X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/4c1958b0db98c7628e91265dd7e99c0c840c1206..HEAD:/plot.go

diff --git a/plot.go b/plot.go
deleted file mode 100644
index 51f5c8236c..0000000000
--- a/plot.go
+++ /dev/null
@@ -1,72 +0,0 @@
-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
-	_ "embed"
-	"flag"
-	"fmt"
-	"io"
-	_ "net/http/pprof"
-
-	"git.arvados.org/arvados.git/sdk/go/arvados"
-)
-
-type pythonPlot struct{}
-
-//go:embed plot.py
-var plotscript string
-
-func (cmd *pythonPlot) 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")
-	inputFilename := flags.String("i", "-", "input `file`")
-	sampleListFilename := flags.String("samples", "", "use second column of `samples.csv` as complete list of sample IDs")
-	phenotypeFilename := flags.String("phenotype", "", "use `phenotype.csv` as id->phenotype mapping (column 0 is sample id)")
-	phenotypeColumn := flags.Int("phenotype-column", 1, "0-based column `index` of phenotype in phenotype.csv file")
-	priority := flags.Int("priority", 500, "container request priority")
-	err = flags.Parse(args)
-	if err == flag.ErrHelp {
-		err = nil
-		return 0
-	} else if err != nil {
-		return 2
-	}
-
-	runner := arvadosContainerRunner{
-		Name:        "lightning plot",
-		Client:      arvados.NewClientFromEnv(),
-		ProjectUUID: *projectUUID,
-		RAM:         4 << 30,
-		VCPUs:       1,
-		Priority:    *priority,
-		Mounts: map[string]map[string]interface{}{
-			"/plot.py": map[string]interface{}{
-				"kind":    "text",
-				"content": plotscript,
-			},
-		},
-	}
-	err = runner.TranslatePaths(inputFilename, sampleListFilename, phenotypeFilename)
-	if err != nil {
-		return 1
-	}
-	runner.Prog = "python3"
-	runner.Args = []string{"/plot.py", *inputFilename, *sampleListFilename, *phenotypeFilename, fmt.Sprintf("%d", *phenotypeColumn), "/mnt/output/plot.png"}
-	var output string
-	output, err = runner.Run()
-	if err != nil {
-		return 1
-	}
-	fmt.Fprintln(stdout, output+"/plot.png")
-	return 0
-}