April 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d7aa747eb7e/ Changeset: 9d7aa747eb7e User: jmchilton Date: 2014-04-10 20:31:46 Summary: Remove unused variable? Affected #: 1 file diff -r 2eb03ce13018bbd46ddf55b296246b355afd7ba4 -r 9d7aa747eb7ee1f01db0821e51bc80f0271204a5 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -422,7 +422,6 @@ // Update input rows var old_body = el.find( "div.inputs" ); var new_body = $("<div class='inputs'></div>"); - var old = old_body.find( "div.input-data-row"); $.each( data.data_inputs, function( i, input ) { var t = node.new_input_terminal( input ); // If already connected save old connection https://bitbucket.org/galaxy/galaxy-central/commits/b51841ba5ce8/ Changeset: b51841ba5ce8 User: jmchilton Date: 2014-04-10 20:31:47 Summary: Refactor interaction between workflows JS and editor JS for adding nodes. Add abstraction into editor for use by galaxy.workflow.js to hide some editor details from workflow code and reduce duplication between add_node_for_tool and add_node_for_module. Affected #: 2 files diff -r 9d7aa747eb7ee1f01db0821e51bc80f0271204a5 -r b51841ba5ce81e0adb416c80123ed28184e4c549 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -892,6 +892,18 @@ return node; } +function add_node( type, title_text, tool_id ) { + // Abstraction for use by galaxy.workflow.js to hide + // some editor details from workflow code and reduce duplication + // between add_node_for_tool and add_node_for_module. + var node = prebuild_node( type, title_text, tool_id ); + workflow.add_node( node ); + workflow.fit_canvas_to_nodes(); + canvas_manager.draw_overview(); + workflow.activate_node( node ); + return node; +} + var ext_to_type = null; var type_to_type = null; diff -r 9d7aa747eb7ee1f01db0821e51bc80f0271204a5 -r b51841ba5ce81e0adb416c80123ed28184e4c549 static/scripts/galaxy.workflows.js --- a/static/scripts/galaxy.workflows.js +++ b/static/scripts/galaxy.workflows.js @@ -320,11 +320,7 @@ // Add a new step to the workflow by tool id function add_node_for_tool( id, title ) { - var node = prebuild_node( 'tool', title, id ); - workflow.add_node( node ); - workflow.fit_canvas_to_nodes(); - canvas_manager.draw_overview(); - workflow.activate_node( node ); + node = add_node( 'tool', title, id ); $.ajax( { url: get_new_module_info_url, data: { type: "tool", tool_id: id, "_": "true" }, @@ -344,11 +340,7 @@ } function add_node_for_module( type, title ) { - node = prebuild_node( type, title ); - workflow.add_node( node ); - workflow.fit_canvas_to_nodes(); - canvas_manager.draw_overview(); - workflow.activate_node( node ); + node = add_node( type, title ); $.ajax( { url: get_new_module_info_url, data: { type: type, "_": "true" }, https://bitbucket.org/galaxy/galaxy-central/commits/8f577a1a3901/ Changeset: 8f577a1a3901 User: jmchilton Date: 2014-04-10 20:31:48 Summary: Outline workflow editor tests. Affected #: 2 files diff -r b51841ba5ce81e0adb416c80123ed28184e4c549 -r 8f577a1a390145aaab909ccbfbd31a78241f2e45 test/qunit/tests/workflow_editor_tests.html --- /dev/null +++ b/test/qunit/tests/workflow_editor_tests.html @@ -0,0 +1,10 @@ +<!doctype html> + +<html> + <head> + <script data-main="../test-common" src="../scripts/libs/require.js"></script> + </head> + <body> + </body> +</html> diff -r b51841ba5ce81e0adb416c80123ed28184e4c549 -r 8f577a1a390145aaab909ccbfbd31a78241f2e45 test/qunit/tests/workflow_editor_tests.js --- /dev/null +++ b/test/qunit/tests/workflow_editor_tests.js @@ -0,0 +1,379 @@ +/* global define, QUnit, module, test, ok, equal, deepEqual, notEqual */ +/* global Workflow, CanvasManager, InputTerminal, Connector, add_node */ +define([ + "galaxy.workflow_editor.canvas", + "jquery", + "sinon-qunit" +], function( + workflowEditor, + $, + sinon +){ + "use strict"; + + // globals cosumed by workflow editor + window.show_form_for_tool = sinon.spy(); + window.workflow = null; + window.canvas_manager = null; + + // Stub used over stubbing issubtype for unit testing datatype comparisons. + var issubtypeStub = null; + + QUnit.moduleStart(function() { + if( issubtypeStub === null) { + issubtypeStub = sinon.stub( window, "issubtype" ); + } + }); + QUnit.moduleDone(function() { + if( issubtypeStub !