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         bundlerversion          = "2.2.19"
  36         singularityversion      = "3.7.4"
  37         pjsversion              = "1.9.8"
  38         geckoversion            = "0.24.0"
  39         gradleversion           = "5.3.1"
  40         nodejsversion           = "v12.22.11"
  41         devtestDatabasePassword = "insecure_arvados_test"
  42         workbench2version       = "5e020488f67b5bc919796e0dc8b0b9f3b3ff23b0"
  43 )
  44
  45 type installCommand struct {
  46         ClusterType    string
  47         SourcePath     string
  48         PackageVersion string
  49         EatMyData      bool
  50 }
  51
  52 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  53         logger := ctxlog.New(stderr, "text", "info")
  54         ctx := ctxlog.Context(context.Background(), logger)
  55         ctx, cancel := context.WithCancel(ctx)
  56         defer cancel()
  57
  58         var err error
  59         defer func() {
  60                 if err != nil {
  61                         logger.WithError(err).Info("exiting")
  62                 }
  63         }()
  64
  65         flags := flag.NewFlagSet(prog, flag.ContinueOnError)
  66         flags.SetOutput(stderr)
  67         versionFlag := flags.Bool("version", false, "Write version information to stdout and exit 0")
  68         flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
  69         flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
  70         flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
  71         flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
  72
  73         if ok, code := cmd.ParseFlags(flags, prog, args, "", stderr); !ok {
  74                 return code
  75         } else if *versionFlag {
  76                 return cmd.Version.RunCommand(prog, args, stdin, stdout, stderr)
  77         }
  78
  79         var dev, test, prod, pkg bool
  80         switch inst.ClusterType {
  81         case "development":
  82                 dev = true
  83         case "test":
  84                 test = true
  85         case "production":
  86                 prod = true
  87         case "package":
  88                 pkg = true
  89         default:
  90                 err = fmt.Errorf("invalid cluster type %q (must be 'development', 'test', 'production', or 'package')", inst.ClusterType)
  91                 return 2
  92         }
  93
  94         if prod {
  95                 err = errors.New("production install is not yet implemented")
  96                 return 1
  97         }
  98
  99         osv, err := identifyOS()
 100         if err != nil {
 101                 return 1
 102         }
 103
 104         listdir, err := os.Open("/var/lib/apt/lists")
 105         if err != nil {
 106                 logger.Warnf("error while checking whether to run apt-get update: %s", err)
 107         } else if names, _ := listdir.Readdirnames(1); len(names) == 0 {
 108                 // Special case for a base docker image where the
 109                 // package cache has been deleted and all "apt-get
 110                 // install" commands will fail unless we fetch repos.
 111                 cmd := exec.CommandContext(ctx, "apt-get", "update")
 112                 cmd.Stdout = stdout
 113                 cmd.Stderr = stderr
 114                 err = cmd.Run()
 115                 if err != nil {
 116                         return 1
 117                 }
 118         }
 119
 120         if inst.EatMyData {
 121                 cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
 122                 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 123                 cmd.Stdout = stdout
 124                 cmd.Stderr = stderr
 125                 err = cmd.Run()
 126                 if err != nil {
 127                         return 1
 128                 }
 129         }
 130
 131         pkgs := prodpkgs(osv)
 132
 133         if pkg {
 134                 pkgs = append(pkgs,
 135                         "dpkg-dev",
 136                         "eatmydata", // install it for later steps, even if we're not using it now
 137                         "rsync",
 138                 )
 139         }
 140
 141         if dev || test || pkg {
 142                 pkgs = append(pkgs,
 143                         "automake",
 144                         "bison",
 145                         "bsdmainutils",
 146                         "build-essential",
 147                         "cadaver",
 148                         "curl",
 149                         "cython3",
 150                         "default-jdk-headless",
 151                         "default-jre-headless",
 152                         "gettext",
 153                         "libattr1-dev",
 154                         "libcrypt-ssleay-perl",
 155                         "libfuse-dev",
 156                         "libgnutls28-dev",
 157                         "libjson-perl",
 158                         "libpam-dev",
 159                         "libpcre3-dev",
 160                         "libpq-dev",
 161                         "libreadline-dev",
 162                         "libssl-dev",
 163                         "libwww-perl",
 164                         "libxml2-dev",
 165                         "libxslt1-dev",
 166                         "linkchecker",
 167                         "lsof",
