Merge branch 'release_18.05' into dev

scripts/common_startup.sh

@@ -246,4 +246,7 @@ if [ $SKIP_CLIENT_BUILD -eq 0 ]; then
         echo "ERROR: Galaxy client build failed. See ./client/README.md for more information, including how to get help."
         exit 1
     fi
+else
+    echo "Regenerating static plugin directories."
+    python ./scripts/plugin_staging.py
 fi

scripts/get_uwsgi_args.py

@@ -23,7 +23,7 @@ ALIASES = {
     'module': ('mount',),   # mount is not actually an alias for module, but we don't want to set module if mount is set
 }
 DEFAULT_ARGS = {
-    '_all_': ('pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'die-on-term', 'hook-master-start', 'enable-threads'),
+    '_all_': ('pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'static-safe', 'die-on-term', 'hook-master-start', 'enable-threads'),
     'galaxy': ('py-call-osafterfork',),
     'reports': (),
     'tool_shed': (),
@@ -92,6 +92,8 @@ def _get_uwsgi_args(cliargs, kwargs):
         'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]),
         'static-map': ('/static/style={here}/static/style/blue'.format(here=os.getcwd()),
                        '/static={here}/static'.format(here=os.getcwd())),
+        'static-safe': ('{here}/config/plugins/visualizations'.format(here=os.getcwd()),
+                        '{here}/config/plugins/interactive_environments'.format(here=os.getcwd())),
         'die-on-term': True,
         'enable-threads': True,
         'hook-master-start': ('unix_signal:2 gracefully_kill_them_all',

scripts/plugin_staging.py

@@ -0,0 +1,28 @@
+import glob
+import os
+import shutil
+
+GXY_ROOT = os.path.abspath(os.path.join(os.path.dirname(os.path.realpath(__file__)), os.pardir))
+
+
+def link_up_static(f):
+    src = os.path.join(GXY_ROOT, 'config/plugins', f)
+    dest = os.path.join(GXY_ROOT, 'static/plugins', f)
+    dest_parent = os.path.abspath(os.path.join(dest, os.pardir))
+    if os.path.exists(dest):
+        # We have to clear out the old staged or linked static to relink.
+        if os.path.islink(dest):
+            os.unlink(dest)
+        else:
+            shutil.rmtree(dest)
+    elif not os.path.exists(dest_parent):
+        # Create parent dir structure to symlink directly to static.
+        os.makedirs(dest_parent)
+    os.symlink(src, dest)
+
+
+if __name__ == "__main__":
+    # This is not awesome, but it's temporary, and it supports two-tier plugin static.
+    for f in glob.glob(os.path.join(GXY_ROOT, 'config/plugins/*/*/static')) + glob.glob(os.path.join(GXY_ROOT, 'config/plugins/*/*/*/static')):
+        f = os.path.relpath(f, os.path.join(GXY_ROOT, 'config/plugins'))
+        link_up_static(f)