Merge branch 'release_17.01' into dev

Conflicts:
	static/maps/mvc/ui/ui-select-content.js.map
	static/scripts/bundled/analysis.bundled.js
	static/scripts/bundled/analysis.bundled.js.map
	static/scripts/bundled/libs.bundled.js.map
	static/scripts/mvc/ui/ui-select-content.js

client/galaxy/scripts/mvc/ui/ui-select-content.js

@@ -11,7 +11,7 @@ var Configurations = {
         { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   multiple: false,   batch: Batch.LINKED     } ],
     data_multiple: [
         { src: 'hda',  icon: 'fa-files-o',  tooltip: 'Multiple datasets',    multiple: true,    batch: Batch.DISABLED   },
-        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   multiple: false,   batch: Batch.DISABLED   } ],
+        { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collections',  multiple: true,    batch: Batch.DISABLED   } ],
     data_collection: [
         { src: 'hdca', icon: 'fa-folder-o', tooltip: 'Dataset collection',   multiple: false,   batch: Batch.DISABLED   } ],
     workflow_data: [

lib/galaxy/model/__init__.py

@@ -3512,6 +3512,14 @@ class DatasetCollectionElement( object, Dictifiable ):
         else:
             return element_object
 
+    @property
+    def dataset_instances( self ):
+        element_object = self.element_object
+        if isinstance( element_object, DatasetCollection ):
+            return element_object.dataset_instances
+        else:
+            return [element_object]
+
     def copy_to_collection( self, collection, destination=None, element_destination=None ):
         element_object = self.element_object
         if element_destination:

lib/galaxy/tools/__init__.py

@@ -153,6 +153,8 @@ GALAXY_LIB_TOOLS_UNVERSIONED = [
 # with the version at which they were fixed.
 GALAXY_LIB_TOOLS_VERSIONED = {
     "sam_to_bam": LooseVersion("1.1.3"),
+    "PEsortedSAM2readprofile": LooseVersion("1.1.1"),
+    "fetchflank": LooseVersion("1.0.1"),
 }
 
 
@@ -2310,9 +2312,10 @@ class DatabaseOperationTool( Tool ):
         for input_dataset in input_datasets.values():
             check_dataset_instance( input_dataset )
 
-        for input_dataset_collection in input_dataset_collections.values():
-            if not input_dataset_collection.collection.populated:
-                raise ToolInputsNotReadyException()
+        for input_dataset_collection_pairs in input_dataset_collections.values():
+            for input_dataset_collection, is_mapped in input_dataset_collection_pairs:
+                if not input_dataset_collection.collection.populated:
+                    raise ToolInputsNotReadyException()
 
             map( check_dataset_instance, input_dataset_collection.dataset_instances )
 

lib/galaxy/tools/actions/model_operations.py

@@ -12,8 +12,12 @@ log = logging.getLogger( __name__ )
 
 class ModelOperationToolAction( DefaultToolAction ):
 
-    def check_inputs_ready( self, tool, trans, incoming, history ):
-        history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history)
+    def check_inputs_ready( self, tool, trans, incoming, history, execution_cache=None ):
+        if execution_cache is None:
+            execution_cache = ToolExecutionCache(trans)
+
+        current_user_roles = execution_cache.current_user_roles
+        history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history, current_user_roles)
 
         tool.check_inputs_ready( inp_data, inp_dataset_collections )
 

lib/galaxy/tools/execute.py

@@ -48,7 +48,7 @@ def execute( trans, tool, param_combinations, history, rerun_remap_job_id=None,
     burst_at = getattr( config, 'tool_submission_burst_at', 10 )
     burst_threads = getattr( config, 'tool_submission_burst_threads', 1 )
 
-    tool_action = tool.action
+    tool_action = tool.tool_action
     if hasattr( tool_action, "check_inputs_ready" ):
         for params in execution_tracker.param_combinations:
             # This will throw an exception if the tool is not ready.

