stats.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         "bufio"
   9         "encoding/json"
  10         "errors"
  11         "flag"
  12         "fmt"
  13         "io"
  14         "io/ioutil"
  15         "net/http"
  16         _ "net/http/pprof"
  17         "os"
  18         "strings"
  19
  20         "git.arvados.org/arvados.git/sdk/go/arvados"
  21         log "github.com/sirupsen/logrus"
  22 )
  23
  24 type statscmd struct {
  25         debugUnplaced bool
  26 }
  27
  28 func (cmd *statscmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  29         var err error
  30         defer func() {
  31                 if err != nil {
  32                         fmt.Fprintf(stderr, "%s\n", err)
  33                 }
  34         }()
  35         flags := flag.NewFlagSet("", flag.ContinueOnError)
  36         flags.SetOutput(stderr)
  37         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  38         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  39         projectUUID := flags.String("project", "", "project `UUID` for output data")
  40         priority := flags.Int("priority", 500, "container request priority")
  41         inputFilename := flags.String("i", "-", "input `file`")
  42         outputFilename := flags.String("o", "-", "output `file`")
  43         flags.BoolVar(&cmd.debugUnplaced, "debug-unplaced", false, "output full list of unplaced tags")
  44         err = flags.Parse(args)
  45         if err == flag.ErrHelp {
  46                 err = nil
  47                 return 0
  48         } else if err != nil {
  49                 return 2
  50         }
  51
  52         if *pprof != "" {
  53                 go func() {
  54                         log.Println(http.ListenAndServe(*pprof, nil))
  55                 }()
  56         }
  57
  58         if !*runlocal {
  59                 if *outputFilename != "-" {
  60                         err = errors.New("cannot specify output file in container mode: not implemented")
  61                         return 1
  62                 }
  63                 runner := arvadosContainerRunner{
  64                         Name:        "lightning stats",
  65                         Client:      arvados.NewClientFromEnv(),
  66                         ProjectUUID: *projectUUID,
  67                         RAM:         16000000000,
  68                         VCPUs:       1,
  69                         Priority:    *priority,
  70                 }
  71                 err = runner.TranslatePaths(inputFilename)
  72                 if err != nil {
  73                         return 1
  74                 }
  75                 runner.Args = []string{"stats", "-local=true", fmt.Sprintf("-debug-unplaced=%v", cmd.debugUnplaced), "-i", *inputFilename, "-o", "/mnt/output/stats.json"}
  76                 var output string
  77                 output, err = runner.Run()
  78                 if err != nil {
  79                         return 1
  80                 }
  81                 fmt.Fprintln(stdout, output+"/stats.json")
  82                 return 0
  83         }
  84
  85         var input io.ReadCloser
  86         if *inputFilename == "-" {
  87                 input = ioutil.NopCloser(stdin)
  88         } else {
  89                 input, err = os.Open(*inputFilename)
  90                 if err != nil {
  91                         return 1
  92                 }
  93                 defer input.Close()
  94         }
  95
  96         var output io.WriteCloser
  97         if *outputFilename == "-" {
  98                 output = nopCloser{stdout}
  99         } else {
 100                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
 101                 if err != nil {
 102                         return 1
 103                 }
 104                 defer output.Close()
 105         }
 106
 107         bufw := bufio.NewWriter(output)
 108         err = cmd.doStats(input, strings.HasSuffix(*inputFilename, ".gz"), bufw)
 109         if err != nil {
 110                 return 1
 111         }
 112         err = bufw.Flush()
 113         if err != nil {
 114                 return 1
 115         }
 116         err = output.Close()
 117         if err != nil {
 118                 return 1
 119         }
 120         return 0
 121 }
 122
 123 func (cmd *statscmd) doStats(input io.Reader, gz bool, output io.Writer) error {
 124         var ret struct {
 125                 Genomes          int
 126                 CalledBases      []int64
 127                 Tags             int
 128                 TagsPlacedNTimes []int // a[x]==y means there were y tags that placed x times
 129                 TileVariants     int
 130                 VariantsBySize   []int
 131                 NCVariantsBySize []int
 132                 UnplacedTags     []string `json:",omitempty"`
 133         }
 134
 135         var tagSet [][]byte
 136         var tagPlacements []int
 137         tileVariantCalls := map[tileLibRef]int{}
 138         err := DecodeLibrary(input, gz, func(ent *LibraryEntry) error {
 139                 ret.Genomes += len(ent.CompactGenomes)
 140                 ret.TileVariants += len(ent.TileVariants)
 141                 if len(ent.TagSet) > 0 {
 142                         if ret.Tags > 0 {
 143                                 return errors.New("invalid input: contains multiple tagsets")
 144                         }
 145                         ret.Tags = len(ent.TagSet)
 146                         tagSet = ent.TagSet
 147                 }
 148                 for _, tv := range ent.TileVariants {
 149                         if need := 1 + len(tv.Sequence) - len(ret.VariantsBySize); need > 0 {
 150                                 ret.VariantsBySize = append(ret.VariantsBySize, make([]int, need)...)
 151                                 ret.NCVariantsBySize = append(ret.NCVariantsBySize, make([]int, need)...)
 152                         }
 153
 154                         calls := 0
 155                         hasNoCalls := false
 156                         for _, b := range tv.Sequence {
 157                                 if b == 'a' || b == 'c' || b == 'g' || b == 't' {
 158                                         calls++
 159                                 } else {
 160                                         hasNoCalls = true
 161                                 }
 162                         }
 163
 164                         if hasNoCalls {
 165                                 ret.NCVariantsBySize[len(tv.Sequence)]++
 166                         } else {
 167                                 ret.VariantsBySize[len(tv.Sequence)]++
 168                         }
 169
 170                         tileVariantCalls[tileLibRef{Tag: tv.Tag, Variant: tv.Variant}] = calls
 171                 }
 172                 for _, g := range ent.CompactGenomes {
 173                         if need := (len(g.Variants)+1)/2 - len(tagPlacements); need > 0 {
 174                                 tagPlacements = append(tagPlacements, make([]int, need)...)
 175                         }
 176                         calledBases := int64(0)
 177                         for idx, v := range g.Variants {
 178                                 if v > 0 {
 179                                         tagPlacements[idx/2]++
 180                                         calledBases += int64(tileVariantCalls[tileLibRef{Tag: tagID(idx / 2), Variant: v}])
 181                                 }
 182                         }
 183                         ret.CalledBases = append(ret.CalledBases, calledBases)
 184                 }
 185                 return nil
 186         })
 187         if err != nil {
 188                 return err
 189         }
 190         for id, p := range tagPlacements {
 191                 for len(ret.TagsPlacedNTimes) <= p {
 192                         ret.TagsPlacedNTimes = append(ret.TagsPlacedNTimes, 0)
 193                 }
 194                 ret.TagsPlacedNTimes[p]++
 195                 if cmd.debugUnplaced && p == 0 {
 196                         ret.UnplacedTags = append(ret.UnplacedTags, fmt.Sprintf("%d %s", id, tagSet[id]))
 197                 }
 198         }
 199
 200         return json.NewEncoder(output).Encode(ret)
 201 }