000}},
+ "output_path": "/mnt/out",
+ "state": arvados.ContainerRequestStateCommitted,
+ "priority": 1,
+ "container_count_max": 1,
+ },
+ })
+ c.Assert(err, check.IsNil)
}
type lsfstub struct {
"-J", arvadostest.LockedContainerUUID,
"-n", "4",
"-D", "11701MB",
- "-R", "rusage[mem=11701MB:tmp=0MB] span[hosts=1]"})
+ "-R", "rusage[mem=11701MB:tmp=0MB] span[hosts=1]",
+ "-R", "select[mem>=11701MB]",
+ "-R", "select[tmp>=0MB]",
+ "-R", "select[ncpus>=4]"})
mtx.Lock()
fakejobq[nextjobid] = args[1]
nextjobid++
"-J", arvadostest.QueuedContainerUUID,
"-n", "4",
"-D", "11701MB",
- "-R", "rusage[mem=11701MB:tmp=45777MB] span[hosts=1]"})
+ "-R", "rusage[mem=11701MB:tmp=45777MB] span[hosts=1]",
+ "-R", "select[mem>=11701MB]",
+ "-R", "select[tmp>=45777MB]",
+ "-R", "select[ncpus>=4]"})
+ mtx.Lock()
+ fakejobq[nextjobid] = args[1]
+ nextjobid++
+ mtx.Unlock()
+ case s.crTooBig.ContainerUUID:
+ c.Check(args, check.DeepEquals, []string{
+ "-J", s.crTooBig.ContainerUUID,
+ "-n", "1",
+ "-D", "954187MB",
+ "-R", "rusage[mem=954187MB:tmp=256MB] span[hosts=1]",
+ "-R", "select[mem>=954187MB]",
+ "-R", "select[tmp>=256MB]",
+ "-R", "select[ncpus>=1]"})
mtx.Lock()
fakejobq[nextjobid] = args[1]
nextjobid++
}
return exec.Command("echo", "submitted job")
case "bjobs":
- c.Check(args, check.DeepEquals, []string{"-u", "all", "-noheader", "-o", "jobid stat job_name:30"})
- out := ""
+ c.Check(args, check.DeepEquals, []string{"-u", "all", "-o", "jobid stat job_name pend_reason", "-json"})
+ var records []map[string]interface{}
for jobid, uuid := range fakejobq {
- out += fmt.Sprintf(`%d %s %s\n`, jobid, "RUN", uuid)
+ stat, reason := "RUN", ""
+ if uuid == s.crTooBig.ContainerUUID {
+ // The real bjobs output includes a trailing ';' here:
+ stat, reason = "PEND", "There are no suitable hosts for the job;"
+ }
+ records = append(records, map[string]interface{}{
+ "JOBID": fmt.Sprintf("%d", jobid),
+ "STAT": stat,
+ "JOB_NAME": uuid,
+ "PEND_REASON": reason,
+ })
}
- c.Logf("bjobs out: %q", out)
- return exec.Command("printf", out)
+ out, err := json.Marshal(map[string]interface{}{
+ "COMMAND": "bjobs",
+ "JOBS": len(fakejobq),
+ "RECORDS": records,
+ })
+ if err != nil {
+ panic(err)
+ }
+ c.Logf("bjobs out: %s", out)
+ return exec.Command("printf", string(out))
case "bkill":
killid, _ := strconv.Atoi(args[0])
if uuid, ok := fakejobq[killid]; !ok {
sudoUser: s.disp.Cluster.Containers.LSF.BsubSudoUser,
}.stubCommand(s, c)
s.disp.Start()
+
deadline := time.Now().Add(20 * time.Second)
for range time.NewTicker(time.Second).C {
if time.Now().After(deadline) {
break
}
// "queuedcontainer" should be running
- if _, ok := s.disp.lsfqueue.JobID(arvadostest.QueuedContainerUUID); !ok {
+ if _, ok := s.disp.lsfqueue.Lookup(arvadostest.QueuedContainerUUID); !ok {
continue
}
// "lockedcontainer" should be cancelled because it
// has priority 0 (no matching container requests)
- if _, ok := s.disp.lsfqueue.JobID(arvadostest.LockedContainerUUID); ok {
+ if _, ok := s.disp.lsfqueue.Lookup(arvadostest.LockedContainerUUID); ok {
+ continue
+ }
+ // "crTooBig" should be cancelled because lsf stub
+ // reports there is no suitable instance type
+ if _, ok := s.disp.lsfqueue.Lookup(s.crTooBig.ContainerUUID); ok {
continue
}
var ctr arvados.Container
if err := s.disp.arvDispatcher.Arv.Get("containers", arvadostest.LockedContainerUUID, nil, &ctr); err != nil {
c.Logf("error getting container state for %s: %s", arvadostest.LockedContainerUUID, err)
continue
- }
- if ctr.State != arvados.ContainerStateQueued {
+ } else if ctr.State != arvados.ContainerStateQueued {
c.Logf("LockedContainer is not in the LSF queue but its arvados record has not been updated to state==Queued (state is %q)", ctr.State)
continue
}
+
+ if err := s.disp.arvDispatcher.Arv.Get("containers", s.crTooBig.ContainerUUID, nil, &ctr); err != nil {
+ c.Logf("error getting container state for %s: %s", s.crTooBig.ContainerUUID, err)
+ continue
+ } else if ctr.State != arvados.ContainerStateCancelled {
+ c.Logf("container %s is not in the LSF queue but its arvados record has not been updated to state==Cancelled (state is %q)", s.crTooBig.ContainerUUID, ctr.State)
+ continue
+ } else {
+ c.Check(ctr.RuntimeStatus["error"], check.Equals, "There are no suitable hosts for the job;")
+ }
c.Log("reached desired state")
break
}
import (
"bytes"
+ "encoding/json"
"fmt"
"os"
"os/exec"
)
type bjobsEntry struct {
- id int
- name string
- stat string
+ ID string `json:"JOBID"`
+ Name string `json:"JOB_NAME"`
+ Stat string `json:"STAT"`
+ PendReason string `json:"PEND_REASON"`
}
type lsfcli struct {
func (cli lsfcli) Bjobs() ([]bjobsEntry, error) {
cli.logger.Debugf("Bjobs()")