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

@@ -69,9 +69,13 @@ class RemoteUser( object ):
             assert self.remote_user_header not in environ
             environ[ self.remote_user_header ] = self.single_user
 
-        # Apache sets REMOTE_USER to the string '(null)' when using the
-        # Rewrite* method for passing REMOTE_USER and a user is
-        # un-authenticated.  Any other possible values need to go here as well.
+        if environ.get(self.remote_user_header, '').startswith('(null)'):
+            # Throw away garbage headers.
+            # Apache sets REMOTE_USER to the string '(null)' when using the
+            # Rewrite* method for passing REMOTE_USER and a user is not authenticated.
+            # Any other possible values need to go here as well.
+            log.debug("Discarding invalid remote user header %s:%s.", self.remote_user_header, environ.get(self.remote_user_header, None))
+            environ.pop(self.remote_user_header)
         if self.remote_user_header in environ:
             # process remote user with configuration options.
             if self.normalize_remote_user_email:
@@ -126,10 +130,7 @@ class RemoteUser( object ):
                 """
                 return self.error( start_response, title, message )
 
-        # Apache sets REMOTE_USER to the string '(null)' when using the
-        # Rewrite* method for passing REMOTE_USER and a user is
-        # un-authenticated.  Any other possible values need to go here as well.
-        if not environ.get(self.remote_user_header, '(null)').startswith('(null)'):
+        if environ.get(self.remote_user_header, None):
             if not environ[ self.remote_user_header ].count( '@' ):
                 if self.maildomain is not None:
                     environ[ self.remote_user_header ] += '@' + self.maildomain

lib/galaxy/web/framework/webapp.py

@@ -385,7 +385,13 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         elif secure_id:
             # API authentication via active session
             # Associate user using existing session
-            self._ensure_valid_session( session_cookie )
+            # This will throw an exception under remote auth with anon users.
+            try:
+                self._ensure_valid_session( session_cookie )
+            except Exception:
+                log.exception("Exception during Session-based API authentication, this was most likely an attempt to use an anonymous cookie under remote authentication (so, no user), which we don't support.")
+                self.user = None
+                self.galaxy_session = None
         else:
             # Anonymous API interaction -- anything but @expose_api_anonymous will fail past here.
             self.user = None
@@ -435,17 +441,13 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
         # cases won't have a cookie set above, so we need to to check some
         # things now.
         if self.app.config.use_remote_user:
-            # If this is an api request, and they've passed a key, we let this go.
-            assert self.app.config.remote_user_header in self.environ, \
-                "use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header
-            remote_user_email = self.environ[ self.app.config.remote_user_header ]
+            remote_user_email = self.environ.get( self.app.config.remote_user_header, None)
             if galaxy_session:
-                # An existing session, make sure correct association exists
-                if galaxy_session.user is None:
+                if remote_user_email and galaxy_session.user is None:
                     # No user, associate
                     galaxy_session.user = self.get_or_create_remote_user( remote_user_email )
                     galaxy_session_requires_flush = True
-                elif (not remote_user_email.startswith('(null)') and  # Apache does this, see remoteuser.py
+                elif (remote_user_email and
                       (galaxy_session.user.email != remote_user_email) and
                       ((not self.app.config.allow_user_impersonation) or
                        (remote_user_email not in self.app.config.admin_users_list))):
@@ -456,9 +458,11 @@ class GalaxyWebTransaction( base.DefaultWebTransaction,
                     user_for_new_session = self.get_or_create_remote_user( remote_user_email )
                     log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session",
                                  remote_user_email, galaxy_session.user.email )
-            else:
+            elif remote_user_email:
                 # No session exists, get/create user for new session
                 user_for_new_session = self.get_or_create_remote_user( remote_user_email )
+            if ((galaxy_session and galaxy_session.user is None) and user_for_new_session is None):
+                raise Exception("Remote Authentication Failure - user is unknown and/or not supplied.")
         else:
             if galaxy_session is not None and galaxy_session.user and galaxy_session.user.external:
                 # Remote user support is not enabled, but there is an existing

