Merge.

CONTRIBUTING.md

@@ -1,12 +1,13 @@
 # Contributing
 
 This document briefly describes how to contribute to the
-galaxy-central core project - also checkout the video of our [2013
-Galaxy Community Conference
-presentation](http://vimeo.com/channels/581875/73486255) on the
-topic. For information on contributing more broadly to the Galaxy
-ecosystem and a deeper discussion of some of these points - please see
-the [Develop](https://wiki.galaxyproject.org/Develop/) section of the
+galaxy-central core project - also checkout our 2013 Galaxy Community
+Conference presentation] on the topic
+([video](http://vimeo.com/channels/581875/73486255),
+[presentation](https://wiki.galaxyproject.org/Documents/Presentations/GCC2013?action=AttachFile&do=view&target=BakerContribute.pdf)). For
+information on contributing more broadly to the Galaxy ecosystem and a
+deeper discussion of some of these points - please see the
+[Develop](https://wiki.galaxyproject.org/Develop/) section of the
 [Galaxy Wiki](https://wiki.galaxyproject.org/).
 
 ## Before you Begin
@@ -80,6 +81,13 @@ the [development mailing list](http://dev.list.galaxyproject.org/).
    
    * A description of how to test the change.
 
+## Ideas
+
+Galaxy's [Trello board](http://bit.ly/gxytrello) is filled with bugs and ideas
+for enhancements, but we maintain a [card](https://trello.com/c/eFdPIdIB) with
+links to smaller issues we believe would make the best entry points for new
+developers.
+
 ## A Quick Note about Tools
 
   For the most part, Galaxy tools should be published to the

client/galaxy/scripts/mvc/tools/tools-form-workflow.js

@@ -275,10 +275,16 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
         /** Request a new model for an already created tool form and updates the form inputs
         */
         _updateModel: function() {
-            // create the request dictionary
+            // link self
             var self = this;
-            var current_state = this.tree.finalize();
-
+            
+            // create the request dictionary
+            var current_state = {
+                tool_id         : this.options.id,
+                tool_version    : this.options.version,
+                inputs          : this.tree.finalize()
+            }
+        
             // log tool state
             console.debug('tools-form-workflow::_refreshForm() - Refreshing states.');
             console.debug(current_state);
@@ -287,11 +293,11 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
             var process_id = this.deferred.register();
 
             // build model url for request
-            var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False';
+            var model_url = galaxy_config.root + 'api/workflows/build_module';
 
             // post job
             Utils.request({
-                type    : 'GET',
+                type    : 'POST',
                 url     : model_url,
                 data    : current_state,
                 success : function(data) {

client/galaxy/scripts/mvc/tools/tools-input.js

@@ -34,8 +34,7 @@ define([], function() {
             this.field.skip = false;
             var v = this.field.value && this.field.value();
             this.field.skip = Boolean(options.optional &&
-                                        ((this.default_value === undefined) ||
-                                        ((this.field.validate && !this.field.validate()) || !v ||
+                                        (((this.field.validate && !this.field.validate()) || !v ||
                                         (v == this.default_value) || (Number(v) == Number(this.default_value)) ||
                                         (JSON.stringify(v) == JSON.stringify(this.default_value)))));
 

client/galaxy/scripts/mvc/tools/tools-section.js

@@ -294,17 +294,20 @@ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet',
             // get id
             var id = input_def.id;
 
+            // add regular/default value if missing
+            if (input_def.value === undefined) {
+                input_def.value = null;
+            }
+            if (input_def.default_value === undefined) {
+                input_def.default_value = input_def.value;
+            }
+            
             // create input field
             var field = this._createField(input_def);
 
             // add to field list
             this.app.field_list[id] = field;
 
-            // fix default value if missing
-            if (input_def.default_value === undefined) {
-                input_def.default_value = input_def.value;
-            }
-
             // create input field wrapper
             var input_element = new InputElement(this.app, {
                 label           : input_def.label,

client/galaxy/scripts/mvc/tools/tools-tree.js

@@ -10,13 +10,13 @@ return Backbone.Model.extend({
     initialize: function(app) {
         this.app = app;
     },
-    
+
     /** Convert dictionary representation into tool api specific flat dictionary format.
     */
     finalize: function(patch) {
         // link this
         var self = this;
-        
+
         // dictionary with api specific identifiers
         this.map_dict = {};
 
@@ -24,24 +24,24 @@ return Backbone.Model.extend({
         if (!this.app.section) {
             return {};
         }
-        
+
         // ensure that dictionary with patching functions exists
         patch = patch || {};
-        
+
         // dictionary formatted for job submission or tool form update
         var result_dict = {};
 