- cmd := cli.command("bjobs", "-u", "all", "-noheader", "-o", "jobid stat job_name:30")
+ cmd := cli.command("bjobs", "-u", "all", "-o", "jobid stat job_name pend_reason", "-json")
buf, err := cmd.Output()
if err != nil {
return nil, errWithStderr(err)
}
- var bjobs []bjobsEntry
- for _, line := range strings.Split(string(buf), "\n") {
- if line == "" {
- continue
- }
- var ent bjobsEntry
- if _, err := fmt.Sscan(line, &ent.id, &ent.stat, &ent.name); err != nil {
- cli.logger.Warnf("ignoring unparsed line in bjobs output: %q", line)
- continue
- }
- bjobs = append(bjobs, ent)
+ var resp struct {
+ Records []bjobsEntry `json:"RECORDS"`
}
- return bjobs, nil
+ err = json.Unmarshal(buf, &resp)
+ return resp.Records, err
}
-func (cli lsfcli) Bkill(id int) error {
- cli.logger.Infof("Bkill(%d)", id)
- cmd := cli.command("bkill", fmt.Sprintf("%d", id))
+func (cli lsfcli) Bkill(id string) error {
+ cli.logger.Infof("Bkill(%s)", id)
+ cmd := cli.command("bkill", id)
buf, err := cmd.CombinedOutput()
if err == nil || strings.Index(string(buf), "already finished") >= 0 {
return nil
latest map[string]bjobsEntry
}
-// JobID waits for the next queue update (so even a job that was only
+// Lookup waits for the next queue update (so even a job that was only
// submitted a nanosecond ago will show up) and then returns the LSF
-// job ID corresponding to the given container UUID.
-func (q *lsfqueue) JobID(uuid string) (int, bool) {
+// queue information corresponding to the given container UUID.
+func (q *lsfqueue) Lookup(uuid string) (bjobsEntry, bool) {
ent, ok := q.getNext()[uuid]
- return ent.id, ok
+ return ent, ok
}
// All waits for the next queue update, then returns the names of all
}
next := make(map[string]bjobsEntry, len(ents))
for _, ent := range ents {
- next[ent.name] = ent
+ next[ent.Name] = ent
}
// Replace q.latest and notify all the
// goroutines that the "next update" they
EndpointLinkGet = APIEndpoint{"GET", "arvados/v1/links/{uuid}", ""}
EndpointLinkList = APIEndpoint{"GET", "arvados/v1/links", ""}
EndpointLinkDelete = APIEndpoint{"DELETE", "arvados/v1/links/{uuid}", ""}
+ EndpointSysTrashSweep = APIEndpoint{"POST", "sys/trash_sweep", ""}
EndpointUserActivate = APIEndpoint{"POST", "arvados/v1/users/{uuid}/activate", ""}
EndpointUserCreate = APIEndpoint{"POST", "arvados/v1/users", "user"}
EndpointUserCurrent = APIEndpoint{"GET", "arvados/v1/users/current", ""}
EndpointUserBatchUpdate = APIEndpoint{"PATCH", "arvados/v1/users/batch_update", ""}
EndpointUserAuthenticate = APIEndpoint{"POST", "arvados/v1/users/authenticate", ""}
EndpointAPIClientAuthorizationCurrent = APIEndpoint{"GET", "arvados/v1/api_client_authorizations/current", ""}
+ EndpointAPIClientAuthorizationCreate = APIEndpoint{"POST", "arvados/v1/api_client_authorizations", "api_client_authorization"}
+ EndpointAPIClientAuthorizationUpdate = APIEndpoint{"PUT", "arvados/v1/api_client_authorizations/{uuid}", "api_client_authorization"}
+ EndpointAPIClientAuthorizationList = APIEndpoint{"GET", "arvados/v1/api_client_authorizations", ""}
+ EndpointAPIClientAuthorizationDelete = APIEndpoint{"DELETE", "arvados/v1/api_client_authorizations/{uuid}", ""}
+ EndpointAPIClientAuthorizationGet = APIEndpoint{"GET", "arvados/v1/api_client_authorizations/{uuid}", ""}
)
type ContainerSSHOptions struct {
SpecimenGet(ctx context.Context, options GetOptions) (Specimen, error)
SpecimenList(ctx context.Context, options ListOptions) (SpecimenList, error)
SpecimenDelete(ctx context.Context, options DeleteOptions) (Specimen, error)
+ SysTrashSweep(ctx context.Context, options struct{}) (struct{}, error)
UserCreate(ctx context.Context, options CreateOptions) (User, error)
UserUpdate(ctx context.Context, options UpdateOptions) (User, error)
UserMerge(ctx context.Context, options UserMergeOptions) (User, error)
UserBatchUpdate(context.Context, UserBatchUpdateOptions) (UserList, error)
UserAuthenticate(ctx context.Context, options UserAuthenticateOptions) (APIClientAuthorization, error)
APIClientAuthorizationCurrent(ctx context.Context, options GetOptions) (APIClientAuthorization, error)
+ APIClientAuthorizationCreate(ctx context.Context, options CreateOptions) (APIClientAuthorization, error)
+ APIClientAuthorizationList(ctx context.Context, options ListOptions) (APIClientAuthorizationList, error)
+ APIClientAuthorizationDelete(ctx context.Context, options DeleteOptions) (APIClientAuthorization, error)
+ APIClientAuthorizationUpdate(ctx context.Context, options UpdateOptions) (APIClientAuthorization, error)
+ APIClientAuthorizationGet(ctx context.Context, options GetOptions) (APIClientAuthorization, error)
}
package arvados
+import "time"
+
// APIClientAuthorization is an arvados#apiClientAuthorization resource.
