Merge pull request #3641 from nsoranzo/merge_17.01

Merge 17.01 into dev

client/galaxy/scripts/mvc/history/history-model.js

@@ -177,7 +177,7 @@ var History = Backbone.Model
         // if we don't flip this, then a fully-fetched list will not be re-checked via fetch
         this.contents.allFetched = false;
         var fetchFn = self.contents.currentPage !== 0
-            ? function(){ return self.contents.fetchPage( 0 ); }
+            ? function(){ return self.contents.fetchPage( self.contents.currentPage ); }
             : function(){ return self.contents.fetchUpdated( lastUpdateTime ); };
         // note: if there was no previous update time, all summary contents will be fetched
         return fetchFn()

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

@@ -369,14 +369,17 @@ var HistoryView = _super.extend(
     }),
 
     _clickPrevPage : function( ev ){
+        this.model.clearUpdateTimeout();
         this.model.contents.fetchPrevPage();
     },
 
     _clickNextPage : function( ev ){
+        this.model.clearUpdateTimeout();
         this.model.contents.fetchNextPage();
     },
 
     _changePageSelect : function( ev ){
+        this.model.clearUpdateTimeout();
         var page = $( ev.currentTarget ).val();
         this.model.contents.fetchPage( page );
     },

client/galaxy/scripts/mvc/history/options-menu.js

@@ -110,36 +110,23 @@ var menu = [
         html    : _l( 'Unhide Hidden Datasets' ),
         anon    : true,
         func    : function() {
+            // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really unhide all hidden datasets?' ) ) ){
-                var filtered = Galaxy.currHistoryPanel.model.contents.hidden();
-                //TODO: batch
-                filtered.ajaxQueue( Backbone.Model.prototype.save, { visible : true })
-                    .done( function(){
-                        Galaxy.currHistoryPanel.renderItems();
-                    })
-                    .fail( function(){
-                        alert( 'There was an error unhiding the datasets' );
-                        console.error( arguments );
-                    });
+                $.post(Galaxy.root + "history/adjust_hidden",
+                       { 'user_action' : 'unhide' },
+                       function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
             }
         },
     },
     {
         html    : _l( 'Delete Hidden Datasets' ),
         anon    : true,
         func    : function() {
+            // TODO: Deprecate this functionality and replace with group dataset selector and action combination
             if( Galaxy && Galaxy.currHistoryPanel && confirm( _l( 'Really delete all hidden datasets?' ) ) ){
-                var filtered = Galaxy.currHistoryPanel.model.contents.hidden();
-                //TODO: batch
-                // both delete *and* unhide them
-                filtered.ajaxQueue( Backbone.Model.prototype.save, { deleted : true, visible: true })
-                    .done( function(){
-                        Galaxy.currHistoryPanel.renderItems();
-                    })
-                    .fail( function(){
-                        alert( 'There was an error deleting the datasets' );
-                        console.error( arguments );
-                    });
+                $.post(Galaxy.root + "history/adjust_hidden",
+                       { 'user_action' : 'delete' },
+                       function(){Galaxy.currHistoryPanel.loadCurrentHistory();});
             }
         },
     },

lib/galaxy/jobs/command_factory.py

@@ -29,7 +29,7 @@
      -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
-GALAXY_PYTHON=`which python`
+GALAXY_PYTHON=`command -v python`
 """
 
 

lib/galaxy/tools/deps/conda_util.py

@@ -82,6 +82,41 @@ def __init__(self, conda_prefix=None, conda_exec=None,
             ensure_channels = None
         self.ensure_channels = ensure_channels
         self.ensured_channels = False
+        self._conda_version = None
+        self._miniconda_version = None
+
+    @property
+    def conda_version(self):
+        if self._conda_version is None:
+            self._guess_conda_version()
+        return self._conda_version
+
+    def _guess_conda_version(self):
+        conda_meta_path = self._conda_meta_path
+        # Perhaps we should call "conda info --json" and parse it but for now we are going
+        # to assume the default.
+        conda_version = LooseVersion(CONDA_VERSION)
+        miniconda_version = "3"
+
+        if os.path.exists(conda_meta_path):
+            for package in os.listdir(conda_meta_path):
+                package_parts = package.split("-")
+                if len(package_parts) < 3:
+                    continue
+                package = '-'.join(package_parts[:-2])
+                version = package_parts[-2]
+                # build = package_parts[-1]
+                if package == "conda":
+                    conda_version = LooseVersion(version)
+                if package == "python" and version.startswith("2"):
+                    miniconda_version = "2"
+
+        self._conda_version = conda_version
+        self._miniconda_version = miniconda_version
+
+    @property
+    def _conda_meta_path(self):
+        return os.path.join(self.conda_prefix, "conda-meta")
 
     def ensure_channels_configured(self):
         if not self.ensured_channels:
@@ -495,7 +530,16 @@ def build_isolated_environment(
                 export_path
             )
             export_paths.append(export_path)
-        create_args = ["--unknown", "--offline"]
+        create_args = ["--unknown"]
+        # Works in 3.19, 4.0 - 4.2 - not in 4.3.
+        # Adjust fix if they fix Conda - xref
+        # - https://github.com/galaxyproject/galaxy/issues/3635
+        # - https://github.com/conda/conda/issues/2035
+        offline_works = conda_context.conda_version < LooseVersion("4.3")
+        if offline_works:
+            create_args.extend(["--offline"])
+        else:
+            create_args.extend(["--use-index-cache"])
         if path is None:
             create_args.extend(["--name", tempdir_name])
         else:

lib/galaxy/web/framework/middleware/remoteuser.py

@@ -147,6 +147,7 @@ def __call__( self, environ, start_response ):
                     """
                     return self.error( start_response, title, message )
             user_accessible_paths = (
+                '/users',
                 '/user/api_keys',
                 '/user/edit_username',
                 '/user/dbkeys',

lib/galaxy/webapps/galaxy/buildapp.py

@@ -78,6 +78,11 @@ def paste_app_factory( global_conf, **kwargs ):
     # Force /history to go to view of current
     webapp.add_route( '/history', controller='history', action='view' )
     webapp.add_route( '/history/view/{id}', controller='history', action='view' )
+    # THIS IS A TEMPORARY ROUTE FOR THE 17.01 RELEASE
+    # This route supports the previous hide/delete-all-hidden functionality in a history.
+    # It will be removed after 17.01.
+    webapp.add_route( '/history/adjust_hidden', controller='history', action='adjust_hidden')
+
     # Force /activate to go to the controller
     webapp.add_route( '/activate', controller='user', action='activate' )
     webapp.add_route( '/login', controller='root', action='login' )

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

@@ -826,6 +826,20 @@ def share( self, trans, id=None, email="", **kwd ):
                                     email=email,
                                     send_to_err=send_to_err )
 
+    @web.expose
+    def adjust_hidden( self, trans, id=None, **kwd ):
+        """ THIS METHOD IS A TEMPORARY ADDITION. It'll allow us to fix the
+        regression in history-wide actions, and will be removed in the first
+        release after 17.01 """
+        action = kwd.get('user_action', None)
+        if action == 'delete':
+            for hda in trans.history.datasets:
+                if not hda.visible:
+                    hda.mark_deleted()
+        elif action == 'unhide':
+            trans.history.unhide_datasets()
+        trans.sa_session.flush()
+
     @web.expose
     @web.require_login( "share restricted histories with other users" )
     def share_restricted( self, trans, id=None, email="", **kwd ):