         // prepare full dictionary
         var dict = {};
-        
+
         // fill dictionary from dom
         this._iterate(this.app.section.$el, dict);
-        
+
         // add identifier and value to job definition
         function add(job_input_id, input_id, input_value) {
             // add entry to result dictionary
             result_dict[job_input_id] = input_value;
-            
+
             // backup id mapping
             self.map_dict[job_input_id] = input_id;
         };
@@ -53,21 +53,21 @@ return Backbone.Model.extend({
                 if (node.input) {
                     // get node
                     var input = node.input;
-                    
+
                     // create identifier
                     var job_input_id = identifier;
                     if (identifier != '') {
                         job_input_id += '|';
                     }
                     job_input_id += input.name;
-                    
+
                     // process input type
                     switch (input.type) {
                         // handle repeats
                         case 'repeat':
                             // section identifier
                             var section_label = 'section-';
-                            
+
                             // collect repeat block identifiers
                             var block_indices = [];
                             var block_prefix = null;
@@ -81,10 +81,10 @@ return Backbone.Model.extend({
                                     }
                                 }
                             }
-                            
+
                             // sort repeat blocks
                             block_indices.sort(function(a,b) { return a - b; });
-                            
+
                             // add to response dictionary in created order
                             var index = 0;
                             for (var i in block_indices) {
@@ -98,10 +98,10 @@ return Backbone.Model.extend({
                             if (patch[input.test_param.type]) {
                                 value = patch[input.test_param.type](value);
                             }
-                            
+
                             // add conditional value
                             add (job_input_id + '|' + input.test_param.name, input.id, value);
-                            
+
                             // identify selected case
                             var selectedCase = self.matchCase(input, value);
                             if (selectedCase != -1) {
@@ -116,22 +116,17 @@ return Backbone.Model.extend({
                             // get field
                             var field = self.app.field_list[input.id];
                             if (field && field.value) {
-                                // get and patch field value
+                                // validate field value
                                 var value = field.value();
-                                if (patch[input.type]) {
-                                    value = patch[input.type](value);
-                                }
-
-                                // validate field value
-                                if (field.skip) {
-                                    continue;
-                                }
-
-                                // validate field value
                                 if (field.validate && !field.validate()) {
                                     value = null;
                                 }
 
+                                // get and patch field value
+                                if (patch[input.type]) {
+                                    value = patch[input.type](value);
+                                }
+
                                 // ignore certain values
                                 if (input.ignore === undefined || (value !== null && input.ignore != value)) {
                                     // add value to submission
@@ -149,20 +144,20 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // start conversion
         convert('', dict);
-        
+
         // return result
         return result_dict;
     },
-    
+
     /** Match job definition identifier to input element identifier
     */
     match: function (job_input_id) {
         return this.map_dict && this.map_dict[job_input_id];
     },
-    
+
     /** Match conditional values to selected cases
     */
     matchCase: function(input, value) {
@@ -174,27 +169,27 @@ return Backbone.Model.extend({
                 value = input.test_param.falsevalue || 'false';
             }
         }
-        
+
         // find selected case
         for (var i in input.cases) {
             if (input.cases[i].value == value) {
                 return i;
             }
         }
-        
+
         // selected case not found
         return -1;
     },
-    
+
     /** Matches identifier from api model to input elements
     */
     matchModel: function(model, callback) {
         // final result dictionary
         var result = {};
-        
+
         // link this
         var self = this;
-        
+
         // search throughout response
         function search (id, head) {
             for (var i in head) {
@@ -224,23 +219,23 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // match all ids and return messages
         search('', model.inputs);
 
         // return matched results
         return result;
     },
-    
+
     /** Matches identifier from api response to input elements
     */
     matchResponse: function(response) {
         // final result dictionary
         var result = {};
-        
+
         // link this
         var self = this;
-        
+
         // search throughout response
         function search (id, head) {
             if (typeof head === 'string') {
@@ -262,14 +257,14 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // match all ids and return messages
         search('', response);
-        
+
         // return matched results
         return result;
     },
-    
+
     /** Iterate through the tool form dom and map it to the dictionary.
     */
     _iterate: function(parent, dict) {
@@ -279,15 +274,15 @@ return Backbone.Model.extend({
         children.each(function() {
             // get child element
             var child = this;
-            
+
             // get id
             var id = $(child).attr('id');
-            
+
             // create new branch
             if ($(child).hasClass('section-row')) {
                 // create sub dictionary
                 dict[id] = {};
-                
+
                 // add input element if it exists
                 var input = self.app.input_list[id];
                 if (input) {
@@ -295,7 +290,7 @@ return Backbone.Model.extend({
                         input : input
                     }
                 }
-                
+
                 // fill sub dictionary
                 self._iterate(child, dict[id]);
             } else {

client/galaxy/scripts/utils/metrics-logger.js

@@ -34,7 +34,7 @@ function MetricsLogger( options ){
     var self = this;
 
     ///** get the current user's id from bootstrapped data or options */
-    self.userId = window.bootstrapped? window.bootstrapped.user.id: null;
+    self.userId = ( window.bootstrapped && window.bootstrapped.user )? window.bootstrapped.user.id: null;
     self.userId = self.userId || options.userId || null;
 
     /** the (optional) console to emit logs to */

config/plugins/visualizations/scatterplot/package.json

@@ -16,8 +16,8 @@
   "devDependencies": {
     "grunt": "~0.4.1",
     "grunt-cli": "~0.1.9",
-    "grunt-contrib-handlebars": "~0.5.10",
     "grunt-contrib-concat": "~0.3.0",
+    "grunt-contrib-handlebars": "^0.9.3",
     "grunt-contrib-uglify": "~0.2.2",
     "grunt-contrib-watch": "~0.5.3"
   }

lib/galaxy/datatypes/dataproviders/column.py

@@ -3,6 +3,9 @@ Providers that provide lists of lists generally where each line of a source
 is further subdivided into multiple data (e.g. columns from a line).
 """
 
+import urllib
+import re
+
 import line
 
 _TODO = """
@@ -34,12 +37,13 @@ class ColumnarDataProvider( line.RegexLineDataProvider ):
         'column_count'  : 'int',
         'column_types'  : 'list:str',
         'parse_columns' : 'bool',
-        'deliminator'   : 'str'
+        'deliminator'   : 'str',
+        'filters'       : 'list:str'
     }
 
     def __init__( self, source, indeces=None,
             column_count=None, column_types=None, parsers=None, parse_columns=True,
-            deliminator='\t', **kwargs ):
+            deliminator='\t', filters=None, **kwargs ):
         """
         :param indeces: a list of indeces of columns to gather from each row
             Optional: will default to `None`.
@@ -103,6 +107,104 @@ class ColumnarDataProvider( line.RegexLineDataProvider ):
             # overwrite with user desired parsers
             self.parsers.update( parsers or {} )
 
