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commit/galaxy-central: 3 new changesets
by Bitbucket 24 Oct '12

24 Oct '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/489e80f86187/ changeset: 489e80f86187 user: jmchilton date: 2012-09-26 04:49:22 summary: Ease tool development by reducing clicking/keystorkes required by developers to repeatedly reload the same tool via admin console. affected #: 2 files diff -r 20144ac9ffa7d15a9738cee2a5c8cb2b4cf1c401 -r 489e80f8618766c5ea3d655adaaea5e6b13d3bc2 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1578,10 +1578,12 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) toolbox = self.app.toolbox + tool_id = None if params.get( 'reload_tool_button', False ): tool_id = params.tool_id message, status = toolbox.reload_tool_by_id( tool_id ) return trans.fill_template( '/admin/reload_tool.mako', + tool_id=tool_id, toolbox=toolbox, message=message, status=status ) diff -r 20144ac9ffa7d15a9738cee2a5c8cb2b4cf1c401 -r 489e80f8618766c5ea3d655adaaea5e6b13d3bc2 templates/admin/reload_tool.mako --- a/templates/admin/reload_tool.mako +++ b/templates/admin/reload_tool.mako @@ -1,6 +1,17 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<script type="text/javascript"> +$().ready(function() { +%if tool_id: + var focus_el = $("input[name=reload_tool_button]"); +%else: + var focus_el = $("select[name=tool_id]"); +%endif + focus_el.focus(); +}); +</script> + %if message: ${render_msg( message, status )} %endif @@ -22,7 +33,11 @@ <% section = val %> %for section_key, section_val in section.elems.items(): %if section_key.startswith( 'tool' ): - <option value="${section_val.id}">${section_val.name}</option> + <% selected_str = "" %> + %if section_val.id == tool_id: + <% selected_str = " selected=\"selected\"" %> + %endif + <option value="${section_val.id}"${selected_str}>${section_val.name}</option> %endif %endfor %endif https://bitbucket.org/galaxy/galaxy-central/changeset/a0b1af3a160f/ changeset: a0b1af3a160f user: jmchilton date: 2012-09-29 03:15:56 summary: Merge with galaxy-central changes. affected #: 232 files Diff too large to display. https://bitbucket.org/galaxy/galaxy-central/changeset/869bcca8756a/ changeset: 869bcca8756a user: dannon date: 2012-10-24 16:54:37 summary: Merged in jmchilton/galaxy-central-reload-tool-improvements (pull request #72) affected #: 3 files diff -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f -r 869bcca8756a32b0b2c482f1ea67623cce110051 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -56,10 +56,12 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) toolbox = self.app.toolbox + tool_id = None if params.get( 'reload_tool_button', False ): tool_id = params.tool_id message, status = toolbox.reload_tool_by_id( tool_id ) return trans.fill_template( '/admin/reload_tool.mako', + tool_id=tool_id, toolbox=toolbox, message=message, status=status ) @@ -1110,4 +1112,4 @@ # Load user from database id = trans.security.decode_id( id ) quota = trans.sa_session.query( trans.model.Quota ).get( id ) - return quota \ No newline at end of file + return quota diff -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f -r 869bcca8756a32b0b2c482f1ea67623cce110051 templates/admin/reload_tool.mako --- a/templates/admin/reload_tool.mako +++ b/templates/admin/reload_tool.mako @@ -1,6 +1,17 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<script type="text/javascript"> +$().ready(function() { +%if tool_id: + var focus_el = $("input[name=reload_tool_button]"); +%else: + var focus_el = $("select[name=tool_id]"); +%endif + focus_el.focus(); +}); +</script> + %if message: ${render_msg( message, status )} %endif @@ -22,7 +33,11 @@ <% section = val %> %for section_key, section_val in section.elems.items(): %if section_key.startswith( 'tool' ): - <option value="${section_val.id}">${section_val.name}</option> + <% selected_str = "" %> + %if section_val.id == tool_id: + <% selected_str = " selected=\"selected\"" %> + %endif + <option value="${section_val.id}"${selected_str}>${section_val.name}</option> %endif %endfor %endif Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 11 new changesets
by Bitbucket 24 Oct '12

24 Oct '12

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8220718b1eeb/ changeset: 8220718b1eeb user: jmchilton date: 2012-10-08 01:22:49 summary: Fix running tools with multi-data parameters. (Extracting and running workflows still broken.) affected #: 2 files diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 8220718b1eebdcb1257a9520f9aa9d23f7b2d3e4 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2224,6 +2224,13 @@ values = input_values[ input.name ] current = values["__current_case__"] wrap_values( input.cases[current].inputs, values ) + elif isinstance( input, DataToolParameter ) and input.multiple: + values = input_values[ input.name ] + input_values[ input.name ] = \ + [DatasetFilenameWrapper( value, + datatypes_registry = self.app.datatypes_registry, + tool = self, + name = input.name ) for value in values] elif isinstance( input, DataToolParameter ): ## FIXME: We're populating param_dict with conversions when ## wrapping values, this should happen as a separate diff -r 05fc04a70a3bcbfaeedfcf6f2ec16a7e38fc7c94 -r 8220718b1eebdcb1257a9520f9aa9d23f7b2d3e4 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1545,9 +1545,30 @@ else: return trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) + + # TODO: Determine if this needs to be overridden. -John + def value_from_basic( self, value, app, ignore_errors=False ): + # HACK: Some things don't deal with unicode well, psycopg problem? + if type( value ) == unicode: + value = str( value ) + # Handle Runtime values (valid for any parameter?) + if isinstance( value, dict ) and '__class__' in value and value['__class__'] == "RuntimeValue": + return RuntimeValue() + # Delegate to the 'to_python' method + if ignore_errors: + try: + return self.to_python( value, app ) + except: + return value + else: + return self.to_python( value, app ) + + def to_string( self, value, app ): if value is None or isinstance( value, str ): return value + elif isinstance( value, list ): + return ",".join( [ val if isinstance( val, str ) else str(val.id) for val in value] ) elif isinstance( value, DummyDataset ): return None return value.id @@ -1557,6 +1578,10 @@ # indicates that the dataset is optional, while '' indicates that it is not. if value is None or value == '' or value == 'None': return value + if isinstance(value, str) and value.find(",") > -1: + values = value.split(",") + # TODO: Optimize. -John + return [app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( val ) ) for val in values] return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) def to_param_dict_string( self, value, other_values={} ): https://bitbucket.org/galaxy/galaxy-central/changeset/4a3d4de46132/ changeset: 4a3d4de46132 user: jmchilton date: 2012-10-08 01:29:54 summary: Fix extracting workflows containing tools with multi-input parameters. affected #: 1 file diff -r 8220718b1eebdcb1257a9520f9aa9d23f7b2d3e4 -r 4a3d4de46132de8e353b48640512fdefab7ea7ca lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -2054,7 +2054,11 @@ # still need to clean them up so we can serialize # if not( prefix ): if tmp: #this is false for a non-set optional dataset - associations.append( ( tmp.hid, prefix + key ) ) + if not isinstance(tmp, list): + associations.append( ( tmp.hid, prefix + key ) ) + else: + associations.extend( [ (t.hid, prefix + key) for t in tmp] ) + # Cleanup the other deprecated crap associated with datasets # as well. Worse, for nested datasets all the metadata is # being pushed into the root. FIXME: MUST REMOVE SOON https://bitbucket.org/galaxy/galaxy-central/changeset/65024c60d545/ changeset: 65024c60d545 user: jmchilton date: 2012-10-08 02:36:46 summary: Progress toward multi-inputs: initial run workflow input page renders, workflows still do not execute, standard workflows seem to continue to work. affected #: 3 files diff -r 4a3d4de46132de8e353b48640512fdefab7ea7ca -r 65024c60d5452cad3d410b41046a472ba3109e41 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1567,10 +1567,12 @@ def to_string( self, value, app ): if value is None or isinstance( value, str ): return value + elif isinstance( value, DummyDataset ): + return None + elif isinstance( value, list) and len(value) > 0 and isinstance( value[0], DummyDataset): + return None elif isinstance( value, list ): return ",".join( [ val if isinstance( val, str ) else str(val.id) for val in value] ) - elif isinstance( value, DummyDataset ): - return None return value.id def to_python( self, value, app ): diff -r 4a3d4de46132de8e353b48640512fdefab7ea7ca -r 65024c60d5452cad3d410b41046a472ba3109e41 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1362,6 +1362,13 @@ # Connections by input name step.input_connections_by_name = \ dict( ( conn.input_name, conn ) for conn in step.input_connections ) + input_connections_by_name = {} + for conn in step.input_connections: + input_name = conn.input_name + if not input_name in input_connections_by_name: + input_connections_by_name[input_name] = [] + input_connections_by_name[input_name].append(conn) + step.input_connections_by_name = input_connections_by_name # Extract just the arguments for this step by prefix p = "%s|" % step.id l = len(p) @@ -1419,10 +1426,15 @@ tool = trans.app.toolbox.get_tool( step.tool_id ) # Connect up def callback( input, value, prefixed_name, prefixed_label ): + replacement = None if isinstance( input, DataToolParameter ): if prefixed_name in step.input_connections_by_name: conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] + if input.multiple: + replacements = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + else: + replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] + return replacement try: visit_input_values( tool.inputs, step.state.inputs, callback ) except KeyError, k: diff -r 4a3d4de46132de8e353b48640512fdefab7ea7ca -r 65024c60d5452cad3d410b41046a472ba3109e41 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -336,9 +336,14 @@ # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) def callback( input, value, prefixed_name, prefixed_label ): + replacement = None if isinstance( input, DataToolParameter ): if connections is None or prefixed_name in input_connections_by_name: - return DummyDataset() + if input.multiple: + replacement = [DummyDataset() for conn in connections] + else: + replacement = DummyDataset() + return replacement visit_input_values( self.tool.inputs, self.state.inputs, callback ) class WorkflowModuleFactory( object ): https://bitbucket.org/galaxy/galaxy-central/changeset/565510047933/ changeset: 565510047933 user: jmchilton date: 2012-10-08 02:49:02 summary: Cleanup some artifacts from last few multi-input commits. affected #: 2 files diff -r 65024c60d5452cad3d410b41046a472ba3109e41 -r 56551004793378fb618fcfc0214669f307dea594 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1545,25 +1545,6 @@ else: return trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) - - # TODO: Determine if this needs to be overridden. -John - def value_from_basic( self, value, app, ignore_errors=False ): - # HACK: Some things don't deal with unicode well, psycopg problem? - if type( value ) == unicode: - value = str( value ) - # Handle Runtime values (valid for any parameter?) - if isinstance( value, dict ) and '__class__' in value and value['__class__'] == "RuntimeValue": - return RuntimeValue() - # Delegate to the 'to_python' method - if ignore_errors: - try: - return self.to_python( value, app ) - except: - return value - else: - return self.to_python( value, app ) - - def to_string( self, value, app ): if value is None or isinstance( value, str ): return value diff -r 65024c60d5452cad3d410b41046a472ba3109e41 -r 56551004793378fb618fcfc0214669f307dea594 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1360,8 +1360,6 @@ for step in workflow.steps: step.upgrade_messages = {} # Connections by input name - step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) input_connections_by_name = {} for conn in step.input_connections: input_name = conn.input_name https://bitbucket.org/galaxy/galaxy-central/changeset/709ce65ca6b2/ changeset: 709ce65ca6b2 user: jmchilton date: 2012-10-08 03:19:40 summary: Fix a typo, now workflows contain multi-dataset inputs run. affected #: 1 file diff -r 56551004793378fb618fcfc0214669f307dea594 -r 709ce65ca6b29b15e89a0913546ffd67e1d3c19d lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1429,11 +1429,12 @@ if prefixed_name in step.input_connections_by_name: conn = step.input_connections_by_name[ prefixed_name ] if input.multiple: - replacements = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] else: replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] return replacement try: + # Replace DummyDatasets with historydatasetassociations visit_input_values( tool.inputs, step.state.inputs, callback ) except KeyError, k: error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) https://bitbucket.org/galaxy/galaxy-central/changeset/bbeb3f333beb/ changeset: bbeb3f333beb user: jmchilton date: 2012-10-12 19:01:06 summary: Fix from Jim Johnson for rerunning jobs with multi-input data parameters. affected #: 1 file diff -r 709ce65ca6b29b15e89a0913546ffd67e1d3c19d -r bbeb3f333beb6f09c7a32ef9299c362f999ff79b lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -199,6 +199,12 @@ if isinstance( value, UnvalidatedValue ): return str( value ) if isinstance( input, DataToolParameter ): + if isinstance(value,list): + values = [] + for val in value: + if val not in history.datasets and val in hda_source_dict: + values.append( hda_source_dict[ val ]) + return values if value not in history.datasets and value in hda_source_dict: return hda_source_dict[ value ] visit_input_values( tool.inputs, params_objects, rerun_callback ) https://bitbucket.org/galaxy/galaxy-central/changeset/db6cabd6760c/ changeset: db6cabd6760c user: jmchilton date: 2012-10-16 16:13:32 summary: Initial work from JJ on enhancing the workflow editor to allow multiple input data parameters. Workflows containing such connections will now display properly, though they cannot be modified. affected #: 3 files diff -r bbeb3f333beb6f09c7a32ef9299c362f999ff79b -r db6cabd6760c09f9a5b49aed7e38e4ef991fee97 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -741,12 +741,14 @@ } # Connections input_connections = step.input_connections + multiple_input = {} # Boolean value indicating if this can be mutliple if step.type is None or step.type == 'tool': # Determine full (prefixed) names of valid input datasets data_input_names = {} def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): data_input_names[ prefixed_name ] = True + multiple_input[input.name] = input.multiple visit_input_values( module.tool.inputs, module.state.inputs, callback ) # Filter # FIXME: this removes connection without displaying a message currently! @@ -766,8 +768,14 @@ # Encode input connections as dictionary input_conn_dict = {} for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) + conn_dict = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + if conn.input_name in multiple_input: + if conn.input_name in input_conn_dict: + input_conn_dict[ conn.input_name ].append( conn_dict ) + else: + input_conn_dict[ conn.input_name ] = [ conn_dict ] + else: + input_conn_dict[ conn.input_name ] = conn_dict step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position @@ -832,13 +840,15 @@ # Second pass to deal with connections between steps for step in steps: # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] + for input_name, conns in step.temp_input_connections.iteritems(): + if conns: + conn_dicts = conns if isinstance(conns,list) else [conns] + for conn_dict in conn_dicts: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] del step.temp_input_connections # Order the steps if possible attach_ordered_steps( workflow, steps ) diff -r bbeb3f333beb6f09c7a32ef9299c362f999ff79b -r db6cabd6760c09f9a5b49aed7e38e4ef991fee97 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -263,6 +263,7 @@ data_inputs.append( dict( name=prefixed_name, label=prefixed_label, + multiple=input.multiple, extensions=input.extensions ) ) visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs @@ -340,7 +341,7 @@ if isinstance( input, DataToolParameter ): if connections is None or prefixed_name in input_connections_by_name: if input.multiple: - replacement = [DummyDataset() for conn in connections] + replacement = [] if not connections else [DummyDataset() for conn in connections] else: replacement = DummyDataset() return replacement diff -r bbeb3f333beb6f09c7a32ef9299c362f999ff79b -r db6cabd6760c09f9a5b49aed7e38e4ef991fee97 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -34,16 +34,17 @@ OutputTerminal.prototype = new Terminal(); -function InputTerminal( element, datatypes ) { +function InputTerminal( element, datatypes, multiple ) { Terminal.call( this, element ); this.datatypes = datatypes; + this.multiple = multiple } InputTerminal.prototype = new Terminal(); $.extend( InputTerminal.prototype, { can_accept: function ( other ) { - if ( this.connectors.length < 1 ) { + if ( this.connectors.length < 1 || this.multiple) { for ( var t in this.datatypes ) { var cat_outputs = new Array(); cat_outputs = cat_outputs.concat(other.datatypes); @@ -163,10 +164,10 @@ this.tool_errors = {}; } $.extend( Node.prototype, { - enable_input_terminal : function( elements, name, types ) { + enable_input_terminal : function( elements, name, types, multiple ) { var node = this; $(elements).each( function() { - var terminal = this.terminal = new InputTerminal( this, types ); + var terminal = this.terminal = new InputTerminal( this, types, multiple ); terminal.node = node; terminal.name = name; $(this).bind( "dropinit", function( e, d ) { @@ -304,7 +305,7 @@ var ibox = $("<div class='inputs'></div>").appendTo( b ); $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); - node.enable_input_terminal( t, input.name, input.extensions ); + node.enable_input_terminal( t, input.name, input.extensions, input.multiple ); var ib = $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ); ib.css({ position:'absolute', left: -1000, @@ -407,7 +408,7 @@ var old = old_body.find( "div.input-data-row"); $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); - node.enable_input_terminal( t, input.name, input.extensions ); + node.enable_input_terminal( t, input.name, input.extensions, input.multiple ); // If already connected save old connection old_body.find( "div[name='" + input.name + "']" ).each( function() { $(this).find( ".input-terminal" ).each( function() { @@ -545,8 +546,10 @@ input_connections[ t.name ] = null; // There should only be 0 or 1 connectors, so this is // really a sneaky if statement + var cons = [] $.each( t.connectors, function ( i, c ) { - input_connections[ t.name ] = { id: c.handle1.node.id, output_name: c.handle1.name }; + cons[i] = { id: c.handle1.node.id, output_name: c.handle1.name }; + input_connections[ t.name ] = cons; }); }); var post_job_actions = {}; @@ -617,11 +620,21 @@ var node = wf.nodes[id]; $.each( step.input_connections, function( k, v ) { if ( v ) { - var other_node = wf.nodes[ v.id ]; - var c = new Connector(); - c.connect( other_node.output_terminals[ v.output_name ], - node.input_terminals[ k ] ); - c.redraw(); + if ($.isArray(v)) { + $.each( v, function (l,x ) { + var other_node = wf.nodes[ x.id ]; + var c = new Connector(); + c.connect( other_node.output_terminals[ x.output_name ], + node.input_terminals[ k ] ); + c.redraw(); + }); + } else { + var other_node = wf.nodes[ v.id ]; + var c = new Connector(); + c.connect( other_node.output_terminals[ v.output_name ], + node.input_terminals[ k ] ); + c.redraw(); + } } }); if(using_workflow_outputs && node.type === 'tool'){ https://bitbucket.org/galaxy/galaxy-central/changeset/b9477d8f7050/ changeset: b9477d8f7050 user: jjohnson date: 2012-10-16 18:47:57 summary: Fix workflow_editor exceptions for multi-input when dragging affected #: 1 file diff -r db6cabd6760c09f9a5b49aed7e38e4ef991fee97 -r b9477d8f7050cf90786e749ce096667a7cfc4725 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -112,6 +112,9 @@ var relativeTop = function( e ) { return $(e).offset().top - canvas_container.offset().top; }; + if (!this.handle1 || !this.handle2) { + return; + } // Find the position of each handle var start_x = relativeLeft( this.handle1.element ) + 5; var start_y = relativeTop( this.handle1.element ) + 5; @@ -175,9 +178,13 @@ // compatible type return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal ); }).bind( "dropstart", function( e, d ) { - d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; + if (d.proxy.terminal) { + d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; + } }).bind( "dropend", function ( e, d ) { - d.proxy.terminal.connectors[0].inner_color = "#FFFFFF"; + if (d.proxy.terminal) { + d.proxy.terminal.connectors[0].inner_color = "#FFFFFF"; + } }).bind( "drop", function( e, d ) { ( new Connector( d.drag.terminal, terminal ) ).redraw(); }).bind( "hover", function() { @@ -191,7 +198,9 @@ $("<div class='buttons'></div>").append( $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function() { $.each( terminal.connectors, function( _, x ) { - x.destroy(); + if (x) { + x.destroy(); + } }); t.remove(); }))) https://bitbucket.org/galaxy/galaxy-central/changeset/eec42e84733b/ changeset: eec42e84733b user: jmchilton date: 2012-10-17 16:53:15 summary: Fix workflow imports/exports for multiple input data parameters. affected #: 1 file diff -r b9477d8f7050cf90786e749ce096667a7cfc4725 -r eec42e84733b60c98c388ebf3291636fe0cfb15a lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -1761,9 +1761,22 @@ input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] # Encode input connections as dictionary input_conn_dict = {} - for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) + unique_input_names = set( [conn.input_name for conn in input_connections] ) + for input_name in unique_input_names: + input_conn_dict[ input_name ] = \ + [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] + # Preserve backward compatability. Previously Galaxy + # assumed input connections would be dictionaries not + # lists of dictionaries, so replace any singleton list + # with just the dictionary so that workflows exported from + # newer Galaxy instances can be used with older Galaxy + # instances if they do no include multiple input + # tools. This should be removed at some point. Mirrored + # hack in _workflow_from_dict should never be removed so + # existing workflow exports continue to function. + for input_name, input_conn in dict(input_conn_dict).iteritems(): + if len(input_conn) == 1: + input_conn_dict[input_name] = input_conn[0] step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position @@ -1828,8 +1841,12 @@ # Second pass to deal with connections between steps for step in steps: # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: conn = model.WorkflowStepConnection() conn.input_step = step conn.input_name = input_name https://bitbucket.org/galaxy/galaxy-central/changeset/ba74363c65be/ changeset: ba74363c65be user: dannon date: 2012-10-24 15:00:30 summary: Merge affected #: 6 files diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2245,6 +2245,13 @@ values = input_values[ input.name ] current = values["__current_case__"] wrap_values( input.cases[current].inputs, values ) + elif isinstance( input, DataToolParameter ) and input.multiple: + values = input_values[ input.name ] + input_values[ input.name ] = \ + [DatasetFilenameWrapper( value, + datatypes_registry = self.app.datatypes_registry, + tool = self, + name = input.name ) for value in values] elif isinstance( input, DataToolParameter ): ## FIXME: We're populating param_dict with conversions when ## wrapping values, this should happen as a separate diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1550,6 +1550,10 @@ return value elif isinstance( value, DummyDataset ): return None + elif isinstance( value, list) and len(value) > 0 and isinstance( value[0], DummyDataset): + return None + elif isinstance( value, list ): + return ",".join( [ val if isinstance( val, str ) else str(val.id) for val in value] ) return value.id def to_python( self, value, app ): @@ -1557,6 +1561,10 @@ # indicates that the dataset is optional, while '' indicates that it is not. if value is None or value == '' or value == 'None': return value + if isinstance(value, str) and value.find(",") > -1: + values = value.split(",") + # TODO: Optimize. -John + return [app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( val ) ) for val in values] return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) def to_param_dict_string( self, value, other_values={} ): diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -189,6 +189,12 @@ if isinstance( value, UnvalidatedValue ): return str( value ) if isinstance( input, DataToolParameter ): + if isinstance(value,list): + values = [] + for val in value: + if val not in history.datasets and val in hda_source_dict: + values.append( hda_source_dict[ val ]) + return values if value not in history.datasets and value in hda_source_dict: return hda_source_dict[ value ] visit_input_values( tool.inputs, params_objects, rerun_callback ) diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -741,12 +741,14 @@ } # Connections input_connections = step.input_connections + multiple_input = {} # Boolean value indicating if this can be mutliple if step.type is None or step.type == 'tool': # Determine full (prefixed) names of valid input datasets data_input_names = {} def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): data_input_names[ prefixed_name ] = True + multiple_input[input.name] = input.multiple visit_input_values( module.tool.inputs, module.state.inputs, callback ) # Filter # FIXME: this removes connection without displaying a message currently! @@ -766,8 +768,14 @@ # Encode input connections as dictionary input_conn_dict = {} for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) + conn_dict = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + if conn.input_name in multiple_input: + if conn.input_name in input_conn_dict: + input_conn_dict[ conn.input_name ].append( conn_dict ) + else: + input_conn_dict[ conn.input_name ] = [ conn_dict ] + else: + input_conn_dict[ conn.input_name ] = conn_dict step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position @@ -832,13 +840,15 @@ # Second pass to deal with connections between steps for step in steps: # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_name = conn_dict['output_name'] - conn.output_step = steps_by_external_id[ conn_dict['id'] ] + for input_name, conns in step.temp_input_connections.iteritems(): + if conns: + conn_dicts = conns if isinstance(conns,list) else [conns] + for conn_dict in conn_dicts: + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_name = conn_dict['output_name'] + conn.output_step = steps_by_external_id[ conn_dict['id'] ] del step.temp_input_connections # Order the steps if possible attach_ordered_steps( workflow, steps ) @@ -1346,8 +1356,13 @@ for step in workflow.steps: step.upgrade_messages = {} # Connections by input name - step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) + input_connections_by_name = {} + for conn in step.input_connections: + input_name = conn.input_name + if not input_name in input_connections_by_name: + input_connections_by_name[input_name] = [] + input_connections_by_name[input_name].append(conn) + step.input_connections_by_name = input_connections_by_name # Extract just the arguments for this step by prefix p = "%s|" % step.id l = len(p) @@ -1405,11 +1420,17 @@ tool = trans.app.toolbox.get_tool( step.tool_id ) # Connect up def callback( input, value, prefixed_name, prefixed_label ): + replacement = None if isinstance( input, DataToolParameter ): if prefixed_name in step.input_connections_by_name: conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] + if input.multiple: + replacement = [outputs[ c.output_step.id ][ c.output_name ] for c in conn] + else: + replacement = outputs[ conn[0].output_step.id ][ conn[0].output_name ] + return replacement try: + # Replace DummyDatasets with historydatasetassociations visit_input_values( tool.inputs, step.state.inputs, callback ) except KeyError, k: error( "Error due to input mapping of '%s' in '%s'. A common cause of this is conditional outputs that cannot be determined until runtime, please review your workflow." % (tool.name, k.message)) @@ -1726,9 +1747,22 @@ input_connections = [ conn for conn in input_connections if conn.input_name in data_input_names ] # Encode input connections as dictionary input_conn_dict = {} - for conn in input_connections: - input_conn_dict[ conn.input_name ] = \ - dict( id=conn.output_step.order_index, output_name=conn.output_name ) + unique_input_names = set( [conn.input_name for conn in input_connections] ) + for input_name in unique_input_names: + input_conn_dict[ input_name ] = \ + [ dict( id=conn.output_step.order_index, output_name=conn.output_name ) for conn in input_connections if conn.input_name == input_name ] + # Preserve backward compatability. Previously Galaxy + # assumed input connections would be dictionaries not + # lists of dictionaries, so replace any singleton list + # with just the dictionary so that workflows exported from + # newer Galaxy instances can be used with older Galaxy + # instances if they do no include multiple input + # tools. This should be removed at some point. Mirrored + # hack in _workflow_from_dict should never be removed so + # existing workflow exports continue to function. + for input_name, input_conn in dict(input_conn_dict).iteritems(): + if len(input_conn) == 1: + input_conn_dict[input_name] = input_conn[0] step_dict['input_connections'] = input_conn_dict # Position step_dict['position'] = step.position @@ -1793,8 +1827,12 @@ # Second pass to deal with connections between steps for step in steps: # Input connections - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: + for input_name, conn_list in step.temp_input_connections.iteritems(): + if not conn_list: + continue + if not isinstance(conn_list, list): # Older style singleton connection + conn_list = [conn_list] + for conn_dict in conn_list: conn = model.WorkflowStepConnection() conn.input_step = step conn.input_name = input_name @@ -2040,7 +2078,11 @@ # still need to clean them up so we can serialize # if not( prefix ): if tmp: #this is false for a non-set optional dataset - associations.append( ( tmp.hid, prefix + key ) ) + if not isinstance(tmp, list): + associations.append( ( tmp.hid, prefix + key ) ) + else: + associations.extend( [ (t.hid, prefix + key) for t in tmp] ) + # Cleanup the other deprecated crap associated with datasets # as well. Worse, for nested datasets all the metadata is # being pushed into the root. FIXME: MUST REMOVE SOON diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -263,6 +263,7 @@ data_inputs.append( dict( name=prefixed_name, label=prefixed_label, + multiple=input.multiple, extensions=input.extensions ) ) visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs @@ -336,9 +337,14 @@ # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) def callback( input, value, prefixed_name, prefixed_label ): + replacement = None if isinstance( input, DataToolParameter ): if connections is None or prefixed_name in input_connections_by_name: - return DummyDataset() + if input.multiple: + replacement = [] if not connections else [DummyDataset() for conn in connections] + else: + replacement = DummyDataset() + return replacement visit_input_values( self.tool.inputs, self.state.inputs, callback ) class WorkflowModuleFactory( object ): diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -34,16 +34,17 @@ OutputTerminal.prototype = new Terminal(); -function InputTerminal( element, datatypes ) { +function InputTerminal( element, datatypes, multiple ) { Terminal.call( this, element ); this.datatypes = datatypes; + this.multiple = multiple } InputTerminal.prototype = new Terminal(); $.extend( InputTerminal.prototype, { can_accept: function ( other ) { - if ( this.connectors.length < 1 ) { + if ( this.connectors.length < 1 || this.multiple) { for ( var t in this.datatypes ) { var cat_outputs = new Array(); cat_outputs = cat_outputs.concat(other.datatypes); @@ -111,6 +112,9 @@ var relativeTop = function( e ) { return $(e).offset().top - canvas_container.offset().top; }; + if (!this.handle1 || !this.handle2) { + return; + } // Find the position of each handle var start_x = relativeLeft( this.handle1.element ) + 5; var start_y = relativeTop( this.handle1.element ) + 5; @@ -163,10 +167,10 @@ this.tool_errors = {}; } $.extend( Node.prototype, { - enable_input_terminal : function( elements, name, types ) { + enable_input_terminal : function( elements, name, types, multiple ) { var node = this; $(elements).each( function() { - var terminal = this.terminal = new InputTerminal( this, types ); + var terminal = this.terminal = new InputTerminal( this, types, multiple ); terminal.node = node; terminal.name = name; $(this).bind( "dropinit", function( e, d ) { @@ -174,9 +178,13 @@ // compatible type return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal ); }).bind( "dropstart", function( e, d ) { - d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; + if (d.proxy.terminal) { + d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; + } }).bind( "dropend", function ( e, d ) { - d.proxy.terminal.connectors[0].inner_color = "#FFFFFF"; + if (d.proxy.terminal) { + d.proxy.terminal.connectors[0].inner_color = "#FFFFFF"; + } }).bind( "drop", function( e, d ) { ( new Connector( d.drag.terminal, terminal ) ).redraw(); }).bind( "hover", function() { @@ -190,7 +198,9 @@ $("<div class='buttons'></div>").append( $("<img/>").attr("src", galaxy_paths.attributes.image_path + '/delete_icon.png').click( function() { $.each( terminal.connectors, function( _, x ) { - x.destroy(); + if (x) { + x.destroy(); + } }); t.remove(); }))) @@ -304,7 +314,7 @@ var ibox = $("<div class='inputs'></div>").appendTo( b ); $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); - node.enable_input_terminal( t, input.name, input.extensions ); + node.enable_input_terminal( t, input.name, input.extensions, input.multiple ); var ib = $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ); ib.css({ position:'absolute', left: -1000, @@ -407,7 +417,7 @@ var old = old_body.find( "div.input-data-row"); $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); - node.enable_input_terminal( t, input.name, input.extensions ); + node.enable_input_terminal( t, input.name, input.extensions, input.multiple ); // If already connected save old connection old_body.find( "div[name='" + input.name + "']" ).each( function() { $(this).find( ".input-terminal" ).each( function() { @@ -545,8 +555,10 @@ input_connections[ t.name ] = null; // There should only be 0 or 1 connectors, so this is // really a sneaky if statement + var cons = [] $.each( t.connectors, function ( i, c ) { - input_connections[ t.name ] = { id: c.handle1.node.id, output_name: c.handle1.name }; + cons[i] = { id: c.handle1.node.id, output_name: c.handle1.name }; + input_connections[ t.name ] = cons; }); }); var post_job_actions = {}; @@ -617,11 +629,21 @@ var node = wf.nodes[id]; $.each( step.input_connections, function( k, v ) { if ( v ) { - var other_node = wf.nodes[ v.id ]; - var c = new Connector(); - c.connect( other_node.output_terminals[ v.output_name ], - node.input_terminals[ k ] ); - c.redraw(); + if ($.isArray(v)) { + $.each( v, function (l,x ) { + var other_node = wf.nodes[ x.id ]; + var c = new Connector(); + c.connect( other_node.output_terminals[ x.output_name ], + node.input_terminals[ k ] ); + c.redraw(); + }); + } else { + var other_node = wf.nodes[ v.id ]; + var c = new Connector(); + c.connect( other_node.output_terminals[ v.output_name ], + node.input_terminals[ k ] ); + c.redraw(); + } } }); if(using_workflow_outputs && node.type === 'tool'){ https://bitbucket.org/galaxy/galaxy-central/changeset/10342b1b167a/ changeset: 10342b1b167a user: dannon date: 2012-10-24 16:31:43 summary: Merge affected #: 4 files diff -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -418,6 +418,13 @@ def sort( self, trans, query, ascending, column_name=None ): """Sort query using this column.""" return GridColumn.sort( self, trans, query, ascending, column_name=column_name ) + def get_single_filter( self, user, a_filter ): + if self.key.find( '.' ) > -1: + a_key = self.key.split( '.' )[1] + else: + a_key = self.key + model_class_key_field = getattr( self.model_class, a_key ) + return model_class_key_field == a_filter class IntegerColumn( TextColumn ): """ diff -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -292,28 +292,25 @@ ] class AdminRepositoryGrid( RepositoryGrid ): + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): + if repository.deleted: + return 'yes' + return '' columns = [ RepositoryGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), - RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ), - RepositoryGrid.DeprecatedColumn( "Deprecated", attach_popup=False ), + RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], + DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -327,6 +324,10 @@ condition=( lambda item: item.deleted ), async_compatible=False ) ) standard_filters = [] + default_filter = {} + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( model.User.table ) class RepositoryMetadataGrid( grids.Grid ): class IdColumn( grids.IntegerColumn ): @@ -335,6 +336,9 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.name + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.user.username class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository @@ -343,42 +347,60 @@ return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - tools_str = '' + tools_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: - for tool_metadata_dict in metadata[ 'tools' ]: - tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + # We used to display the following, but grid was too cluttered. + #for tool_metadata_dict in metadata[ 'tools' ]: + # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + return '%d' % len( metadata[ 'tools' ] ) return tools_str class DatatypesColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - datatypes_str = '' + datatypes_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'datatypes' in metadata: - for datatype_metadata_dict in metadata[ 'datatypes' ]: - datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + # We used to display the following, but grid was too cluttered. + #for datatype_metadata_dict in metadata[ 'datatypes' ]: + # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + return '%d' % len( metadata[ 'datatypes' ] ) return datatypes_str class WorkflowsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - workflows_str = '' + workflows_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'workflows' in metadata: - workflows_str += '<b>Workflows:</b><br/>' + # We used to display the following, but grid was too cluttered. + #workflows_str += '<b>Workflows:</b><br/>' # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - workflow_tups = metadata[ 'workflows' ] - workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] - for workflow_metadata_dict in workflow_metadata_dicts: - workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + #workflow_tups = metadata[ 'workflows' ] + #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] + #for workflow_metadata_dict in workflow_metadata_dicts: + # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + return '%d' % len( metadata[ 'workflows' ] ) return workflows_str + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deleted: + return 'yes' + return '' + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deprecated: + return 'yes' + return '' class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.malicious + if repository_metadata.malicious: + return 'yes' + return '' # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata @@ -393,16 +415,14 @@ model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), attach_popup=True ), - RevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tools", - attach_popup=False ), - DatatypesColumn( "Datatypes", - attach_popup=False ), - WorkflowsColumn( "Workflows", - attach_popup=False ), - MaliciousColumn( "Malicious", - attach_popup=False ) + OwnerColumn( "Owner", attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + ToolsColumn( "Tools", attach_popup=False ), + DatatypesColumn( "Datatypes", attach_popup=False ), + WorkflowsColumn( "Workflows", attach_popup=False ), + DeletedColumn( "Deleted", attach_popup=False ), + DeprecatedColumn( "Deprecated", attach_popup=False ), + MaliciousColumn( "Malicious", attach_popup=False ) ] operations = [ grids.GridOperation( "Delete", allow_multiple=False, @@ -416,8 +436,7 @@ use_paging = True def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository.table ) \ - .filter( model.Repository.table.c.deprecated == False ) + .join( model.Repository.table ) class AdminController( BaseUIController, Admin ): diff -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -39,7 +39,8 @@ if category.repositories: viewable_repositories = 0 for rca in category.repositories: - viewable_repositories += 1 + if not rca.repository.deleted and not rca.repository.deprecated: + viewable_repositories += 1 return viewable_repositories return 0 title = "Categories" @@ -191,8 +192,6 @@ link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), - grids.CommunityRatingColumn( "Average Rating", key="rating" ), - EmailAlertsColumn( "Alert", attach_popup=False ), # Columns that are valid for filtering but are not visible. EmailColumn( "Email", model_class=model.User, @@ -201,11 +200,7 @@ RepositoryCategoryColumn( "Category", model_class=model.Category, key="Category.name", - visible=False ), - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + visible=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[0], columns[1] ], @@ -222,7 +217,9 @@ preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) \ + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) @@ -257,7 +254,8 @@ async_compatible=False ) ] def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.user_id == trans.user.id ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.user_id == trans.user.id ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) @@ -283,7 +281,8 @@ filterable="standard" ) ) def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.user_id == trans.user.id, + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.user_id == trans.user.id, model.Repository.table.c.deprecated == True ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ @@ -341,11 +340,7 @@ RepositoryGrid.RepositoryCategoryColumn( "Category", model_class=model.Category, key="Category.name", - visible=False ), - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + visible=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], @@ -375,7 +370,8 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) # Return an empty query. - return [] + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.id < 0 ) class ValidRepositoryGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as deprecated. @@ -435,7 +431,8 @@ if 'id' in kwd: # The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id. return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) \ .join( model.RepositoryCategoryAssociation.table ) \ @@ -444,7 +441,8 @@ model.RepositoryMetadata.table.c.downloadable == True ) ) # The user performed a free text search on the ValidCategoryGrid. return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ @@ -501,7 +499,8 @@ changeset_revision ) ) return trans.sa_session.query( model.RepositoryMetadata ) \ .join( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ) \ .filter( or_( *clause_list ) ) \ .order_by( model.Repository.name ) @@ -556,7 +555,8 @@ # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we # are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: - # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository id to pass on. + # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository + # id to pass on. try: repository = get_repository_by_name( trans, kwd[ 'id' ] ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) diff -r ba74363c65bee1e90a4ae6346cbd7f2d3ff9a6b3 -r 10342b1b167a6f7290b8f3dc1d00c2d2b77e046f lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -222,7 +222,7 @@ properties=dict( repositories=relation( RepositoryCategoryAssociation, secondary=Repository.table, primaryjoin=( Category.table.c.id == RepositoryCategoryAssociation.table.c.category_id ), - secondaryjoin=( ( RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id ) & ( Repository.table.c.deprecated == False ) ) ) ) ) + secondaryjoin=( RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id ) ) ) ) assign_mapper( context, Repository, Repository.table, properties = dict( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for the Category.repositories mapper.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f56ec1622b27/ changeset: f56ec1622b27 user: greg date: 2012-10-24 16:24:11 summary: Fix for the Category.repositories mapper. affected #: 1 file diff -r 25ff502e7faa7e6030545a3035b5e98ee584ab5a -r f56ec1622b278da8d759805e70d3a7ac61596328 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -222,7 +222,7 @@ properties=dict( repositories=relation( RepositoryCategoryAssociation, secondary=Repository.table, primaryjoin=( Category.table.c.id == RepositoryCategoryAssociation.table.c.category_id ), - secondaryjoin=( ( RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id ) & ( Repository.table.c.deprecated == False ) ) ) ) ) + secondaryjoin=( RepositoryCategoryAssociation.table.c.repository_id == Repository.table.c.id ) ) ) ) assign_mapper( context, Repository, Repository.table, properties = dict( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Grid cleanup in the tool shed repository controller.