Merge pull request #5491 from nsoranzo/release_18.01_fix_common_startup_for_bare_clone

[18.01] Fix common_startup.sh for galaxy tarballs

client/package.json

@@ -36,7 +36,7 @@
     "build-production": "NODE_ENV=production gulp stage-libs && concurrently \"yarn run style\" \"yarn run webpack-production\" \"yarn run gulp clean && yarn run gulp-production\" && yarn run save-build-hash",
     "build-production-maps": "NODE_ENV=production gulp stage-libs && concurrently \"yarn run style\" \"yarn run webpack-production-maps\" \"yarn run gulp clean && yarn run gulp-production-maps\" && yarn run save-build-hash",
     "webpack": "webpack -d",
-    "save-build-hash": "git rev-parse HEAD > ../static/client_build_hash.txt",
+    "save-build-hash": "(git rev-parse HEAD 2>/dev/null || echo '') >../static/client_build_hash.txt",
     "webpack-watch": "webpack -d --watch",
     "webpack-production": "webpack -p",
     "webpack-production-maps": "GXY_BUILD_SOURCEMAPS=1 webpack -p",

lib/galaxy/dependencies/pipfiles/develop/Pipfile

@@ -23,3 +23,4 @@ Sphinx = "*"
 sphinx_rtd_theme = "*"
 lxml = "*"
 recommonmark = "*"
+nodeenv = "*"

lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock

@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "7da6298d5a5d49c87941125b449f37cc26c44d80f94d3d35a211463aa1efcf10"
+            "sha256": "5050d55a5cfaa22fddfa05d7edd3b2102a632d322266917f36a2c05f2522bcbb"
         },
         "host-environment-markers": {
             "implementation_name": "cpython",
@@ -156,6 +156,12 @@
             ],
             "version": "==2.0.0"
         },
+        "nodeenv": {
+            "hashes": [
+                "sha256:98835dab727f94a713eacc7234e3db6777a55cafb60f391485011899e5c818df"
+            ],
+            "version": "==1.2.0"
+        },
         "nose": {
             "hashes": [
                 "sha256:dadcddc0aefbf99eea214e0f1232b94f2fa9bd98fa8353711dacb112bfcbbb2a",

lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt

@@ -33,3 +33,4 @@ chardet==3.0.4 --hash=sha256:fc323ffcaeaed0e0a02bf4d117757b98aed530d9ed4531e3e15
 nose==1.3.7 --hash=sha256:dadcddc0aefbf99eea214e0f1232b94f2fa9bd98fa8353711dacb112bfcbbb2a  --hash=sha256:9ff7c6cc443f8c51994b34a667bbcf45afd6d945be7477b52e97516fd17c53ac  --hash=sha256:f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98
 requests==2.18.4 --hash=sha256:6a1b267aa90cac58ac3a765d067950e7dbbf75b1da07e895d1f594193a40a38b  --hash=sha256:9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e
 idna==2.6 --hash=sha256:8c7309c718f94b3a625cb648ace320157ad16ff131ae0af362c9f21b80ef6ec4  --hash=sha256:2c6a5de3089009e3da7c5dde64a141dbc8551d5b7f6cf4ed7c2568d0cc520a8f
+nodeenv==1.2.0 --hash=sha256:98835dab727f94a713eacc7234e3db6777a55cafb60f391485011899e5c818df

lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt

@@ -33,3 +33,4 @@ chardet==3.0.4
 nose==1.3.7
 requests==2.18.4
 idna==2.6
+nodeenv==1.2.0

scripts/common_startup.sh

@@ -49,6 +49,18 @@ RMFILES="
     lib/pkg_resources.pyc
 "
 
+# return true if $1 is in $VIRTUAL_ENV else false
+in_venv() {
+    case $1 in
+        $VIRTUAL_ENV*)
+            return 0
+            ;;
+        ''|*)
+            return 1
+            ;;
+    esac
+}
+
 if [ $COPY_SAMPLE_FILES -eq 1 ]; then
 	# Create any missing config/location files
 	for sample in $SAMPLES; do
@@ -65,30 +77,23 @@ for rmfile in $RMFILES; do
     [ -f "$rmfile" ] && rm -f "$rmfile"
 done
 