+        filters = filters or []
+        self.column_filters = []
+        for filter_ in filters:
+            parsed = self.parse_filter( filter_ )
+            #TODO: might be better to error on bad filter/None here
+            if callable( parsed ):
+                self.column_filters.append( parsed )
+
+    def parse_filter( self, filter_param_str ):
+        split = filter_param_str.split( '-', 3 )
+        if not len( split ) == 3:
+            return None
+        column, op, val = split
+
+        # better checking v. len and indeces
+        column = int( column )
+        if column > len( self.column_types ):
+            return None
+        if self.column_types[ column ] in ( 'float', 'int' ):
+            return self.create_numeric_filter( column, op, val )
+        if self.column_types[ column ] in ( 'str' ):
+            return self.create_string_filter( column, op, val )
+        if self.column_types[ column ] in ( 'list' ):
+            return self.create_list_filter( column, op, val )
+        return None
+
+    def create_numeric_filter( self, column, op, val ):
+        """
+        Return an anonymous filter function that will be passed the array
+        of parsed columns. Return None if no filter function can be 
+        created for the given params.
+
+        The function will compare the column at index `column` against `val`
+        using the given op where op is one of: 
+            lt: less than, le: less than or equal to,
+            eq: equal to, ne: not equal to,
+            ge: greather than or equal to, gt: greater than
+
+        `val` is cast as float here and will return None if there's a parsing error.
+        """
+        try:
+            val = float( val )
+        except ValueError:
+            return None
+        if   'lt' == op:
+            return lambda d: d[column] < val
+        elif 'le' == op:
+            return lambda d: d[column] <= val
+        elif 'eq' == op:
+            return lambda d: d[column] == val
+        elif 'ne' == op:
+            return lambda d: d[column] != val
+        elif 'ge' == op:
+            return lambda d: d[column] >= val
+        elif 'gt' == op:
+            return lambda d: d[column] > val
+        return None
+
+    def create_string_filter( self, column, op, val ):
+        """
+        Return an anonymous filter function that will be passed the array
+        of parsed columns. Return None if no filter function can be 
+        created for the given params.
+
+        The function will compare the column at index `column` against `val`
+        using the given op where op is one of: 
+            eq: exactly matches,
+            has: the column contains the substring `val`,
+            re: the column matches the regular expression in `val`
+        """
+        if   'eq' == op:
+            return lambda d: d[column] == val
+        elif 'has' == op:
+            return lambda d: val in d[column]
+        elif 're' == op:
+            val = urllib.unquote_plus( val )
+            val = re.compile( val )
+            return lambda d: val.match( d[column] ) is not None
+        return None
+
+    def create_list_filter( self, column, op, val ):
+        """
+        Return an anonymous filter function that will be passed the array
+        of parsed columns. Return None if no filter function can be 
+        created for the given params.
+
+        The function will compare the column at index `column` against `val`
+        using the given op where op is one of: 
+            eq: the list `val` exactly matches the list in the column,
+            has: the list in the column contains the sublist `val`,
+        """
+        if   'eq' == op:
+            val = self.parse_value( val, 'list' )
+            return lambda d: d[column] == val
+        elif 'has' == op:
+            return lambda d: val in d[column]
+        return None
+
     def get_default_parsers( self ):
         """
         Return parser dictionary keyed for each columnar type
@@ -140,6 +242,39 @@ class ColumnarDataProvider( line.RegexLineDataProvider ):
             #'gffstrand': # -, +, ?, or '.' for None, etc.
         }
 
+    def filter( self, line ):
+        line = super( ColumnarDataProvider, self ).filter( line )
+        if line == None:
+            return line
+        columns = self.parse_columns_from_line( line )
+        return self.filter_by_columns( columns )
+
+    def parse_columns_from_line( self, line ):
+        """
+        Returns a list of the desired, parsed columns.
+        :param line: the line to parse
+        :type line: str
+        """
+        #TODO: too much going on in this loop - the above should all be precomputed AMAP...
+        all_columns = line.split( self.deliminator )
+        # if no indeces were passed to init, return all columns
+        selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) )
+        parsed_columns = []
+        for parser_index, column_index in enumerate( selected_indeces ):
+            parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) )
+        return parsed_columns
+
+    def parse_column_at_index( self, columns, parser_index, index ):
+        """
+        Get the column type for the parser from `self.column_types` or `None`
+        if the type is unavailable.
+        """
+        try:
+            return self.parse_value( columns[ index ], self.get_column_type( parser_index ) )
+        # if a selected index is not within columns, return None
+        except IndexError, index_err:
+            return None
+
     def parse_value( self, val, type ):
         """
         Attempt to parse and return the given value based on the given type.
@@ -173,51 +308,11 @@ class ColumnarDataProvider( line.RegexLineDataProvider ):
         except IndexError, ind_err:
             return None
 
