Merge release_15.07 into dev

client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js

@@ -568,7 +568,8 @@ var PairedCollectionCreator = Backbone.View.extend( baseMVC.LoggableMixin ).exte
      */
     createList : function( name ){
         var creator = this,
-            url = '/api/histories/' + this.historyId + '/contents/dataset_collections';
+            root = ( window.Galaxy && Galaxy.options.root )? Galaxy.options.root : '/',
+            url = root + 'api/histories/' + this.historyId + '/contents/dataset_collections';
 
         //TODO: use ListPairedCollection.create()
         var ajaxData = {

config/datatypes_conf.xml.sample

@@ -106,7 +106,7 @@
         <display file="igb/gtf.xml" />
     </datatype>
     <datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" />
-    <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />
+    <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" display_in_upload="True"/>
     <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/>
     <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true" description="File must start with definition line in the following format (columns may be in any order)." >
       <converter file="interval_to_bed_converter.xml" target_datatype="bed"/>

config/galaxy.ini.sample

@@ -973,9 +973,10 @@ use_interactive = True
 
 # Very large metadata values can cause Galaxy crashes.  This will allow
 # limiting the maximum metadata key size (in bytes used in memory, not the end
-# result database value size) Galaxy will attempt to save with a dataset.  0 to
-# disable this feature.  5000000 seems to be a reasonable size.
-#max_metadata_value_size = 0
+# result database value size) Galaxy will attempt to save with a dataset.  Use
+# 0 to disable this feature.  The default is 5MB, but as low as 1MB seems to be
+# a reasonable size.
+#max_metadata_value_size = 5242880
 
 # If (for example) you run on a cluster and your datasets (by default,
 # database/files/) are mounted read-only, this option will override tool output

lib/galaxy/config.py

@@ -146,7 +146,7 @@ def __init__( self, **kwargs ):
         self.tool_secret = kwargs.get( "tool_secret", "" )
         self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
         self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) )
-        self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 0 ) )
+        self.max_metadata_value_size = int( kwargs.get( "max_metadata_value_size", 5242880 ) )
         self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
         self.normalize_remote_user_email = string_as_bool( kwargs.get( "normalize_remote_user_email", "False" ) )
         self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )

lib/galaxy/datatypes/metadata.py

@@ -754,7 +754,7 @@ def __get_filename_override():
                         if dataset_path.real_path == metadata_files.dataset.file_name:
                             return dataset_path.false_path or dataset_path.real_path
                 return ""
-            line = "%s,%s,%s,%s,%s,%s" % (
+            line = '"%s,%s,%s,%s,%s,%s"' % (
                 metadata_path_on_compute(metadata_files.filename_in),
                 metadata_path_on_compute(metadata_files.filename_kwds),
                 metadata_path_on_compute(metadata_files.filename_out),
@@ -826,16 +826,16 @@ def __get_filename_override():
                 sa_session.add( metadata_files )
                 sa_session.flush()
             metadata_files_list.append( metadata_files )
-        args = "%s %s %s %s" % ( datatypes_config,
-                                 job_metadata,
-                                 " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ),
-                                 max_metadata_value_size)
+        args = '"%s" "%s" %s %s' % ( datatypes_config,
+                                     job_metadata,
+                                     " ".join( map( __metadata_files_list_to_cmd_line, metadata_files_list ) ),
+                                     max_metadata_value_size)
         if include_command:
             # return command required to build
             fd, fp = tempfile.mkstemp( suffix='.py', dir=tmp_dir, prefix="set_metadata_" )
             metadata_script_file = abspath( fp )
             os.fdopen( fd, 'w' ).write( 'from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()' )
-            return "python %s %s" % ( metadata_path_on_compute(metadata_script_file), args )
+            return 'python "%s" %s' % ( metadata_path_on_compute(metadata_script_file), args )
         else:
             # return args to galaxy_ext.metadata.set_metadata required to build
             return args

lib/galaxy/datatypes/registry.py

@@ -641,11 +641,13 @@ def load_external_metadata_tool( self, toolbox ):
                   <requirement type="package">samtools</requirement>
               </requirements>
               <action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/>
-              <command>python $set_metadata $__SET_EXTERNAL_METADATA_COMMAND_LINE__</command>
+              <command>python "${set_metadata}" ${__SET_EXTERNAL_METADATA_COMMAND_LINE__}</command>
               <inputs>
                 <param format="data" name="input1" type="data" label="File to set metadata on."/>
                 <param name="__ORIGINAL_DATASET_STATE__" type="hidden" value=""/>
-                <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value=""/>
+                <param name="__SET_EXTERNAL_METADATA_COMMAND_LINE__" type="hidden" value="">
+                  <sanitizer sanitize="False"/>
+                </param>
               </inputs>
               <configfiles>
                 <configfile name="set_metadata">from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()</configfile>

lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py

@@ -60,13 +60,17 @@ def get_account_info(self, trans, key_id, secret):
         """
         Get EC2 Account Info
         """
-        account_info = {}
-        cml = cloudman.launch.CloudManLauncher(key_id, secret)
-        ec2_conn = cml.connect_ec2(key_id, secret)
-        kps = ec2_conn.get_all_key_pairs()
-        account_info['clusters'] = cml.get_clusters_pd()
-        account_info['keypairs'] = [akp.name for akp in kps]
-        return dumps(account_info)
+        try:
+            account_info = {}
+            cml = cloudman.launch.CloudManLauncher(key_id, secret)
+            ec2_conn = cml.connect_ec2(key_id, secret)
+            kps = ec2_conn.get_all_key_pairs()
+            account_info['clusters'] = cml.get_clusters_pd()
+            account_info['keypairs'] = [akp.name for akp in kps]
+            return dumps(account_info)
+        except EC2ResponseError as e:
+            trans.response.status = 400
+            return e.message
 
     @web.expose
     def launch_instance(self, trans, cluster_name, password, key_id, secret,

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

@@ -569,7 +569,7 @@ def structure( self, trans, id=None, **kwargs ):
         hda_dictionaries = history_data[ 'contents' ]
 
         jobs = ( trans.sa_session.query( trans.app.model.Job )
-                 .filter( trans.app.model.Job.user == trans.user )
+                 .filter( trans.app.model.Job.user == history_to_view.user )
                  .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all()
         jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs )