lib/install/deps.go

   1 // Copyright (C) The Arvados Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package install
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "context"
  11         "errors"
  12         "flag"
  13         "fmt"
  14         "io"
  15         "os"
  16         "os/exec"
  17         "os/user"
  18         "path/filepath"
  19         "strconv"
  20         "strings"
  21         "syscall"
  22         "time"
  23
  24         "git.arvados.org/arvados.git/lib/cmd"
  25         "git.arvados.org/arvados.git/sdk/go/ctxlog"
  26         "github.com/lib/pq"
  27 )
  28
  29 var Command cmd.Handler = &installCommand{}
  30
  31 const goversion = "1.17.7"
  32
  33 const (
  34         rubyversion             = "2.7.5"
  35         singularityversion      = "3.7.4"
  36         pjsversion              = "1.9.8"
  37         geckoversion            = "0.24.0"
  38         gradleversion           = "5.3.1"
  39         nodejsversion           = "v12.22.2"
  40         devtestDatabasePassword = "insecure_arvados_test"
  41         workbench2version       = "cfa81dfc3041cb459c8a0918a2732dfcf3a11d40"
  42 )
  43
  44 type installCommand struct {
  45         ClusterType    string
  46         SourcePath     string
  47         PackageVersion string
  48         EatMyData      bool
  49 }
  50
  51 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  52         logger := ctxlog.New(stderr, "text", "info")
  53         ctx := ctxlog.Context(context.Background(), logger)
  54         ctx, cancel := context.WithCancel(ctx)
  55         defer cancel()
  56
  57         var err error
  58         defer func() {
  59                 if err != nil {
  60                         logger.WithError(err).Info("exiting")
  61                 }
  62         }()
  63
  64         flags := flag.NewFlagSet(prog, flag.ContinueOnError)
  65         flags.SetOutput(stderr)
  66         versionFlag := flags.Bool("version", false, "Write version information to stdout and exit 0")
  67         flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
  68         flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
  69         flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
  70         flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
  71
  72         if ok, code := cmd.ParseFlags(flags, prog, args, "", stderr); !ok {
  73                 return code
  74         } else if *versionFlag {
  75                 return cmd.Version.RunCommand(prog, args, stdin, stdout, stderr)
  76         }
  77
  78         var dev, test, prod, pkg bool
  79         switch inst.ClusterType {
  80         case "development":
  81                 dev = true
  82         case "test":
  83                 test = true
  84         case "production":
  85                 prod = true
  86         case "package":
  87                 pkg = true
  88         default:
  89                 err = fmt.Errorf("invalid cluster type %q (must be 'development', 'test', 'production', or 'package')", inst.ClusterType)
  90                 return 2
  91         }
  92
  93         if prod {
  94                 err = errors.New("production install is not yet implemented")
  95                 return 1
  96         }
  97
  98         osv, err := identifyOS()
  99         if err != nil {
 100                 return 1
 101         }
 102
 103         listdir, err := os.Open("/var/lib/apt/lists")
 104         if err != nil {
 105                 logger.Warnf("error while checking whether to run apt-get update: %s", err)
 106         } else if names, _ := listdir.Readdirnames(1); len(names) == 0 {
 107                 // Special case for a base docker image where the
 108                 // package cache has been deleted and all "apt-get
 109                 // install" commands will fail unless we fetch repos.