 168                         "make",
 169                         "net-tools",
 170                         "pandoc",
 171                         "perl-modules",
 172                         "pkg-config",
 173                         "postgresql",
 174                         "postgresql-contrib",
 175                         "python3-dev",
 176                         "python3-venv",
 177                         "python3-virtualenv",
 178                         "r-base",
 179                         "r-cran-testthat",
 180                         "r-cran-devtools",
 181                         "r-cran-knitr",
 182                         "r-cran-markdown",
 183                         "r-cran-roxygen2",
 184                         "r-cran-xml",
 185                         "sudo",
 186                         "uuid-dev",
 187                         "wget",
 188                         "xvfb",
 189                 )
 190                 if test {
 191                         if osv.Debian && osv.Major <= 10 {
 192                                 pkgs = append(pkgs, "iceweasel")
 193                         } else {
 194                                 pkgs = append(pkgs, "firefox")
 195                         }
 196                 }
 197                 if dev || test {
 198                         pkgs = append(pkgs, "squashfs-tools") // for singularity
 199                 }
 200                 switch {
 201                 case osv.Debian && osv.Major >= 10:
 202                         pkgs = append(pkgs, "libcurl4")
 203                 default:
 204                         pkgs = append(pkgs, "libcurl3")
 205                 }
 206                 cmd := exec.CommandContext(ctx, "apt-get")
 207                 if inst.EatMyData {
 208                         cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
 209                 }
 210                 cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
 211                 cmd.Args = append(cmd.Args, pkgs...)
 212                 cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 213                 cmd.Stdout = stdout
 214                 cmd.Stderr = stderr
 215                 err = cmd.Run()
 216                 if err != nil {
 217                         return 1
 218                 }
 219         }
 220
 221         os.Mkdir("/var/lib/arvados", 0755)
 222         os.Mkdir("/var/lib/arvados/tmp", 0700)
 223         if prod || pkg {
 224                 u, er := user.Lookup("www-data")
 225                 if er != nil {
 226                         err = fmt.Errorf("user.Lookup(%q): %w", "www-data", er)
 227                         return 1
 228                 }
 229                 uid, _ := strconv.Atoi(u.Uid)
 230                 gid, _ := strconv.Atoi(u.Gid)
 231                 os.Mkdir("/var/lib/arvados/wwwtmp", 0700)
 232                 err = os.Chown("/var/lib/arvados/wwwtmp", uid, gid)
 233                 if err != nil {
 234                         return 1
 235                 }
 236         }
 237         rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
 238         if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
 239                 logger.Print("ruby " + rubyversion + " already installed")
 240         } else {
 241                 err = inst.runBash(`
 242 tmp="$(mktemp -d)"
 243 trap 'rm -r "${tmp}"' ERR EXIT
 244 wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
 245 cd "${tmp}/ruby-`+rubyversion+`"
 246 ./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
 247 make -j8
 248 make install
 249 /var/lib/arvados/bin/gem install bundler --no-document
 250 `, stdout, stderr)
 251                 if err != nil {
 252                         return 1
 253                 }
 254         }
 255
 256         if !prod {
 257                 if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
 258                         logger.Print("go " + goversion + " already installed")
 259                 } else {
 260                         err = inst.runBash(`
 261 cd /tmp
 262 rm -rf /var/lib/arvados/go/
 263 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
 264 ln -sfv /var/lib/arvados/go/bin/* /usr/local/bin/
 265 `, stdout, stderr)
 266                         if err != nil {
 267                                 return 1
 268                         }
 269                 }
 270         }
 271
 272         if !prod && !pkg {
 273                 if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
 274                         logger.Print("phantomjs " + pjsversion + " already installed")
 275                 } else {
 276                         err = inst.runBash(`
 277 PJS=phantomjs-`+pjsversion+`-linux-x86_64
 278 wget --progress=dot:giga -O- https://cache.arvados.org/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
 279 ln -sfv /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
 280 `, stdout, stderr)
 281                         if err != nil {
 282                                 return 1
 283                         }
 284                 }
 285
 286                 if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
 287                         logger.Print("geckodriver " + geckoversion + " already installed")
 288                 } else {
 289                         err = inst.runBash(`
 290 GD=v`+geckoversion+`
 291 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
 292 ln -sfv /var/lib/arvados/bin/geckodriver /usr/local/bin/
