import (
"bufio"
+ "errors"
"flag"
"fmt"
"io"
- "log"
+ "io/ioutil"
"net/http"
_ "net/http/pprof"
+ "os"
+ "git.arvados.org/arvados.git/sdk/go/arvados"
"github.com/kshedden/gonpy"
+ log "github.com/sirupsen/logrus"
)
-type exportNumpy struct {
- output io.Writer
-}
+type exportNumpy struct{}
func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
var err error
flags := flag.NewFlagSet("", flag.ContinueOnError)
flags.SetOutput(stderr)
pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+ runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
+ projectUUID := flags.String("project", "", "project `UUID` for output data")
+ priority := flags.Int("priority", 500, "container request priority")
+ inputFilename := flags.String("i", "-", "input `file`")
+ outputFilename := flags.String("o", "-", "output `file`")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
} else if err != nil {
return 2
}
- cmd.output = stdout
if *pprof != "" {
go func() {
}()
}
- cgs, err := ReadCompactGenomes(stdin)
+ if !*runlocal {
+ if *outputFilename != "-" {
+ err = errors.New("cannot specify output file in container mode: not implemented")
+ return 1
+ }
+ runner := arvadosContainerRunner{
+ Name: "lightning export-numpy",
+ Client: arvados.NewClientFromEnv(),
+ ProjectUUID: *projectUUID,
+ RAM: 64000000000,
+ VCPUs: 2,
+ Priority: *priority,
+ }
+ err = runner.TranslatePaths(inputFilename)
+ if err != nil {
+ return 1
+ }
+ runner.Args = []string{"export-numpy", "-local=true", "-i", *inputFilename, "-o", "/mnt/output/library.npy"}
+ var output string
+ output, err = runner.Run()
+ if err != nil {
+ return 1
+ }
+ fmt.Fprintln(stdout, output+"/library.npy")
+ return 0
+ }
+
+ var input io.ReadCloser
+ if *inputFilename == "-" {
+ input = ioutil.NopCloser(stdin)
+ } else {
+ input, err = os.Open(*inputFilename)
+ if err != nil {
+ return 1
+ }
+ defer input.Close()
+ }
+ cgs, err := ReadCompactGenomes(input)
+ if err != nil {
+ return 1
+ }
+ err = input.Close()
if err != nil {
return 1
}
out[row*cols+i] = uint16(v)
}
}
- w := bufio.NewWriter(cmd.output)
- npw, err := gonpy.NewWriter(nopCloser{w})
+
+ var output io.WriteCloser
+ if *outputFilename == "-" {
+ output = nopCloser{stdout}
+ } else {
+ output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
+ if err != nil {
+ return 1
+ }
+ defer output.Close()
+ }
+ bufw := bufio.NewWriter(output)
+ npw, err := gonpy.NewWriter(nopCloser{bufw})
if err != nil {
return 1
}
npw.Shape = []int{rows, cols}
npw.WriteUint16(out)
- err = w.Flush()
+ err = bufw.Flush()
+ if err != nil {
+ return 1
+ }
+ err = output.Close()
if err != nil {
return 1
}