 110                 cmd := exec.CommandContext(ctx, "apt-get", "update")
 111                 cmd.Stdout = stdout
 112                 cmd.Stderr = stderr
 113                 err = cmd.Run()
 114                 if err != nil {
 115                         return 1
 116                 }
 117         }
 118
 119         if inst.EatMyData {
 120                 cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
 121                 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 122                 cmd.Stdout = stdout
 123                 cmd.Stderr = stderr
 124                 err = cmd.Run()
 125                 if err != nil {
 126                         return 1
 127                 }
 128         }
 129
 130         pkgs := prodpkgs(osv)
 131
 132         if pkg {
 133                 pkgs = append(pkgs,
 134                         "dpkg-dev",
 135                         "eatmydata", // install it for later steps, even if we're not using it now
 136                         "rsync",
 137                 )
 138         }
 139
 140         if dev || test || pkg {
 141                 pkgs = append(pkgs,
 142                         "automake",
 143                         "bison",
 144                         "bsdmainutils",
 145                         "build-essential",
 146                         "cadaver",
 147                         "curl",
 148                         "cython3",
 149                         "default-jdk-headless",
 150                         "default-jre-headless",
 151                         "gettext",
 152                         "libattr1-dev",
 153                         "libcrypt-ssleay-perl",
 154                         "libfuse-dev",
 155                         "libgnutls28-dev",
 156                         "libjson-perl",
 157                         "libpam-dev",
 158                         "libpcre3-dev",
 159                         "libpq-dev",
 160                         "libreadline-dev",
 161                         "libssl-dev",
 162                         "libwww-perl",
 163                         "libxml2-dev",
 164                         "libxslt1-dev",
 165                         "linkchecker",
 166                         "lsof",
 167                         "make",
 168                         "net-tools",
 169                         "pandoc",
 170                         "perl-modules",
 171                         "pkg-config",
 172                         "postgresql",
 173                         "postgresql-contrib",
 174                         "python3-dev",
 175                         "python3-venv",
 176                         "python3-virtualenv",
 177                         "r-base",
 178                         "r-cran-testthat",
 179                         "r-cran-devtools",
 180                         "r-cran-knitr",
 181                         "r-cran-markdown",
 182                         "r-cran-roxygen2",
 183                         "r-cran-xml",
 184                         "sudo",
 185                         "uuid-dev",
 186                         "wget",
 187                         "xvfb",
 188                 )
 189                 if test {
 190                         if osv.Debian && osv.Major <= 10 {
 191                                 pkgs = append(pkgs, "iceweasel")
 192                         } else {
 193                                 pkgs = append(pkgs, "firefox")
 194                         }
 195                 }
 196                 if dev || test {
 197                         pkgs = append(pkgs, "squashfs-tools") // for singularity
 198                 }
 199                 switch {
 200                 case osv.Debian && osv.Major >= 10:
 201                         pkgs = append(pkgs, "libcurl4")
 202                 default:
 203                         pkgs = append(pkgs, "libcurl3")
 204                 }
 205                 cmd := exec.CommandContext(ctx, "apt-get")
 206                 if inst.EatMyData {
 207                         cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
 208                 }
 209                 cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
 210                 cmd.Args = append(cmd.Args, pkgs...)
 211                 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 212                 cmd.Stdout = stdout
 213                 cmd.Stderr = stderr
 214                 err = cmd.Run()
 215                 if err != nil {
 216                         return 1
 217                 }
 218         }
 219
 220         os.Mkdir("/var/lib/arvados", 0755)
 221         os.Mkdir("/var/lib/arvados/tmp", 0700)
 222         if prod || pkg {
 223                 u, er := user.Lookup("www-data")
 224                 if er != nil {
 225                         err = fmt.Errorf("user.Lookup(%q): %w", "www-data", er)
