Merge remote-tracking branch 'upstream/dev' into hashtags

.ci/flake8_wrapper_docstrings.sh

@@ -7,7 +7,7 @@ set -e
 # D3XX - Quoting issues.
 # D401 - First line should be in imperative mood 
 # D403 - First word of the first line should be properly capitalized
-args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D401,D403"
+args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
 
 # If the first argument is --include, lint the modules expected to pass. If
 # the first argument is --exclude, lint all modules the full Galaxy linter lints

.ci/jenkins/selenium/run_tests.sh

@@ -97,6 +97,12 @@ done;
 export GALAXY_TEST_SELENIUM_REMOTE=1
 export GALAXY_TEST_SELENIUM_REMOTE_PORT="${SELENIUM_PORT}"
 
+# Retry all failed Selenium tests a second time to deal
+# with transiently failing tests. Failure information for
+# first tests is still populated in database/test_errors
+# and available at the top of the Jenkins test report.
+export GALAXY_TEST_SELENIUM_RETRIES=1
+
 # Access Galaxy on localhost via port $GALAXY_PORT
 export GALAXY_TEST_PORT="${GALAXY_PORT}"
 

CITATION

@@ -16,7 +16,7 @@ following publications:
   a platform for interactive large-scale genome analysis." 
   Genome Research. 2005 Oct; 15(10):1451-5.
 
-See also: http://wiki.galaxyproject.org/CitingGalaxy
+See also: https://galaxyproject.org/citing-galaxy
 
 
 

client/galaxy/scripts/apps/analysis.js

@@ -69,6 +69,18 @@ window.app = function app( options, bootstrapped ){
     Galaxy.currHistoryPanel = historyPanel.historyView;
     Galaxy.currHistoryPanel.listenToGalaxy( Galaxy );
 
+    var routingMessage = Backbone.View.extend({
+        initialize: function(options) {
+            this.message = options.message || "Undefined Message";
+            this.msg_status = options.type || 'info';
+            this.render();
+		},
+        render: function(){
+            this.$el.html(_.escape(this.message)).addClass(this.msg_status + "message");
+        }
+    });
+
+
     // .................................................... routes
     /**  */
     Galaxy.router = new ( Backbone.Router.extend({
@@ -98,7 +110,7 @@ window.app = function app( options, bootstrapped ){
                 if ( this.authenticate( args, name ) ) {
                     callback.apply( this, args );
                 } else {
-                    this.push( Galaxy.root );
+                    this.loginRequired();
                 }
             }
         },
@@ -117,6 +129,10 @@ window.app = function app( options, bootstrapped ){
             'show_user_form'
         ],
 
+        loginRequired: function() {
+            centerPanel.display( new routingMessage({type: 'error', message: "You must be logged in to make this request."}) );
+        },
+
         authenticate: function( args, name ) {
             return ( Galaxy.user && Galaxy.user.id ) || this.require_login.indexOf( name ) == -1;
         },
@@ -209,4 +225,4 @@ window.app = function app( options, bootstrapped ){
             pushState   : true,
         });
     });
-};
+};

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

@@ -151,7 +151,7 @@ var CitationListView = Backbone.View.extend({
                 ' citations explicitly at this time. When writing up your analysis, please manually',
                 ' review your histories and find all references',
                 ' that should be cited in order to completely describe your work. Also, please remember to',
-                ' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',
+                ' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',
                 '</div>',
             ].join('');
         } else {

client/galaxy/scripts/mvc/library/library-folderlist-view.js

@@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({
       '</table>',
       '<div class="empty-folder-message" style="display:none;">',
           'This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up',
-          ' please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
+          ' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
           ' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
       '</div>'
       ].join(''));

client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js

@@ -1151,7 +1151,7 @@ var FolderToolbarView = Backbone.View.extend({
               ' Details',
             '</button>',
             '<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
-              '<a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank">',
+              '<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">',
                 '<button class="primary-button" type="button">',
                   '<span class="fa fa-question-circle"></span>',
                   '&nbsp;Help',

client/galaxy/scripts/mvc/library/library-librarylist-view.js

@@ -232,7 +232,7 @@ var LibraryListView = Backbone.View.extend({
           '<% } else{ %>',
             '<div>',
               'There are no libraries visible to you here. If you expected some to show up please consult the',
-              ' <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
+              ' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
               ' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
             '</div>',
           '<% }%>',

client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js

@@ -192,7 +192,7 @@ var LibraryToolbarView = Backbone.View.extend({
                 '</span>',
               '<% } %>',
               '<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
-                '<a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank">',
+                '<a href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">',
                   '<button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button>',
                 '</a>',
               '</span>',

