plot.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         _ "embed"
   9         "flag"
  10         "fmt"
  11         "io"
  12         _ "net/http/pprof"
  13
  14         "git.arvados.org/arvados.git/sdk/go/arvados"
  15 )
  16
  17 type pythonPlot struct{}
  18
  19 //go:embed plot.py
  20 var plotscript string
  21
  22 func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  23         var err error
  24         defer func() {
  25                 if err != nil {
  26                         fmt.Fprintf(stderr, "%s\n", err)
  27                 }
  28         }()
  29         flags := flag.NewFlagSet("", flag.ContinueOnError)
  30         flags.SetOutput(stderr)
  31         projectUUID := flags.String("project", "", "project `UUID` for output data")
  32         inputFilename := flags.String("i", "-", "input `file`")
  33         sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
  34         phenotypeFilename := flags.String("phenotype", "", "use `phenotype.csv` as id->phenotype mapping (column 0 is sample id)")
  35         phenotypeColumn := flags.Int("phenotype-column", 1, "0-based column `index` of phenotype in phenotype.csv file")
  36         priority := flags.Int("priority", 500, "container request priority")
  37         err = flags.Parse(args)
  38         if err == flag.ErrHelp {
  39                 err = nil
  40                 return 0
  41         } else if err != nil {
  42                 return 2
  43         }
  44
  45         runner := arvadosContainerRunner{
  46                 Name:        "lightning plot",
  47                 Client:      arvados.NewClientFromEnv(),
  48                 ProjectUUID: *projectUUID,
  49                 RAM:         4 << 30,
  50                 VCPUs:       1,
  51                 Priority:    *priority,
  52                 Mounts: map[string]map[string]interface{}{
  53                         "/plot.py": map[string]interface{}{
  54                                 "kind":    "text",
  55                                 "content": plotscript,
  56                         },
  57                 },
  58         }
  59         err = runner.TranslatePaths(inputFilename, sampleListFilename, phenotypeFilename)
  60         if err != nil {
  61                 return 1
  62         }
  63         runner.Prog = "python3"
  64         runner.Args = []string{"/plot.py", *inputFilename, *sampleListFilename, *phenotypeFilename, fmt.Sprintf("%d", *phenotypeColumn), "/mnt/output/plot.png"}
  65         var output string
  66         output, err = runner.Run()
  67         if err != nil {
  68                 return 1
  69         }
  70         fmt.Fprintln(stdout, output+"/plot.png")
  71         return 0
  72 }