Merge branch 'dev' into unify_label_name_000

.ci/flake8_blacklist.txt

@@ -5,3 +5,4 @@ database/
 doc/source/conf.py
 eggs/
 lib/galaxy/util/jstree.py
+lib/galaxy/web/proxy/js/node_modules/

client/galaxy/scripts/mvc/grid/grid-view.js

@@ -155,18 +155,6 @@ return Backbone.View.extend({
             });
         });
 
-        // Initialize autocomplete for text inputs in search UI.
-        var t1 = this.$el.find('#input-tags-filter');
-        if (t1.length) {
-            t1.autocomplete(this.grid.history_tag_autocomplete_url,
-                { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
-        }
-        var t2 = this.$el.find('#input-name-filter');
-        if (t2.length) {
-            t2.autocomplete(this.grid.history_name_autocomplete_url,
-                { selectFirst: false, autoFill: false, highlight: false, mustMatch: false });
-        }
-
         // Initialize standard, advanced search toggles.
         this.$el.find('.advanced-search-toggle').each( function() {
             $(this).off();

config/plugins/interactive_environments/jupyter/config/allowed_images.yml.sample

@@ -6,7 +6,7 @@
 # appropriate `apt-get/pip install` statements.
 ---
 -
-    image: bgruening/docker-jupyter-notebook:16.01
+    image: bgruening/docker-jupyter-notebook:16.01.1
     description: |
         The Jupyter notebook is the next iteration of IPython, allowing
         analysis in many different languages. This image features the Python,

lib/galaxy/auth/providers/ldap_ad.py

@@ -15,7 +15,7 @@
 
 
 def _get_subs(d, k, params):
-    if k not in d:
+    if k not in d or not d[k]:
         raise ConfigurationError("Missing '%s' parameter in LDAP options" % k)
     return str(d[k]).format(**params)
 
@@ -25,17 +25,17 @@ def _parse_ldap_options(ldap, options_unparsed):
     if not options_unparsed:
         return []
 
-    if "=" not in options_unparsed:
-        log.error("LDAP authenticate: Invalid syntax in <ldap-options>. Syntax should be option1=value1,option2=value2")
-        return []
-
     ldap_options = []
 
     # Valid options must start with this prefix. See help(ldap)
     prefix = "OPT_"
 
     for opt in options_unparsed.split(","):
-        key, value = opt.split("=")
+        try:
+            key, value = opt.split("=")
+        except ValueError:
+            log.warning("LDAP authenticate: Invalid syntax '%s' inside <ldap-options> element. Syntax should be option1=value1,option2=value2" % opt)
+            continue
 
         try:
             pair = []
@@ -109,14 +109,18 @@ def authenticate(self, email, username, password, options):
         else:
             ldap_options = _parse_ldap_options(ldap, ldap_options_raw)
 
-        if 'search-fields' in options:
-            try:
-                # setup connection
-                ldap.set_option(ldap.OPT_REFERRALS, 0)
+        try:
+            # setup connection
+            ldap.set_option(ldap.OPT_REFERRALS, 0)
 
-                for opt in ldap_options:
-                    ldap.set_option(*opt)
+            for opt in ldap_options:
+                ldap.set_option(*opt)
+        except Exception:
+            log.exception('LDAP authenticate: set_option exception')
+            return (failure_mode, '', '')
 
+        if 'search-fields' in options:
+            try:
                 l = ldap.initialize(_get_subs(options, 'server', params))
                 l.protocol_version = 3
 
@@ -155,17 +159,9 @@ def authenticate(self, email, username, password, options):
 
         # bind as user to check their credentials
         try:
-            # setup connection
-            ldap.set_option(ldap.OPT_REFERRALS, 0)
-
-            for opt in ldap_options:
-                ldap.set_option(*opt)
-
             l = ldap.initialize(_get_subs(options, 'server', params))
             l.protocol_version = 3
             bind_password = _get_subs(options, 'bind-password', params)
-            if not bind_password:
-                raise RuntimeError('LDAP authenticate: empty password')
             l.simple_bind_s(_get_subs(
                 options, 'bind-user', params), bind_password)
             try:

lib/galaxy/visualization/plugins/plugin.py

@@ -274,7 +274,16 @@ def get_api_key():
             render_vars[ 'plugin_path' ] = os.path.abspath( self.path )
 
         if self.config.get( 'plugin_type', 'visualization' ) == "interactive_environment":
-            request = self.INTENV_REQUEST_FACTORY( trans, self )
+            try:
+                request = self.INTENV_REQUEST_FACTORY( trans, self )
+            except:
+                log.exception("IE plugin request handling failed")
+                return trans.fill_template( 'message.mako',
+                    message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format(
+                        admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format(
+                            admin_mail=trans.app.config.error_email_to)
+                        if trans.app.config.error_email_to else 'Galaxy administrator'),
+                    status='error')
             render_vars[ "ie_request" ] = request
 
         template_filename = self.config[ 'entry_point' ][ 'file' ]

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -1261,21 +1261,6 @@ def set_accessible_async( self, trans, id=None, accessible=False ):
         return
         # TODO: used in page/editor.mako
 
-    @web.expose
-    def name_autocomplete_data( self, trans, q=None, limit=None, timestamp=None ):
-        """Return autocomplete data for history names"""
-        user = trans.get_user()
-        if not user:
-            return
-
-        ac_data = ""
-        for history in ( trans.sa_session.query( model.History )
-                         .filter_by( user=user )
-                         .filter( func.lower( model.History.name ).like(q.lower() + "%") ) ):
-            ac_data = ac_data + history.name + "\n"
-        return ac_data
-        # TODO: used in grid_base.mako
-
     @web.expose
     @web.require_login( "rename histories" )
     def rename( self, trans, id=None, name=None, **kwd ):

scripts/bootstrap_history.py

@@ -100,15 +100,17 @@
 **Feature3**
   Feature description.
 
-`Github <https://github.com/galaxyproject/galaxy>`__
-===========================================================
+Get Galaxy
+==========
+
+The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
 
-New Galaxy repository
+To get a new Galaxy repository run:
   .. code-block:: shell
 
       $$ git clone -b release_${release} https://github.com/galaxyproject/galaxy.git
 
-Update of existing Galaxy repository
+To update an existing Galaxy repository run:
   .. code-block:: shell
 
       $$ git checkout release_${release} && git pull --ff-only origin release_${release}

templates/grid_base.mako

@@ -101,8 +101,6 @@
         'cur_page_num'                  : cur_page_num,
         'num_pages'                     : num_pages,
         'num_page_links'                : num_page_links,
-        'history_tag_autocomplete_url'  : url( controller='tag', action='tag_autocomplete_data', item_class=item_class ),
-        ## 'history_name_autocomplete_url' : url( controller='history', action='name_autocomplete_data' ),
         'status'                        : status,
         'message'                       : util.restore_text(message),
         'global_actions'                : [],

tools/data_source/upload.py

@@ -95,6 +95,7 @@ def add_file( dataset, registry, json_file, output_path ):
             file_err( 'Unable to fetch %s\n%s' % ( dataset.path, str( e ) ), dataset, json_file )
             return
         dataset.path = temp_name
+        dataset.name = os.path.basename( dataset.name )
     # See if we have an empty file
     if not os.path.exists( dataset.path ):
         file_err( 'Uploaded temporary file (%s) does not exist.' % dataset.path, dataset, json_file )