*.asc
sdk/java-v2/build.gradle
sdk/java-v2/settings.gradle
-sdk/cwl/tests/wf/feddemo
\ No newline at end of file
+sdk/cwl/tests/wf/feddemo
+go.mod
+go.sum
github.com/imdario/mergo v0.3.8-0.20190415133143-5ef87b449ca7
github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect
github.com/jmcvetta/randutil v0.0.0-20150817122601-2bb1b664bcff
+ github.com/jmoiron/sqlx v1.2.0
github.com/julienschmidt/httprouter v1.2.0
github.com/karalabe/xgo v0.0.0-20191115072854-c5ccff8648a7 // indirect
github.com/kevinburke/ssh_config v0.0.0-20171013211458-802051befeb5 // indirect
github.com/go-ldap/ldap v3.0.3+incompatible/go.mod h1:qfd9rJvER9Q0/D/Sqn1DfHRoBp40uXYvFoEVrNEPqRc=
github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE=
github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk=
+github.com/go-sql-driver/mysql v1.4.0/go.mod h1:zAC/RDZ24gD3HViQzih4MyKcchzm+sOG5ZlKdlhCg5w=
github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY=
github.com/gogo/protobuf v1.1.1 h1:72R+M5VuhED/KujmZVcIquuo8mBgX4oVda//DQb3PXo=
github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
github.com/jmcvetta/randutil v0.0.0-20150817122601-2bb1b664bcff/go.mod h1:ddfPX8Z28YMjiqoaJhNBzWHapTHXejnB5cDCUWDwriw=
github.com/jmespath/go-jmespath v0.0.0-20180206201540-c2b33e8439af h1:pmfjZENx5imkbgOkpRUYLnmbU7UEFbjtDA2hxJ1ichM=
github.com/jmespath/go-jmespath v0.0.0-20180206201540-c2b33e8439af/go.mod h1:Nht3zPeWKUH0NzdCt2Blrr5ys8VGpn0CEB0cQHVjt7k=
+github.com/jmoiron/sqlx v1.2.0 h1:41Ip0zITnmWNR/vHV+S4m+VoUivnWY5E4OJfLZjCJMA=
+github.com/jmoiron/sqlx v1.2.0/go.mod h1:1FEQNm3xlJgrMD+FBdI9+xvCksHtbpVBBw5dYhBSsks=
github.com/json-iterator/go v1.1.6/go.mod h1:+SdeFBvtyEkXs7REEP0seUULqWtbJapLOCVDaaPEHmU=
github.com/json-iterator/go v1.1.7/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/uOdHXbAo4=
github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU=
github.com/konsorten/go-windows-terminal-sequences v1.0.1 h1:mweAR1A6xJ3oS2pRaGiHgQ4OO8tzTaLawm8vnODuwDk=
github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ=
github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod h1:+0opPa2QZZtGFBFZlji/RkVcI2GknAs/DXo4wKdlNEc=
+github.com/lib/pq v1.0.0/go.mod h1:5WUZQaWbwv1U+lTReE5YruASi9Al49XbQIvNi/34Woo=
github.com/lib/pq v1.3.0 h1:/qkRGz8zljWiDcFvgpwUpwIAPu3r07TDvs3Rws+o/pU=
github.com/lib/pq v1.3.0/go.mod h1:5WUZQaWbwv1U+lTReE5YruASi9Al49XbQIvNi/34Woo=
github.com/marstr/guid v1.1.1-0.20170427235115-8bdf7d1a087c h1:ouxemItv3B/Zh008HJkEXDYCN3BIRyNHxtUN7ThJ5Js=
github.com/marstr/guid v1.1.1-0.20170427235115-8bdf7d1a087c/go.mod h1:74gB1z2wpxxInTG6yaqA7KrtM0NZ+RbrcqDvYHefzho=
+github.com/mattn/go-sqlite3 v1.9.0/go.mod h1:FPy6KqzDD04eiIsT53CuJW3U88zkxoIYsOqkbpncsNc=
github.com/matttproud/golang_protobuf_extensions v1.0.1 h1:4hp9jkHxhMHkqkrB3Ix0jegS5sx/RkqARlsWZ6pIwiU=
github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0=
github.com/mitchellh/go-homedir v0.0.0-20161203194507-b8bc1bf76747 h1:eQox4Rh4ewJF+mqYPxCkmBAirRnPaHEB26UkNuPyjlk=
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+// Package api provides types used by controller/server-component
+// packages.
