X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ee7d60f02525760a2480157011659e7b2210f6b8..ba56503f90d099a215fb7375f5cb1cc1ac667e2c:/lib/install/deps.go

diff --git a/lib/install/deps.go b/lib/install/deps.go
index f9b962fdd8..8df3fba532 100644
--- a/lib/install/deps.go
+++ b/lib/install/deps.go
@@ -14,6 +14,7 @@ import (
 	"io"
 	"os"
 	"os/exec"
+	"os/user"
 	"path/filepath"
 	"strconv"
 	"strings"
@@ -33,6 +34,7 @@ type installCommand struct {
 	ClusterType    string
 	SourcePath     string
 	PackageVersion string
+	EatMyData      bool
 }
 
 func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
@@ -54,6 +56,7 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 	flags.StringVar(&inst.ClusterType, "type", "production", "cluster `type`: development, test, production, or package")
 	flags.StringVar(&inst.SourcePath, "source", "/arvados", "source tree location (required for -type=package)")
 	flags.StringVar(&inst.PackageVersion, "package-version", "0.0.0", "version string to embed in executable files")
+	flags.BoolVar(&inst.EatMyData, "eatmydata", false, "use eatmydata to speed up install")
 	err = flags.Parse(args)
 	if err == flag.ErrHelp {
 		err = nil
@@ -108,22 +111,36 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 		}
 	}
 
+	if inst.EatMyData {
+		cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends", "eatmydata")
+		cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
+		cmd.Stdout = stdout
+		cmd.Stderr = stderr
+		err = cmd.Run()
+		if err != nil {
+			return 1
+		}
+	}
+
 	pkgs := prodpkgs(osv)
 
 	if pkg {
 		pkgs = append(pkgs,
 			"dpkg-dev",
+			"eatmydata", // install it for later steps, even if we're not using it now
 			"rsync",
 		)
 	}
 
 	if dev || test || pkg {
 		pkgs = append(pkgs,
+			"automake",
+			"bison",
 			"bsdmainutils",
 			"build-essential",
 			"cadaver",
-			"cython",
-			"daemontools", // lib/boot uses setuidgid to drop privileges when running as root
+			"curl",
+			"cython3",
 			"default-jdk-headless",
 			"default-jre-headless",
 			"gettext",
@@ -135,7 +152,7 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"libjson-perl",
 			"libpam-dev",
 			"libpcre3-dev",
-			"libpython2.7-dev",
+			"libpq-dev",
 			"libreadline-dev",
 			"libssl-dev",
 			"libwww-perl",
@@ -143,6 +160,7 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"libxslt1-dev",
 			"linkchecker",
 			"lsof",
+			"make",
 			"net-tools",
 			"pandoc",
 			"perl-modules",
@@ -150,11 +168,16 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 			"postgresql",
 			"postgresql-contrib",
 			"python3-dev",
-			"python-epydoc",
+			"python3-venv",
+			"python3-virtualenv",
 			"r-base",
 			"r-cran-testthat",
+			"r-cran-devtools",
+			"r-cran-knitr",
+			"r-cran-markdown",
+			"r-cran-roxygen2",
+			"r-cran-xml",
 			"sudo",
-			"virtualenv",
 			"wget",
 			"xvfb",
 		)
@@ -164,7 +187,11 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 		default:
 			pkgs = append(pkgs, "libcurl3")
 		}
-		cmd := exec.CommandContext(ctx, "apt-get", "install", "--yes", "--no-install-recommends")
+		cmd := exec.CommandContext(ctx, "apt-get")
+		if inst.EatMyData {
+			cmd = exec.CommandContext(ctx, "eatmydata", "apt-get")
+		}
+		cmd.Args = append(cmd.Args, "install", "--yes", "--no-install-recommends")
 		cmd.Args = append(cmd.Args, pkgs...)
 		cmd.Env = append(os.Environ(), "DEBIAN_FRONTEND=noninteractive")
 		cmd.Stdout = stdout
@@ -176,21 +203,35 @@ func (inst *installCommand) RunCommand(prog string, args []string, stdin io.Read
 	}
 
