From 291f97cecfaa2dcee2c332c1192b506c551552ee Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Mon, 2 Mar 2020 16:49:48 -0500 Subject: [PATCH] Run "import" in arvados container. Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- arvados.go | 167 ++++++++++++++++++++++++++++++++++++++++++++ exportnumpy_test.go | 4 +- go.mod | 13 +++- go.sum | 50 ++++++++++++- import.go | 40 +++++++++++ 5 files changed, 267 insertions(+), 7 deletions(-) create mode 100644 arvados.go diff --git a/arvados.go b/arvados.go new file mode 100644 index 0000000000..f121542117 --- /dev/null +++ b/arvados.go @@ -0,0 +1,167 @@ +package main + +import ( + "errors" + "fmt" + "io/ioutil" + "log" + "os" + "regexp" + + "git.arvados.org/arvados.git/sdk/go/arvados" + "git.arvados.org/arvados.git/sdk/go/arvadosclient" + "git.arvados.org/arvados.git/sdk/go/keepclient" + "golang.org/x/crypto/blake2b" +) + +type arvadosContainerRunner struct { + Client *arvados.Client + Name string + ProjectUUID string + Args []string + Mounts map[string]string +} + +var ( + collectionInPathRe = regexp.MustCompile(`^(.*/)?([0-9a-f]{32}\+[0-9]+|[0-9a-z]{5}-[0-9a-z]{5}-[0-9a-z]{15})(/.*)?$`) +) + +func (runner *arvadosContainerRunner) Run() error { + if runner.ProjectUUID == "" { + return errors.New("cannot run arvados container: ProjectUUID not provided") + } + prog := "/mnt/cmd/lightning" + cmdUUID, err := runner.makeCommandCollection() + if err != nil { + return err + } + command := append([]string{prog}, runner.Args...) + mounts := map[string]map[string]interface{}{ + "/mnt/cmd": { + "kind": "collection", + "uuid": cmdUUID, + }, + "/mnt/output": { + "kind": "tmp", + "writable": true, + "capacity": 100000000000, + }, + } + for uuid, mnt := range runner.Mounts { + mounts[mnt] = map[string]interface{}{ + "kind": "collection", + "uuid": uuid, + } + } + cpus := 16 + rc := arvados.RuntimeConstraints{ + VCPUs: cpus, + RAM: 64000000000, + KeepCacheRAM: (1 << 26) * 2 * int64(cpus), + } + var cr arvados.ContainerRequest + err = runner.Client.RequestAndDecode(&cr, "POST", "arvados/v1/container_requests", nil, map[string]interface{}{ + "container_request": map[string]interface{}{ + "owner_uuid": runner.ProjectUUID, + "name": runner.Name, + "container_image": "lightning-runtime", + "command": command, + "mounts": mounts, + "use_existing": true, + "output_path": "/mnt/output", + "runtime_constraints": rc, + "priority": 1, + "state": arvados.ContainerRequestStateCommitted, + }, + }) + log.Print(cr.UUID) + return err +} + +func (runner *arvadosContainerRunner) TranslatePaths(paths ...*string) error { + if runner.Mounts == nil { + runner.Mounts = make(map[string]string) + } + for _, path := range paths { + if *path == "" { + continue + } + m := collectionInPathRe.FindStringSubmatch(*path) + if m == nil { + return fmt.Errorf("cannot find uuid in path: %q", *path) + } + uuid := m[2] + mnt, ok := runner.Mounts[uuid] + if !ok { + mnt = "/mnt/" + uuid + runner.Mounts[uuid] = mnt + } + *path = mnt + m[3] + } + return nil +} + +func (runner *arvadosContainerRunner) makeCommandCollection() (string, error) { + exe, err := ioutil.ReadFile("/proc/self/exe") + if err != nil { + return "", err + } + b2 := blake2b.Sum256(exe) + cname := fmt.Sprintf("lightning-%x", b2) + var existing arvados.CollectionList + err = runner.Client.RequestAndDecode(&existing, "GET", "arvados/v1/collections", nil, arvados.ListOptions{ + Limit: 1, + Count: "none", + Filters: []arvados.Filter{ + {"name", "=", cname}, + {"owner_uuid", "=", runner.ProjectUUID}, + }, + }) + if