== null) { + issubtypeStub.restore(); + issubtypeStub = null; + } + }); + + var with_canvas_container = function( f ) { + var canvas_container = $("<div id='canvas-container'>"); + $("body").append( canvas_container ); + f( canvas_container ); + canvas_container.remove(); + }; + + var with_workflow_global = function( f ) { + var overview = $( "<div id='overview'><canvas id='overview-canvas'></canvas><div id='overview-viewport'></div></div>" ); + var canvas_viewport = $( "<div id='canvas-viewport'><div id='canvas-container'></div></div>" ); + + $("body").append( overview, canvas_viewport ); + window.canvas_manager = new CanvasManager( canvas_viewport, overview ); + with_canvas_container( function( canvas_container ) { + window.workflow = new Workflow( canvas_container ); + f( window.workflow ); + window.workflow = null; + } ); + window.canvas_manager = null; + overview.remove(); + canvas_viewport.remove(); + }; + + module( "Input terminal model test", { + setup: function() { + this.node = { }; + this.element = $( "<div>" ); + this.input_terminal = new InputTerminal( this.element, [ "txt" ] ); + this.input_terminal.node = this.node; + }, + test_connector: function( attr ) { + var connector = attr || {}; + this.input_terminal.connectors.push( connector ); + return connector; + }, + with_test_connector: function( attr, f ) { + this.test_connector( attr ); + f(); + this.reset_connectors(); + }, + reset_connectors: function( ) { + this.input_terminal.connectors = []; + }, + test_accept: function( other ) { + other = other || { node: {}, datatypes: [ "txt" ] }; + return this.input_terminal.can_accept( other ); + } + } ); + + test( "test connect", function() { + this.node.changed = sinon.spy(); + + var connector = {}; + this.input_terminal.connect( connector ); + + // Assert node changed called + ok( this.node.changed.called ); + // Assert connectors updated + ok( this.input_terminal.connectors[ 0 ] === connector ); + } ); + + test( "test disconnect", function() { + this.node.changed = sinon.spy(); + + var connector = this.test_connector( {} ); + this.input_terminal.disconnect( connector ); + + // Assert node changed called + ok( this.node.changed.called ); + // Assert connectors updated + equal( this.input_terminal.connectors.length, 0 ); + } ); + + test( "test redraw", function() { + var connector = this.test_connector( { redraw: sinon.spy() } ); + this.input_terminal.redraw(); + // Assert connectors were redrawn + ok( connector.redraw.called ); + } ); + + test( "test destroy", function() { + var connector = this.test_connector( { destroy: sinon.spy() } ); + + this.input_terminal.destroy(); + // Assert connectors were redrawn + ok( connector.destroy.called ); + } ); + + test( "can accept correct datatype", function() { + issubtypeStub.returns(true); + ok( this.test_accept() ) ; + } ); + + test( "cannot accept incorrect datatypes", function() { + issubtypeStub.returns(false); + ok( ! this.test_accept() ); + } ); + + test( "can accept inputs", function() { + issubtypeStub.returns(false); + // Other is data input module - always accept (currently - could be + // more intelligent by looking at what else input is connected to. + var other = { node: {}, datatypes: [ "input" ] }; + ok( this.test_accept( other ) ); + } ); + + test( "cannot accept when already connected", function() { + issubtypeStub.returns(true); + var self = this; + // If other is subtype but already connected, cannot accept + this.with_test_connector( {}, function() { + ok( ! self.test_accept() ); + } ); + } ); + + module( "Connector test", { + + } ); + + test( "connects only if both valid handles", function() { + var input = { connect: sinon.spy() }; + var output = { connect: sinon.spy() }; + new Connector( input, null ); + new Connector( null, output ); + // Not attempts to connect... + ok( ! input.connect.called ); + ok( ! output.connect.called ); + + new Connector( input, output ); + ok( input.connect.called ); + ok( output.connect.called ); + }); + + test( "default attributes", function() { + var input = { connect: sinon.spy() }; + var output = { connect: sinon.spy() }; + var connector = new Connector( input, output ); + + equal( connector.dragging, false ); + equal( connector.canvas, null ); + equal( connector.inner_color, "#FFFFFF" ); + equal( connector.outer_color, "#D8B365" ); + } ); + + test( "destroy", function() { + var input = { connect: sinon.spy(), disconnect: sinon.spy() }; + var output = { connect: sinon.spy(), disconnect: sinon.spy() }; + var connector = new Connector( input, output ); + + connector.destroy(); + ok( input.disconnect.called ); + ok( output.disconnect.called ); + } ); + + test( "initial redraw", function() { + with_canvas_container( function( canvas_container ) { + var input = { connect: sinon.spy(), element: $("<div>") }; + var output = { connect: sinon.spy(), element: $("<div>") }; + var connector = new Connector( input, output ); + + connector.redraw(); + // Ensure canvas gets set + ok( connector.canvas ); + // Ensure it gest added to canvas container + equal( canvas_container.children()[ 0 ], connector.canvas ); + } ); + } ); + + module( "Node unit test", { + setup: function() { + this.input_terminal = { destroy: sinon.spy(), redraw: sinon.spy() }; + this.output_terminal = { destroy: sinon.spy(), redraw: sinon.spy() }; + this.element = $("<div><div class='toolFormBody'></div></div>"); + this.node = new Node( this.element ); + this.node.input_terminals.i1 = this.input_terminal; + this.node.output_terminals.o1 = this.output_terminal; + }, + $: function( selector ) { + return $( this.node.element.find( selector ) ); + }, + expect_workflow_node_changed: function( f ) { + var node = this.node; + with_workflow_global( function( workflow ) { + var node_changed_spy = sinon.spy( workflow, "node_changed" ); + f(); + ok( node_changed_spy.calledWith( node ) ); + } ); + }, + init_field_data_simple: function() { + var data = { + data_inputs: [ {name: "input1", extensions: [ "data" ] } ], + data_outputs: [ {name: "output1", extensions: [ "data" ] } ], + }; + this.node.init_field_data( data ); + }, + update_field_data_with_new_input: function() { + var new_data = { + data_inputs: [ + { name: "input1", extensions: [ "data" ] }, + { name: "extra_0|input1", extensions: [ "data" ] }, + ], + data_outputs: [ {name: "output1", extensions: [ "data" ] } ], + post_job_actions: "{}" + }; + this.node.update_field_data( new_data ); + } + } ); + + test( "make active", function() { + ok( ! this.element.hasClass( "toolForm-active" ) ); + this.node.make_active(); + ok( this.element.hasClass( "toolForm-active" ) ); + } ); + + test( "destroy", function() { + var test = this; + with_workflow_global( function( workflow ) { + var remove_node_spy = sinon.spy( workflow, "remove_node" ); + test.node.destroy(); + ok( test.input_terminal.destroy.called ); + ok( test.output_terminal.destroy.called ); + ok( remove_node_spy.calledWith( test.node ) ); + } ); + } ); + + test( "error", function() { + // Test body of toolFormBody div updated and workflow notified of change. + var test = this; + this.expect_workflow_node_changed( function() { + test.node.error( "TOOL ERROR" ); + equal( $( test.$(".toolFormBody").children()[ 0 ] ).html(), "TOOL ERROR" ); + } ); + } ); + + test( "init_field_data properties", function() { + var node = this.node; + this.expect_workflow_node_changed( function( ) { + var data = { + data_inputs: [], + data_outputs: [], + type: "tool", + name: "cat1", + form_html: "<form>", + tool_state: "ok", + tool_errors: false, + tooltip: "tool tooltip", + annotation: "tool annotation", + workflow_outputs: [ "out1" ], + }; + node.init_field_data( data ); + equal( node.type, "tool" ); + equal( node.name, "cat1" ); + equal( node.form_html, "<form>" ); + equal( node.tool_state, "ok" ); + equal( node.tooltip, "tool tooltip" ); + equal( node.annotation, "tool annotation" ); + deepEqual( node.post_job_actions, {} ); + deepEqual( node.workflow_outputs, [ "out1" ] ); + } ); + } ); + + test( "init_field_data data", function() { + var test = this; + this.expect_workflow_node_changed( function( ) { + // pre-init not tool form body... + equal( test.$( ".output-terminal" ).length, 0 ); + equal( test.$( ".input-terminal" ).length, 0 ); + equal( test.$( ".rule" ).length, 0 ); + + test.init_field_data_simple(); + + // After init tool form should have three "rows"/divs - , inputs div, one output, and rule... + equal( test.$( ".output-terminal" ).length, 1 ); + equal( test.$( ".input-terminal" ).length, 1 ); + equal( test.$( ".rule" ).length, 1 ); + + equal( test.$( ".toolFormBody" ).children().length, 3 ); + } ); + } ); + + test( "update_field_data updated data inputs and outputs", function() { + var test = this; + this.expect_workflow_node_changed( function( ) { + // Call init with one input and output. + test.init_field_data_simple(); + + test.update_field_data_with_new_input(); + + // Now there are 2 inputs... + equal( test.$( ".input-terminal" ).length, 2 ); + equal( test.