X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0fbc2ee6f150426919eaf3ab9361208aa2968a70..32b8eda74f24d1df963a18da5f8023b15d209ca9:/build/run-tests.sh

diff --git a/build/run-tests.sh b/build/run-tests.sh
index 5260a2b6a9..9081d99bb5 100755
--- a/build/run-tests.sh
+++ b/build/run-tests.sh
@@ -69,7 +69,12 @@ apps/workbench_functionals (*)
 apps/workbench_integration (*)
 apps/workbench_benchmark
 apps/workbench_profile
+cmd/arvados-client
 doc
+lib/cli
+lib/cmd
+lib/crunchstat
+lib/dispatchcloud
 services/api
 services/arv-git-httpd
 services/crunchstat
@@ -104,6 +109,7 @@ sdk/go/asyncbuf
 sdk/go/stats
 sdk/go/crunchrunner
 sdk/cwl
+sdk/R
 tools/sync-groups
 tools/crunchstat-summary
 tools/keep-exercise
@@ -128,6 +134,7 @@ VENV3DIR=
 PYTHONPATH=
 GEMHOME=
 PERLINSTALLBASE=
+R_LIBS=
 
 short=
 only_install=
@@ -235,6 +242,18 @@ sanity_checks() {
     which Xvfb || fatal "No xvfb. Try: apt-get install xvfb"
     echo -n 'graphviz: '
     dot -V || fatal "No graphviz. Try: apt-get install graphviz"
+
+    if [[ "$NEED_SDK_R" = true ]]; then
+      # R SDK stuff
+      echo -n 'R: '
+      which R || fatal "No R. Try: apt-get install r-base"
+      echo -n 'testthat: '
+      R -q -e "library('testthat')" || fatal "No testthat. Try: apt-get install r-cran-testthat"
+      # needed for roxygen2, needed for devtools, needed for R sdk
+      pkg-config --exists libxml-2.0 || fatal "No libxml2. Try: apt-get install libxml2-dev"
+      # needed for pkgdown, builds R SDK doc pages
+      which pandoc || fatal "No pandoc. Try: apt-get install pandoc"
+    fi
 }
 
 rotate_logfile() {
@@ -304,6 +323,18 @@ do
     esac
 done
 
+# R SDK installation is very slow (~360s in a clean environment) and only
+# required when testing it. Skip that step if it is not needed.
+NEED_SDK_R=true
+
+if [[ ! -z "${only}" && "${only}" != "sdk/R" ]]; then
+  NEED_SDK_R=false
+fi
+
+if [[ ! -z "${skip}" && "${skip}" == "sdk/R" ]]; then
+  NEED_SDK_R=false
+fi
+
 start_services() {
     echo 'Starting API, keepproxy, keep-web, ws, arv-git-httpd, and nginx ssl proxy...'
     if [[ ! -d "$WORKSPACE/services/api/log" ]]; then
@@ -363,7 +394,7 @@ if [[ -z "$temp" ]]; then
 fi
 
 # Set up temporary install dirs (unless existing dirs were supplied)
-for tmpdir in VENVDIR VENV3DIR GOPATH GEMHOME PERLINSTALLBASE
+for tmpdir in VENVDIR VENV3DIR GOPATH GEMHOME PERLINSTALLBASE R_LIBS
 do
     if [[ -z "${!tmpdir}" ]]; then
         eval "$tmpdir"="$temp/$tmpdir"
@@ -472,26 +503,50 @@ setup_virtualenv() {
 export PERLINSTALLBASE
 export PERLLIB="$PERLINSTALLBASE/lib/perl5:${PERLLIB:+$PERLLIB}"
 
+export R_LIBS
+
 export GOPATH
 mkdir -p "$GOPATH/src/git.curoverse.com"
-rmdir --parents "$GOPATH/src/git.curoverse.com/arvados.git/tmp/GOPATH"
-ln -sfT "$WORKSPACE" "$GOPATH/src/git.curoverse.com/arvados.git" \
+rmdir -v --parents --ignore-fail-on-non-empty "$GOPATH/src/git.curoverse.com/arvados.git/tmp/GOPATH"
+for d in \
+    "$GOPATH/src/git.curoverse.com/arvados.git/arvados.git" \
+    "$GOPATH/src/git.curoverse.com/arvados.git"; do
+    [[ -d "$d" ]] && rmdir "$d"
+    [[ -h "$d" ]] && rm "$d"
+done
+ln -vsnfT "$WORKSPACE" "$GOPATH/src/git.curoverse.com/arvados.git" \
     || fatal "symlink failed"
 go get -v github.com/kardianos/govendor \
     || fatal "govendor install failed"
+cd "$GOPATH/src/git.curoverse.com/arvados.git" \
+    || fatal
+# Remove cached source dirs in workdir. Otherwise, they won't qualify
+# as +missing or +external below, and we won't be able to detect that
+# they're missing from vendor/vendor.json.
+rm -r vendor/*/
+go get -v -d ...
+"$GOPATH/bin/govendor" sync \
+    || fatal "govendor sync failed"
+[[ -z $("$GOPATH/bin/govendor" list +unused +missing +external | tee /dev/stderr) ]] \
+    || fatal "vendor/vendor.json has unused or missing dependencies -- try:
+* govendor remove +unused
+* govendor add +missing +external
+"
+cd "$WORKSPACE"
+
 