err != nil { + return "", err + } + if len(existing.Items) > 0 { + uuid := existing.Items[0].UUID + log.Printf("using existing collection %q named %q (did not verify whether content matches)", uuid, cname) + return uuid, nil + } + log.Printf("writing lightning binary to new collection %q", cname) + ac, err := arvadosclient.New(runner.Client) + if err != nil { + return "", err + } + kc := keepclient.New(ac) + var coll arvados.Collection + fs, err := coll.FileSystem(runner.Client, kc) + if err != nil { + return "", err + } + f, err := fs.OpenFile("lightning", os.O_CREATE|os.O_WRONLY, 0777) + if err != nil { + return "", err + } + _, err = f.Write(exe) + if err != nil { + return "", err + } + err = f.Close() + if err != nil { + return "", err + } + mtxt, err := fs.MarshalManifest(".") + if err != nil { + return "", err + } + err = runner.Client.RequestAndDecode(&coll, "POST", "arvados/v1/collections", nil, map[string]interface{}{ + "collection": map[string]interface{}{ + "owner_uuid": runner.ProjectUUID, + "manifest_text": mtxt, + "name": cname, + }, + }) + if err != nil { + return "", err + } + log.Printf("collection: %#v", coll) + return coll.UUID, nil +} diff --git a/exportnumpy_test.go b/exportnumpy_test.go index 4bef7bd1e8..91921a8502 100644 --- a/exportnumpy_test.go +++ b/exportnumpy_test.go @@ -14,8 +14,8 @@ var _ = check.Suite(&exportSuite{}) func (s *exportSuite) TestFastaToNumpy(c *check.C) { var buffer bytes.Buffer - exited := (&importer{}).RunCommand("import", []string{"-tag-library", "testdata/tags", "-ref", "testdata/ref", "testdata/a.1.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr) - c.Check(exited, check.Equals, 0) + exited := (&importer{}).RunCommand("import", []string{"-local=true", "-tag-library", "testdata/tags", "-ref", "testdata/ref", "testdata/a.1.fasta"}, &bytes.Buffer{}, &buffer, os.Stderr) + c.Assert(exited, check.Equals, 0) var output bytes.Buffer exited = (&exportNumpy{}).RunCommand("export-numpy", nil, &buffer, &output, os.Stderr) c.Check(exited, check.Equals, 0) diff --git a/go.mod b/go.mod index 7e35d3e8bc..91be95e4f1 100644 --- a/go.mod +++ b/go.mod @@ -3,8 +3,15 @@ module github.com/curii/lightning go 1.13 require ( - git.arvados.org/arvados.git v0.0.0-20200107160329-7db3857d78a0 + git.arvados.org/arvados.git v0.0.0-20200228212437-894d7e9c3adf + github.com/gogo/protobuf v1.3.1 // indirect + github.com/golang/protobuf v1.3.4 // indirect + github.com/konsorten/go-windows-terminal-sequences v1.0.2 // indirect github.com/kshedden/gonpy v0.0.0-20190510000443-66c21fac4672 - golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2 - gopkg.in/check.v1 v1.0.0-20161208181325-20d25e280405 + github.com/prometheus/client_golang v1.4.1 // indirect + github.com/prometheus/procfs v0.0.10 // indirect + golang.org/x/crypto v0.0.0-20200221231518-2aa609cf4a9d + golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527 // indirect + gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 + gopkg.in/yaml.v2 v2.2.8 // indirect ) diff --git a/go.sum b/go.sum index f7279df446..322870aefa 100644 --- a/go.sum +++ b/go.sum @@ -1,8 +1,8 @@ cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= -git.arvados.org/arvados.git v0.0.0-20200107160329-7db3857d78a0 h1:Jd6ic7+NjLGT9xs5sxHQzLYoeTevyo4AOBJjxMHwRso= -git.arvados.org/arvados.git v0.0.0-20200107160329-7db3857d78a0/go.mod h1:mBINrAVO/QPkpIjFUDdfdynfy6HLsfWGbMlaCPCH8iA= +git.arvados.org/arvados.git v0.0.0-20200228212437-894d7e9c3adf h1:DaFOmEkjD79eDdCXOllKN/11oqlVPHoQRbBKu0qUIWo= +git.arvados.org/arvados.git