type APIClientAuthorization struct {
- UUID string `json:"uuid"`
- APIToken string `json:"api_token"`
- ExpiresAt string `json:"expires_at"`
- Scopes []string `json:"scopes"`
+ UUID string `json:"uuid"`
+ APIClientID int `json:"api_client_id"`
+ APIToken string `json:"api_token"`
+ CreatedAt time.Time `json:"created_at"`
+ CreatedByIPAddress string `json:"created_by_ip_address"`
+ DefaultOwnerUUID string `json:"default_owner_uuid"`
+ Etag string `json:"etag"`
+ ExpiresAt time.Time `json:"expires_at"`
+ LastUsedAt time.Time `json:"last_used_at"`
+ LastUsedByIPAddress string `json:"last_used_by_ip_address"`
+ ModifiedAt time.Time `json:"modified_at"`
+ ModifiedByClientUUID string `json:"modified_by_client_uuid"`
+ ModifiedByUserUUID string `json:"modified_by_user_uuid"`
+ OwnerUUID string `json:"owner_uuid"`
+ Scopes []string `json:"scopes"`
+ UserID int `json:"user_id"`
}
// APIClientAuthorizationList is an arvados#apiClientAuthorizationList resource.
return err
}
switch {
+ case resp.StatusCode == http.StatusNoContent:
+ return nil
case resp.StatusCode == http.StatusOK && dst == nil:
return nil
case resp.StatusCode == http.StatusOK:
as.appendCall(ctx, as.SpecimenDelete, options)
return arvados.Specimen{}, as.Error
}
+func (as *APIStub) SysTrashSweep(ctx context.Context, options struct{}) (struct{}, error) {
+ as.appendCall(ctx, as.SysTrashSweep, options)
+ return struct{}{}, as.Error
+}
func (as *APIStub) UserCreate(ctx context.Context, options arvados.CreateOptions) (arvados.User, error) {
as.appendCall(ctx, as.UserCreate, options)
return arvados.User{}, as.Error
as.appendCall(ctx, as.APIClientAuthorizationCurrent, options)
return arvados.APIClientAuthorization{}, as.Error
}
+func (as *APIStub) APIClientAuthorizationCreate(ctx context.Context, options arvados.CreateOptions) (arvados.APIClientAuthorization, error) {
+ as.appendCall(ctx, as.APIClientAuthorizationCreate, options)
+ return arvados.APIClientAuthorization{}, as.Error
+}
+func (as *APIStub) APIClientAuthorizationUpdate(ctx context.Context, options arvados.UpdateOptions) (arvados.APIClientAuthorization, error) {
+ as.appendCall(ctx, as.APIClientAuthorizationUpdate, options)
+ return arvados.APIClientAuthorization{}, as.Error
+}
+func (as *APIStub) APIClientAuthorizationDelete(ctx context.Context, options arvados.DeleteOptions) (arvados.APIClientAuthorization, error) {
+ as.appendCall(ctx, as.APIClientAuthorizationDelete, options)
+ return arvados.APIClientAuthorization{}, as.Error
+}
+func (as *APIStub) APIClientAuthorizationList(ctx context.Context, options arvados.ListOptions) (arvados.APIClientAuthorizationList, error) {
+ as.appendCall(ctx, as.APIClientAuthorizationList, options)
+ return arvados.APIClientAuthorizationList{}, as.Error
+}
+func (as *APIStub) APIClientAuthorizationGet(ctx context.Context, options arvados.GetOptions) (arvados.APIClientAuthorization, error) {
+ as.appendCall(ctx, as.APIClientAuthorizationGet, options)
+ return arvados.APIClientAuthorization{}, as.Error
+}
func (as *APIStub) appendCall(ctx context.Context, method interface{}, options interface{}) {
as.mtx.Lock()
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package arvadostest
+
+import "git.arvados.org/arvados.git/sdk/go/arvados"
+
+// Test that *APIStub implements arvados.API
+var _ arvados.API = &APIStub{}
private String groupClass;
@JsonProperty("description")
private String description;
- @JsonProperty("writable_by")
+ @JsonProperty(value = "writable_by", access = JsonProperty.Access.WRITE_ONLY)
private List<String> writableBy;
@JsonProperty("delete_at")
private LocalDateTime deleteAt;
@JsonInclude(JsonInclude.Include.NON_NULL)
@JsonIgnoreProperties(ignoreUnknown = true)
-@JsonPropertyOrder({ "name", "head_kind", "head_uuid", "link_class" })
+@JsonPropertyOrder({"name", "head_kind", "head_uuid", "link_class"})
public class Link extends Item {
@JsonProperty("name")
private String name;
- @JsonProperty("head_kind")
+ @JsonProperty(value = "head_kind", access = JsonProperty.Access.WRITE_ONLY)
private String headKind;
@JsonProperty("head_uuid")
private String headUuid;
+ @JsonProperty("tail_uuid")
+ private String tailUuid;
+ @JsonProperty(value = "tail_kind", access = JsonProperty.Access.WRITE_ONLY)
+ private String tailKind;
@JsonProperty("link_class")
private String linkClass;
return headUuid;
}
+ public String getTailUuid() {
+ return tailUuid;
+ }
+
+ public String getTailKind() {
+ return tailKind;
+ }
+
public String getLinkClass() {
return linkClass;
}
this.headUuid = headUuid;
}
+ public void setTailUuid(String tailUuid) {
+ this.tailUuid = tailUuid;
+ }
+
+ public void setTailKind(String tailKind) {
+ this.tailKind = tailKind;
+ }
+
public void setLinkClass(String linkClass) {
this.linkClass = linkClass;
}
--- /dev/null
+/*
+ * Copyright (C) The Arvados Authors. All rights reserved.
