import.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "compress/gzip"
   6         "encoding/gob"
   7         "errors"
   8         "flag"
   9         "fmt"
  10         "io"
  11         "net/http"
  12         _ "net/http/pprof"
  13         "os"
  14         "os/exec"
  15         "path/filepath"
  16         "regexp"
  17         "runtime"
  18         "sort"
  19         "strings"
  20         "sync"
  21         "sync/atomic"
  22         "time"
  23
  24         "git.arvados.org/arvados.git/sdk/go/arvados"
  25         log "github.com/sirupsen/logrus"
  26 )
  27
  28 type importer struct {
  29         tagLibraryFile string
  30         refFile        string
  31         outputFile     string
  32         projectUUID    string
  33         runLocal       bool
  34         skipOOO        bool
  35         encoder        *gob.Encoder
  36 }
  37
  38 func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  39         var err error
  40         defer func() {
  41                 if err != nil {
  42                         fmt.Fprintf(stderr, "%s\n", err)
  43                 }
  44         }()
  45         flags := flag.NewFlagSet("", flag.ContinueOnError)
  46         flags.SetOutput(stderr)
  47         flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`")
  48         flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
  49         flags.StringVar(&cmd.outputFile, "o", "-", "output `file`")
  50         flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for output data")
  51         flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
  52         flags.BoolVar(&cmd.skipOOO, "skip-ooo", false, "skip out-of-order tags")
  53         priority := flags.Int("priority", 500, "container request priority")
  54         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  55         loglevel := flags.String("loglevel", "info", "logging threshold (trace, debug, info, warn, error, fatal, or panic)")
  56         err = flags.Parse(args)
  57         if err == flag.ErrHelp {
  58                 err = nil
  59                 return 0
  60         } else if err != nil {
  61                 return 2
  62         } else if cmd.tagLibraryFile == "" {
  63                 fmt.Fprintln(os.Stderr, "cannot import without -tag-library argument")
  64                 return 2
  65         } else if flags.NArg() == 0 {
  66                 flags.Usage()
  67                 return 2
  68         }
  69
  70         if *pprof != "" {
  71                 go func() {
  72                         log.Println(http.ListenAndServe(*pprof, nil))
  73                 }()
  74         }
  75
  76         lvl, err := log.ParseLevel(*loglevel)
  77         if err != nil {
  78                 return 2
  79         }
  80         log.SetLevel(lvl)
  81
  82         if !cmd.runLocal {
  83                 runner := arvadosContainerRunner{
  84                         Name:        "lightning import",
  85                         Client:      arvados.NewClientFromEnv(),
  86                         ProjectUUID: cmd.projectUUID,
  87                         RAM:         60000000000,
  88                         VCPUs:       16,
  89                         Priority:    *priority,
  90                 }
  91                 err = runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile)
  92                 if err != nil {
  93                         return 1
  94                 }
  95                 inputs := flags.Args()
  96                 for i := range inputs {
  97                         err = runner.TranslatePaths(&inputs[i])
  98                         if err != nil {
  99                                 return 1
 100                         }
 101                 }
 102                 if cmd.outputFile == "-" {
 103                         cmd.outputFile = "/mnt/output/library.gob"
 104                 } else {
 105                         // Not yet implemented, but this should write
 106                         // the collection to an existing collection,
 107                         // possibly even an in-place update.
