Run "filter" and "export" in arvados containers.

[lightning.git] / exportnumpy.go

diff --git a/exportnumpy.go b/exportnumpy.go
index d11b7431d5a6bc73dc4711035dfdda9bf992d6fb..e8854ace8c55f88a8cadf2f2e0b67682808b33c5 100644 (file)
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -2,13 +2,16 @@ package main
 
 import (
        "bufio"
+       "errors"
        "flag"
        "fmt"
        "io"
        "log"
        "net/http"
        _ "net/http/pprof"
+       "os"
 
+       "git.arvados.org/arvados.git/sdk/go/arvados"
        "github.com/kshedden/gonpy"
 )
 
@@ -26,6 +29,10 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
        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")
+       inputFilename := flags.String("i", "", "input `file`")
+       outputFilename := flags.String("o", "", "output `file`")
        err = flags.Parse(args)
        if err == flag.ErrHelp {
                err = nil
@@ -41,6 +48,30 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                }()
        }
 
+       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,
+               }
+               err = runner.TranslatePaths(inputFilename)
+               if err != nil {
+                       return 1
+               }
+               runner.Args = []string{"export-numpy", "-local=true", "-i", *inputFilename, "-o", "/mnt/output/library.npy"}
+               err = runner.Run()
+               if err != nil {
+                       return 1
+               }
+               return 0
+       }
+
        cgs, err := ReadCompactGenomes(stdin)
        if err != nil {
                return 1
@@ -58,14 +89,29 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
                        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{cmd.output}
+       } 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
        }