v0.0.0-20200228212437-894d7e9c3adf/go.mod h1:AgfRQKQQM8/38MUWiRuXoK9Le1LC8pvhmhHeG0mJaLk= github.com/AdRoll/goamz v0.0.0-20170825154802-2731d20f46f4/go.mod h1:bix3XpsJxNavm6XVKAuEFzG+1W3ORxj7hvbIrFr7Sqs= github.com/Azure/azure-sdk-for-go v19.1.0+incompatible/go.mod h1:9XXNKU+eRnpl9moKnB4QOLf1HestfXbmab5FXxiDBjc= github.com/Azure/go-autorest v10.15.2+incompatible/go.mod h1:r+4oMnoxhatjLLJ6zxSWATqVooLgysK6ZNox3g/xq24= @@ -14,6 +14,7 @@ github.com/alecthomas/template v0.0.0-20190718012654-fb15b899a751/go.mod h1:LOuy github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= github.com/alecthomas/units v0.0.0-20190717042225-c3de453c63f4/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= github.com/anmitsu/go-shlex v0.0.0-20161002113705-648efa622239/go.mod h1:2FmKhYUyUczH0OGQWaF5ceTx0UBShxjsH6f8oGKYe2c= +github.com/arvados/cgofuse v1.2.0/go.mod h1:79WFV98hrkRHK9XPhh2IGGOwpFSjocsWubgxAs2KhRc= github.com/aws/aws-sdk-go v1.25.30/go.mod h1:KmX6BPdI08NWTb3/sm4ZGu5ShLoqVDhKgpiN924inxo= github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= @@ -21,6 +22,8 @@ github.com/beorn7/perks v1.0.1 h1:VlbKKnNfV8bJzeqoa4cOKqO6bYr3WgKZxO8Z16+hsOM= github.com/beorn7/perks v1.0.1/go.mod h1:G2ZrVWU2WbWT9wwq4/hrbKbnv/1ERSJQ0ibhJ6rlkpw= github.com/cespare/xxhash/v2 v2.1.0 h1:yTUvW7Vhb89inJ+8irsUqiWjh8iT6sQPZiQzI6ReGkA= github.com/cespare/xxhash/v2 v2.1.0/go.mod h1:dgIUBU3pDso/gPgZ1osOZ0iQf77oPR28Tjxl5dIMyVM= +github.com/cespare/xxhash/v2 v2.1.1 h1:6MnRN8NT7+YBpUIWxHtefFZOKTAPgGjpQSxqLNn0+qY= +github.com/cespare/xxhash/v2 v2.1.1/go.mod h1:VGX0DQ3Q6kWi7AoAeZDth3/j3BFtOZR5XLFGgcrjCOs= github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= github.com/coreos/go-oidc v2.1.0+incompatible/go.mod h1:CgnwVTmzoESiwO9qyAFEMiHoZ1nMCKZlZ9V6mm3/LKc= github.com/coreos/go-systemd v0.0.0-20180108085132-cc4f39464dc7/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4= @@ -45,6 +48,8 @@ github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V 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/gogo/protobuf v1.3.1 h1:DqDEcV5aeaTmdFBePNpYsp3FlcVH/2ISVVM9Qf8PSls= +github.com/gogo/protobuf v1.3.1/go.mod h1:SlYgWuQ5SjCEi6WLHjHCa1yvBfUnHcTbrrZtXPKa29o= github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= github.com/golang/mock v1.2.0/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= @@ -52,10 +57,15 @@ github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5y github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= github.com/golang/protobuf v1.3.2 h1:6nsPYzhq5kReh6QImI3k5qWzO4PEbvbIW2cwSfR/6xs= github.com/golang/protobuf v1.3.2/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= +github.com/golang/protobuf v1.3.4 h1:87PNWwrRvUSnqS4dlcBU/ftvOIBep4sYuBLlh6rX2wk= +github.com/golang/protobuf v1.3.4/go.mod h1:vzj43D7+SQXF/4pzW/hwtAqwc6iTitCiVSaWz5lYuqw= github.com/google/btree v0.0.0-20180813153112-4030bb1f1f0c/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ= github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M= github.com/google/go-cmp v0.3.0 h1:crn/baboCvb5fXaQ0IJ1SGTsTVrWpDsCWC8EGETZijY= github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= +github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= +github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= +github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/google/gofuzz v1.0.0/go.mod h1:dBl0BpW6vV/+mYPU4Po3pmUjxk6FQPldtuIdl/M65Eg= github.com/google/martian v2.1.0+incompatible/go.mod h1:9I4somxYTbIHy5NJKHRl3wXiIaQGbYVAs8BPL6v8lEs= github.com/google/pprof