 108                         err = errors.New("cannot specify output file in container mode: not implemented")
 109                         return 1
 110                 }
 111                 runner.Args = append([]string{"import", "-local=true", "-loglevel=" + *loglevel, fmt.Sprintf("-skip-ooo=%v", cmd.skipOOO), "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
 112                 var output string
 113                 output, err = runner.Run()
 114                 if err != nil {
 115                         return 1
 116                 }
 117                 fmt.Fprintln(stdout, output+"/library.gob")
 118                 return 0
 119         }
 120
 121         infiles, err := listInputFiles(flags.Args())
 122         if err != nil {
 123                 return 1
 124         }
 125
 126         tilelib, err := cmd.loadTileLibrary()
 127         if err != nil {
 128                 return 1
 129         }
 130         go func() {
 131                 for range time.Tick(10 * time.Minute) {
 132                         log.Printf("tilelib.Len() == %d", tilelib.Len())
 133                 }
 134         }()
 135
 136         var output io.WriteCloser
 137         if cmd.outputFile == "-" {
 138                 output = nopCloser{stdout}
 139         } else {
 140                 output, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
 141                 if err != nil {
 142                         return 1
 143                 }
 144                 defer output.Close()
 145         }
 146         bufw := bufio.NewWriter(output)
 147         cmd.encoder = gob.NewEncoder(bufw)
 148
 149         err = cmd.tileInputs(tilelib, infiles)
 150         if err != nil {
 151                 return 1
 152         }
 153         err = bufw.Flush()
 154         if err != nil {
 155                 return 1
 156         }
 157         err = output.Close()
 158         if err != nil {
 159                 return 1
 160         }
 161         return 0
 162 }
 163
 164 func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, error) {
 165         var input io.ReadCloser
 166         input, err := os.Open(infile)
 167         if err != nil {
 168                 return nil, err
 169         }
 170         defer input.Close()
 171         if strings.HasSuffix(infile, ".gz") {
 172                 input, err = gzip.NewReader(input)
 173                 if err != nil {
 174                         return nil, err
 175                 }
 176                 defer input.Close()
 177         }
 178         return tilelib.TileFasta(infile, input)
 179 }
 180
 181 func (cmd *importer) loadTileLibrary() (*tileLibrary, error) {
 182         log.Printf("tag library %s load starting", cmd.tagLibraryFile)
 183         f, err := os.Open(cmd.tagLibraryFile)
 184         if err != nil {
 185                 return nil, err
 186         }
 187         defer f.Close()
 188         var rdr io.ReadCloser = f
 189         if strings.HasSuffix(cmd.tagLibraryFile, ".gz") {
 190                 rdr, err = gzip.NewReader(f)
 191                 if err != nil {
 192                         return nil, fmt.Errorf("%s: gzip: %s", cmd.tagLibraryFile, err)
 193                 }
 194                 defer rdr.Close()
 195         }
 196         var taglib tagLibrary
 197         err = taglib.Load(rdr)
 198         if err != nil {
 199                 return nil, err
 200         }
 201         if taglib.Len() < 1 {
 202                 return nil, fmt.Errorf("cannot tile: tag library is empty")
 203         }
 204         log.Printf("tag library %s load done", cmd.tagLibraryFile)
 205         return &tileLibrary{taglib: &taglib, skipOOO: cmd.skipOOO}, nil
 206 }
 207
 208 func listInputFiles(paths []string) (files []string, err error) {
 209         for _, path := range paths {
 210                 if fi, err := os.Stat(path); err != nil {
 211                         return nil, fmt.Errorf("%s: stat failed: %s", path, err)
 212                 } else if !fi.IsDir() {
 213                         if !strings.HasSuffix(path, ".2.fasta") || strings.HasSuffix(path, ".2.fasta.gz") {
 214                                 files = append(files, path)
 215                         }
 216                         continue
 217                 }
 218                 d, err := os.Open(path)
 219                 if err != nil {
 220                         return nil, fmt.Errorf("%s: open failed: %s", path, err)
 221                 }
 222                 defer d.Close()
 223                 names, err := d.Readdirnames(0)
 224                 if err != nil {
 225                         return nil, fmt.Errorf("%s: readdir failed: %s", path, err)
 226                 }
 227                 sort.Strings(names)
 228                 for _, name := range names {
 229                         if strings.HasSuffix(name, ".vcf") || strings.HasSuffix(name, ".vcf.gz") {
 230                                 files = append(files, filepath.Join(path, name))
 231                         } else if strings.HasSuffix(name, ".1.fasta") || strings.HasSuffix(name, ".1.fasta.gz") {
 232                                 files = append(files, filepath.Join(path, name))
 233                         }
 234                 }
 235                 d.Close()
 236         }
 237         for _, file := range files {
 238                 if strings.HasSuffix(file, ".1.fasta") || strings.HasSuffix(file, ".1.fasta.gz") {
 239                         continue
 240                 } else if _, err := os.Stat(file + ".csi"); err == nil {
 241                         continue
 242                 } else if _, err = os.Stat(file + ".tbi"); err == nil {
 243                         continue
 244                 } else {
 245                         return nil, fmt.Errorf("%s: cannot read without .tbi or .csi index file", file)
 246                 }
 247         }
 248         return
 249 }
 250
 251 func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
 252         starttime := time.Now()
 253         errs := make(chan error, 1)
 254         todo := make(chan func() error, len(infiles)*2)
 255         var encodeJobs sync.WaitGroup
 256         for _, infile := range infiles {
 257                 infile := infile
 258                 var phases sync.WaitGroup
 259                 phases.Add(2)
 260                 variants := make([][]tileVariantID, 2)
 261                 if strings.HasSuffix(infile, ".1.fasta") || strings.HasSuffix(infile, ".1.fasta.gz") {
 262                         todo <- func() error {
 263                                 defer phases.Done()
 264                                 log.Printf("%s starting", infile)