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/25ff502e7faa/ changeset: 25ff502e7faa user: greg date: 2012-10-24 16:23:08 summary: Grid cleanup in the tool shed repository controller. affected #: 1 file diff -r 2350e6e0ca9c6ad885de9fac9d196dc07c45d074 -r 25ff502e7faa7e6030545a3035b5e98ee584ab5a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -39,7 +39,8 @@ if category.repositories: viewable_repositories = 0 for rca in category.repositories: - viewable_repositories += 1 + if not rca.repository.deleted and not rca.repository.deprecated: + viewable_repositories += 1 return viewable_repositories return 0 title = "Categories" @@ -191,8 +192,6 @@ link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), - grids.CommunityRatingColumn( "Average Rating", key="rating" ), - EmailAlertsColumn( "Alert", attach_popup=False ), # Columns that are valid for filtering but are not visible. EmailColumn( "Email", model_class=model.User, @@ -201,11 +200,7 @@ RepositoryCategoryColumn( "Category", model_class=model.Category, key="Category.name", - visible=False ), - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + visible=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, description", cols_to_filter=[ columns[0], columns[1] ], @@ -222,7 +217,9 @@ preserve_state = False use_paging = True def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) \ + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) @@ -257,7 +254,8 @@ async_compatible=False ) ] def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.user_id == trans.user.id ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.user_id == trans.user.id ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) @@ -283,7 +281,8 @@ filterable="standard" ) ) def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.user_id == trans.user.id, + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.user_id == trans.user.id, model.Repository.table.c.deprecated == True ) ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ @@ -341,11 +340,7 @@ RepositoryGrid.RepositoryCategoryColumn( "Category", model_class=model.Category, key="Category.name", - visible=False ), - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) + visible=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name", cols_to_filter=[ columns[0] ], @@ -375,7 +370,8 @@ .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) # Return an empty query. - return [] + return trans.sa_session.query( model.Repository ) \ + .filter( model.Repository.table.c.id < 0 ) class ValidRepositoryGrid( RepositoryGrid ): # This grid filters out repositories that have been marked as deprecated. @@ -435,7 +431,8 @@ if 'id' in kwd: # The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id. return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) \ .join( model.RepositoryCategoryAssociation.table ) \ @@ -444,7 +441,8 @@ model.RepositoryMetadata.table.c.downloadable == True ) ) # The user performed a free text search on the ValidCategoryGrid. return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) \ .outerjoin( model.RepositoryCategoryAssociation.table ) \ @@ -501,7 +499,8 @@ changeset_revision ) ) return trans.sa_session.query( model.RepositoryMetadata ) \ .join( model.Repository ) \ - .filter( model.Repository.table.c.deprecated == False ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ .join( model.User.table ) \ .filter( or_( *clause_list ) ) \ .order_by( model.Repository.name ) @@ -556,7 +555,8 @@ # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we # are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: - # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository id to pass on. + # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository + # id to pass on. try: repository = get_repository_by_name( trans, kwd[ 'id' ] ) kwd[ 'id' ] = trans.security.encode_id( repository.id ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Grid cleanup in the tool shed admin controller.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2350e6e0ca9c/ changeset: 2350e6e0ca9c user: greg date: 2012-10-24 16:21:45 summary: Grid cleanup in the tool shed admin controller. affected #: 1 file diff -r 25a93da96e03431557e1418fd4cf70ab7b6ec427 -r 2350e6e0ca9c6ad885de9fac9d196dc07c45d074 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -292,28 +292,25 @@ ] class AdminRepositoryGrid( RepositoryGrid ): + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): + if repository.deleted: + return 'yes' + return '' columns = [ RepositoryGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=True ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), RepositoryGrid.UserColumn( "Owner", model_class=model.User, link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), attach_popup=False, key="User.username" ), - RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ), - RepositoryGrid.DeprecatedColumn( "Deprecated", attach_popup=False ), + RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], + DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -327,6 +324,10 @@ condition=( lambda item: item.deleted ), async_compatible=False ) ) standard_filters = [] + default_filter = {} + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( model.User.table ) class RepositoryMetadataGrid( grids.Grid ): class IdColumn( grids.IntegerColumn ): @@ -335,6 +336,9 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.name + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.user.username class RevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository @@ -343,42 +347,60 @@ return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - tools_str = '' + tools_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: - for tool_metadata_dict in metadata[ 'tools' ]: - tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + # We used to display the following, but grid was too cluttered. + #for tool_metadata_dict in metadata[ 'tools' ]: + # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + return '%d' % len( metadata[ 'tools' ] ) return tools_str class DatatypesColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - datatypes_str = '' + datatypes_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'datatypes' in metadata: - for datatype_metadata_dict in metadata[ 'datatypes' ]: - datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + # We used to display the following, but grid was too cluttered. + #for datatype_metadata_dict in metadata[ 'datatypes' ]: + # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + return '%d' % len( metadata[ 'datatypes' ] ) return datatypes_str class WorkflowsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - workflows_str = '' + workflows_str = '0' if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'workflows' in metadata: - workflows_str += '<b>Workflows:</b><br/>' + # We used to display the following, but grid was too cluttered. + #workflows_str += '<b>Workflows:</b><br/>' # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - workflow_tups = metadata[ 'workflows' ] - workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] - for workflow_metadata_dict in workflow_metadata_dicts: - workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + #workflow_tups = metadata[ 'workflows' ] + #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] + #for workflow_metadata_dict in workflow_metadata_dicts: + # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + return '%d' % len( metadata[ 'workflows' ] ) return workflows_str + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deleted: + return 'yes' + return '' + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deprecated: + return 'yes' + return '' class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.malicious + if repository_metadata.malicious: + return 'yes' + return '' # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata @@ -393,16 +415,14 @@ model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), attach_popup=True ), - RevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tools", - attach_popup=False ), - DatatypesColumn( "Datatypes", - attach_popup=False ), - WorkflowsColumn( "Workflows", - attach_popup=False ), - MaliciousColumn( "Malicious", - attach_popup=False ) + OwnerColumn( "Owner", attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + ToolsColumn( "Tools", attach_popup=False ), + DatatypesColumn( "Datatypes", attach_popup=False ), + WorkflowsColumn( "Workflows", attach_popup=False ), + DeletedColumn( "Deleted", attach_popup=False ), + DeprecatedColumn( "Deprecated", attach_popup=False ), + MaliciousColumn( "Malicious", attach_popup=False ) ] operations = [ grids.GridOperation( "Delete", allow_multiple=False, @@ -416,8 +436,7 @@ use_paging = True def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository.table ) \ - .filter( model.Repository.table.c.deprecated == False ) + .join( model.Repository.table ) class AdminController( BaseUIController, Admin ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Override the grid's TextColumn.get_single_filter() method for the BooleanColumn so the BooleanColumn can be used in grids.