static/scripts/bundled/libs.bundled.js

@@ -1,4 +1,4 @@
-!function(t){function e(i){if(n[i])return n[i].exports;var s=n[i]={exports:{},id:i,loaded:!1};return t[i].call(s.exports,s,s.exports,e),s.loaded=!0,s.exports}var i=window.webpackJsonp;window.webpackJsonp=function(o,r){for(var a,l,u=0,c=[];u<o.length;u++)l=o[u],s[l]&&c.push.apply(c,s[l]),s[l]=0;for(a in r)t[a]=r[a];for(i&&i(o,r);c.length;)c.shift().call(null,e);if(r[0])return n[0]=0,e(0)};var n={},s={2:0};return e.e=function(t,i){if(0===s[t])return i.call(null,e);if(void 0!==s[t])s[t].push(i);else{s[t]=[i];var n=document.getElementsByTagName("head")[0],o=document.createElement("script");o.type="text/javascript",o.charset="utf-8",o.async=!0,o.src=e.p+""+t+"."+({3:"analysis",4:"login"}[t]||t)+".bundled.js",n.appendChild(o)}},e.m=t,e.c=n,e.p="",e(0)}([function(t,e,i){i(133),i(1),i(107),i(69),i(66),i(67),i(68),i(105),i(65),i(102),i(64),i(104),i(2),i(3),i(86),i(62),i(10),t.exports=i(132)},function(t,e,i){var n,s;/*!
+!function(t){function e(i){if(n[i])return n[i].exports;var s=n[i]={exports:{},id:i,loaded:!1};return t[i].call(s.exports,s,s.exports,e),s.loaded=!0,s.exports}var i=window.webpackJsonp;window.webpackJsonp=function(o,r){for(var a,l,u=0,c=[];u<o.length;u++)l=o[u],s[l]&&c.push.apply(c,s[l]),s[l]=0;for(a in r)Object.prototype.hasOwnProperty.call(r,a)&&(t[a]=r[a]);for(i&&i(o,r);c.length;)c.shift().call(null,e);if(r[0])return n[0]=0,e(0)};var n={},s={2:0};return e.e=function(t,i){if(0===s[t])return i.call(null,e);if(void 0!==s[t])s[t].push(i);else{s[t]=[i];var n=document.getElementsByTagName("head")[0],o=document.createElement("script");o.type="text/javascript",o.charset="utf-8",o.async=!0,o.src=e.p+""+t+"."+({3:"analysis",4:"login"}[t]||t)+".bundled.js",n.appendChild(o)}},e.m=t,e.c=n,e.p="",e(0)}([function(t,e,i){i(133),i(1),i(107),i(69),i(66),i(67),i(68),i(105),i(65),i(102),i(64),i(104),i(2),i(3),i(86),i(62),i(10),t.exports=i(132)},function(t,e,i){var n,s;/*!
 	 * jQuery JavaScript Library v1.12.4
 	 * http://jquery.com/
 	 *

test/api/test_workflows.py

@@ -895,6 +895,50 @@ steps:
         content = self.dataset_populator.get_history_dataset_content( history_id )
         self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0")
 
+    def test_filter_failed_mapping( self ):
+        history_id = self.dataset_populator.new_history()
+        summary = self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - type: collection
+    label: input_c
+steps:
+  - label: mixed_collection
+    tool_id: exit_code_from_file
+    state:
+       input:
+         $link: input_c
+
+  - label: filtered_collection
+    tool_id: "__FILTER_FAILED_DATASETS__"
+    state:
+      input:
+        $link: mixed_collection#out_file1
+
+  - tool_id: cat1
+    state:
+      input1:
+        $link: filtered_collection
+test_data:
+  input_c:
+    type: list
+    elements:
+      - identifier: i1
+        content: "0"
+      - identifier: i2
+        content: "1"
+""", history_id=history_id, wait=True, assert_ok=False)
+        jobs = summary.jobs
+
+        def filter_jobs_by_tool(tool_id):
+            return [j for j in summary.jobs if j["tool_id"] == tool_id]
+
+        assert len(filter_jobs_by_tool("upload1")) == 2, jobs
+        assert len(filter_jobs_by_tool("exit_code_from_file")) == 2, jobs
+        assert len(filter_jobs_by_tool("__FILTER_FAILED_DATASETS__")) == 1, jobs
+        # Follow proves one job was filtered out of the result of cat1
+        assert len(filter_jobs_by_tool("cat1")) == 1, jobs
+
     def test_workflow_request( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_queue" )
         workflow_request, history_id = self._setup_workflow_run( workflow )

test/qunit/tests/ui_tests.js

@@ -698,11 +698,11 @@ define([ 'test-app', 'mvc/ui/ui-misc', 'mvc/ui/ui-select-content', 'mvc/ui/ui-dr
                 firstvalue      : 'id0',
                 firstlabel      : 'hid0: name0',
                 firstmultiple   : true,
-                totalmultiple   : 1,
+                totalmultiple   : 2,
                 lastvalue       : 'id2',
                 lastlabel       : 'hid2: name2',
                 lastlength      : 3,
-                lastmultiple    : false });
+                lastmultiple    : true });
 
         select.model.set( 'multiple', false );
         select.model.set( 'type', 'data_collection' );