 265                                 defer log.Printf("%s done", infile)
 266                                 tseqs, err := cmd.tileFasta(tilelib, infile)
 267                                 variants[0] = tseqs.Variants()
 268                                 return err
 269                         }
 270                         infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
 271                         todo <- func() error {
 272                                 defer phases.Done()
 273                                 log.Printf("%s starting", infile2)
 274                                 defer log.Printf("%s done", infile2)
 275                                 tseqs, err := cmd.tileFasta(tilelib, infile2)
 276                                 variants[1] = tseqs.Variants()
 277                                 return err
 278                         }
 279                 } else {
 280                         for phase := 0; phase < 2; phase++ {
 281                                 phase := phase
 282                                 todo <- func() error {
 283                                         defer phases.Done()
 284                                         log.Printf("%s phase %d starting", infile, phase+1)
 285                                         defer log.Printf("%s phase %d done", infile, phase+1)
 286                                         tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
 287                                         variants[phase] = tseqs.Variants()
 288                                         return err
 289                                 }
 290                         }
 291                 }
 292                 encodeJobs.Add(1)
 293                 go func() {
 294                         defer encodeJobs.Done()
 295                         phases.Wait()
 296                         if len(errs) > 0 {
 297                                 return
 298                         }
 299                         ntags := len(variants[0])
 300                         if ntags < len(variants[1]) {
 301                                 ntags = len(variants[1])
 302                         }
 303                         flat := make([]tileVariantID, ntags*2)
 304                         for i := 0; i < ntags; i++ {
 305                                 for hap := 0; hap < 2; hap++ {
 306                                         if i < len(variants[hap]) {
 307                                                 flat[i*2+hap] = variants[hap][i]
 308                                         }
 309                                 }
 310                         }
 311                         err := cmd.encoder.Encode(LibraryEntry{
 312                                 CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},
 313                         })
 314                         if err != nil {
 315                                 select {
 316                                 case errs <- err:
 317                                 default:
 318                                 }
 319                         }
 320                 }()
 321         }
 322         go close(todo)
 323         var tileJobs sync.WaitGroup
 324         var running int64
 325         for i := 0; i < runtime.NumCPU()*9/8+1; i++ {
 326                 tileJobs.Add(1)
 327                 atomic.AddInt64(&running, 1)
 328                 go func() {
 329                         defer tileJobs.Done()
 330                         defer atomic.AddInt64(&running, -1)
 331                         for fn := range todo {
 332                                 if len(errs) > 0 {
 333                                         return
 334                                 }
 335                                 err := fn()
 336                                 if err != nil {
 337                                         select {
 338                                         case errs <- err:
 339                                         default:
 340                                         }
 341                                 }
 342                                 remain := len(todo) + int(atomic.LoadInt64(&running)) - 1
 343                                 ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
 344                                 eta := time.Now().Add(ttl)
 345                                 log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
 346                         }
 347                 }()
 348         }
 349         tileJobs.Wait()
 350         encodeJobs.Wait()
 351         go close(errs)
 352         return <-errs
 353 }
 354
 355 func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, err error) {
 356         if cmd.refFile == "" {
 357                 err = errors.New("cannot import vcf: reference data (-ref) not specified")
 358                 return
 359         }
 360         args := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase + 1), infile}
 361         indexsuffix := ".tbi"
 362         if _, err := os.Stat(infile + ".csi"); err == nil {
 363                 indexsuffix = ".csi"
 364         }
 365         if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err == nil && len(out) > 0 {
 366                 args = append([]string{
 367                         "docker", "run", "--rm",
 368                         "--log-driver=none",
 369                         "--volume=" + infile + ":" + infile + ":ro",
 370                         "--volume=" + infile + indexsuffix + ":" + infile + indexsuffix + ":ro",
 371                         "--volume=" + cmd.refFile + ":" + cmd.refFile + ":ro",
 372                         "lightning-runtime",
 373                 }, args...)
 374         }
 375         consensus := exec.Command(args[0], args[1:]...)
 376         consensus.Stderr = os.Stderr
 377         stdout, err := consensus.StdoutPipe()
 378         defer stdout.Close()
 379         if err != nil {
 380                 return
 381         }
 382         err = consensus.Start()
 383         if err != nil {
 384                 return
 385         }
 386         defer consensus.Wait()
 387         tileseq, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout)
 388         if err != nil {
 389                 return
 390         }
 391         err = stdout.Close()
 392         if err != nil {
 393                 return
 394         }
 395         err = consensus.Wait()
 396         if err != nil {
 397                 err = fmt.Errorf("%s phase %d: bcftools: %s", infile, phase, err)
 398                 return
 399         }
 400         return
 401 }