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -279,7 +279,7 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
                 _.each( options.requirements, function( req, i ) {
                     requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) );
                 });
-                var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://wiki.galaxyproject.org/Tools/Requirements' ).text( 'here' );
+                var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' );
                 return $( '<span/>' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' );
             }
             return 'No requirements found.';

client/galaxy/scripts/mvc/user/user-preferences.js

@@ -153,7 +153,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
             return  '<p class="ui-panel-footer">' +
                         'You are using <strong>' + options.nice_total_disk_usage + '</strong> of disk space in this Galaxy instance. ' +
                         ( Galaxy.config.enable_quotas ? 'Your disk quota is: <strong>' + options.quota + '</strong>. ' : '' ) +
-                        'Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
+                        'Is your usage more than expected? See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
                     '</p>';
         }
     });

client/galaxy/scripts/mvc/workflow/workflow-forms.js

@@ -151,7 +151,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
                     type        : 'text',
                     value       : '',
                     ignore      : '',
-                    help        : 'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
+                    help        : 'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
                 },{
                     action      : 'ChangeDatatypeAction',
                     pja_arg     : 'newtype',

client/galaxy/scripts/viz/phyloviz.js

@@ -741,7 +741,7 @@ var HeaderButtons = Backbone.View.extend({
                 $("#nodeSelectionView").show();
             } },
             { icon_class: 'information', title: 'Phyloviz Help', on_click: function() {
-                window.open('https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree');
+                window.open('https://galaxyproject.org/learn/visualization/phylogenetic-tree/');
                 // https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit
             } }
         ],

config/galaxy.ini.sample

@@ -11,9 +11,10 @@
 # values are set to the default value.  Relative paths are relative to the root
 # Galaxy directory.
 #
-# Examples of many of these options are explained in more detail in the wiki:
+# Examples of many of these options are explained in more detail in the Galaxy
+# Community Hub.
 #
-#   https://wiki.galaxyproject.org/Admin/Config
+#   https://galaxyproject.org/admin/config
 #
 # Config hackers are encouraged to check there before asking for help.
 
@@ -179,7 +180,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # Path to the directory in which tool dependencies are placed.  This is used by
 # the Tool Shed to install dependencies and can also be used by administrators
 # to manually install or link to dependencies.  For details, see:
-#   https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
+#   https://galaxyproject.org/admin/config/tool-dependencies
 # Set the string to None to explicitly disable tool dependency handling.
 # If this option is set to none or an invalid path, installing tools with dependencies
 # from the Tool Shed will fail.
@@ -305,9 +306,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # applied to the ToolDataTableManager at server start up.
 #shed_tool_data_table_config = config/shed_tool_data_table_conf.xml
 
-# Directory where data used by tools is located, see the samples in that
-# directory and the wiki for help:
-#   https://wiki.galaxyproject.org/Admin/DataIntegration
+# Directory where data used by tools is located.  See the samples in that
+# directory and the Galaxy Community Hub for help:
+# https://galaxyproject.org/admin/data-integration
 #tool_data_path = tool-data
 
 # Directory where Tool Data Table related files will be placed
@@ -483,7 +484,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 
 # URL of the support resource for the galaxy instance.  Used in activation
 # emails.
-#instance_resource_url = https://wiki.galaxyproject.org/
+#instance_resource_url = https://galaxyproject.org/
 
 # E-mail domains blacklist is used for filtering out users that are using
 # disposable email address during the registration.  If their address domain
@@ -544,7 +545,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
 # bypass security to display datasets.  Please be aware that there are security
 # implications if this is allowed.  More details (including required changes to
 # the proxy server config) are available in the Apache proxy documentation on
-# the wiki.
+# the Galaxy Community Hub.
 #
 # The list of servers in this sample config are for the UCSC Main, Test and
 # Archaea browsers, but the default if left commented is to not allow any
@@ -615,19 +616,19 @@ nglims_config_file = tool-data/nglims.yaml
 #logo_url = /
 
 # The URL linked by the "Wiki" link in the "Help" menu.
-#wiki_url = https://wiki.galaxyproject.org/
+#wiki_url = https://galaxyproject.org/
 
 # The URL linked by the "Support" link in the "Help" menu.
-#support_url = https://wiki.galaxyproject.org/Support
+#support_url = https://galaxyproject.org/support
 
 # The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
-#citation_url = https://wiki.galaxyproject.org/CitingGalaxy
+#citation_url = https://galaxyproject.org/citing-galaxy
 
 # The URL linked by the "Search" link in the "Help" menu.
-#search_url = http://galaxyproject.org/search/usegalaxy/
+#search_url = https://galaxyproject.org/search/
 
 # The URL linked by the "Mailing Lists" link in the "Help" menu.
-#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists
+#mailing_lists_url = https://galaxyproject.org/mailing-lists
 
 # The URL linked by the "Videos" link in the "Help" menu.
 #screencasts_url = https://vimeo.com/galaxyproject
@@ -892,8 +893,9 @@ use_interactive = True
 
 # -- Data Libraries
 
-# These library upload options are described in much more detail in the wiki:
-#   https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
+# These library upload options are described in much more detail in the Galaxy
+# Community Hub:
+# https://galaxyproject.org/data-libraries/
 
 # Add an option to the library upload form which allows administrators to
 # upload a directory of files.
@@ -979,7 +981,7 @@ use_interactive = True
 # User authentication can be delegated to an upstream proxy server (usually
 # Apache).  The upstream proxy should set a REMOTE_USER header in the request.
 # Enabling remote user disables regular logins.  For more information, see:
-#   https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
+#   https://galaxyproject.org/admin/config/apache-proxy
 #use_remote_user = False
 