-    def parse_column_at_index( self, columns, parser_index, index ):
-        """
-        Get the column type for the parser from `self.column_types` or `None`
-        if the type is unavailable.
-        """
-        try:
-            return self.parse_value( columns[ index ], self.get_column_type( parser_index ) )
-        # if a selected index is not within columns, return None
-        except IndexError, index_err:
-            return None
-
-    def parse_columns_from_line( self, line ):
-        """
-        Returns a list of the desired, parsed columns.
-        :param line: the line to parse
-        :type line: str
-        """
-        #TODO: too much going on in this loop - the above should all be precomputed AMAP...
-        all_columns = line.split( self.deliminator )
-        # if no indeces were passed to init, return all columns
-        selected_indeces = self.selected_column_indeces or list( xrange( len( all_columns ) ) )
-        parsed_columns = []
-        for parser_index, column_index in enumerate( selected_indeces ):
-            parsed_columns.append( self.parse_column_at_index( all_columns, parser_index, column_index ) )
-        return parsed_columns
-
-    def __iter__( self ):
-        parent_gen = super( ColumnarDataProvider, self ).__iter__()
-        for line in parent_gen:
-            columns = self.parse_columns_from_line( line )
-            yield columns
-
-    #TODO: implement column filters here and not below - flatten hierarchy
-
-class FilteredByColumnDataProvider( ColumnarDataProvider ):
-    """
-    Data provider that provide a list of columns from the lines of its source
-    _only_ if they pass a given filter function.
-
-    e.g. column #3 is type int and > N
-    """
-    # TODO: how to do this and still have limit and offset work?
-    def __init__( self, source, **kwargs ):
-        raise NotImplementedError()
-        super( FilteredByColumnDataProvider, self ).__init__( source, **kwargs )
+    def filter_by_columns( self, columns ):
+        for filter_fn in self.column_filters:
+            if not filter_fn( columns ):
+                return None
+        return columns
 
 
 class DictDataProvider( ColumnarDataProvider ):

lib/galaxy/jobs/runners/util/cli/job/slurm.py

@@ -7,7 +7,7 @@ try:
 except ImportError:
     # Not in Galaxy, map Galaxy job states to Pulsar ones.
     from galaxy.util import enum
-    job_states = enum(RUNNING='running', OK='complete', QUEUED='queued')
+    job_states = enum(RUNNING='running', OK='complete', QUEUED='queued', ERROR="failed")
 
 from ..job import BaseJobExec
 
@@ -59,10 +59,10 @@ class Slurm(BaseJobExec):
         return 'scancel %s' % job_id
 
     def get_status(self, job_ids=None):
-        return 'squeue -a -o \\"%A %t\\"'
+        return "squeue -a -o '%A %t'"
 
     def get_single_status(self, job_id):
-        return 'squeue -a -o \\"%A %t\\" -j ' + job_id
+        return "squeue -a -o '%A %t' -j " + job_id
 
     def parse_status(self, status, job_ids):
         # Get status for each job, skipping header.
@@ -80,6 +80,7 @@ class Slurm(BaseJobExec):
             # Job still on cluster and has state.
             id, state = status[1].split()
             return self._get_job_state(state)
+        # else line like "slurm_load_jobs error: Invalid job id specified"
         return job_states.OK
 
     def _get_job_state(self, state):

lib/galaxy/managers/users.py

@@ -199,6 +199,42 @@ class UserManager( base.ModelManager, deletable.PurgableManagerMixin ):
         #TODO: use quota manager
         return self.app.quota_agent.get_percent( user=user )
 
+    def tags_used( self, trans, user, tag_models=None ):
+        """
+        Return a list of distinct 'user_tname:user_value' strings that the
+        given user has used.
+        """
+        #TODO: simplify and unify with tag manager
+        if self.is_anonymous( user ):
+            return []
+
+        # get all the taggable model TagAssociations
+        if not tag_models:
+            tag_models = [ v.tag_assoc_class for v in self.app.tag_handler.item_tag_assoc_info.values() ]
+        # create a union of subqueries for each for this user - getting only the tname and user_value
+        all_tags_query = None
+        for tag_model in tag_models:
+            subq = ( self.app.model.context.query( tag_model.user_tname, tag_model.user_value )
+                        .filter( tag_model.user == trans.user ) )
+            all_tags_query = subq if all_tags_query is None else all_tags_query.union( subq )
+
+        # if nothing init'd the query, bail
+        if all_tags_query is None:
+            return []
+
+        # boil the tag tuples down into a sorted list of DISTINCT name:val strings
+        tags = all_tags_query.distinct().all()
+        tags = [( ( name + ':' + val ) if val else name ) for name, val in tags ]
+        return sorted( tags )
+
+    def has_requests( self, trans, user ):
+        """
+        """
+        if self.is_anonymous( user ):
+            return False
+        request_types = self.app.security_agent.get_accessible_request_types( trans, user )
+        return ( user.requests or request_types )
+
 
 class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
 
@@ -214,21 +250,22 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'id', 'email', 'username'
         ])
         self.add_view( 'detailed', [
-            'update_time',
-            'create_time',
-
-            'deleted',
-            'purged',
-            'active',
+            #'update_time',
+            #'create_time',
 
             'total_disk_usage',
             'nice_total_disk_usage',
             'quota_percent'
-        #    'preferences',
-        #    # all tags
-        #    'tags',
-        #    # all annotations
-        #    'annotations'
+
+            #'deleted',
+            #'purged',
+            #'active',
+
+            #'preferences',
+            # all tags
+            'tags_used',
+            ## all annotations
+            #'annotations'
         ], include_keys_from='summary' )
 
     def add_serializers( self ):
@@ -240,7 +277,13 @@ class UserSerializer( base.ModelSerializer, deletable.PurgableSerializerMixin ):
             'create_time'   : self.serialize_date,
             'update_time'   : self.serialize_date,
             'is_admin'      : lambda t, i, k: self.user_manager.is_admin( t, i ),
-            'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i )
+
+            'total_disk_usage' : lambda t, i, k: float( i.total_disk_usage ),
+            'quota_percent' : lambda t, i, k: self.user_manager.quota( t, i ),
+
+            'tags_used'     : lambda t, i, k: self.user_manager.tags_used( t, i ),
+            #TODO: 'has_requests' is more apt
+            'requests'      : lambda t, i, k: self.user_manager.has_requests( t, i )
         })
 