+ *
+ * SPDX-License-Identifier: AGPL-3.0 OR Apache-2.0
+ *
+ */
+
+package org.arvados.client.api.client;
+
+import okhttp3.mockwebserver.RecordedRequest;
+import org.arvados.client.api.model.Link;
+import org.arvados.client.api.model.LinkList;
+import org.arvados.client.test.utils.ArvadosClientMockedWebServerTest;
+import org.arvados.client.test.utils.RequestMethod;
+import org.junit.Test;
+
+import static org.arvados.client.test.utils.ApiClientTestUtils.assertAuthorizationHeader;
+import static org.arvados.client.test.utils.ApiClientTestUtils.assertRequestMethod;
+import static org.arvados.client.test.utils.ApiClientTestUtils.assertRequestPath;
+import static org.arvados.client.test.utils.ApiClientTestUtils.getResponse;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.Assert.assertEquals;
+
+public class LinkApiClientTest extends ArvadosClientMockedWebServerTest {
+
+ private static final String RESOURCE = "links";
+
+ private final LinksApiClient client = new LinksApiClient(CONFIG);
+
+ @Test
+ public void listLinks() throws Exception {
+ // given
+ server.enqueue(getResponse("links-list"));
+
+ // when
+ LinkList actual = client.list();
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertThat(actual.getItemsAvailable()).isEqualTo(2);
+ }
+
+ @Test
+ public void getLink() throws Exception {
+ // given
+ server.enqueue(getResponse("links-get"));
+
+ String uuid = "arkau-o0j2j-huxuaxbi46s1yml";
+
+ // when
+ Link actual = client.get(uuid);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE + "/" + uuid);
+ assertRequestMethod(request, RequestMethod.GET);
+ assertEquals(actual.getUuid(), uuid);
+ assertEquals(actual.getName(), "can_read");
+ assertEquals(actual.getHeadKind(), "arvados#group");
+ assertEquals(actual.getHeadUuid(), "arkau-j7d0g-fcedae2076pw56h");
+ assertEquals(actual.getTailUuid(), "ardev-tpzed-n3kzq4fvoks3uw4");
+ assertEquals(actual.getTailKind(), "arvados#user");
+ assertEquals(actual.getLinkClass(), "permission");
+ }
+
+ @Test
+ public void createLink() throws Exception {
+ // given
+ server.enqueue(getResponse("links-create"));
+
+ String name = "Star Link";
+
+ Link collection = new Link();
+ collection.setName(name);
+
+ // when
+ Link actual = client.create(collection);
+
+ // then
+ RecordedRequest request = server.takeRequest();
+ assertAuthorizationHeader(request);
+ assertRequestPath(request, RESOURCE);
+ assertRequestMethod(request, RequestMethod.POST);
+ assertThat(actual.getName()).isEqualTo(name);
+ assertEquals(actual.getName(), name);
+ assertEquals(actual.getUuid(), "arkau-o0j2j-huxuaxbi46s1yml");
+ assertEquals(actual.getHeadKind(), "arvados#group");
+ assertEquals(actual.getHeadUuid(), "arkau-j7d0g-fcedae2076pw56h");
+ assertEquals(actual.getTailUuid(), "ardev-tpzed-n3kzq4fvoks3uw4");
+ assertEquals(actual.getTailKind(), "arvados#user");
+ assertEquals(actual.getLinkClass(), "star");
+ }
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/links/arkau-o0j2j-huxuaxbi46s1yml",
+ "kind": "arvados#link",
+ "etag": "zw1rlnbig0kpm9btw8us3pn9",
+ "uuid": "arkau-o0j2j-huxuaxbi46s1yml",
+ "owner_uuid": "arkau-tpzed-000000000000000",
+ "created_at": "2021-11-30T08:45:04.373354745Z",
+ "modified_by_client_uuid": null,
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2021-11-30T08:45:04.374489000Z",
+ "tail_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "link_class": "star",
+ "name": "Star Link",
+ "head_uuid": "arkau-j7d0g-fcedae2076pw56h",
+ "head_kind": "arvados#group",
+ "tail_kind": "arvados#user",
+ "properties": {}
+}
\ No newline at end of file
--- /dev/null
+{
+ "href": "/links/arkau-o0j2j-huxuaxbi46s1yml",
+ "kind": "arvados#link",
+ "etag": "zw1rlnbig0kpm9btw8us3pn9",
+ "uuid": "arkau-o0j2j-huxuaxbi46s1yml",
+ "owner_uuid": "arkau-tpzed-000000000000000",
+ "created_at": "2021-11-30T08:45:04.373354745Z",
+ "modified_by_client_uuid": null,
+ "modified_by_user_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "modified_at": "2021-11-30T08:45:04.374489000Z",
+ "tail_uuid": "ardev-tpzed-n3kzq4fvoks3uw4",
+ "link_class": "permission",
+ "name": "can_read",
+ "head_uuid": "arkau-j7d0g-fcedae2076pw56h",
+ "head_kind": "arvados#group",
+ "tail_kind": "arvados#user",
+ "properties": {}
+}
\ No newline at end of file
--- /dev/null
+{
+ "kind": "arvados#linkList",
+ "etag": "",
+ "self_link": "",
+ "offset": 0,
+ "limit": 100,
+ "items": [
+ {
+ "href": "/links/arkau-o0j2j-x2b4rdadxs2fizn",
+ "kind": "arvados#link",
+ "etag": "dkhtr9tvp9zfy0d90xjn7w1t7",
+ "uuid": "arkau-o0j2j-x2b4rdadxs2fizn",
+ "owner_uuid": "arkau-j7d0g-publicfavorites",
+ "created_at": "2021-10-27T12:00:06.607794000Z",