 	os.Mkdir("/var/lib/arvados", 0755)
-	rubyversion := "2.5.7"
+	os.Mkdir("/var/lib/arvados/tmp", 0700)
+	if prod || pkg {
+		os.Mkdir("/var/lib/arvados/wwwtmp", 0700)
+		u, er := user.Lookup("www-data")
+		if er != nil {
+			err = fmt.Errorf("user.Lookup(%q): %w", "www-data", er)
+			return 1
+		}
+		uid, _ := strconv.Atoi(u.Uid)
+		gid, _ := strconv.Atoi(u.Gid)
+		err = os.Chown("/var/lib/arvados/wwwtmp", uid, gid)
+		if err != nil {
+			return 1
+		}
+	}
+	rubyversion := "2.7.2"
+	rubymajorversion := rubyversion[:strings.LastIndex(rubyversion, ".")]
 	if haverubyversion, err := exec.Command("/var/lib/arvados/bin/ruby", "-v").CombinedOutput(); err == nil && bytes.HasPrefix(haverubyversion, []byte("ruby "+rubyversion)) {
 		logger.Print("ruby " + rubyversion + " already installed")
 	} else {
-		err = runBash(`
-mkdir -p /var/lib/arvados/tmp
-tmp=/var/lib/arvados/tmp/ruby-`+rubyversion+`
-trap "rm -r ${tmp}" ERR
-wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/2.5/ruby-`+rubyversion+`.tar.gz | tar -C /var/lib/arvados/tmp -xzf -
-cd ${tmp}
-./configure --disable-install-doc --prefix /var/lib/arvados
+		err = inst.runBash(`
+tmp="$(mktemp -d)"
+trap 'rm -r "${tmp}"' ERR EXIT
+wget --progress=dot:giga -O- https://cache.ruby-lang.org/pub/ruby/`+rubymajorversion+`/ruby-`+rubyversion+`.tar.gz | tar -C "${tmp}" -xzf -
+cd "${tmp}/ruby-`+rubyversion+`"
+./configure --disable-install-static-library --enable-shared --disable-install-doc --prefix /var/lib/arvados
 make -j8
 make install
-/var/lib/arvados/bin/gem install bundler
-rm -r ${tmp}
+/var/lib/arvados/bin/gem install bundler --no-document
 `, stdout, stderr)
 		if err != nil {
 			return 1
@@ -198,11 +239,11 @@ rm -r ${tmp}
 	}
 
 	if !prod {
-		goversion := "1.14"
+		goversion := "1.16.3"
 		if havegoversion, err := exec.Command("/usr/local/bin/go", "version").CombinedOutput(); err == nil && bytes.HasPrefix(havegoversion, []byte("go version go"+goversion+" ")) {
 			logger.Print("go " + goversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 cd /tmp
 wget --progress=dot:giga -O- https://storage.googleapis.com/golang/go`+goversion+`.linux-amd64.tar.gz | tar -C /var/lib/arvados -xzf -
 ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
@@ -218,7 +259,7 @@ ln -sf /var/lib/arvados/go/bin/* /usr/local/bin/
 		if havepjsversion, err := exec.Command("/usr/local/bin/phantomjs", "--version").CombinedOutput(); err == nil && string(havepjsversion) == "1.9.8\n" {
 			logger.Print("phantomjs " + pjsversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 PJS=phantomjs-`+pjsversion+`-linux-x86_64
 wget --progress=dot:giga -O- https://bitbucket.org/ariya/phantomjs/downloads/$PJS.tar.bz2 | tar -C /var/lib/arvados -xjf -
 ln -sf /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
@@ -232,7 +273,7 @@ ln -sf /var/lib/arvados/$PJS/bin/phantomjs /usr/local/bin/
 		if havegeckoversion, err := exec.Command("/usr/local/bin/geckodriver", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegeckoversion), " "+geckoversion+" ") {
 			logger.Print("geckodriver " + geckoversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 GD=v`+geckoversion+`
 wget --progress=dot:giga -O- https://github.com/mozilla/geckodriver/releases/download/$GD/geckodriver-$GD-linux64.tar.gz | tar -C /var/lib/arvados/bin -xzf - geckodriver
 ln -sf /var/lib/arvados/bin/geckodriver /usr/local/bin/
@@ -242,11 +283,11 @@ ln -sf /var/lib/arvados/bin/geckodriver /usr/local/bin/
 			}
 		}
 