     def serialize_current_anonymous_user( self, trans, user, keys ):

lib/galaxy/tools/__init__.py

@@ -2250,13 +2250,12 @@ class Tool( object, Dictifiable ):
 
         return tool_dict
 
-    def to_json (self, trans, **kwd):
+    def to_json (self, trans, kwd={}, is_dynamic=True):
         """
         Recursively creates a tool dictionary containing repeats, dynamic options and updated states.
         """
         job_id = kwd.get('__job_id__', None)
         dataset_id = kwd.get('__dataset_id__', None)
-        is_dynamic = string_as_bool(kwd.get('__is_dynamic__', True))
 
         # load job details if provided
         job = None

lib/galaxy/tools/parameters/basic.py

@@ -1618,6 +1618,8 @@ class DrillDownSelectToolParameter( SelectToolParameter ):
             return UnvalidatedValue( None )
         initial_values = []
         recurse_options( initial_values, self.get_options( trans=trans, other_values=context ) )
+        if len( initial_values ) == 0:
+            initial_values = None
         return initial_values
 
     def value_to_display_text( self, value, app ):

lib/galaxy/web/__init__.py

@@ -19,6 +19,7 @@ from framework.decorators import _future_expose_api_anonymous
 from framework.decorators import _future_expose_api_raw
 from framework.decorators import _future_expose_api_raw_anonymous
 from framework.decorators import _future_expose_api_anonymous_and_sessionless
+from framework.decorators import _future_expose_api_raw_anonymous_and_sessionless
 
 from framework.formbuilder import form
 from framework.formbuilder import FormBuilder

lib/galaxy/web/framework/decorators.py

@@ -344,3 +344,6 @@ def _future_expose_api_raw( func ):
 
 def _future_expose_api_raw_anonymous( func ):
     return _future_expose_api( func, to_json=False, user_required=False )
+
+def _future_expose_api_raw_anonymous_and_sessionless( func ):
+    return _future_expose_api( func, to_json=False, user_required=False, user_or_session_required=False )

lib/galaxy/webapps/galaxy/api/job_files.py

@@ -8,8 +8,8 @@ from galaxy import exceptions
 from galaxy import util
 from galaxy import model
 from galaxy.web.base.controller import BaseAPIController
-from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous
-from galaxy.web import _future_expose_api_raw_anonymous as expose_api_raw_anonymous
+from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless
+from galaxy.web import _future_expose_api_raw_anonymous_and_sessionless as expose_api_raw_anonymous_and_sessionless
 
 
 import logging
@@ -28,7 +28,7 @@ class JobFilesAPIController( BaseAPIController ):
     security model for tool execution.
     """
 
-    @expose_api_raw_anonymous
+    @expose_api_raw_anonymous_and_sessionless
     def index( self, trans, job_id, **kwargs ):
         """
         index( self, trans, job_id, **kwargs )
@@ -54,7 +54,7 @@ class JobFilesAPIController( BaseAPIController ):
         path = kwargs.get("path", None)
         return open(path, 'rb')
 
-    @expose_api_anonymous
+    @expose_api_anonymous_and_sessionless
     def create( self, trans, job_id, payload, **kwargs ):
         """
         create( self, trans, job_id, payload, **kwargs )

lib/galaxy/webapps/galaxy/api/tools.py

@@ -76,14 +76,10 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
         GET /api/tools/{tool_id}/build
         Returns a tool model including dynamic parameters and updated values, repeats block etc.
         """
-        tool_id = urllib.unquote_plus( id )
         tool_version = kwd.get( 'tool_version', None )
-        tool = self.app.toolbox.get_tool( tool_id, tool_version )
-        if not tool:
-            trans.response.status = 500
-            return { 'error': 'Could not find tool with id \'%s\'' % tool_id }
-        return tool.to_json(trans, **kwd)
-    
+        tool = self._get_tool( id, tool_version=tool_version, user=trans.user )
+        return tool.to_json(trans, kwd)
+
     @_future_expose_api
     @web.require_admin
     def reload( self, trans, tool_id, **kwd ):

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -6,6 +6,8 @@ from __future__ import absolute_import
 
 import uuid
 import logging
+import copy
+import urllib
 from sqlalchemy import desc, or_, and_
 from galaxy import exceptions, util
 from galaxy.model.item_attrs import UsesAnnotations
@@ -17,6 +19,7 @@ from galaxy.web.base.controller import SharableMixin
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_config
+from galaxy.workflow.modules import module_factory
 
 log = logging.getLogger(__name__)
 
@@ -305,6 +308,52 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
             raise exceptions.RequestParameterInvalidException( message )
         return self.workflow_contents_manager.workflow_to_dict( trans, stored_workflow, style="instance" )
 