 # If use_remote_user is enabled and your external authentication
@@ -1022,7 +1024,7 @@ use_interactive = True
 # users (email addresses).  These users will have access to the Admin section
 # of the server, and will have access to create users, groups, roles,
 # libraries, and more.  For more information, see:
-#   https://wiki.galaxyproject.org/Admin/Interface
+#   https://galaxyproject.org/admin/
 #admin_users = None
 
 # Force everyone to log in (disable anonymous access).
@@ -1213,7 +1215,7 @@ use_interactive = True
 # separate Galaxy into multiple processes.  There are more than one way to do
 # this, and they are explained in detail in the documentation:
 #
-#   https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
+#   https://galaxyproject.org/admin/config/performance/scaling
 
 # By default, Galaxy manages and executes jobs from within a single process and
 # notifies itself of new jobs via in-memory queues.  Jobs are run locally on
@@ -1302,7 +1304,7 @@ use_interactive = True
 # actual user instead of as the user running the Galaxy server process.  For
 # details on these options, see the documentation at:
 #
-# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
+# https://galaxyproject.org/admin/config/performance/cluster
 #
 #drmaa_external_runjob_script = scripts/drmaa_external_runner.py
 #drmaa_external_killjob_script = scripts/drmaa_external_killer.py

config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample

@@ -45,6 +45,10 @@
 # inside your container to which Galaxy should connect the UI.
 #docker_connect_port = None
 
+# Set the following value to false if Docker volumes between Galaxy server and Docker
+# container cannot or should not be used.
+#use_volumes = True
+
 # To run containers in Docker Swarm mode on (an existing swarm), set the
 # following option to True *and*:
 # - set docker_connect_port above. For Jupyter the # port should most likely be

config/plugins/interactive_environments/jupyter/templates/jupyter.mako

@@ -17,19 +17,26 @@ if ie_request.attr.PASSWORD_AUTH:
 else:
     PASSWORD = "none"
 
+additional_ids = trans.request.params.get('additional_dataset_ids', None)
+
 ## Jupyter Notbook Specific
 if hda.datatype.__class__.__name__ == "Ipynb":
     DATASET_HID = hda.hid
 else:
     DATASET_HID = None
+    if not additional_ids:
+        additional_ids = str(trans.security.encode_id( hda.id ) )
+    else:
+        additional_ids += "," + trans.security.encode_id( hda.id )
 
 # Add all environment variables collected from Galaxy's IE infrastructure
 ie_request.launch(
     image=trans.request.params.get('image_tag', None),
-    additional_ids=trans.request.params.get('additional_dataset_ids', None),
+    additional_ids=additional_ids if ie_request.use_volumes else None,
     env_override={
         'notebook_password': PASSWORD,
         'dataset_hid': DATASET_HID,
+        'additional_ids': additional_ids if not ie_request.use_volumes else None,
     }
 )
 

config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample

@@ -47,6 +47,10 @@ password_auth = True
 # inside your container to which Galaxy should connect the UI.
 #docker_connect_port = None
 
+# Set the following value to false if Docker volumes between Galaxy server and Docker
+# container cannot or should not be used.
+#use_volumes = True
+
 # To run containers in Docker Swarm mode on (an existing swarm), set the
 # following option to True *and*:
 # - set docker_connect_port above. For erasche/docker-rstudio-notebook the port

config/plugins/interactive_environments/rstudio/templates/rstudio.mako

@@ -13,16 +13,23 @@ USERNAME = "rstudio"
 # Then override it again
 ie_request.notebook_pw = "rstudio"
 
+additional_ids = trans.request.params.get('additional_dataset_ids', None)
+if not additional_ids:
+    additional_ids = str(trans.security.encode_id( hda.id ) )
+else:
+    additional_ids += "," + trans.security.encode_id( hda.id )
+
 DATASET_HID = hda.hid
 
 # Add all environment variables collected from Galaxy's IE infrastructure
 ie_request.launch(
     image=trans.request.params.get('image_tag', None),
-    additional_ids=trans.request.params.get('additional_dataset_ids', None),
+    additional_ids=additional_ids if ie_request.use_volumes else None,
     env_override={
         'notebook_username': USERNAME,
         'notebook_password': PASSWORD,
         'dataset_hid': DATASET_HID,
+        'additional_ids': additional_ids if not ie_request.use_volumes else None,
     }
 )
 

lib/galaxy/config.py

@@ -369,8 +369,9 @@ def __init__( self, **kwargs ):
         self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
         self.message_box_content = kwargs.get( 'message_box_content', None )
         self.message_box_class = kwargs.get( 'message_box_class', 'info' )
-        self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
-        self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
+        self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' )
+        self.citation_url = kwargs.get( 'citation_url', 'https://galaxyproject.org/citing-galaxy' )
+        self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
         self.blog_url = kwargs.get( 'blog_url', None )
         self.screencasts_url = kwargs.get( 'screencasts_url', None )
         self.library_import_dir = kwargs.get( 'library_import_dir', None )