 226                         return 1
 227                 }
 228                 uid, _ := strconv.Atoi(u.Uid)
 229                 gid, _ := strconv.Atoi(u.Gid)
 230                 os.Mkdir("/var/lib/arvados/wwwtmp", 0700)
 231                 err = os.Chown("/var/lib/arvados/wwwtmp", uid, gid)
 232                 if err != nil {
 233                         return 1
 234                 }
 235         }
 236         rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
 237         if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
 238                 logger.Print("ruby " + rubyversion + " already installed")
 239         } else {
 240                 err = inst.runBash(`
 241 tmp="$(mktemp -d)"
 242 trap 'rm -r "${tmp}"' ERR EXIT
 243 wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
 244 cd "${tmp}/ruby-`+rubyversion+`"
 245 ./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
 246 make -j8
 247 make install
 248 /var/lib/arvados/bin/gem install bundler --no-document
 249 `, stdout, stderr)
 250                 if err != nil {
 251                         return 1
 252                 }
 253         }
 254
 255         if !prod {
 256                 if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
 257                         logger.Print("go " + goversion + " already installed")
 258                 } else {
 259                         err = inst.runBash(`
 260 cd /tmp
 261 rm -rf /var/lib/arvados/go/
 262 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
 263 ln -sfv /var/lib/arvados/go/bin/* /usr/local/bin/
 264 `, stdout, stderr)
 265                         if err != nil {
 266                                 return 1
 267                         }
 268                 }
 269         }
 270
 271         if !prod && !pkg {
 272                 if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
 273                         logger.Print("phantomjs " + pjsversion + " already installed")
 274                 } else {
 275                         err = inst.runBash(`
 276 PJS=phantomjs-`+pjsversion+`-linux-x86_64
 277 wget --progress=dot:giga -O- https://cache.arvados.org/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
 278 ln -sfv /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
 279 `, stdout, stderr)
 280                         if err != nil {
 281                                 return 1
 282                         }
 283                 }
 284
 285                 if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
 286                         logger.Print("geckodriver " + geckoversion + " already installed")
 287                 } else {
 288                         err = inst.runBash(`
 289 GD=v`+geckoversion+`
 290 wget --progress=dot:giga -O- https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz | tar -C /var/lib/arvados/bin -xzf - geckodriver
 291 ln -sfv /var/lib/arvados/bin/geckodriver /usr/local/bin/
 292 `, stdout, stderr)
 293                         if err != nil {
 294                                 return 1
 295                         }
 296                 }
 297
 298                 if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
 299                         logger.Print("gradle " + gradleversion + " already installed")
 300                 } else {
 301                         err = inst.runBash(`
 302 G=`+gradleversion+`
 303 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
 304 trap "rm ${zip}" ERR
 305 wget --progress=dot:giga -O${zip} https://services.gradle.org/distributions/gradle-${G}-bin.zip
 306 unzip -o -d /var/lib/arvados ${zip}
 307 ln -sfv /var/lib/arvados/gradle-${G}/bin/gradle /usr/local/bin/
 308 rm ${zip}
 309 `, stdout, stderr)
 310                         if err != nil {
 311                                 return 1
 312                         }
 313                 }
 314
 315                 if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
 316                         logger.Print("singularity " + singularityversion + " already installed")
 317                 } else if dev || test {
 318                         err = inst.runBash(`
 319 S=`+singularityversion+`
 320 tmp=/var/lib/arvados/tmp/singularity
 321 trap "rm -r ${tmp}" ERR EXIT
 322 cd /var/lib/arvados/tmp
 323 git clone https://github.com/sylabs/singularity
 324 cd singularity
 325 git checkout v${S}
 326 ./mconfig --prefix=/var/lib/arvados
 327 make -C ./builddir
 328 make -C ./builddir install
 329 `, stdout, stderr)
 330                         if err != nil {
 331                                 return 1
 332                         }
 333                 }
 334
 335                 // The entry in /etc/locale.gen is "en_US.UTF-8"; once
 336                 // it's installed, locale -a reports it as
 337                 // "en_US.utf8".
