X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/3528563917b200e6126452aec5fd7b77af0fc1c2..d59f4efde5eece7d3b3ea965895397c8ad4c936e:/plot.go

diff --git a/plot.go b/plot.go
index 6705f146c0..0367b1241a 100644
--- a/plot.go
+++ b/plot.go
@@ -1,4 +1,8 @@
-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
 
 import (
 	"flag"
@@ -24,6 +28,7 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 	inputFilename := flags.String("i", "-", "input `file`")
 	sampleCSVFilename := flags.String("labels-csv", "", "use first two columns of `labels.csv` as id->color mapping")
 	sampleFastaDirname := flags.String("sample-fasta-dir", "", "`directory` containing fasta input files")
+	priority := flags.Int("priority", 500, "container request priority")
 	err = flags.Parse(args)
 	if err == flag.ErrHelp {
 		err = nil
@@ -36,8 +41,9 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 		Name:        "lightning plot",
 		Client:      arvados.NewClientFromEnv(),
 		ProjectUUID: *projectUUID,
-		RAM:         1 << 30,
+		RAM:         4 << 30,
 		VCPUs:       1,
+		Priority:    *priority,
 		Mounts: map[string]map[string]interface{}{
 			"/plot.py": map[string]interface{}{
 				"kind":    "text",
@@ -51,10 +57,12 @@ func (cmd *pythonPlot) RunCommand(prog string, args []string, stdin io.Reader, s
 	}
 	runner.Prog = "python3"
 	runner.Args = []string{"/plot.py", *inputFilename, *sampleCSVFilename, *sampleFastaDirname, "/mnt/output/plot.png"}
-	err = runner.Run()
+	var output string
+	output, err = runner.Run()
 	if err != nil {
 		return 1
 	}
+	fmt.Fprintln(stdout, output+"/plot.png")
 	return 0
 }
 
@@ -112,7 +120,10 @@ if sys.argv[2]:
         'PJL': 'blueviolet',
     }
     for fnm in sorted(labels.keys()):
-        colors.append(labelcolors[labels[fnm]])
+        if labels[fnm] in labelcolors:
+            colors.append(labelcolors[labels[fnm]])
+        else:
+            colors.append('black')
 
 from matplotlib.figure import Figure
 from matplotlib.patches import Polygon