 setup_virtualenv "$VENVDIR" --python python2.7
 . "$VENVDIR/bin/activate"
 
 # Needed for run_test_server.py which is used by certain (non-Python) tests.
 pip freeze 2>/dev/null | egrep ^PyYAML= \
-    || pip install PyYAML >/dev/null \
+    || pip install --no-cache-dir PyYAML >/dev/null \
     || fatal "pip install PyYAML failed"
 
-# Preinstall forked version of libcloud, because nodemanager "pip install"
+# Preinstall libcloud, because nodemanager "pip install"
 # won't pick it up by default.
 pip freeze 2>/dev/null | egrep ^apache-libcloud==$LIBCLOUD_PIN \
-    || pip install --pre --ignore-installed https://github.com/curoverse/libcloud/archive/apache-libcloud-$LIBCLOUD_PIN.zip >/dev/null \
+    || pip install --pre --ignore-installed --no-cache-dir apache-libcloud>=$LIBCLOUD_PIN >/dev/null \
     || fatal "pip install apache-libcloud failed"
 
 # We need an unreleased (as of 2017-08-17) llfuse bugfix, otherwise our fuse test suite deadlocks.
@@ -660,11 +715,17 @@ do_test_once() {
 }
 
 do_install() {
-    if [[ -z "${only_install}" || "${only_install}" == "${1}" ]]; then
-        retry do_install_once ${@}
-    else
-        title "Skipping $1 install"
-    fi
+  skipit=false
+
+  if [[ -z "${only_install}" || "${only_install}" == "${1}" ]]; then
+      retry do_install_once ${@}
+  else
+      skipit=true
+  fi
+
+  if [[ "$skipit" = true ]]; then
+    title "Skipping $1 install"
+  fi
 }
 
 do_install_once() {
@@ -738,6 +799,14 @@ install_ruby_sdk() {
 }
 do_install sdk/ruby ruby_sdk
 
+install_R_sdk() {
+  if [[ "$NEED_SDK_R" = true ]]; then
+    cd "$WORKSPACE/sdk/R" \
+       && R --quiet --vanilla --file=install_deps.R
+  fi
+}
+do_install sdk/R R_sdk
+
 install_perl_sdk() {
     cd "$WORKSPACE/sdk/perl" \
         && perl Makefile.PL INSTALL_BASE="$PERLINSTALLBASE" \
@@ -813,6 +882,8 @@ install_apiserver() {
         && mkdir -p tmp/git \
         && cd tmp/git \
         && tar xf ../../test/test.git.tar \
+        && mkdir -p internal.git \
+        && git --git-dir internal.git init \
             || return 1
 
     cd "$WORKSPACE/services/api" \
@@ -822,11 +893,13 @@ install_apiserver() {
 }
 do_install services/api apiserver
 
-cd "$GOPATH/src/git.curoverse.com/arvados.git" && \
-    "$GOPATH/bin/govendor" sync -v || \
-        fatal "govendor sync failed"
 declare -a gostuff
 gostuff=(
+    cmd/arvados-client
+    lib/cli
+    lib/cmd
+    lib/crunchstat
+    lib/dispatchcloud
     sdk/go/arvados
     sdk/go/arvadosclient
     sdk/go/blockdigest
@@ -837,7 +910,6 @@ gostuff=(
     sdk/go/asyncbuf
     sdk/go/crunchrunner
     sdk/go/stats
-    lib/crunchstat
     services/arv-git-httpd
     services/crunchstat
     services/health
@@ -906,6 +978,15 @@ test_ruby_sdk() {
 }
 do_test sdk/ruby ruby_sdk
 
+test_R_sdk() {
+  if [[ "$NEED_SDK_R" = true ]]; then
+    cd "$WORKSPACE/sdk/R" \
+        && R --quiet --file=run_test.R
+  fi
+}
+
+do_test sdk/R R_sdk
+
 test_cli() {
     cd "$WORKSPACE/sdk/cli" \
         && mkdir -p /tmp/keep \