 338                 wantlocale := "en_US.UTF-8"
 339                 if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
 340                         logger.Print("locale " + wantlocale + " already installed")
 341                 } else {
 342                         err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
 343                         if err != nil {
 344                                 return 1
 345                         }
 346                 }
 347
 348                 var pgc struct {
 349                         Version       string
 350                         Cluster       string
 351                         Port          int
 352                         Status        string
 353                         Owner         string
 354                         DataDirectory string
 355                         LogFile       string
 356                 }
 357                 if pgLsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
 358                         err = fmt.Errorf("pg_lsclusters: %s", err2)
 359                         return 1
 360                 } else if pgclusters := strings.Split(strings.TrimSpace(string(pgLsclusters)), "\n"); len(pgclusters) != 1 {
 361                         logger.Warnf("pg_lsclusters returned %d postgresql clusters -- skipping postgresql initdb/startup, hope that's ok", len(pgclusters))
 362                 } else if _, err = fmt.Sscanf(pgclusters[0], "%s %s %d %s %s %s %s", &pgc.Version, &pgc.Cluster, &pgc.Port, &pgc.Status, &pgc.Owner, &pgc.DataDirectory, &pgc.LogFile); err != nil {
 363                         err = fmt.Errorf("error parsing pg_lsclusters output: %s", err)
 364                         return 1
 365                 } else if pgc.Status == "online" {
 366                         logger.Infof("postgresql cluster %s-%s is online", pgc.Version, pgc.Cluster)
 367                 } else {
 368                         logger.Infof("postgresql cluster %s-%s is %s; trying to start", pgc.Version, pgc.Cluster, pgc.Status)
 369                         cmd := exec.Command("pg_ctlcluster", "--foreground", pgc.Version, pgc.Cluster, "start")
 370                         cmd.Stdout = stdout
 371                         cmd.Stderr = stderr
 372                         err = cmd.Start()
 373                         if err != nil {
 374                                 return 1
 375                         }
 376                         defer func() {
 377                                 cmd.Process.Signal(syscall.SIGTERM)
 378                                 logger.Info("sent SIGTERM; waiting for postgres to shut down")
 379                                 cmd.Wait()
 380                         }()
 381                         err = waitPostgreSQLReady()
 382                         if err != nil {
 383                                 return 1
 384                         }
 385                 }
 386
 387                 if os.Getpid() == 1 {
 388                         // We are the init process (presumably in a
 389                         // docker container) so although postgresql is
 390                         // installed, it's not running, and initdb
 391                         // might never have been run.
 392                 }
 393
 394                 var needcoll []string
 395                 // If the en_US.UTF-8 locale wasn't installed when
 396                 // postgresql initdb ran, it needs to be added
 397                 // explicitly before we can use it in our test suite.
 398                 for _, collname := range []string{"en_US", "en_US.UTF-8"} {
 399                         cmd := exec.Command("sudo", "-u", "postgres", "psql", "-t", "-c", "SELECT 1 FROM pg_catalog.pg_collation WHERE collname='"+collname+"' AND collcollate IN ('en_US.UTF-8', 'en_US.utf8')")
 400                         cmd.Dir = "/"
 401                         out, err2 := cmd.CombinedOutput()
 402                         if err != nil {
 403                                 err = fmt.Errorf("error while checking postgresql collations: %s", err2)
 404                                 return 1
 405                         }
 406                         if strings.Contains(string(out), "1") {
 407                                 logger.Infof("postgresql supports collation %s", collname)
 408                         } else {
 409                                 needcoll = append(needcoll, collname)
 410                         }
 411                 }
 412                 if len(needcoll) > 0 && os.Getpid() != 1 {
 413                         // In order for the CREATE COLLATION statement
 414                         // below to work, the locale must have existed
 415                         // when PostgreSQL started up. If we're
 416                         // running as init, we must have started
 417                         // PostgreSQL ourselves after installing the
 418                         // locales. Otherwise, it might need a
 419                         // restart, so we attempt to restart it with
 420                         // systemd.