-# Check client build state.
-if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
-    gitbranch=$(git rev-parse --abbrev-ref HEAD)
-    if [ "$gitbranch" = "dev" ]; then
-        # We're on dev.  This branch (only, currently) doesn't have build
-        # artifacts.  We should probabably swap to a list of releases?
-        # Compare hash.
-        if [ -f static/client_build_hash.txt ]; then
-            githash=$(git rev-parse HEAD)
-            statichash=$(cat static/client_build_hash.txt)
-            if [ "$githash" = "$statichash" ]; then
-                SKIP_CLIENT_BUILD=1
-            fi
-        fi
-    else
-        # Not on dev.  We're not going to bug people about building.
-        SKIP_CLIENT_BUILD=1
-    fi
-    if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
-        echo "The Galaxy client build is out of date.  Please run 'make client' or your choice of client build target (client-*)."
-        echo "If you're sure you'd like to skip this check, you can run galaxy with the --skip-client-build flag, though this is not recommended as the client and server code will potentially be out of sync."
-        echo "See ./client/README.md in the Galaxy repository for more information, including how to get help if you're having trouble."
-        exit 1
-    fi
+# Determine branch (if using git)
+if command -v git >/dev/null && [ -d .git ]; then
+    GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD)
+    case $GIT_BRANCH in
+        release_*|master)
+            # All non-release branches should build the client as necessary
+            SKIP_CLIENT_BUILD=1
+            ;;
+        *)
+            # Ensure nodeenv is installed
+            DEV_WHEELS=1
+            # SKIP_CLIENT_BUILD will default to false, but can be overridden by the command line argument
+            ;;
+    esac
+else
+    GIT_BRANCH=0
+    DEV_WHEELS=1
 fi
 
 : ${GALAXY_CONFIG_FILE:=config/galaxy.yml}
@@ -115,7 +120,7 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
             # Ensure Python is a supported version before creating .venv
             python ./scripts/check_python.py || exit 1
             if command -v virtualenv >/dev/null; then
-                virtualenv -p python2.7 "$GALAXY_VIRTUAL_ENV"
+                virtualenv -p "$(command -v python)" "$GALAXY_VIRTUAL_ENV"
             else
                 vvers=13.1.2
                 vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
@@ -183,3 +188,48 @@ if [ $FETCH_WHEELS -eq 1 ]; then
     GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print('\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE')))")
     [ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}" --extra-index-url "${PYPI_INDEX_URL}"
 fi
+
+# Check client build state.
+if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
+    if [ -f static/client_build_hash.txt ]; then
+        # If git is not used and static/client_build_hash.txt is present, next
+        # client rebuilds must be done manually by the admin
+        if [ "$GIT_BRANCH" = "0" ]; then
+            SKIP_CLIENT_BUILD=1
+        else
+            # Compare hash.
+            githash=$(git rev-parse HEAD)
+            statichash=$(cat static/client_build_hash.txt)
+            if [ "$githash" = "$statichash" ]; then
+                SKIP_CLIENT_BUILD=1
+            else
+                echo "The Galaxy client is out of date and will be built now."
+            fi
+        fi
+    else
+        echo "The Galaxy client has not yet been built and will be built now."
+    fi
+fi
+
+# Build client if necessary.
+if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
+    # Ensure dependencies are installed
+    if [ -n "$VIRTUAL_ENV" ]; then
+        if ! in_venv "$(command -v node)"; then
+            echo "Installing node into $VIRTUAL_ENV with nodeenv."
+            nodeenv -p
+        fi
+        if ! in_venv "$(command -v yarn)"; then
+            echo "Installing yarn into $VIRTUAL_ENV with npm."
+            npm install --global yarn
+        fi
+    else
+        echo "WARNING: Galaxy client build needed but there is no virtualenv enabled. Build may fail."
+    fi
+
+    # Build client
+    if ! make client; then
+        echo "ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help."
+        exit 1
+    fi
+fi