v0.0.0-20181206194817-3ea8567a2e57/go.mod h1:zfwlbNMJ+OItoe0UupaVj+oy1omPYYDuagoSzA8v9mc= @@ -71,12 +81,23 @@ github.com/jmcvetta/randutil v0.0.0-20150817122601-2bb1b664bcff/go.mod h1:ddfPX8 github.com/jmespath/go-jmespath v0.0.0-20180206201540-c2b33e8439af/go.mod h1:Nht3zPeWKUH0NzdCt2Blrr5ys8VGpn0CEB0cQHVjt7k= 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/json-iterator/go v1.1.9/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/uOdHXbAo4= github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU= github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w= +github.com/karalabe/xgo v0.0.0-20191115072854-c5ccff8648a7/go.mod h1:iYGcTYIPUvEWhFo6aKUuLchs+AV4ssYdyuBbQJZGcBk= github.com/kevinburke/ssh_config v0.0.0-20171013211458-802051befeb5/go.mod h1:CT57kijsi8u/K/BOFA39wgDQJ9CxiF4nAY/ojJ6r6mM= +github.com/kisielk/errcheck v1.2.0/go.mod h1:/BMXB+zMLi60iA8Vv6Ksmxu/1UDYcXs4uQLJ+jE2L00= +github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck= 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/konsorten/go-windows-terminal-sequences v1.0.2 h1:DB17ag19krx9CFsz4o3enTrPXyIXCl+2iCXH/aMAp9s= +github.com/konsorten/go-windows-terminal-sequences v1.0.2/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/kr/pretty v0.1.0 h1:L/CwN0zerZDmRFUapSPitk6f+Q3+0za1rQkzVuMiMFI= +github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo= +github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ= +github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE= +github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI= github.com/kshedden/gonpy v0.0.0-20190510000443-66c21fac4672 h1:LQLnybCU54zB8Gj8c1DPeZEheIAn3eZ8Cc9fYqM4ac8= github.com/kshedden/gonpy v0.0.0-20190510000443-66c21fac4672/go.mod h1:+uEXxXG0RlfBPqG1tq5QN/F2jRlcuY0dExSONLpEwcA= github.com/lib/pq v0.0.0-20171126050459-83612a56d3dd/go.mod h1:5WUZQaWbwv1U+lTReE5YruASi9Al49XbQIvNi/34Woo= @@ -101,17 +122,26 @@ github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXP github.com/prometheus/client_golang v1.0.0/go.mod h1:db9x61etRT2tGnBNRi70OPL5FsnadC4Ky3P0J6CfImo= github.com/prometheus/client_golang v1.2.1 h1:JnMpQc6ppsNgw9QPAGF6Dod479itz7lvlsMzzNayLOI= github.com/prometheus/client_golang v1.2.1/go.mod h1:XMU6Z2MjaRKVu/dC1qupJI9SiNkDYzz3xecMgSW/F+U= +github.com/prometheus/client_golang v1.4.1 h1:FFSuS004yOQEtDdTq+TAOLP5xUq63KqAFYyOi8zA+Y8= +github.com/prometheus/client_golang v1.4.1/go.mod h1:e9GMxYsXl05ICDXkRhurwBS4Q3OK1iX/F2sw+iXX5zU= github.com/prometheus/client_model v0.0.0-20180712105110-5c3871d89910/go.mod h1:MbSGuTsp3dbXC40dX6PRTWyKYBIrTGTE9sqQNg2J8bo= github.com/prometheus/client_model v0.0.0-20190129233127-fd36f4220a90/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA= github.com/prometheus/client_model v0.0.0-20190812154241-14fe0d1b01d4 h1:gQz4mCbXsO+nc9n1hCxHcGA3Zx3Eo+UHZoInFGUIXNM= github.com/prometheus/client_model v0.0.0-20190812154241-14fe0d1b01d4/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA= +github.com/prometheus/client_model v0.2.0 h1:uq5h0d+GuxiXLJLNABMgp2qUWDPiLvgCzz2dUR+/W/M= +github.com/prometheus/client_model v0.2.0/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA= github.com/prometheus/common v0.4.1/go.mod h1:TNfzLD0ON7rHzMJeJkieUDPYmFC7Snx/y86RQel1bk4= github.com/prometheus/common v0.7.0 h1:L+1lyG48J1zAQXA3RBX/nG/B3gjlHq0zTt2tlbJLyCY= github.com/prometheus/common v0.7.0/go.mod h1:DjGbpBbp5NYNiECxcL/VnbXCCaQpKd3tt26CguLLsqA= +github.com/prometheus/common v0.9.1 h1:KOMtN28tlbam3/7ZKEYKHhKoJZYYj3gMH4uc62x7X7U= +github.com/prometheus/common v0.9.1/go.mod