 421                         if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
 422                                 logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
 423                         } else if err = waitPostgreSQLReady(); err != nil {
 424                                 return 1
 425                         }
 426                 }
 427                 for _, collname := range needcoll {
 428                         cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE COLLATION \""+collname+"\" (LOCALE = \"en_US.UTF-8\")")
 429                         cmd.Stdout = stdout
 430                         cmd.Stderr = stderr
 431                         cmd.Dir = "/"
 432                         err = cmd.Run()
 433                         if err != nil {
 434                                 err = fmt.Errorf("error adding postgresql collation %s: %s", collname, err)
 435                                 return 1
 436                         }
 437                 }
 438
 439                 withstuff := "WITH LOGIN SUPERUSER ENCRYPTED PASSWORD " + pq.QuoteLiteral(devtestDatabasePassword)
 440                 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "ALTER ROLE arvados "+withstuff)
 441                 cmd.Dir = "/"
 442                 if err := cmd.Run(); err == nil {
 443                         logger.Print("arvados role exists; superuser privileges added, password updated")
 444                 } else {
 445                         cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE ROLE arvados "+withstuff)
 446                         cmd.Dir = "/"
 447                         cmd.Stdout = stdout
 448                         cmd.Stderr = stderr
 449                         err = cmd.Run()
 450                         if err != nil {
 451                                 return 1
 452                         }
 453                 }
 454         }
 455
 456         if !prod {
 457                 if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
 458                         logger.Print("nodejs " + nodejsversion + " already installed")
 459                 } else {
 460                         err = inst.runBash(`
 461 NJS=`+nodejsversion+`
 462 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
 463 ln -sfv /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
 464 `, stdout, stderr)
 465                         if err != nil {
 466                                 return 1
 467                         }
 468                 }
 469
 470                 if haveyarnversion, err := exec.Command("/usr/local/bin/yarn", "--version").CombinedOutput(); err == nil && len(haveyarnversion) > 0 {
 471                         logger.Print("yarn " + strings.TrimSpace(string(haveyarnversion)) + " already installed")
 472                 } else {
 473                         err = inst.runBash(`
 474 npm install -g yarn
 475 ln -sfv /var/lib/arvados/node-`+nodejsversion+`-linux-x64/bin/{yarn,yarnpkg} /usr/local/bin/
 476 `, stdout, stderr)
 477                         if err != nil {
 478                                 return 1
 479                         }
 480                 }
 481
 482                 if havewb2version, err := exec.Command("git", "--git-dir=/var/lib/arvados/arvados-workbench2/.git", "log", "-n1", "--format=%H").CombinedOutput(); err == nil && string(havewb2version) == workbench2version+"\n" {
 483                         logger.Print("workbench2 repo is already at " + workbench2version)
 484                 } else {
 485                         err = inst.runBash(`
 486 V=`+workbench2version+`
 487 cd /var/lib/arvados
 488 if [[ ! -e arvados-workbench2 ]]; then
 489   git clone https://git.arvados.org/arvados-workbench2.git
 490   cd arvados-workbench2
 491   git checkout $V
 492 else
 493   cd arvados-workbench2
 494   if ! git checkout $V; then
 495     git fetch
 496     git checkout $V
 497   fi
 498 fi
 499 rm -rf build
 500 `, stdout, stderr)
 501                         if err != nil {
 502                                 return 1
 503                         }
 504                 }
 505
 506                 if err = inst.runBash(`
 507 cd /var/lib/arvados/arvados-workbench2
 508 yarn install
 509 `, stdout, stderr); err != nil {
 510                         return 1
 511                 }
 512         }
 513
 514         if prod || pkg {
 515                 // Install Go programs to /var/lib/arvados/bin/
 516                 for _, srcdir := range []string{
 517                         "cmd/arvados-client",
 518                         "cmd/arvados-server",
 519                         "services/arv-git-httpd",
 520                         "services/crunch-dispatch-local",
 521                         "services/crunch-dispatch-slurm",
 522                         "services/health",
 523                         "services/keep-balance",
 524                         "services/keep-web",
 525                         "services/keepproxy",
 526                         "services/keepstore",
 527                         "services/ws",
 528                 } {
 529                         fmt.Fprintf(stderr, "building %s...\n", srcdir)
 530                         cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
 531                         cmd.Env = append(cmd.Env, os.Environ()...)