by Bitbucket 24 Oct '12

24 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/25a93da96e03/ changeset: 25a93da96e03 user: greg date: 2012-10-24 15:51:17 summary: Override the grid's TextColumn.get_single_filter() method for the BooleanColumn so the BooleanColumn can be used in grids. affected #: 1 file diff -r 33db1925e701664785735160f3738dfde97fc2e6 -r 25a93da96e03431557e1418fd4cf70ab7b6ec427 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -418,6 +418,13 @@ def sort( self, trans, query, ascending, column_name=None ): """Sort query using this column.""" return GridColumn.sort( self, trans, query, ascending, column_name=column_name ) + def get_single_filter( self, user, a_filter ): + if self.key.find( '.' ) > -1: + a_key = self.key.split( '.' )[1] + else: + a_key = self.key + model_class_key_field = getattr( self.model_class, a_key ) + return model_class_key_field == a_filter class IntegerColumn( TextColumn ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Handle weak Python 2.5 unicode string handling in the tool shed.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/33db1925e701/ changeset: 33db1925e701 user: greg date: 2012-10-23 22:52:25 summary: Handle weak Python 2.5 unicode string handling in the tool shed. affected #: 2 files diff -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 -r 33db1925e701664785735160f3738dfde97fc2e6 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -50,7 +50,7 @@ break if found: break - full_path = os.path.abspath( os.path.join( root, name ) ) + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) tool = self.toolbox.load_tool( full_path ) return generate_tool_guid( repository_clone_url, tool ) def get_proprietary_tool_panel_elems( self, latest_tool_migration_script_number ): diff -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 -r 33db1925e701664785735160f3738dfde97fc2e6 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -685,7 +685,7 @@ metadata_dict[ 'readme' ] = relative_path_to_readme # See if we have a tool config. elif name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) if os.path.getsize( full_path ) > 0: if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the problematic Repository.ReviewedRevisions mapper from the tool shed model.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/70ae646e6892/ changeset: 70ae646e6892 user: greg date: 2012-10-23 22:20:05 summary: Eliminate the problematic Repository.ReviewedRevisions mapper from the tool shed model. affected #: 3 files diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -156,11 +156,9 @@ def changeset_revision_reviewed_by_user( trans, user, repository, changeset_revision ): """Determine if the current changeset revision has been reviewed by the current user.""" changeset_revision_reviewed_by_user = False - for reviewed_revision in repository.reviewed_revisions: - if reviewed_revision.changeset_revision == changeset_revision: - for review in repository.reviews: - if review.changeset_revision == changeset_revision and review.user == user: - return True + for review in repository.reviews: + if review.changeset_revision == changeset_revision and review.user == user: + return True return False def check_file_contents( trans ): # See if any admin users have chosen to receive email alerts when a repository is updated. @@ -505,13 +503,15 @@ def get_previous_repository_reviews( trans, repository, changeset_revision ): """Return an ordered dictionary of repository reviews up to and including the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path ) - reviewed_revision_hashes = [ reviewed_revisions.changeset_revision for reviewed_revisions in repository.reviewed_revisions ] + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] previous_reviews_dict = odict() for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: previous_rev, previous_changeset_revision_label = get_rev_label_from_changeset_revision( repo, previous_changeset_revision ) - revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, trans.security.encode_id( repository.id ), previous_changeset_revision ) + revision_reviews = get_reviews_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + previous_changeset_revision ) previous_reviews_dict[ previous_changeset_revision ] = dict( changeset_revision_label=previous_changeset_revision_label, reviews=revision_reviews ) return previous_reviews_dict @@ -701,7 +701,7 @@ def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path ) - reviewed_revision_hashes = [ reviewed_revisions.changeset_revision for reviewed_revisions in repository.reviewed_revisions ] + reviewed_revision_hashes = [ review.changeset_revision for review in repository.reviews ] for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): previous_changeset_revision = str( repo.changectx( changeset ) ) if previous_changeset_revision in reviewed_revision_hashes: diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1530,7 +1530,7 @@ if current_user: # See if the current user owns any repositories that have been reviewed. for repository in current_user.active_repositories: - if repository.reviewed_revisions: + if repository.reviews: has_reviewed_repositories = True break # See if the current user has any repositories that have been marked as deprecated. diff -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 -r 70ae646e6892e7bb5a05500c99b4cfcc22495a37 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -239,12 +239,7 @@ reviewers=relation( User, secondary=RepositoryReview.table, primaryjoin=( Repository.table.c.id == RepositoryReview.table.c.repository_id ), - secondaryjoin=( RepositoryReview.table.c.user_id == User.table.c.id ) ), - reviewed_revisions=relation( RepositoryMetadata, - secondary=RepositoryReview.table, - foreign_keys=[ RepositoryMetadata.table.c.repository_id, RepositoryMetadata.table.c.changeset_revision ], - primaryjoin=( Repository.table.c.id == RepositoryMetadata.table.c.repository_id ), - secondaryjoin=( ( RepositoryMetadata.table.c.repository_id == RepositoryReview.table.c.repository_id ) & ( RepositoryMetadata.table.c.changeset_revision == RepositoryReview.table.c.changeset_revision ) ) ) ) ) + secondaryjoin=( RepositoryReview.table.c.user_id == User.table.c.id ) ) ) ) assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Circster, enhancements for chords: (a) adjust chords when datasets added/removed from visualization; (b) use config to color; and (c) enable dynamic addition of chord/interaction datasets.