h1:yhUN8i9wzaXS3w1O07YhxHEBxD+W35wd8bs7vj7HSQ4= github.com/prometheus/procfs v0.0.0-20181005140218-185b4288413d/go.mod h1:c3At6R/oaqEKCNdg8wHV1ftS6bRYblBhIjjI8uT2IGk= github.com/prometheus/procfs v0.0.2/go.mod h1:TjEm7ze935MbeOT/UhFTIMYKhuLP4wbCsTZCD3I8kEA= github.com/prometheus/procfs v0.0.5 h1:3+auTFlqw+ZaQYJARz6ArODtkaIwtvBTx3N2NehQlL8= github.com/prometheus/procfs v0.0.5/go.mod h1:4A/X28fw3Fc593LaREMrKMqOKvUAntwMDaekg4FpcdQ= +github.com/prometheus/procfs v0.0.8/go.mod h1:7Qr8sr6344vo1JqZ6HhLceV9o3AJ1Ff+GxbHq6oeK9A= +github.com/prometheus/procfs v0.0.10 h1:QJQN3jYQhkamO4mhfUWqdDH2asK7ONOI9MTWjyAxNKM= +github.com/prometheus/procfs v0.0.10/go.mod h1:7Qr8sr6344vo1JqZ6HhLceV9o3AJ1Ff+GxbHq6oeK9A= github.com/satori/go.uuid v1.2.1-0.20180103174451-36e9d2ebbde5/go.mod h1:dA0hQrYB0VpLJoorglMZABFdXlWrHn1NEOzdhQKdks0= github.com/sergi/go-diff v1.0.0/go.mod h1:0CfEIISq7TuYL3j771MWULgwwjU+GofnZX9QAmXWZgo= github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= @@ -129,6 +159,8 @@ go.opencensus.io v0.21.0/go.mod h1:mSImk1erAIZhrmZN+AvHh14ztQfjbGwt4TtuofqLduU= golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2 h1:VklqNMn3ovrHsnt90PveolxSbWFaJdECFbxSq0Mqo2M= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= +golang.org/x/crypto v0.0.0-20200221231518-2aa609cf4a9d h1:1ZiEyfaQIg3Qh0EoqpwAakHVhecoE5wlSg5GjnafJGw= +golang.org/x/crypto v0.0.0-20200221231518-2aa609cf4a9d/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto= golang.org/x/exp v0.0.0-20190121172915-509febef88a4/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= golang.org/x/lint v0.0.0-20190227174305-5b3e6a55c961/go.mod h1:wehouNa3lNwaWXcvxsM5YxQ5yQlVC4a0KAMCusXpPoU= @@ -141,6 +173,7 @@ golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73r golang.org/x/net v0.0.0-20190108225652-1e06a53dbb7e/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= golang.org/x/net v0.0.0-20190213061140-3a22650c66bd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= +golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/net v0.0.0-20190503192946-f4e77d36d62c/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/net v0.0.0-20190613194153-d28f0bde5980/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= @@ -151,25 +184,33 @@ golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJ golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= 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 v0.0.0-20190911185100-cd5d95a43a6e/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 v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= +golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190422165155-953cdadca894/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190507160741-ecd444e8653b/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191010194322-b09406accb47/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191105231009-c1f44814a5cd h1:3x5uuvBgE6oaXJjCOvpCC1IpgJogqQ+PqGGU3ZxAgII= golang.org/x/sys v0.0.0-20191105231009-c1f44814a5cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20200122134326-e047566fdf82/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527 h1:uYVVQ9WP/Ds2ROhcaGPeIdVq0RIXVLwsHlnvJ+cT1So= +golang.org/x/sys v0.0.0-20200302150141-5c8b2ff67527/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= 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= golang.org/x/time v0.0.0-20181108054448-85acf8d2951c/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= +golang.org/x/tools v0.0.0-20181030221726-6c7e314b6563/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190226205152-f727befe758c/go.mod