 532                         cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
 533                         cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 534                         cmd.Stdout = stdout
 535                         cmd.Stderr = stderr
 536                         err = cmd.Run()
 537                         if err != nil {
 538                                 return 1
 539                         }
 540                 }
 541
 542                 // Copy assets from source tree to /var/lib/arvados/share
 543                 cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
 544                 cmd.Stdout = stdout
 545                 cmd.Stderr = stderr
 546                 err = cmd.Run()
 547                 if err != nil {
 548                         return 1
 549                 }
 550
 551                 // Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
 552                 for dstdir, srcdir := range map[string]string{
 553                         "railsapi":   "services/api",
 554                         "workbench1": "apps/workbench",
 555                 } {
 556                         fmt.Fprintf(stderr, "building %s...\n", srcdir)
 557                         cmd := exec.Command("rsync",
 558                                 "-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
 559                                 "--exclude", "/coverage",
 560                                 "--exclude", "/log",
 561                                 "--exclude", "/tmp",
 562                                 "--exclude", "/vendor",
 563                                 "--exclude", "/config/environments",
 564                                 "./", "/var/lib/arvados/"+dstdir+"/")
 565                         cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 566                         cmd.Stdout = stdout
 567                         cmd.Stderr = stderr
 568                         err = cmd.Run()
 569                         if err != nil {
 570                                 return 1
 571                         }
 572                         for _, cmdline := range [][]string{
 573                                 {"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
 574                                 {"touch", "log/production.log"},
 575                                 {"chown", "-R", "--from=root", "www-data:www-data", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
 576                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:2.2.19"},
 577                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
 578                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
 579                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
 580                         } {
 581                                 cmd = exec.Command(cmdline[0], cmdline[1:]...)
 582                                 cmd.Dir = "/var/lib/arvados/" + dstdir
 583                                 cmd.Stdout = stdout
 584                                 cmd.Stderr = stderr
 585                                 fmt.Fprintf(stderr, "... %s\n", cmd.Args)
 586                                 err = cmd.Run()
 587                                 if err != nil {
 588                                         return 1
 589                                 }
 590                         }
 591                         cmd = exec.Command("sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "validate-install")
 592                         cmd.Dir = "/var/lib/arvados/" + dstdir
 593                         cmd.Stdout = stdout
 594                         cmd.Stderr = stderr
 595                         err = cmd.Run()
 596                         if err != nil && !strings.Contains(err.Error(), "exit status 2") {
 597                                 // Exit code 2 indicates there were warnings (like
 598                                 // "other passenger installations have been detected",
 599                                 // which we can't expect to avoid) but no errors.
 600                                 // Other non-zero exit codes (1, 9) indicate errors.