+package api
+
+import "context"
+
+// A RoutableFunc calls an API method (sometimes via a wrapped
+// RoutableFunc) that has real argument types.
+//
+// (It is used by ctrlctx to manage database transactions, so moving
+// it to the router package would cause a circular dependency
+// router->arvadostest->ctrlctx->router.)
+type RoutableFunc func(ctx context.Context, opts interface{}) (interface{}, error)
import (
"context"
- "database/sql"
"errors"
"fmt"
"net/http"
"time"
"git.arvados.org/arvados.git/lib/controller/federation"
- "git.arvados.org/arvados.git/lib/controller/localdb"
"git.arvados.org/arvados.git/lib/controller/railsproxy"
"git.arvados.org/arvados.git/lib/controller/router"
+ "git.arvados.org/arvados.git/lib/ctrlctx"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/health"
"git.arvados.org/arvados.git/sdk/go/httpserver"
+ "github.com/jmoiron/sqlx"
_ "github.com/lib/pq"
)
proxy *proxy
secureClient *http.Client
insecureClient *http.Client
- pgdb *sql.DB
+ pgdb *sqlx.DB
pgdbMtx sync.Mutex
}
Routes: health.Routes{"ping": func() error { _, err := h.db(context.TODO()); return err }},
})
- rtr := router.New(federation.New(h.Cluster), localdb.WrapCallsInTransactions(h.db))
+ rtr := router.New(federation.New(h.Cluster), ctrlctx.WrapCallsInTransactions(h.db))
mux.Handle("/arvados/v1/config", rtr)
mux.Handle("/"+arvados.EndpointUserAuthenticate.Path, rtr)
var errDBConnection = errors.New("database connection error")
-func (h *Handler) db(ctx context.Context) (*sql.DB, error) {
+func (h *Handler) db(ctx context.Context) (*sqlx.DB, error) {
h.pgdbMtx.Lock()
defer h.pgdbMtx.Unlock()
if h.pgdb != nil {
return h.pgdb, nil
}
- db, err := sql.Open("postgres", h.Cluster.PostgreSQL.Connection.String())
+ db, err := sqlx.Open("postgres", h.Cluster.PostgreSQL.Connection.String())
if err != nil {
ctxlog.FromContext(ctx).WithError(err).Error("postgresql connect failed")
return nil, errDBConnection
func NewConn(cluster *arvados.Cluster) *Conn {
railsProxy := railsproxy.NewConn(cluster)
- return &Conn{
+ var conn Conn
+ conn = Conn{
cluster: cluster,
railsProxy: railsProxy,
loginController: chooseLoginController(cluster, railsProxy),
}
+ return &conn
}
func (conn *Conn) Logout(ctx context.Context, opts arvados.LogoutOptions) (arvados.LogoutResponse, error) {
"strings"
"git.arvados.org/arvados.git/lib/controller/rpc"
+ "git.arvados.org/arvados.git/lib/ctrlctx"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/auth"
"git.arvados.org/arvados.git/sdk/go/httpserver"
return
}
token := target.Query().Get("api_token")
- tx, err := currenttx(ctx)
+ tx, err := ctrlctx.CurrentTx(ctx)
if err != nil {
return
}
}
var exp sql.NullString
var scopes []byte
- err = tx.QueryRowContext(ctx, "select uuid, api_token, expires_at, scopes from api_client_authorizations where api_token=$1", tokensecret).Scan(&resp.UUID, &resp.APIToken, &exp, &scopes)
+ 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
}
import (
"context"
- "database/sql"
"encoding/json"
"net"
"net/http"
"git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/controller/railsproxy"
+ "git.arvados.org/arvados.git/lib/ctrlctx"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadostest"