+ "modified_by_client_uuid": null,
+ "modified_by_user_uuid": "arlog-tpzed-fyiau9qwo7ytntu",
+ "modified_at": "2021-10-27T12:00:06.609840000Z",
+ "tail_uuid": "arkau-j7d0g-publicfavorites",
+ "link_class": "star",
+ "name": "pRED Data Commons Service - Open access",
+ "head_uuid": "arkau-j7d0g-sfhw8b1uson0hwh",
+ "head_kind": "arvados#group",
+ "tail_kind": "arvados#group",
+ "properties": {}
+ },
+ {
+ "href": "/links/arkau-o0j2j-r5am4lz9gnu488k",
+ "kind": "arvados#link",
+ "etag": "9nt0c2xn5oz1jzjzawlycmehz",
+ "uuid": "arkau-o0j2j-r5am4lz9gnu488k",
+ "owner_uuid": "arkau-j7d0g-publicfavorites",
+ "created_at": "2021-06-23T14:58:06.189520000Z",
+ "modified_by_client_uuid": null,
+ "modified_by_user_uuid": "arlog-tpzed-xzjyeljl6co7vlz",
+ "modified_at": "2021-06-23T14:58:06.196208000Z",
+ "tail_uuid": "arkau-j7d0g-publicfavorites",
+ "link_class": "star",
+ "name": "Open Targets Genetics",
+ "head_uuid": "arkau-j7d0g-pj5wysmpy5wn8yo",
+ "head_kind": "arvados#group",
+ "tail_kind": "arvados#group",
+ "properties": {}
+ }
+ ],
+ "items_available": 2
+}
\ No newline at end of file
files.sort()
for f in files:
filepath = os.path.join(root, f)
+ if not os.path.isfile(filepath):
+ self.logger.warning("Skipping non-regular file '{}'".format(filepath))
+ continue
# Add its size to the total bytes count (if applicable)
if self.follow_links or (not os.path.islink(filepath)):
if self.bytes_expected is not None:
import apiclient
import ciso8601
import datetime
-import hashlib
import json
import logging
import mock
+import multiprocessing
import os
import pwd
import random
import time
import unittest
import uuid
-import yaml
import arvados
import arvados.commands.put as arv_put
shutil.rmtree(self.small_files_dir)
shutil.rmtree(self.tempdir_with_symlink)
+ def test_non_regular_files_are_ignored_except_symlinks_to_dirs(self):
+ def pfunc(x):
+ with open(x, 'w') as f:
+ f.write('test')
+ fifo_filename = 'fifo-file'
+ fifo_path = os.path.join(self.tempdir_with_symlink, fifo_filename)
+ self.assertTrue(os.path.islink(os.path.join(self.tempdir_with_symlink, 'linkeddir')))
+ os.mkfifo(fifo_path)
+ producer = multiprocessing.Process(target=pfunc, args=(fifo_path,))
+ producer.start()
+ cwriter = arv_put.ArvPutUploadJob([self.tempdir_with_symlink])
+ cwriter.start(save_collection=False)
+ if producer.exitcode is None:
+ # If the producer is still running, kill it. This should always be
+ # before any assertion that may fail.
+ producer.terminate()
+ producer.join(1)
+ self.assertIn('linkeddir', cwriter.manifest_text())
+ self.assertNotIn(fifo_filename, cwriter.manifest_text())
+
def test_symlinks_are_followed_by_default(self):
self.assertTrue(os.path.islink(os.path.join(self.tempdir_with_symlink, 'linkeddir')))
self.assertTrue(os.path.islink(os.path.join(self.tempdir_with_symlink, 'linkedfile')))
}
}
+ discovery[:resources]['sys'] = {
+ methods: {
+ get: {
+ id: "arvados.sys.trash_sweep",
+ path: "sys/trash_sweep",
+ httpMethod: "POST",
+ description: "apply scheduled trash and delete operations",
+ parameters: {
+ },
+ parameterOrder: [
+ ],
+ response: {
+ },
+ scopes: [
+ "https://api.arvados.org/auth/arvados",
+ "https://api.arvados.org/auth/arvados.readonly"
+ ]
+ },
+ }
+ }
+
Rails.configuration.API.DisabledAPIs.each do |method, _|
ctrl, action = method.to_s.split('.', 2)
discovery[:resources][ctrl][:methods].delete(action.to_sym)
#
# SPDX-License-Identifier: AGPL-3.0
-require 'current_api_client'
+class SysController < ApplicationController
+ skip_before_action :find_object_by_uuid
+ skip_before_action :render_404_if_no_object
+ before_action :admin_required
-module SweepTrashedObjects
- extend CurrentApiClient
-
- def self.delete_project_and_contents(p_uuid)
- p = Group.find_by_uuid(p_uuid)
- if !p || p.group_class != 'project'
- raise "can't sweep group '#{p_uuid}', it may not exist or not be a project"
- end
- # First delete sub projects
- Group.where({group_class: 'project', owner_uuid: p_uuid}).each do |sub_project|
- delete_project_and_contents(sub_project.uuid)
- end
- # Next, iterate over all tables which have owner_uuid fields, with some
- # exceptions, and delete records owned by this project
- skipped_classes = ['Group', 'User']
- ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |klass|
- if !skipped_classes.include?(klass.name) && klass.columns.collect(&:name).include?('owner_uuid')
- klass.where({owner_uuid: p_uuid}).destroy_all
- end
- end
- # Finally delete the project itself
- p.destroy
- end
-
- def self.sweep_now
+ def trash_sweep
act_as_system_user do
# Sweep trashed collections
Collection.