 601                                 return 1
 602                         }
 603                 }
 604
 605                 // Install workbench2 app to /var/lib/arvados/workbench2/
 606                 if err = inst.runBash(`
 607 cd /var/lib/arvados/arvados-workbench2
 608 VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
 609 rsync -a --delete-after build/ /var/lib/arvados/workbench2/
 610 `, stdout, stderr); err != nil {
 611                         return 1
 612                 }
 613         }
 614
 615         return 0
 616 }
 617
 618 type osversion struct {
 619         Debian bool
 620         Ubuntu bool
 621         Centos bool
 622         Major  int
 623 }
 624
 625 func identifyOS() (osversion, error) {
 626         var osv osversion
 627         f, err := os.Open("/etc/os-release")
 628         if err != nil {
 629                 return osv, err
 630         }
 631         defer f.Close()
 632
 633         kv := map[string]string{}
 634         scanner := bufio.NewScanner(f)
 635         for scanner.Scan() {
 636                 line := strings.TrimSpace(scanner.Text())
 637                 if strings.HasPrefix(line, "#") {
 638                         continue
 639                 }
 640                 toks := strings.SplitN(line, "=", 2)
 641                 if len(toks) != 2 {
 642                         return osv, fmt.Errorf("invalid line in /etc/os-release: %q", line)
 643                 }
 644                 k := toks[0]
 645                 v := strings.Trim(toks[1], `"`)
 646                 if v == toks[1] {
 647                         v = strings.Trim(v, `'`)
 648                 }
 649                 kv[k] = v
 650         }
 651         if err = scanner.Err(); err != nil {
 652                 return osv, err
 653         }
 654         switch kv["ID"] {
 655         case "ubuntu":
 656                 osv.Ubuntu = true
 657         case "debian":
 658                 osv.Debian = true
 659         case "centos":
 660                 osv.Centos = true
 661         default:
 662                 return osv, fmt.Errorf("unsupported ID in /etc/os-release: %q", kv["ID"])
 663         }
 664         vstr := kv["VERSION_ID"]
 665         if i := strings.Index(vstr, "."); i > 0 {
 666                 vstr = vstr[:i]
 667         }
 668         osv.Major, err = strconv.Atoi(vstr)
 669         if err != nil {
 670                 return osv, fmt.Errorf("incomprehensible VERSION_ID in /etc/os-release: %q", kv["VERSION_ID"])
 671         }
 672         return osv, nil
 673 }
 674
 675 func waitPostgreSQLReady() error {
 676         for deadline := time.Now().Add(10 * time.Second); ; {
 677                 output, err := exec.Command("pg_isready").CombinedOutput()
 678                 if err == nil {
 679                         return nil
 680                 } else if time.Now().After(deadline) {
 681                         return fmt.Errorf("timed out waiting for pg_isready (%q)", output)
 682                 } else {
 683                         time.Sleep(time.Second)
 684                 }
 685         }
 686 }
 687
 688 func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
 689         cmd := exec.Command("bash", "-")
 690         if inst.EatMyData {
 691                 cmd = exec.Command("eatmydata", "bash", "-")
 692         }
 693         cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
 694         cmd.Stdout = stdout
 695         cmd.Stderr = stderr
 696         return cmd.Run()
 697 }
 698
 699 func prodpkgs(osv osversion) []string {
 700         pkgs := []string{
 701                 "ca-certificates",
 702                 "curl",
 703                 "fuse",
 704                 "git",
 705                 "gitolite3",
 706                 "graphviz",
 707                 "haveged",
 708                 "libcurl3-gnutls",
 709                 "libxslt1.1",
 710                 "nginx",
 711                 "python",
 712                 "sudo",
 713         }
 714         if osv.Debian || osv.Ubuntu {
 715                 if osv.Debian && osv.Major == 8 {
 716                         pkgs = append(pkgs, "libgnutls-deb0-28") // sdk/cwl
 717                 } else if osv.Debian && osv.Major >= 10 || osv.Ubuntu && osv.Major >= 16 {
 718                         pkgs = append(pkgs, "python3-distutils") // sdk/cwl
 719                 }
 720                 return append(pkgs,
 721                         "g++",
 722                         "libcurl4-openssl-dev", // services/api
 723                         "libpq-dev",
 724                         "libpython2.7", // services/fuse
 725                         "mime-support", // keep-web
 726                         "zlib1g-dev",   // services/api
 727                 )
 728         } else if osv.Centos {
 729                 return append(pkgs,
 730                         "fuse-libs", // services/fuse
 731                         "gcc",
 732                         "gcc-c++",
 733                         "libcurl-devel",    // services/api
 734                         "mailcap",          // keep-web
 735                         "postgresql-devel", // services/api
 736                 )
 737         } else {
 738                 panic("os version not supported")
 739         }
 740 }
 741
 742 func ProductionDependencies() ([]string, error) {
 743         osv, err := identifyOS()
 744         if err != nil {
 745                 return nil, err
 746         }
 747         return prodpkgs(osv), nil
 748 }