Run "import" in arvados container.

[lightning.git] / import.go

diff --git a/import.go b/import.go
index 49a7c7a885b2e1478a6b31b9e5bcda4cdbdd24fd..0f224670767698fd609b49f62426a0dbaae898df 100644 (file)
--- 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