h1:9Yl7xja0Znq3iFh3HoIrodX9oNMXvdceNzlUR8zjMvY= golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= 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/xerrors v0.0.0-20191204190536-9bdfabe68543 h1:E7g+9GITq07hpfrRu66IVDexMakfv52eLZ2CXBWiKr4= +golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= google.golang.org/api v0.4.0/go.mod h1:8k5glujaEP+g9n7WNsDg8QP6cUVNI86fCNMcbazEtwE= google.golang.org/api v0.13.0/go.mod h1:iLdEw5Ide6rF15KTC1Kkl0iskquN2gFfn9o9XIsbkAI= google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= @@ -185,6 +226,8 @@ gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLks 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/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo= +gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/square/go-jose.v2 v2.3.1/go.mod h1:M9dMgbHiYLoDGQrXy7OpJDJWiKiU//h+vD76mk0e1AI= gopkg.in/src-d/go-billy.v4 v4.0.1/go.mod h1:ZHSF0JP+7oD97194otDUCD7Ofbk63+xFcfWP5bT6h+Q= gopkg.in/src-d/go-git-fixtures.v3 v3.5.0/go.mod h1:dLBcvytrw/TYZsNTWCnkNF2DSIlzWYqTe3rJR56Ac7g= @@ -194,6 +237,9 @@ gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.4 h1:/eiJrUcujPVeJ3xlSWaiNi3uSVmDGBK1pDHUHAnao1I= gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= +gopkg.in/yaml.v2 v2.2.5/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= +gopkg.in/yaml.v2 v2.2.8 h1:obN1ZagJSUGI0Ek/LBmuj4SNLPfIny3KsKFopxRdj10= +gopkg.in/yaml.v2 v2.2.8/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= 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= honnef.co/go/tools v0.0.0-20190418001031-e561f6794a2a/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= diff --git a/import.go b/import.go index 49a7c7a885..0f22467076 100644 --- a/import.go +++ b/import.go @@ -21,12 +21,16 @@ import ( "sync" "sync/atomic" "time" + + "git.arvados.org/arvados.git/sdk/go/arvados" ) type importer struct { tagLibraryFile string refFile string outputFile string + projectUUID string + runLocal bool encoder *gob.Encoder } @@ -42,6 +46,8 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`") flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`") flags.StringVar(&cmd.outputFile, "o", "", "output `file`") + flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for storing intermediate and output data") + flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)") pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`") err = flags.Parse(args) if err == flag.ErrHelp { @@ -63,6 +69,40 @@ func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, std }() } + if !cmd.runLocal { + runner := arvadosContainerRunner{ + Name: "lightning import", + Client: arvados.NewClientFromEnv(), + ProjectUUID: cmd.projectUUID, + } + err = runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile) + if err != nil { + return 1 + } + inputs := flags.Args() + for i := range inputs { + err = runner.TranslatePaths(&inputs[i]) + if err != nil { + return 1 + } + } + if cmd.outputFile == "" { + cmd.outputFile = "/mnt/output/library.gob" + } else { + // Not yet implemented, but this should write + // the collection to an existing collection, + // possibly even an in-place update. + err = errors.New("cannot specify output file in container mode: not implemented") + return 1 + } + runner.Args = append([]string{"import", "-local=true", "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...) + err = runner.Run() + if err != nil { + return 1 + } + return 0 + } + infiles, err := listInputFiles(flags.Args()) if err != nil { return 1 -- 2.30.2