+    @expose_api
+    def build_module( self, trans, payload={}):
+        """
+        POST /api/workflows/build_module
+        Builds module details including a tool model for the workflow editor.
+        """
+        tool_id         = payload.get( 'tool_id', None )
+        tool_version    = payload.get( 'tool_version', None )
+        tool_inputs     = payload.get( 'inputs', None )
+        annotation      = payload.get( 'annotation', '' )
+        
+        # load tool
+        tool = self._get_tool( tool_id, tool_version=tool_version, user=trans.user )
+        
+        # initialize module
+        trans.workflow_building_mode = True
+        module = module_factory.from_dict( trans, {
+            'type'          : 'tool',
+            'tool_id'       : tool.id,
+            'tool_state'    : None
+        } )
+        
+        # create tool model and default tool state (if missing)
+        tool_model = module.tool.to_json(trans, tool_inputs, is_dynamic=False)
+        module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
+        return {
+            'tool_model'        : tool_model,
+            'tool_state'        : module.get_state(),
+            'data_inputs'       : module.get_data_inputs(),
+            'data_outputs'      : module.get_data_outputs(),
+            'tool_errors'       : module.get_errors(),
+            'form_html'         : module.get_config_form(),
+            'annotation'        : annotation,
+            'post_job_actions'  : module.get_post_job_actions(tool_inputs)
+        }
+
+    #
+    # -- Helper methods --
+    #
+    def _get_tool( self, id, tool_version=None, user=None ):
+        id = urllib.unquote_plus( id )
+        tool = self.app.toolbox.get_tool( id, tool_version )
+        if not tool or not tool.allow_user_access( user ):
+            raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id)
+        return tool
+
     def __api_import_new_workflow( self, trans, payload, **kwd ):
         data = payload['workflow']
 

lib/galaxy/webapps/galaxy/buildapp.py

@@ -217,6 +217,7 @@ def populate_api_routes( webapp, app ):
     webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' )
     webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' )
     webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' )
+    webapp.mapper.connect( '/api/workflows/build_module', action='build_module', controller="workflows" )
     webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' )
     webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' )
     webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" )

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -609,7 +609,6 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         This is used for the form shown in the right pane when a node
         is selected.
         """
-
         tool_state = incoming.pop('tool_state', None)
         trans.workflow_building_mode = True
         module = module_factory.from_dict( trans, {
@@ -617,22 +616,7 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
             'tool_id': tool_id,
             'tool_state': tool_state
         } )
-        
-        # create tool model and default tool state (if missing)
-        if type == 'tool' and not tool_state:
-            tool_model = module.tool.to_json(trans, **incoming)
-            module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
-            return {
-                'tool_model': tool_model,
-                'tool_state': module.get_state(),
-                'data_inputs': module.get_data_inputs(),
-                'data_outputs': module.get_data_outputs(),
-                'tool_errors': module.get_errors(),
-                'form_html': module.get_config_form(),
-                'annotation': annotation,
-                'post_job_actions': module.get_post_job_actions(incoming)
-            }
-        
+
         # update module state
         module.update_state( incoming )
         
@@ -669,7 +653,8 @@ class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMix
         module = module_factory.new( trans, type, **kwargs )
         tool_model = None
         if type == 'tool':
-            tool_model = module.tool.to_json(trans)
+            tool_model = module.tool.to_json(trans, is_dynamic=False)
+            module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
         return {
             'type': module.type,
             'name': module.get_name(),

static/scripts/mvc/tools/tools-form-workflow.js

@@ -275,10 +275,16 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
         /** Request a new model for an already created tool form and updates the form inputs
         */
         _updateModel: function() {
-            // create the request dictionary
+            // link self
             var self = this;
-            var current_state = this.tree.finalize();
-
+            
+            // create the request dictionary
+            var current_state = {
+                tool_id         : this.options.id,
+                tool_version    : this.options.version,
+                inputs          : this.tree.finalize()
+            }
+        
             // log tool state
             console.debug('tools-form-workflow::_refreshForm() - Refreshing states.');
             console.debug(current_state);
@@ -287,11 +293,11 @@ define(['utils/utils', 'mvc/tools/tools-form-base'],
             var process_id = this.deferred.register();
 
             // build model url for request
-            var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False';
+            var model_url = galaxy_config.root + 'api/workflows/build_module';
 
             // post job
             Utils.request({
-                type    : 'GET',
+                type    : 'POST',
                 url     : model_url,
                 data    : current_state,
                 success : function(data) {

static/scripts/mvc/tools/tools-input.js

@@ -34,8 +34,7 @@ define([], function() {
             this.field.skip = false;
             var v = this.field.value && this.field.value();
             this.field.skip = Boolean(options.optional &&
-                                        ((this.default_value === undefined) ||
-                                        ((this.field.validate && !this.field.validate()) || !v ||
+                                        (((this.field.validate && !this.field.validate()) || !v ||
                                         (v == this.default_value) || (Number(v) == Number(this.default_value)) ||
                                         (JSON.stringify(v) == JSON.stringify(this.default_value)))));
 

static/scripts/mvc/tools/tools-section.js

@@ -294,17 +294,20 @@ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-portlet',
             // get id
             var id = input_def.id;
 
+            // add regular/default value if missing
+            if (input_def.value === undefined) {
+                input_def.value = null;
+            }
+            if (input_def.default_value === undefined) {
+                input_def.default_value = input_def.value;
+            }
+            
             // create input field
             var field = this._createField(input_def);
 
             // add to field list
             this.app.field_list[id] = field;
 
-            // fix default value if missing
-            if (input_def.default_value === undefined) {
-                input_def.default_value = input_def.value;
-            }
-
             // create input field wrapper
             var input_element = new InputElement(this.app, {
                 label           : input_def.label,

static/scripts/mvc/tools/tools-tree.js

@@ -10,13 +10,13 @@ return Backbone.Model.extend({
     initialize: function(app) {
         this.app = app;
     },
-    
+
     /** Convert dictionary representation into tool api specific flat dictionary format.
     */
     finalize: function(patch) {
         // link this
         var self = this;
-        
+
         // dictionary with api specific identifiers
         this.map_dict = {};
 