"git.arvados.org/arvados.git/sdk/go/auth"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"github.com/bradleypeabody/godap"
+ "github.com/jmoiron/sqlx"
check "gopkg.in/check.v1"
)
cluster *arvados.Cluster
ctrl *ldapLoginController
ldap *godap.LDAPServer // fake ldap server that accepts auth goodusername/goodpassword
- db *sql.DB
+ db *sqlx.DB
// transaction context
ctx context.Context
- rollback func()
+ rollback func() error
}
func (s *LDAPSuite) TearDownSuite(c *check.C) {
Cluster: s.cluster,
RailsProxy: railsproxy.NewConn(s.cluster),
}
- s.db = testdb(c, s.cluster)
+ s.db = arvadostest.DB(c, s.cluster)
}
func (s *LDAPSuite) SetUpTest(c *check.C) {
- s.ctx, s.rollback = testctx(c, s.db)
+ tx, err := s.db.Beginx()
+ c.Assert(err, check.IsNil)
+ s.ctx = ctrlctx.NewWithTransaction(context.Background(), tx)
+ s.rollback = tx.Rollback
}
func (s *LDAPSuite) TearDownTest(c *check.C) {
- s.rollback()
+ if s.rollback != nil {
+ s.rollback()
+ }
}
func (s *LDAPSuite) TestLoginSuccess(c *check.C) {
"net/http"
"strings"
+ "git.arvados.org/arvados.git/lib/controller/api"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/auth"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
type router struct {
mux *mux.Router
backend arvados.API
- wrapCalls func(RoutableFunc) RoutableFunc
+ wrapCalls func(api.RoutableFunc) api.RoutableFunc
}
// New returns a new router (which implements the http.Handler
// the returned method is used in its place. This can be used to
// install hooks before and after each API call and alter responses;
// see localdb.WrapCallsInTransaction for an example.
-func New(backend arvados.API, wrapCalls func(RoutableFunc) RoutableFunc) *router {
+func New(backend arvados.API, wrapCalls func(api.RoutableFunc) api.RoutableFunc) *router {
rtr := &router{
mux: mux.NewRouter(),
backend: backend,
return rtr
}
-type RoutableFunc func(ctx context.Context, opts interface{}) (interface{}, error)
-
func (rtr *router) addRoutes() {
for _, route := range []struct {
endpoint arvados.APIEndpoint
defaultOpts func() interface{}
- exec RoutableFunc
+ exec api.RoutableFunc
}{
{
arvados.EndpointConfigGet,
"GET": "HEAD", // Accept HEAD at any GET route
}
-func (rtr *router) addRoute(endpoint arvados.APIEndpoint, defaultOpts func() interface{}, exec RoutableFunc) {
+func (rtr *router) addRoute(endpoint arvados.APIEndpoint, defaultOpts func() interface{}, exec api.RoutableFunc) {
methods := []string{endpoint.Method}
if alt, ok := altMethod[endpoint.Method]; ok {
methods = append(methods, alt)
//
// SPDX-License-Identifier: AGPL-3.0
-package localdb
+package ctrlctx
import (
"context"
- "database/sql"
"errors"
"sync"
- "git.arvados.org/arvados.git/lib/controller/router"
+ "git.arvados.org/arvados.git/lib/controller/api"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "github.com/jmoiron/sqlx"
+ _ "github.com/lib/pq"
+)
+
+var (
+ ErrNoTransaction = errors.New("bug: there is no transaction in this context")
+ ErrContextFinished = errors.New("refusing to start a transaction after wrapped function already returned")
)
// WrapCallsInTransactions returns a call wrapper (suitable for
//
// The wrapper calls getdb() to get a database handle before each API
// call.