where('is_trashed = false and trash_at < statement_timestamp()').
update_all('is_trashed = true')
- # Sweep trashed projects and their contents
+ # Sweep trashed projects and their contents (as well as role
+ # groups that were trashed before #18340 when that was
+ # disallowed)
Group.
- where({group_class: 'project'}).
where('delete_at is not null and delete_at < statement_timestamp()').each do |project|
delete_project_and_contents(project.uuid)
end
Group.
- where({group_class: 'project'}).
where('is_trashed = false and trash_at < statement_timestamp()').
update_all('is_trashed = true')
# Sweep expired tokens
ActiveRecord::Base.connection.execute("DELETE from api_client_authorizations where expires_at <= statement_timestamp()")
end
+ head :no_content
end
- def self.sweep_if_stale
- return if Rails.configuration.Collections.TrashSweepInterval <= 0
- exp = Rails.configuration.Collections.TrashSweepInterval.seconds
- need = false
- Rails.cache.fetch('SweepTrashedObjects', expires_in: exp) do
- need = true
+ protected
+
+ def delete_project_and_contents(p_uuid)
+ p = Group.find_by_uuid(p_uuid)
+ if !p
+ raise "can't sweep group '#{p_uuid}', it may not exist"
+ end
+ # First delete sub projects
+ Group.where({group_class: 'project', owner_uuid: p_uuid}).each do |sub_project|
+ delete_project_and_contents(sub_project.uuid)
end
- if need
- Thread.new do
- Thread.current.abort_on_exception = false
- begin
- sweep_now
- rescue => e
- Rails.logger.error "#{e.class}: #{e}\n#{e.backtrace.join("\n\t")}"
- ensure
- # Rails 5.1+ makes test threads share a database connection, so we can't
- # close a connection shared with other threads.
- # https://github.com/rails/rails/commit/deba47799ff905f778e0c98a015789a1327d5087
- if Rails.env != "test"
- ActiveRecord::Base.connection.close
- end
- end
+ # Next, iterate over all tables which have owner_uuid fields, with some
+ # exceptions, and delete records owned by this project
+ skipped_classes = ['Group', 'User']
+ ActiveRecord::Base.descendants.reject(&:abstract_class?).each do |klass|
+ if !skipped_classes.include?(klass.name) && klass.columns.collect(&:name).include?('owner_uuid')
+ klass.where({owner_uuid: p_uuid}).destroy_all
end
end
+ # Finally delete the project itself
+ p.destroy
end
end
# SPDX-License-Identifier: AGPL-3.0
require 'arvados/keep'
-require 'sweep_trashed_objects'
require 'trashable'
class Collection < ArvadosModel
super - ["manifest_text", "storage_classes_desired", "storage_classes_confirmed", "current_version_uuid"]
end
- def self.where *args
- SweepTrashedObjects.sweep_if_stale
- super
- end
-
protected
# Although the defaults for these columns is already set up on the schema,
end
end
+ post '/sys/trash_sweep', to: 'sys#trash_sweep'
+
if Rails.env == 'test'
post '/database/reset', to: 'database#reset'
end
ActiveRecord::Base.connection.exec_query "SET LOCAL enable_mergejoin to true;"
+ # Now that we have recomputed a set of permissions, delete any
+ # rows from the materialized_permissions table where (target_uuid,
+ # user_uuid) is not present or has perm_level=0 in the recomputed
+ # set.
ActiveRecord::Base.connection.exec_delete %{
delete from #{PERMISSION_VIEW} where
target_uuid in (select target_uuid from #{temptable_perms}) and
},
"update_permissions.delete"
+ # Now insert-or-update permissions in the recomputed set. The
+ # WHERE clause is important to avoid redundantly updating rows
+ # that haven't actually changed.
