+++ /dev/null
-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
- _ "embed"
- "flag"
- "fmt"
- "io"
- "os/exec"
- "strings"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
-)
-
-type manhattanPlot struct{}
-
-//go:embed manhattan.py
-var manhattanPy string
-
-func (cmd *manhattanPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
- var err error
- defer func() {
- if err != nil {
- fmt.Fprintf(stderr, "%s\n", err)
- }
- }()
- flags := flag.NewFlagSet("", flag.ContinueOnError)
- flags.SetOutput(stderr)
- projectUUID := flags.String("project", "", "project `UUID` for output data")
- inputDirectory := flags.String("i", "-", "input `directory` (output of slice-numpy -single-onehot)")
- outputFilename := flags.String("o", "", "output `filename` (e.g., './plot.png')")
- priority := flags.Int("priority", 500, "container request priority")
- runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
- err = flags.Parse(args)
- if err == flag.ErrHelp {
- err = nil
- return 0
- } else if err != nil {
- return 2
- } else if flags.NArg() > 0 {
- err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
- return 2
- }
-
- runner := arvadosContainerRunner{
- Name: "lightning manhattan",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: *projectUUID,
- RAM: 4 << 30,
- VCPUs: 1,
- Priority: *priority,
- Mounts: map[string]map[string]interface{}{
- "/manhattan.py": map[string]interface{}{
- "kind": "text",
- "content": manhattanPy,
- },
- },
- }
- if !*runlocal {
- err = runner.TranslatePaths(inputDirectory)
- if err != nil {
- return 1
- }
- *outputFilename = "/mnt/output/plot.png"
- }
- args = []string{
- *inputDirectory,
- *outputFilename,
- }
- if *runlocal {
- if *outputFilename == "" {
- fmt.Fprintln(stderr, "error: must specify -o filename.png in local mode (or try -help)")
- return 1
- }
- cmd := exec.Command("python3", append([]string{"-"}, args...)...)
- cmd.Stdin = strings.NewReader(manhattanPy)
- cmd.Stdout = stdout
- cmd.Stderr = stderr
- err = cmd.Run()
- if err != nil {
- return 1
- }
- return 0
- }
- runner.Prog = "python3"
- runner.Args = append([]string{"/manhattan.py"}, args...)
- var output string
- output, err = runner.Run()
- if err != nil {
- return 1
- }
- fmt.Fprintln(stdout, output+"/plot.png")
- return 0
-}