// 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 }