ActiveRecord::Base.connection.exec_query %{
insert into #{PERMISSION_VIEW} (user_uuid, target_uuid, perm_level, traverse_owned)
select user_uuid, target_uuid, val as perm_level, traverse_owned from #{temptable_perms} where val>0
-on conflict (user_uuid, target_uuid) do update set perm_level=EXCLUDED.perm_level, traverse_owned=EXCLUDED.traverse_owned;
+on conflict (user_uuid, target_uuid) do update
+set perm_level=EXCLUDED.perm_level, traverse_owned=EXCLUDED.traverse_owned
+where #{PERMISSION_VIEW}.user_uuid=EXCLUDED.user_uuid and
+ #{PERMISSION_VIEW}.target_uuid=EXCLUDED.target_uuid and
+ (#{PERMISSION_VIEW}.perm_level != EXCLUDED.perm_level or
+ #{PERMISSION_VIEW}.traverse_owned != EXCLUDED.traverse_owned);
},
"update_permissions.insert"
--- /dev/null
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: AGPL-3.0
+
+require 'test_helper'
+
+class SysControllerTest < ActionController::TestCase
+ include CurrentApiClient
+ include DbCurrentTime
+
+ test "trash_sweep - delete expired tokens" do
+ assert_not_empty ApiClientAuthorization.where(uuid: api_client_authorizations(:expired).uuid)
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ assert_empty ApiClientAuthorization.where(uuid: api_client_authorizations(:expired).uuid)
+ end
+
+ test "trash_sweep - fail with non-admin token" do
+ authorize_with :active
+ post :trash_sweep
+ assert_response 403
+ end
+
+ test "trash_sweep - move collections to trash" do
+ c = collections(:trashed_on_next_sweep)
+ refute_empty Collection.where('uuid=? and is_trashed=false', c.uuid)
+ assert_raises(ActiveRecord::RecordNotUnique) do
+ act_as_user users(:active) do
+ Collection.create!(owner_uuid: c.owner_uuid,
+ name: c.name)
+ end
+ end
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ c = Collection.where('uuid=? and is_trashed=true', c.uuid).first
+ assert c
+ act_as_user users(:active) do
+ assert Collection.create!(owner_uuid: c.owner_uuid,
+ name: c.name)
+ end
+ end
+
+ test "trash_sweep - delete collections" do
+ uuid = 'zzzzz-4zz18-3u1p5umicfpqszp' # deleted_on_next_sweep
+ assert_not_empty Collection.where(uuid: uuid)
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ assert_empty Collection.where(uuid: uuid)
+ end
+
+ test "trash_sweep - delete referring links" do
+ uuid = collections(:trashed_on_next_sweep).uuid
+ act_as_system_user do
+ assert_raises ActiveRecord::RecordInvalid do
+ # Cannot create because :trashed_on_next_sweep is already trashed
+ Link.create!(head_uuid: uuid,
+ tail_uuid: system_user_uuid,
+ link_class: 'whatever',
+ name: 'something')
+ end
+
+ # Bump trash_at to now + 1 minute
+ Collection.where(uuid: uuid).
+ update(trash_at: db_current_time + (1).minute)
+
+ # Not considered trashed now
+ Link.create!(head_uuid: uuid,
+ tail_uuid: system_user_uuid,
+ link_class: 'whatever',
+ name: 'something')
+ end
+ past = db_current_time
+ Collection.where(uuid: uuid).
+ update_all(is_trashed: true, trash_at: past, delete_at: past)
+ assert_not_empty Collection.where(uuid: uuid)
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ assert_empty Collection.where(uuid: uuid)
+ end
+
+ test "trash_sweep - move projects to trash" do
+ p = groups(:trashed_on_next_sweep)
+ assert_empty Group.where('uuid=? and is_trashed=true', p.uuid)
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+ assert_not_empty Group.where('uuid=? and is_trashed=true', p.uuid)
+ end
+
+ test "trash_sweep - delete projects and their contents" do
+ g_foo = groups(:trashed_project)
+ g_bar = groups(:trashed_subproject)
+ g_baz = groups(:trashed_subproject3)
+ col = collections(:collection_in_trashed_subproject)
+ job = jobs(:job_in_trashed_project)
+ cr = container_requests(:cr_in_trashed_project)
+ # Save how many objects were before the sweep
+ user_nr_was = User.all.length
+ coll_nr_was = Collection.all.length
+ group_nr_was = Group.where('group_class<>?', 'project').length
+ project_nr_was = Group.where(group_class: 'project').length
+ cr_nr_was = ContainerRequest.all.length
+ job_nr_was = Job.all.length
+ assert_not_empty Group.where(uuid: g_foo.uuid)
+ assert_not_empty Group.where(uuid: g_bar.uuid)
+ assert_not_empty Group.where(uuid: g_baz.uuid)
+ assert_not_empty Collection.where(uuid: col.uuid)
+ assert_not_empty Job.where(uuid: job.uuid)
+ assert_not_empty ContainerRequest.where(uuid: cr.uuid)
+
+ authorize_with :admin
+ post :trash_sweep
+ assert_response :success
+
+ assert_empty Group.where(uuid: g_foo.uuid)
+ assert_empty Group.where(uuid: g_bar.uuid)
+ assert_empty Group.where(uuid: g_baz.uuid)
+ assert_empty Collection.where(uuid: col.uuid)
+ assert_empty Job.where(uuid: job.uuid)
+ assert_empty ContainerRequest.where(uuid: cr.uuid)