@@ -24,24 +24,24 @@ return Backbone.Model.extend({
         if (!this.app.section) {
             return {};
         }
-        
+
         // ensure that dictionary with patching functions exists
         patch = patch || {};
-        
+
         // dictionary formatted for job submission or tool form update
         var result_dict = {};
 
         // prepare full dictionary
         var dict = {};
-        
+
         // fill dictionary from dom
         this._iterate(this.app.section.$el, dict);
-        
+
         // add identifier and value to job definition
         function add(job_input_id, input_id, input_value) {
             // add entry to result dictionary
             result_dict[job_input_id] = input_value;
-            
+
             // backup id mapping
             self.map_dict[job_input_id] = input_id;
         };
@@ -53,21 +53,21 @@ return Backbone.Model.extend({
                 if (node.input) {
                     // get node
                     var input = node.input;
-                    
+
                     // create identifier
                     var job_input_id = identifier;
                     if (identifier != '') {
                         job_input_id += '|';
                     }
                     job_input_id += input.name;
-                    
+
                     // process input type
                     switch (input.type) {
                         // handle repeats
                         case 'repeat':
                             // section identifier
                             var section_label = 'section-';
-                            
+
                             // collect repeat block identifiers
                             var block_indices = [];
                             var block_prefix = null;
@@ -81,10 +81,10 @@ return Backbone.Model.extend({
                                     }
                                 }
                             }
-                            
+
                             // sort repeat blocks
                             block_indices.sort(function(a,b) { return a - b; });
-                            
+
                             // add to response dictionary in created order
                             var index = 0;
                             for (var i in block_indices) {
@@ -98,10 +98,10 @@ return Backbone.Model.extend({
                             if (patch[input.test_param.type]) {
                                 value = patch[input.test_param.type](value);
                             }
-                            
+
                             // add conditional value
                             add (job_input_id + '|' + input.test_param.name, input.id, value);
-                            
+
                             // identify selected case
                             var selectedCase = self.matchCase(input, value);
                             if (selectedCase != -1) {
@@ -116,22 +116,17 @@ return Backbone.Model.extend({
                             // get field
                             var field = self.app.field_list[input.id];
                             if (field && field.value) {
-                                // get and patch field value
+                                // validate field value
                                 var value = field.value();
-                                if (patch[input.type]) {
-                                    value = patch[input.type](value);
-                                }
-
-                                // validate field value
-                                if (field.skip) {
-                                    continue;
-                                }
-
-                                // validate field value
                                 if (field.validate && !field.validate()) {
                                     value = null;
                                 }
 
+                                // get and patch field value
+                                if (patch[input.type]) {
+                                    value = patch[input.type](value);
+                                }
+
                                 // ignore certain values
                                 if (input.ignore === undefined || (value !== null && input.ignore != value)) {
                                     // add value to submission
@@ -149,20 +144,20 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // start conversion
         convert('', dict);
-        
+
         // return result
         return result_dict;
     },
-    
+
     /** Match job definition identifier to input element identifier
     */
     match: function (job_input_id) {
         return this.map_dict && this.map_dict[job_input_id];
     },
-    
+
     /** Match conditional values to selected cases
     */
     matchCase: function(input, value) {
@@ -174,27 +169,27 @@ return Backbone.Model.extend({
                 value = input.test_param.falsevalue || 'false';
             }
         }
-        
+
         // find selected case
         for (var i in input.cases) {
             if (input.cases[i].value == value) {
                 return i;
             }
         }
-        
+
         // selected case not found
         return -1;
     },
-    
+
     /** Matches identifier from api model to input elements
     */
     matchModel: function(model, callback) {
         // final result dictionary
         var result = {};
-        
+
         // link this
         var self = this;
-        
+
         // search throughout response
         function search (id, head) {
             for (var i in head) {
@@ -224,23 +219,23 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // match all ids and return messages
         search('', model.inputs);
 
         // return matched results
         return result;
     },
-    
+
     /** Matches identifier from api response to input elements
     */
     matchResponse: function(response) {
         // final result dictionary
         var result = {};
-        
+
         // link this
         var self = this;
-        
+
         // search throughout response
         function search (id, head) {
             if (typeof head === 'string') {
@@ -262,14 +257,14 @@ return Backbone.Model.extend({
                 }
             }
         }
-        
+
         // match all ids and return messages
         search('', response);
-        
+
         // return matched results
         return result;
     },
-    
+
     /** Iterate through the tool form dom and map it to the dictionary.
     */
     _iterate: function(parent, dict) {
@@ -279,15 +274,15 @@ return Backbone.Model.extend({
         children.each(function() {
             // get child element
             var child = this;
-            
+
             // get id
             var id = $(child).attr('id');
-            
+
             // create new branch
             if ($(child).hasClass('section-row')) {
                 // create sub dictionary
                 dict[id] = {};
-                
+
                 // add input element if it exists
                 var input = self.app.input_list[id];
                 if (input) {
@@ -295,7 +290,7 @@ return Backbone.Model.extend({
                         input : input
                     }
                 }
-                
+
                 // fill sub dictionary
                 self._iterate(child, dict[id]);
             } else {

static/scripts/packed/mvc/tools/tools-form-workflow.js

@@ -1 +1 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
+define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});