-		nodejsversion := "v8.15.1"
+		nodejsversion := "v10.23.1"
 		if havenodejsversion, err := exec.Command("/usr/local/bin/node", "--version").CombinedOutput(); err == nil && string(havenodejsversion) == nodejsversion+"\n" {
 			logger.Print("nodejs " + nodejsversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 NJS=`+nodejsversion+`
 wget --progress=dot:giga -O- https://nodejs.org/dist/${NJS}/node-${NJS}-linux-x64.tar.xz | sudo tar -C /var/lib/arvados -xJf -
 ln -sf /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
@@ -260,9 +301,8 @@ ln -sf /var/lib/arvados/node-${NJS}-linux-x64/bin/{node,npm} /usr/local/bin/
 		if havegradleversion, err := exec.Command("/usr/local/bin/gradle", "--version").CombinedOutput(); err == nil && strings.Contains(string(havegradleversion), "Gradle "+gradleversion+"\n") {
 			logger.Print("gradle " + gradleversion + " already installed")
 		} else {
-			err = runBash(`
+			err = inst.runBash(`
 G=`+gradleversion+`
-mkdir -p /var/lib/arvados/tmp
 zip=/var/lib/arvados/tmp/gradle-${G}-bin.zip
 trap "rm ${zip}" ERR
 wget --progress=dot:giga -O${zip} https://services.gradle.org/distributions/gradle-${G}-bin.zip
@@ -282,7 +322,7 @@ rm ${zip}
 		if havelocales, err := exec.Command("locale", "-a").CombinedOutput(); err == nil && bytes.Contains(havelocales, []byte(strings.Replace(wantlocale+"\n", "UTF-", "utf", 1))) {
 			logger.Print("locale " + wantlocale + " already installed")
 		} else {
-			err = runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
+			err = inst.runBash(`sed -i 's/^# *\(`+wantlocale+`\)/\1/' /etc/locale.gen && locale-gen`, stdout, stderr)
 			if err != nil {
 				return 1
 			}
@@ -297,10 +337,10 @@ rm ${zip}
 			DataDirectory string
 			LogFile       string
 		}
-		if pg_lsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
+		if pgLsclusters, err2 := exec.Command("pg_lsclusters", "--no-header").CombinedOutput(); err2 != nil {
 			err = fmt.Errorf("pg_lsclusters: %s", err2)
 			return 1
-		} else if pgclusters := strings.Split(strings.TrimSpace(string(pg_lsclusters)), "\n"); len(pgclusters) != 1 {
+		} else if pgclusters := strings.Split(strings.TrimSpace(string(pgLsclusters)), "\n"); len(pgclusters) != 1 {
 			logger.Warnf("pg_lsclusters returned %d postgresql clusters -- skipping postgresql initdb/startup, hope that's ok", len(pgclusters))
 		} 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 {
 			err = fmt.Errorf("error parsing pg_lsclusters output: %s", err)
@@ -361,7 +401,7 @@ rm ${zip}
 			// locales. Otherwise, it might need a
 			// restart, so we attempt to restart it with
 			// systemd.
-			if err = runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
+			if err = inst.runBash(`sudo systemctl restart postgresql`, stdout, stderr); err != nil {
 				logger.Warn("`systemctl restart postgresql` failed; hoping postgresql does not need to be restarted")
 			} else if err = waitPostgreSQLReady(); err != nil {
 				return 1
@@ -396,14 +436,21 @@ rm ${zip}
 		}
 	}
 