 293 `, stdout, stderr)
 294                         if err != nil {
 295                                 return 1
 296                         }
 297                 }
 298
 299                 if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
 300                         logger.Print("gradle " + gradleversion + " already installed")
 301                 } else {
 302                         err = inst.runBash(`
 303 G=`+gradleversion+`
 304 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
 305 trap "rm ${zip}" ERR
 306 wget --progress=dot:giga -O${zip} https://services.gradle.org/distributions/gradle-${G}-bin.zip
 307 unzip -o -d /var/lib/arvados ${zip}
 308 ln -sfv /var/lib/arvados/gradle-${G}/bin/gradle /usr/local/bin/
 309 rm ${zip}
 310 `, stdout, stderr)
 311                         if err != nil {
 312                                 return 1
 313                         }
 314                 }
 315
 316                 if havesingularityversion, err := exec.Command("/var/lib/arvados/bin/singularity", "--version").CombinedOutput(); err == nil && strings.Contains(string(havesingularityversion), singularityversion) {
 317                         logger.Print("singularity " + singularityversion + " already installed")
 318                 } else if dev || test {
 319                         err = inst.runBash(`
 320 S=`+singularityversion+`
 321 tmp=/var/lib/arvados/tmp/singularity
 322 trap "rm -r ${tmp}" ERR EXIT
 323 cd /var/lib/arvados/tmp
 324 git clone https://github.com/sylabs/singularity
 325 cd singularity
 326 git checkout v${S}
 327 ./mconfig --prefix=/var/lib/arvados
 328 make -C ./builddir
 329 make -C ./builddir install
 330 `, stdout, stderr)
 331                         if err != nil {
 332                                 return 1
 333                         }
 334                 }
 335
 336                 // The entry in /etc/locale.gen is "en_US.UTF-8"; once
 337                 // it's installed, locale -a reports it as
 338                 // "en_US.utf8".
 339                 wantlocale := "en_US.UTF-8"
 340                 if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
 341                         logger.Print("locale " + wantlocale + " already installed")
 342                 } else {
 343                         err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
 344                         if err != nil {
 345                                 return 1
 346                         }
 347                 }
 348
 349                 var pgc struct {
 350                         Version       string
 351                         Cluster       string
 352                         Port          int
 353                         Status        string
 354                         Owner         string
 355                         DataDirectory string
 356                         LogFile       string
 357                 }
 358                 if pgLsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
 359                         err = fmt.Errorf("pg_lsclusters: %s", err2)
 360                         return 1
 361                 } else if pgclusters := strings.Split(strings.TrimSpace(string(pgLsclusters)), "\n"); len(pgclusters) != 1 {
 362                         logger.Warnf("pg_lsclusters returned %d postgresql clusters -- skipping postgresql initdb/startup, hope that's ok", len(pgclusters))
 363                 } 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 {
 364                         err = fmt.Errorf("error parsing pg_lsclusters output: %s", err)
 365                         return 1
 366                 } else if pgc.Status == "online" {
 367                         logger.Infof("postgresql cluster %s-%s is online", pgc.Version, pgc.Cluster)
 368                 } else {
 369                         logger.Infof("postgresql cluster %s-%s is %s; trying to start", pgc.Version, pgc.Cluster, pgc.Status)
 370                         cmd := exec.Command("pg_ctlcluster", "--foreground", pgc.Version, pgc.Cluster, "start")
 371                         cmd.Stdout = stdout
 372                         cmd.Stderr = stderr
 373                         err = cmd.Start()
 374                         if err != nil {
 375                                 return 1
 376                         }
 377                         defer func() {
 378                                 cmd.Process.Signal(syscall.SIGTERM)
 379                                 logger.Info("sent SIGTERM; waiting for postgres to shut down")
 380                                 cmd.Wait()
 381                         }()
 382                         err = waitPostgreSQLReady()
 383                         if err != nil {
 384                                 return 1
 385                         }
 386                 }
 387
 388                 if os.Getpid() == 1 {
 389                         // We are the init process (presumably in a
 390                         // docker container) so although postgresql is
 391                         // installed, it's not running, and initdb
 392                         // might never have been run.
 393                 }
 394
 395                 var needcoll []string
 396                 // If the en_US.UTF-8 locale wasn't installed when
 397                 // postgresql initdb ran, it needs to be added
 398                 // explicitly before we can use it in our test suite.
