Fix some tests.

[lightning.git] / pca.go

diff --git a/pca.go b/pca.go
deleted file mode 100644 (file)
index f02cee7..0000000
--- a/pca.go
+++ /dev/null
@@ -1,58 +0,0 @@
-package main
-
-import (
-       "flag"
-       "fmt"
-       "io"
-       _ "net/http/pprof"
-
-       "git.arvados.org/arvados.git/sdk/go/arvados"
-)
-
-type pythonPCA struct{}
-
-func (cmd *pythonPCA) 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`")
-       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 pca",
-               Client:      arvados.NewClientFromEnv(),
-               ProjectUUID: *projectUUID,
-               RAM:         440000000000,
-               VCPUs:       1,
-               Priority:    *priority,
-       }
-       err = runner.TranslatePaths(inputFilename)
-       if err != nil {
-               return 1
-       }
-       runner.Prog = "python3"
-       runner.Args = []string{"-c", `import sys
-import scipy
-from sklearn.decomposition import PCA
-scipy.save(sys.argv[2], PCA(n_components=4).fit_transform(scipy.load(sys.argv[1])))`, *inputFilename, "/mnt/output/pca.npy"}
-       var output string
-       output, err = runner.Run()
-       if err != nil {
-               return 1
-       }
-       fmt.Fprintln(stdout, output+"/pca.npy")
-       return 0
-}