+ # No unwanted deletions should have happened
+ assert_equal user_nr_was, User.all.length
+ assert_equal coll_nr_was-2, # collection_in_trashed_subproject
+ Collection.all.length # & deleted_on_next_sweep collections
+ assert_equal group_nr_was, Group.where('group_class<>?', 'project').length
+ assert_equal project_nr_was-3, Group.where(group_class: 'project').length
+ assert_equal cr_nr_was-1, ContainerRequest.all.length
+ assert_equal job_nr_was-1, Job.all.length
+ end
+
+end
# Generally, new routes should appear under /arvados/v1/. If
# they appear elsewhere, that might have been caused by default
# rails generator behavior that we don't want.
- assert_match(/^\/(|\*a|arvados\/v1\/.*|auth\/.*|login|logout|database\/reset|discovery\/.*|static\/.*|themes\/.*|assets|_health\/.*)(\(\.:format\))?$/,
+ assert_match(/^\/(|\*a|arvados\/v1\/.*|auth\/.*|login|logout|database\/reset|discovery\/.*|static\/.*|sys\/trash_sweep|themes\/.*|assets|_health\/.*)(\(\.:format\))?$/,
route.path.spec.to_s,
"Unexpected new route: #{route.path.spec}")
end
# SPDX-License-Identifier: AGPL-3.0
require 'test_helper'
-require 'sweep_trashed_objects'
class ApiClientAuthorizationTest < ActiveSupport::TestCase
include CurrentApiClient
end
end
- test "delete expired in SweepTrashedObjects" do
- assert_not_empty ApiClientAuthorization.where(uuid: api_client_authorizations(:expired).uuid)
- SweepTrashedObjects.sweep_now
- assert_empty ApiClientAuthorization.where(uuid: api_client_authorizations(:expired).uuid)
- end
-
test "accepts SystemRootToken" do
assert_nil ApiClientAuthorization.validate(token: "xxxSystemRootTokenxxx")
# SPDX-License-Identifier: AGPL-3.0
require 'test_helper'
-require 'sweep_trashed_objects'
require 'fix_collection_versions_timestamps'
class CollectionTest < ActiveSupport::TestCase
assert_includes(coll_uuids, collections(:docker_image).uuid)
end
- test "move collections to trash in SweepTrashedObjects" do
- c = collections(:trashed_on_next_sweep)
- refute_empty Collection.where('uuid=? and is_trashed=false', c.uuid)
- assert_raises(ActiveRecord::RecordNotUnique) do
- act_as_user users(:active) do
- Collection.create!(owner_uuid: c.owner_uuid,
- name: c.name)
- end
- end
- SweepTrashedObjects.sweep_now
- c = Collection.where('uuid=? and is_trashed=true', c.uuid).first
- assert c
- act_as_user users(:active) do
- assert Collection.create!(owner_uuid: c.owner_uuid,
- name: c.name)
- end
- end
-
- test "delete collections in SweepTrashedObjects" do
- uuid = 'zzzzz-4zz18-3u1p5umicfpqszp' # deleted_on_next_sweep
- assert_not_empty Collection.where(uuid: uuid)
- SweepTrashedObjects.sweep_now
- assert_empty Collection.where(uuid: uuid)
- end
-
- test "delete referring links in SweepTrashedObjects" do
- uuid = collections(:trashed_on_next_sweep).uuid
- act_as_system_user do
- assert_raises ActiveRecord::RecordInvalid do
- # Cannot create because :trashed_on_next_sweep is already trashed
- Link.create!(head_uuid: uuid,
- tail_uuid: system_user_uuid,
- link_class: 'whatever',
- name: 'something')
- end
-
- # Bump trash_at to now + 1 minute
- Collection.where(uuid: uuid).
- update(trash_at: db_current_time + (1).minute)
-
- # Not considered trashed now
- Link.create!(head_uuid: uuid,
- tail_uuid: system_user_uuid,
- link_class: 'whatever',
- name: 'something')
- end
- past = db_current_time
- Collection.where(uuid: uuid).
- update_all(is_trashed: true, trash_at: past, delete_at: past)
- assert_not_empty Collection.where(uuid: uuid)
- SweepTrashedObjects.sweep_now
- assert_empty Collection.where(uuid: uuid)
- end
-
test "empty names are exempt from name uniqueness" do
act_as_user users(:active) do
c1 = Collection.new(name: nil, manifest_text: '', owner_uuid: groups(:aproject).uuid)
assert User.readable_by(users(:admin)).where(uuid: u_bar.uuid).any?
end
- test "move projects to trash in SweepTrashedObjects" do
- p = groups(:trashed_on_next_sweep)
- assert_empty Group.where('uuid=? and is_trashed=true', p.uuid)
- SweepTrashedObjects.sweep_now
- assert_not_empty Group.where('uuid=? and is_trashed=true', p.uuid)
- end
-
- test "delete projects and their contents in SweepTrashedObjects" do
- g_foo = groups(:trashed_project)
- g_bar = groups(:trashed_subproject)
- g_baz = groups(:trashed_subproject3)
- col = collections(:collection_in_trashed_subproject)
- job = jobs(:job_in_trashed_project)
- cr = container_requests(:cr_in_trashed_project)
- # Save how many objects were before the sweep
- user_nr_was = User.all.length
- coll_nr_was = Collection.all.length
- group_nr_was = Group.where('group_class<>?', 'project').length
- project_nr_was = Group.where(group_class: 'project').length
- cr_nr_was = ContainerRequest.all.length
- job_nr_was = Job.all.length
- assert_not_empty Group.where(uuid: g_foo.uuid)
- assert_not_empty Group.where(uuid: g_bar.uuid)
- assert_not_empty Group.where(uuid: g_baz.uuid)
- assert_not_empty Collection.where(uuid: col.uuid)
- assert_not_empty Job.where(uuid: job.uuid)
- assert_not_empty ContainerRequest.where(uuid: cr.uuid)
- SweepTrashedObjects.sweep_now
- assert_empty Group.where(uuid: g_foo.uuid)
- assert_empty Group.where(uuid: g_bar.uuid)
- assert_empty Group.where(uuid: g_baz.uuid)
- assert_empty Collection.where(uuid: col.uuid)
- assert_empty Job.where(uuid: job.uuid)
- assert_empty ContainerRequest.where(uuid: cr.uuid)
- # No unwanted deletions should have happened
- assert_equal user_nr_was, User.all.length
- assert_equal coll_nr_was-2, # collection_in_trashed_subproject
- Collection.all.length # & deleted_on_next_sweep collections
- assert_equal group_nr_was, Group.where('group_class<>?', 'project').length
- assert_equal project_nr_was-3, Group.where(group_class: 'project').length
- assert_equal cr_nr_was-1, ContainerRequest.all.length
- assert_equal job_nr_was-1, Job.all.length
- end
-
test "project names must be displayable in a filesystem" do
set_user_from_auth :active
["", "{SOLIDUS}"].each do |subst|
projects / arvados.git / commitdiff