-func WrapCallsInTransactions(getdb func(context.Context) (*sql.DB, error)) func(router.RoutableFunc) router.RoutableFunc {
- return func(origFunc router.RoutableFunc) router.RoutableFunc {
+func WrapCallsInTransactions(getdb func(context.Context) (*sqlx.DB, error)) func(api.RoutableFunc) api.RoutableFunc {
+ return func(origFunc api.RoutableFunc) api.RoutableFunc {
return func(ctx context.Context, opts interface{}) (_ interface{}, err error) {
- ctx, finishtx := starttx(ctx, getdb)
+ ctx, finishtx := New(ctx, getdb)
defer finishtx(&err)
return origFunc(ctx, opts)
}
}
}
-// ContextWithTransaction returns a child context in which the given
+// NewWithTransaction returns a child context in which the given
// transaction will be used by any localdb API call that needs one.
// The caller is responsible for calling Commit or Rollback on tx.
-func ContextWithTransaction(ctx context.Context, tx *sql.Tx) context.Context {
+func NewWithTransaction(ctx context.Context, tx *sqlx.Tx) context.Context {
txn := &transaction{tx: tx}
txn.setup.Do(func() {})
return context.WithValue(ctx, contextKeyTransaction, txn)
var contextKeyTransaction = contextKeyT("transaction")
type transaction struct {
- tx *sql.Tx
+ tx *sqlx.Tx
err error
- getdb func(context.Context) (*sql.DB, error)
+ getdb func(context.Context) (*sqlx.DB, error)
setup sync.Once
}
-type transactionFinishFunc func(*error)
+type finishFunc func(*error)
-// starttx returns a new child context that can be used with
-// currenttx(). It does not open a database transaction until the
-// first call to currenttx().
+// New returns a new child context that can be used with
+// CurrentTx(). It does not open a database transaction until the
+// first call to CurrentTx().
//
// The caller must eventually call the returned finishtx() func to
// commit or rollback the transaction, if any.
//
// func example(ctx context.Context) (err error) {
-// ctx, finishtx := starttx(ctx, dber)
+// ctx, finishtx := New(ctx, dber)
// defer finishtx(&err)
// // ...
-// tx, err := currenttx(ctx)
+// tx, err := CurrentTx(ctx)
// if err != nil {
// return fmt.Errorf("example: %s", err)
// }
//
// If *err is non-nil, finishtx() rolls back the transaction, and
// does not modify *err.
-func starttx(ctx context.Context, getdb func(context.Context) (*sql.DB, error)) (context.Context, transactionFinishFunc) {
+func New(ctx context.Context, getdb func(context.Context) (*sqlx.DB, error)) (context.Context, finishFunc) {
txn := &transaction{getdb: getdb}
return context.WithValue(ctx, contextKeyTransaction, txn), func(err *error) {
txn.setup.Do(func() {
// Using (*sync.Once)Do() prevents a future
- // call to currenttx() from opening a
+ // call to CurrentTx() from opening a
// transaction which would never get committed
- // or rolled back. If currenttx() hasn't been
+ // or rolled back. If CurrentTx() hasn't been
// called before now, future calls will return
// this error.
- txn.err = errors.New("refusing to start a transaction after wrapped function already returned")
+ txn.err = ErrContextFinished
})
if txn.tx == nil {
// we never [successfully] started a transaction
}
}
-func currenttx(ctx context.Context) (*sql.Tx, error) {
+func CurrentTx(ctx context.Context) (*sqlx.Tx, error) {
txn, ok := ctx.Value(contextKeyTransaction).(*transaction)
if !ok {
- return nil, errors.New("bug: there is no transaction in this context")
+ return nil, ErrNoTransaction
}
txn.setup.Do(func() {
if db, err := txn.getdb(ctx); err != nil {
txn.err = err
} else {
- txn.tx, txn.err = db.Begin()
+ txn.tx, txn.err = db.Beginx()
}
})
return txn.tx, txn.err
//
// SPDX-License-Identifier: AGPL-3.0
-package localdb
+package ctrlctx
import (
"context"
- "database/sql"
"sync"
"sync/atomic"
+ "testing"
"git.arvados.org/arvados.git/lib/config"
- "git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
+ "github.com/jmoiron/sqlx"
_ "github.com/lib/pq"
check "gopkg.in/check.v1"
)
-// testdb returns a DB connection for the given cluster config.