 399                 for _, collname := range []string{"en_US", "en_US.UTF-8"} {
 400                         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')")
 401                         cmd.Dir = "/"
 402                         out, err2 := cmd.CombinedOutput()
 403                         if err != nil {
 404                                 err = fmt.Errorf("error while checking postgresql collations: %s", err2)
 405                                 return 1
 406                         }
 407                         if strings.Contains(string(out), "1") {
 408                                 logger.Infof("postgresql supports collation %s", collname)
 409                         } else {
 410                                 needcoll = append(needcoll, collname)
 411                         }
 412                 }
 413                 if len(needcoll) > 0 && os.Getpid() != 1 {
 414                         // In order for the CREATE COLLATION statement
 415                         // below to work, the locale must have existed
 416                         // when PostgreSQL started up. If we're
 417                         // running as init, we must have started
 418                         // PostgreSQL ourselves after installing the
 419                         // locales. Otherwise, it might need a
 420                         // restart, so we attempt to restart it with
 421                         // systemd.
 422                         if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
 423                                 logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
 424                         } else if err = waitPostgreSQLReady(); err != nil {
 425                                 return 1
 426                         }
 427                 }
 428                 for _, collname := range needcoll {
 429                         cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE COLLATION \""+collname+"\" (LOCALE = \"en_US.UTF-8\")")
 430                         cmd.Stdout = stdout
 431                         cmd.Stderr = stderr
 432                         cmd.Dir = "/"
 433                         err = cmd.Run()
 434                         if err != nil {
 435                                 err = fmt.Errorf("error adding postgresql collation %s: %s", collname, err)
 436                                 return 1
 437                         }
 438                 }
 439
 440                 withstuff := "WITH LOGIN SUPERUSER ENCRYPTED PASSWORD " + pq.QuoteLiteral(devtestDatabasePassword)
 441                 cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "ALTER ROLE arvados "+withstuff)
 442                 cmd.Dir = "/"
 443                 if err := cmd.Run(); err == nil {
 444                         logger.Print("arvados role exists; superuser privileges added, password updated")
 445                 } else {
 446                         cmd := exec.Command("sudo", "-u", "postgres", "psql", "-c", "CREATE ROLE arvados "+withstuff)
 447                         cmd.Dir = "/"
 448                         cmd.Stdout = stdout
 449                         cmd.Stderr = stderr
 450                         err = cmd.Run()
 451                         if err != nil {
 452                                 return 1
 453                         }
 454                 }
 455         }
 456
 457         if !prod {
 458                 if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
 459                         logger.Print("nodejs " + nodejsversion + " already installed")
 460                 } else {
 461                         err = inst.runBash(`
 462 NJS=`+nodejsversion+`
 463 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
 464 ln -sfv /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
 465 `, stdout, stderr)
 466                         if err != nil {
 467                                 return 1
 468                         }
 469                 }
 470
 471                 if haveyarnversion, err := exec.Command("/usr/local/bin/yarn", "--version").CombinedOutput(); err == nil && len(haveyarnversion) > 0 {
 472                         logger.Print("yarn " + strings.TrimSpace(string(haveyarnversion)) + " already installed")
 473                 } else {
 474                         err = inst.runBash(`
 475 npm install -g yarn
 476 ln -sfv /var/lib/arvados/node-`+nodejsversion+`-linux-x64/bin/{yarn,yarnpkg} /usr/local/bin/
 477 `, stdout, stderr)
 478                         if err != nil {
 479                                 return 1
 480                         }
 481                 }
 482
 483                 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" {
 484                         logger.Print("workbench2 repo is already at " + workbench2version)
 485                 } else {
 486                         err = inst.runBash(`
 487 V=`+workbench2version+`
 488 cd /var/lib/arvados
 489 if [[ ! -e arvados-workbench2 ]]; then
 490   git clone https://git.arvados.org/arvados-workbench2.git
 491   cd arvados-workbench2
 492   git checkout $V
 493 else
 494   cd arvados-workbench2
 495   if ! git checkout $V; then
 496     git fetch
 497     git checkout $V
 498   fi
 499 fi
 500 rm -rf build
 501 `, stdout, stderr)
 502                         if err != nil {
 503                                 return 1
 504                         }
 505                 }
 506
 507                 if err = inst.runBash(`
 508 cd /var/lib/arvados/arvados-workbench2
 509 yarn install
 510 `, stdout, stderr); err != nil {
 511                         return 1
 512                 }
 513         }
 514
 515         if prod || pkg {
 516                 // Install Go programs to /var/lib/arvados/bin/
 517                 for _, srcdir := range []string{
 518                         "cmd/arvados-client",
 519                         "cmd/arvados-server",
 520                         "services/arv-git-httpd",
 521                         "services/crunch-dispatch-local",
 522                         "services/crunch-dispatch-slurm",
 523                         "services/health",
 524                         "services/keep-balance",
 525                         "services/keep-web",
 526                         "services/keepproxy",
 527                         "services/keepstore",
 528                         "services/ws",
 529                 } {
 530                         fmt.Fprintf(stderr, "building %s...\n", srcdir)
 531                         cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion+" -s -w")
 532                         cmd.Env = append(cmd.Env, os.Environ()...)