-	if pkg {
+	if prod || pkg {
 		// Install Rails apps to /var/lib/arvados/{railsapi,workbench1}/
 		for dstdir, srcdir := range map[string]string{
 			"railsapi":   "services/api",
 			"workbench1": "apps/workbench",
 		} {
 			fmt.Fprintf(stderr, "building %s...\n", srcdir)
-			cmd := exec.Command("rsync", "-a", "--no-owner", "--delete-after", "--exclude", "/tmp", "--exclude", "/log", "--exclude", "/vendor", "./", "/var/lib/arvados/"+dstdir+"/")
+			cmd := exec.Command("rsync",
+				"-a", "--no-owner", "--no-group", "--delete-after", "--delete-excluded",
+				"--exclude", "/coverage",
+				"--exclude", "/log",
+				"--exclude", "/tmp",
+				"--exclude", "/vendor",
+				"--exclude", "/config/environments",
+				"./", "/var/lib/arvados/"+dstdir+"/")
 			cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 			cmd.Stdout = stdout
 			cmd.Stderr = stderr
@@ -412,20 +459,19 @@ rm ${zip}
 				return 1
 			}
 			for _, cmdline := range [][]string{
-				{"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.passenger"},
+				{"mkdir", "-p", "log", "tmp", ".bundle", "/var/www/.gem", "/var/www/.bundle", "/var/www/.passenger"},
 				{"touch", "log/production.log"},
-				// {"chown", "-R", "root:root", "."},
-				{"chown", "-R", "www-data:www-data", "/var/www/.gem", "/var/www/.passenger", "log", "tmp", ".bundle", "Gemfile.lock", "config.ru", "config/environment.rb"},
-				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--no-rdoc", "--no-ri", "--conservative", "bundler:1.16.6", "bundler:1.17.3", "bundler:2.0.2"},
+				{"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"},
+				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/gem", "install", "--user", "--conservative", "--no-document", "bundler:1.16.6", "bundler:1.17.3", "bundler:2.0.2"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "install", "--deployment", "--jobs", "8", "--path", "/var/www/.gem"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "build-native-support"},
 				{"sudo", "-u", "www-data", "/var/lib/arvados/bin/bundle", "exec", "passenger-config", "install-standalone-runtime"},
 			} {
 				cmd = exec.Command(cmdline[0], cmdline[1:]...)
-				cmd.Env = append([]string{}, os.Environ()...)
 				cmd.Dir = "/var/lib/arvados/" + dstdir
 				cmd.Stdout = stdout
 				cmd.Stderr = stderr
+				fmt.Fprintf(stderr, "... %s\n", cmd.Args)
 				err = cmd.Run()
 				if err != nil {
 					return 1
@@ -461,7 +507,8 @@ rm ${zip}
 		} {
 			fmt.Fprintf(stderr, "building %s...\n", srcdir)
 			cmd := exec.Command("go", "install", "-ldflags", "-X git.arvados.org/arvados.git/lib/cmd.version="+inst.PackageVersion+" -X main.version="+inst.PackageVersion)
-			cmd.Env = append([]string{"GOBIN=/var/lib/arvados/bin"}, os.Environ()...)
+			cmd.Env = append(cmd.Env, os.Environ()...)
+			cmd.Env = append(cmd.Env, "GOBIN=/var/lib/arvados/bin")
 			cmd.Dir = filepath.Join(inst.SourcePath, srcdir)
 			cmd.Stdout = stdout
 			cmd.Stderr = stderr
@@ -470,6 +517,15 @@ rm ${zip}
 				return 1
 			}
 		}
+
+		// Copy assets from source tree to /var/lib/arvados/share
+		cmd := exec.Command("install", "-v", "-t", "/var/lib/arvados/share", filepath.Join(inst.SourcePath, "sdk/python/tests/nginx.conf"))
+		cmd.Stdout = stdout
+		cmd.Stderr = stderr
+		err = cmd.Run()
+		if err != nil {
+			return 1
+		}
 	}
 
 	return 0
@@ -545,8 +601,11 @@ func waitPostgreSQLReady() error {
 	}
 }
 
-func runBash(script string, stdout, stderr io.Writer) error {
+func (inst *installCommand) runBash(script string, stdout, stderr io.Writer) error {
 	cmd := exec.Command("bash", "-")
+	if inst.EatMyData {
+		cmd = exec.Command("eatmydata", "bash", "-")
+	}
 	cmd.Stdin = bytes.NewBufferString("set -ex -o pipefail\n" + script)
 	cmd.Stdout = stdout
 	cmd.Stderr = stderr
@@ -555,8 +614,6 @@ func runBash(script string, stdout, stderr io.Writer) error {
 
 func prodpkgs(osv osversion) []string {
 	pkgs := []string{
-		"automake",
-		"bison",
 		"ca-certificates",
 		"curl",
 		"fuse",
@@ -566,9 +623,9 @@ func prodpkgs(osv osversion) []string {
 		"haveged",
 		"libcurl3-gnutls",
 		"libxslt1.1",
-		"make",
 		"nginx",
 		"python",
+		"sudo",
 	}
 	if osv.Debian || osv.Ubuntu {
 		if osv.Debian && osv.Major == 8 {