-func testdb(c *check.C, cluster *arvados.Cluster) *sql.DB {
- db, err := sql.Open("postgres", cluster.PostgreSQL.Connection.String())
- c.Assert(err, check.IsNil)
- return db
-}
-
-// testctx returns a context suitable for running a test case in a new
-// transaction, and a rollback func which the caller should call after
-// the test.
-func testctx(c *check.C, db *sql.DB) (ctx context.Context, rollback func()) {
- tx, err := db.Begin()
- c.Assert(err, check.IsNil)
- return ContextWithTransaction(context.Background(), tx), func() {
- c.Check(tx.Rollback(), check.IsNil)
- }
+// Gocheck boilerplate
+func Test(t *testing.T) {
+ check.TestingT(t)
}
var _ = check.Suite(&DatabaseSuite{})
c.Assert(err, check.IsNil)
var getterCalled int64
- getter := func(context.Context) (*sql.DB, error) {
+ getter := func(context.Context) (*sqlx.DB, error) {
atomic.AddInt64(&getterCalled, 1)
- return testdb(c, cluster), nil
+ db, err := sqlx.Open("postgres", cluster.PostgreSQL.Connection.String())
+ c.Assert(err, check.IsNil)
+ return db, nil
}
wrapper := WrapCallsInTransactions(getter)
wrappedFunc := wrapper(func(ctx context.Context, opts interface{}) (interface{}, error) {
- txes := make([]*sql.Tx, 20)
+ txes := make([]*sqlx.Tx, 20)
var wg sync.WaitGroup
for i := range txes {
i := i
wg.Add(1)
go func() {
- // Concurrent calls to currenttx(),
+ // Concurrent calls to CurrentTx(),
// with different children of the same
// parent context, will all return the
// same transaction.
defer wg.Done()
ctx, cancel := context.WithCancel(ctx)
defer cancel()
- tx, err := currenttx(ctx)
+ tx, err := CurrentTx(ctx)
c.Check(err, check.IsNil)
txes[i] = tx
}()
c.Check(err, check.IsNil)
c.Check(getterCalled, check.Equals, int64(1))
- // When a wrapped func returns without calling currenttx(),
- // calling currenttx() later shouldn't start a new
+ // When a wrapped func returns without calling CurrentTx(),
+ // calling CurrentTx() later shouldn't start a new
// transaction.
var savedctx context.Context
ok, err = wrapper(func(ctx context.Context, opts interface{}) (interface{}, error) {
})(context.Background(), "blah")
c.Check(ok, check.Equals, true)
c.Check(err, check.IsNil)
- tx, err := currenttx(savedctx)
+ tx, err := CurrentTx(savedctx)
c.Check(tx, check.IsNil)
c.Check(err, check.NotNil)
}
--- /dev/null
+// Copyright (C) The Arvados Authors. All rights reserved.
+//
+// SPDX-License-Identifier: Apache-2.0
+
+package arvadostest
+
+import (
+ "context"
+
+ "git.arvados.org/arvados.git/lib/ctrlctx"
+ "git.arvados.org/arvados.git/sdk/go/arvados"
+ "github.com/jmoiron/sqlx"
+ _ "github.com/lib/pq"
+ "gopkg.in/check.v1"
+)
+
+// DB returns a DB connection for the given cluster config.
+func DB(c *check.C, cluster *arvados.Cluster) *sqlx.DB {
+ db, err := sqlx.Open("postgres", cluster.PostgreSQL.Connection.String())
+ c.Assert(err, check.IsNil)
+ return db
+}
+
+// TransactionContext returns a context suitable for running a test
+// case in a new transaction, and a rollback func which the caller
+// should call after the test.
+func TransactionContext(c *check.C, db *sqlx.DB) (ctx context.Context, rollback func()) {
+ tx, err := db.Beginx()
+ c.Assert(err, check.IsNil)
+ return ctrlctx.NewWithTransaction(context.Background(), tx), func() {
+ c.Check(tx.Rollback(), check.IsNil)
+ }
+}
projects / arvados.git / commitdiff