static/scripts/packed/mvc/tools/tools-input.js

@@ -1 +1 @@
-define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&((this.default_value===undefined)||((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});
+define([],function(){return Backbone.View.extend({initialize:function(d,c){this.app=d;this.text_enable=d.options.text_enable||"Enable";this.text_disable=d.options.text_disable||"Disable";this.field=c.field;this.default_value=c.default_value;this.setElement(this._template(c));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);this.field.skip=false;var b=this.field.value&&this.field.value();this.field.skip=Boolean(c.optional&&(((this.field.validate&&!this.field.validate())||!b||(b==this.default_value)||(Number(b)==Number(this.default_value))||(JSON.stringify(b)==JSON.stringify(this.default_value)))));this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.show();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html(this.text_disable)}else{this.reset();this.$field.hide();this.$title_optional.html(this.text_enable);this.field.value&&this.field.value(this.default_value)}this.app.trigger("refresh")},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+=a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})});

static/scripts/packed/mvc/tools/tools-tree.js

@@ -1 +1 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(g[u.type]){v=g[u.type](v)}if(t.skip){continue}if(t.validate&&!t.validate()){v=null}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.app=b},finalize:function(g){var b=this;this.map_dict={};if(!this.app.section){return{}}g=g||{};var f={};var e={};this._iterate(this.app.section.$el,e);function d(j,i,h){f[j]=h;b.map_dict[j]=i}function c(p,s){for(var n in s){var k=s[n];if(k.input){var u=k.input;var o=p;if(p!=""){o+="|"}o+=u.name;switch(u.type){case"repeat":var j="section-";var x=[];var r=null;for(var w in k){var q=w.indexOf(j);if(q!=-1){q+=j.length;x.push(parseInt(w.substr(q)));if(!r){r=w.substr(0,q)}}}x.sort(function(y,i){return y-i});var n=0;for(var l in x){c(o+"_"+n++,k[r+x[l]])}break;case"conditional":var v=b.app.field_list[u.id].value();if(g[u.test_param.type]){v=g[u.test_param.type](v)}d(o+"|"+u.test_param.name,u.id,v);var h=b.matchCase(u,v);if(h!=-1){c(o,s[u.id+"-section-"+h])}break;case"section":c("",k);break;default:var t=b.app.field_list[u.id];if(t&&t.value){var v=t.value();if(t.validate&&!t.validate()){v=null}if(g[u.type]){v=g[u.type](v)}if(u.ignore===undefined||(v!==null&&u.ignore!=v)){d(o,u.id,v);if(u.payload){for(var m in u.payload){d(m,u.id,u.payload[m])}}}}}}}}c("",e);return f},match:function(b){return this.map_dict&&this.map_dict[b]},matchCase:function(b,d){if(b.test_param.type=="boolean"){if(d=="true"){d=b.test_param.truevalue||"true"}else{d=b.test_param.falsevalue||"false"}}for(var c in b.cases){if(b.cases[c].value==d){return c}}return -1},matchModel:function(d,f){var b={};var c=this;function e(g,p){for(var m in p){var k=p[m];var n=k.name;if(g!=""){n=g+"|"+n}switch(k.type){case"repeat":for(var l in k.cache){e(n+"_"+l,k.cache[l])}break;case"conditional":var q=k.test_param&&k.test_param.value;var h=c.matchCase(k,q);if(h!=-1){e(n,k.cases[h].inputs)}break;default:var o=c.map_dict[n];if(o){f(o,k)}}}}e("",d.inputs);return b},matchResponse:function(d){var b={};var c=this;function e(l,j){if(typeof j==="string"){var g=c.map_dict[l];if(g){b[g]=j}}else{for(var h in j){var f=h;if(l!==""){var k="|";if(j instanceof Array){k="_"}f=l+k+f}e(f,j[h])}}}e("",d);return b},_iterate:function(d,e){var b=this;var c=$(d).children();c.each(function(){var h=this;var g=$(h).attr("id");if($(h).hasClass("section-row")){e[g]={};var f=b.app.input_list[g];if(f){e[g]={input:f}}b._iterate(h,e[g])}else{b._iterate(h,e)}})}})});

static/scripts/utils/metrics-logger.js

@@ -34,7 +34,7 @@ function MetricsLogger( options ){
     var self = this;
 
     ///** get the current user's id from bootstrapped data or options */
-    self.userId = window.bootstrapped? window.bootstrapped.user.id: null;
+    self.userId = ( window.bootstrapped && window.bootstrapped.user )? window.bootstrapped.user.id: null;
     self.userId = self.userId || options.userId || null;
 
     /** the (optional) console to emit logs to */

templates/webapps/galaxy/tool_form.mako

@@ -10,7 +10,7 @@ ${h.css('base', 'jquery-ui/smoothness/jquery-ui')}
         ## This avoids making two separate requests since the classic form requires the mako anyway.
         params = dict(trans.request.params)
         params['__dataset_id__'] = params.get('id', None)
-        self.form_config = tool.to_json(trans, **params)
+        self.form_config = tool.to_json(trans, params)
         self.form_config.update({
             'id'                : tool.id,
             'job_id'            : trans.security.encode_id( job.id ) if job else None,

templates/webapps/galaxy/workflow/editor_tool_form.mako

@@ -6,11 +6,9 @@
         ## TEMPORARY: create tool dictionary in mako while both tool forms are in use.
         ## This avoids making two separate requests since the classic form requires the mako anyway.
         from galaxy.tools.parameters import params_to_incoming
-        incoming = {
-            '__is_dynamic__' : False
-        }
+        incoming = {}
         params_to_incoming( incoming, tool.inputs, module.state.inputs, trans.app, to_html=False)
-        self.form_config = tool.to_json(trans, **incoming)
+        self.form_config = tool.to_json(trans, incoming, is_dynamic=False)
         self.form_config.update({
             'id'                : tool.id,
             'job_id'            : trans.security.encode_id( job.id ) if job else None,