 533                         cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
 534                         cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 535                         cmd.Stdout = stdout
 536                         cmd.Stderr = stderr
 537                         err = cmd.Run()
 538                         if err != nil {
 539                                 return 1
 540                         }
 541                 }
 542
 543                 // Copy assets from source tree to /var/lib/arvados/share
 544                 cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
 545                 cmd.Stdout = stdout
 546                 cmd.Stderr = stderr
 547                 err = cmd.Run()
 548                 if err != nil {
 549                         return 1
 550                 }
 551
 552                 // Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
 553                 for dstdir, srcdir := range map[string]string{
 554                         "railsapi":   "services/api",
 555                         "workbench1": "apps/workbench",
 556                 } {
 557                         fmt.Fprintf(stderr, "building %s...\n", srcdir)
 558                         cmd := exec.Command("rsync",
 559                                 "-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
 560                                 "--exclude", "/coverage",
 561                                 "--exclude", "/log",
 562                                 "--exclude", "/tmp",
 563                                 "--exclude", "/vendor",
 564                                 "--exclude", "/config/environments",
 565                                 "./", "/var/lib/arvados/"+dstdir+"/")
 566                         cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 567                         cmd.Stdout = stdout
 568                         cmd.Stderr = stderr
 569                         err = cmd.Run()
 570                         if err != nil {
 571                                 return 1
 572                         }
 573                         for _, cmdline := range [][]string{
 574                                 {"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
 575                                 {"touch", "log/production.log"},
 576                                 {"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"},
 577                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:" + bundlerversion},
 578                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem", "--without", "development test diagnostics performance"},
 579                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
 580                                 {"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
 581                         } {
 582                                 cmd = exec.Command(cmdline[0], cmdline[1:]...)
 583                                 cmd.Dir = "/var/lib/arvados/" + dstdir
 584                                 cmd.Stdout = stdout
 585                                 cmd.Stderr = stderr
 586                                 fmt.Fprintf(stderr, "... %s\n", cmd.Args)
 587                                 err = cmd.Run()
 588                                 if err != nil {
 589                                         return 1
 590                                 }
 591                         }
 592                         cmd = exec.Command("sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "validate-install")
 593                         cmd.Dir = "/var/lib/arvados/" + dstdir
 594                         cmd.Stdout = stdout
 595                         cmd.Stderr = stderr
 596                         err = cmd.Run()
 597                         if err != nil && !strings.Contains(err.Error(), "exit status 2") {
 598                                 // Exit code 2 indicates there were warnings (like
 599                                 // "other passenger installations have been detected",
 600                                 // which we can't expect to avoid) but no errors.
 601                                 // Other non-zero exit codes (1, 9) indicate errors.
 602                                 return 1
 603                         }
 604                 }
 605
 606                 // Install workbench2 app to /var/lib/arvados/workbench2/
 607                 if err = inst.runBash(`
 608 cd /var/lib/arvados/arvados-workbench2
 609 VERSION="`+inst.PackageVersion+`" BUILD_NUMBER=1 GIT_COMMIT="`+workbench2version[:9]+`" yarn build
 610 rsync -a --delete-after build/ /var/lib/arvados/workbench2/
 611 `, stdout, stderr); err != nil {
 612                         return 1
 613                 }
 614         }
 615
 616         return 0
 617 }
 618
 619 type osversion struct {
 620         Debian bool
 621         Ubuntu bool
 622         Centos bool
 623         Major  int
 624 }
 625
 626 func identifyOS() (osversion, error) {
 627         var osv osversion
 628         f, err := os.Open("/etc/os-release")
 629         if err != nil {
 630                 return osv, err
 631         }
 632         defer f.Close()
 633
 634         kv := map[string]string{}
 635         scanner := bufio.NewScanner(f)
 636         for scanner.Scan() {
 637                 line := strings.TrimSpace(scanner.Text())
 638                 if strings.HasPrefix(line, "#") {
 639                         continue
 640                 }
 641                 toks := strings.SplitN(line, "=", 2)
 642                 if len(toks) != 2 {
 643                         return osv, fmt.Errorf("invalid line in /etc/os-release: %q", line)
 644                 }
 645                 k := toks[0]
 646                 v := strings.Trim(toks[1], `"`)
 647                 if v == toks[1] {
 648                         v = strings.Trim(v, `'`)
 649                 }
 650                 kv[k] = v
 651         }
 652         if err = scanner.Err(); err != nil {
 653                 return osv, err
 654         }
 655         switch kv["ID"] {
 656         case "ubuntu":
 657                 osv.Ubuntu = true
 658         case "debian":
 659                 osv.Debian = true
 660         case "centos":
 661                 osv.Centos = true
 662         default:
 663                 return osv, fmt.Errorf("unsupported ID in /etc/os-release: %q", kv["ID"])
 664         }
 665         vstr := kv["VERSION_ID"]
 666         if i := strings.Index(vstr, "."); i > 0 {
 667                 vstr = vstr[:i]
 668         }
 669         osv.Major, err = strconv.Atoi(vstr)
 670         if err != nil {
 671                 return osv, fmt.Errorf("incomprehensible VERSION_ID in /etc/os-release: %q", kv["VERSION_ID"])
 672         }
 673         return osv, nil
 674 }
 675
 676 func waitPostgreSQLReady() error {
 677         for deadline := time.Now().Add(10 * time.Second); ; {
 678                 output, err := exec.Command("pg_isready").CombinedOutput()
 679                 if err == nil {
 680                         return nil
 681                 } else if time.Now().After(deadline) {
 682                         return fmt.Errorf("timed out waiting for pg_isready (%q)", output)
 683                 } else {
 684                         time.Sleep(time.Second)
 685                 }
 686         }
 687 }
 688
 689 func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
 690         cmd := exec.Command("bash", "-")
 691         if inst.EatMyData {
 692                 cmd = exec.Command("eatmydata", "bash", "-")
 693         }
 694         cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
 695         cmd.Stdout = stdout
 696         cmd.Stderr = stderr
 697         return cmd.Run()
 698 }
 699
 700 func prodpkgs(osv osversion) []string {
 701         pkgs := []string{
 702                 "ca-certificates",
 703                 "curl",
 704                 "fuse",
 705                 "git",
 706                 "gitolite3",
 707                 "graphviz",
 708                 "haveged",
 709                 "libcurl3-gnutls",
 710                 "libxslt1.1",
 711                 "nginx",
 712                 "python",
 713                 "sudo",
 714         }
 715         if osv.Debian || osv.Ubuntu {
 716                 if osv.Debian && osv.Major == 8 {
 717                         pkgs = append(pkgs, "libgnutls-deb0-28") // sdk/cwl
 718                 } else if osv.Debian && osv.Major >= 10 || osv.Ubuntu && osv.Major >= 16 {
 719                         pkgs = append(pkgs, "python3-distutils") // sdk/cwl
 720                 }
 721                 return append(pkgs,
 722                         "g++",
 723                         "libcurl4-openssl-dev", // services/api
 724                         "libpq-dev",
 725                         "libpython2.7", // services/fuse
 726                         "mime-support", // keep-web
 727                         "zlib1g-dev",   // services/api
 728                 )
 729         } else if osv.Centos {
 730                 return append(pkgs,
 731                         "fuse-libs", // services/fuse
 732                         "gcc",
 733                         "gcc-c++",
 734                         "libcurl-devel",    // services/api
 735                         "mailcap",          // keep-web
 736                         "postgresql-devel", // services/api
 737                 )
 738         } else {
 739                 panic("os version not supported")
 740         }
 741 }
 742
 743 func ProductionDependencies() ([]string, error) {
 744         osv, err := identifyOS()
 745         if err != nil {
 746                 return nil, err
 747         }
 748         return prodpkgs(osv), nil
 749 }