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d6ce5e2a1cdb/ changeset: d6ce5e2a1cdb user: jgoecks date: 2012-10-23 21:41:48 summary: Circster, enhancements for chords: (a) adjust chords when datasets added/removed from visualization; (b) use config to color; and (c) enable dynamic addition of chord/interaction datasets. affected #: 3 files diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -19,6 +19,7 @@ from paste.httpexceptions import * from galaxy.exceptions import * from galaxy.model import NoConverterException, ConverterDependencyException +from galaxy.datatypes.interval import ChromatinInteractions from Cheetah.Template import Template @@ -602,7 +603,7 @@ return visualization - def _get_genome_data( self, trans, dataset, dbkey=None, source='index' ): + def _get_genome_data( self, trans, dataset, dbkey=None ): """ Returns genome-wide data for dataset if available; if not, message is returned. """ @@ -621,6 +622,11 @@ if message: rval = message else: + # HACK: chromatin interactions tracks use data as source. + source = 'index' + if isinstance( dataset.datatype, ChromatinInteractions ): + source = 'data' + data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset, source=source ) diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -8,7 +8,6 @@ from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genome.visual_analytics import get_dataset_job from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider -from galaxy.datatypes.interval import ChromatinInteractions from .library import LibraryListGrid @@ -753,12 +752,8 @@ tracks = viz_config.get( 'tracks', [] ) for track in tracks: dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - # HACK: chromatin interactions tracks use data as source. - source = 'index' - if isinstance( dataset.datatype, ChromatinInteractions ): - source = 'data' - genome_data = self._get_genome_data( trans, dataset, dbkey, source=source ) + genome_data = self._get_genome_data( trans, dataset, dbkey ) if not isinstance( genome_data, str ): track[ 'preloaded_data' ] = genome_data diff -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 -r d6ce5e2a1cdb8645f3490043b151f2b271f4b2b4 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -200,31 +200,53 @@ * Render a single track on the outside of the current visualization. */ add_track: function(new_track) { - // Recompute and update track bounds. - var new_track_bounds = this.get_tracks_bounds(); - _.each(this.circular_views, function(track_view, i) { - track_view.update_radius_bounds(new_track_bounds[i]); - }); + if (new_track.get('track_type') === 'DiagonalHeatmapTrack') { + // Added chords track. + var innermost_radius_bounds = this.circular_views[0].radius_bounds, + new_view = new CircsterChromInteractionsTrackView({ + el: d3.select('g.tracks').append('g')[0], + track: new_track, + radius_bounds: innermost_radius_bounds, + genome: this.genome, + total_gap: this.total_gap + }); + new_view.render(); + this.chords_views.push(new_view); + } + else { + // Added circular track. - // Render new track. - var track_index = this.circular_views.length, - track_view_class = (new_track.get('track_type') === 'LineTrack' ? - CircsterBigWigTrackView : - CircsterSummaryTreeTrackView ), - track_view = new track_view_class({ - el: d3.select('g.tracks').append('g')[0], - track: new_track, - radius_bounds: new_track_bounds[track_index], - genome: this.genome, - total_gap: this.total_gap + // Recompute and update track bounds. + var new_track_bounds = this.get_tracks_bounds(); + _.each(this.circular_views, function(track_view, i) { + track_view.update_radius_bounds(new_track_bounds[i]); }); - track_view.render(); - this.circular_views.push(track_view); - // Update label track. - var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; - track_bounds[1] = track_bounds[0]; - this.label_track_view.update_radius_bounds(track_bounds); + // Update chords tracks. + _.each(this.chords_views, function(track_view) { + track_view.update_radius_bounds(new_track_bounds[0]); + }); + + // Render new track. + var track_index = this.circular_views.length, + track_view_class = (new_track.get('track_type') === 'LineTrack' ? + CircsterBigWigTrackView : + CircsterSummaryTreeTrackView ), + track_view = new track_view_class({ + el: d3.select('g.tracks').append('g')[0], + track: new_track, + radius_bounds: new_track_bounds[track_index], + genome: this.genome, + total_gap: this.total_gap + }); + track_view.render(); + this.circular_views.push(track_view); + + // Update label track. + var track_bounds = new_track_bounds[ new_track_bounds.length-1 ]; + track_bounds[1] = track_bounds[0]; + this.label_track_view.update_radius_bounds(track_bounds); + } }, /** @@ -269,6 +291,15 @@ }, /** + * Get fill color from config. + */ + get_fill_color: function() { + var color = this.track.get('config').get_value('block_color'); + if (!color) { color = this.track.get('config').get_value('color'); } + return color; + }, + + /** * Render track's data by adding SVG elements to parent. */ render: function() { @@ -382,10 +413,8 @@ }); // Add new data path and apply preferences. - var prefs = self.track.get('prefs'), - block_color = prefs.block_color; - if (!block_color) { block_color = prefs.color; } - self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', block_color).style('fill', block_color); + var color = self.get_fill_color(); + self._render_chrom_data(self.parent_elt, chrom_arc, data).style('stroke', color).style('fill', color); }); }); @@ -463,10 +492,8 @@ }); // Apply prefs to all track data. - var config = track.get('config'), - block_color = config.get_value('block_color'); - if (!block_color) { block_color = config.get_value('color'); } - self.parent_elt.selectAll('path.chrom-data').style('stroke', block_color).style('fill', block_color); + var color = self.get_fill_color(); + self.parent_elt.selectAll('path.chrom-data').style('stroke', color).style('fill', color); rendered_deferred.resolve(svg); }); @@ -653,7 +680,7 @@ // When data is ready, render track. $.when(self.track.get('data_manager').data_is_ready()).then(function() { - // Convert genome-wide data in chord data. + // When data has been fetched, render track. $.when(self.track.get('data_manager').get_genome_wide_data(self.genome)).then(function(genome_wide_data) { var chord_data = [], chroms_info = self.genome.get_chroms_info(); @@ -685,13 +712,18 @@ .selectAll("path") .data(chord_data) .enter().append("path") - .style("fill", '000') + .style("fill", self.get_fill_color()) .attr("d", d3.svg.chord().radius(self.radius_bounds[0])) .style("opacity", 1); }); }); }, + update_radius_bounds: function(radius_bounds) { + this.radius_bounds = radius_bounds; + this.parent_elt.selectAll("path").transition().attr("d", d3.svg.chord().radius(this.radius_bounds[0])); + }, + /** * Returns radians for a genomic position. */ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Clarify the various url protocols that are supported by the tool shed repository upload component.
by Bitbucket 23 Oct '12

23 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f23c2b0ef005/ changeset: f23c2b0ef005 user: greg date: 2012-10-23 21:23:51 summary: Clarify the various url protocols that are supported by the tool shed repository upload component. affected #: 1 file diff -r bad5602cdf998dff9c2aecf478dc4ed1a797a023 -r f23c2b0ef005f1e44299d11fd8fbe5077fe850f0 templates/webapps/community/repository/upload.mako --- a/templates/webapps/community/repository/upload.mako +++ b/templates/webapps/community/repository/upload.mako @@ -85,10 +85,10 @@ <input name="url" type="textfield" value="${url | h}" size="40"/></div><div class="toolParamHelp" style="clear: both;"> - Enter a URL to upload your files via http. URLs that point to mercurial repositories (URLs that start with hg:// or hgs://) - are allowed. This mechanism results in the tip revision of an external mercurial repository being added to the tool shed - repository as a single new changeset. The revision history of the originating external mercurial repository is not uploaded - to the tool shed repository. + Enter a url to upload your files. In addition to http and ftp urls, urls that point to mercurial repositories (urls that start + with hg:// or hgs://) are allowed. This mechanism results in the tip revision of an external mercurial repository being added + to the tool shed repository as a single new changeset. The revision history of the originating external mercurial repository is + not uploaded to the tool shed repository. </div><div style="clear: both"></div></div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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