$( ".output-terminal" ).length, 1 ); + equal( test.$( ".rule" ).length, 1 ); + } ); + } ); + + test( "update_field_data preserves connectors", function() { + var test = this; + var node = this.node; + this.expect_workflow_node_changed( function( ) { + // Call init with one input and output. + test.init_field_data_simple(); + + var connector = new Connector(); + var old_input_terminal = node.input_terminals.input1; + old_input_terminal.connectors.push( connector ); + + test.update_field_data_with_new_input(); + + var new_input_terminal = node.input_terminals.input1; + equal( old_input_terminal, old_input_terminal ); + notEqual( old_input_terminal, new_input_terminal ); + equal( connector, new_input_terminal.connectors[ 0 ] ); + } ); + } ); + + test( "update_field_data destroys old terminals", function() { + var test = this; + var node = this.node; + this.expect_workflow_node_changed( function( ) { + var data = { + data_inputs: [ { name: "input1", extensions: [ "data" ] }, + { name: "willDisappear", extensions: [ "data" ] } ], + data_outputs: [ {name: "output1", extensions: [ "data" ] } ], + }; + node.init_field_data( data ); + + var old_input_terminal = node.input_terminals.willDisappear; + var destroy_spy = sinon.spy( old_input_terminal, "destroy" ); + // Update + test.update_field_data_with_new_input(); + + ok( destroy_spy.called ); + } ); + } ); + + module( "add_node" ); + + test( "node added to workflow", function() { + with_workflow_global( function( workflow ) { + var add_node_spy = sinon.spy( workflow, "add_node" ); + var node = add_node( "tool", "Cat Files", "cat1" ); + ok( add_node_spy.calledWith( node ) ); + } ); + } ); + +}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/bacb1a3c0eaa/ Changeset: bacb1a3c0eaa User: jmchilton Date: 2014-04-10 20:31:48 Summary: Simplify enable_output_terminal and enable_output_terminal in workflow editor. These functions were taking in a single element and then looping through it. I hope this is not some intententional jQuery pattern to change the value of 'this' I don't quite understand and is just a remnant of when some loop over inputs was on the inside of this function or some other such refactoring. Affected #: 1 file diff -r 8f577a1a390145aaab909ccbfbd31a78241f2e45 -r bacb1a3c0eaa0fd21ddc9f5099cb65bd2c826a9c static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -172,101 +172,98 @@ } $.extend( Node.prototype, { new_input_terminal : function( input ) { - var t = $("<div class='terminal input-terminal'></div>"); + var t = $("<div class='terminal input-terminal'></div>")[ 0 ]; this.enable_input_terminal( t, input.name, input.extensions, input.multiple ); return t; }, - enable_input_terminal : function( elements, name, types, multiple ) { + enable_input_terminal : function( element, name, types, multiple ) { var node = this; - $(elements).each( function() { - var terminal = this.terminal = new InputTerminal( this, types, multiple ); - terminal.node = node; - terminal.name = name; - $(this).bind( "dropinit", function( e, d ) { - // Accept a dragable if it is an output terminal and has a - // compatible type - return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal ); - }).bind( "dropstart", function( e, d ) { - if (d.proxy.terminal) { - d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; - } - }).bind( "dropend", function ( e, d ) { - 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() { - // If connected, create a popup to allow disconnection - if ( terminal.connectors.length > 0 ) { - // Create callout - var t = $("<div class='callout'></div>") - .css( { display: 'none' } ) - .appendTo( "body" ) - .append( - $("<div class='button'></div>").append( - $("<div/>").addClass("fa-icon-button fa fa-times").click( function() { - $.each( terminal.connectors, function( _, x ) { - if (x) { - x.destroy(); - } - }); - t.remove(); - }))) - .bind( "mouseleave", function() { - $(this).remove(); - }); - // Position it and show - t.css({ - top: $(this).offset().top - 2, - left: $(this).offset().left - t.width(), - 'padding-right': $(this).width() - }).show(); - } - }); - node.input_terminals[name] = terminal; + + var terminal = element.terminal = new InputTerminal( element, types, multiple ); + terminal.node = node; + terminal.name = name; + $(element).bind( "dropinit", function( e, d ) { + // Accept a dragable if it is an output terminal and has a + // compatible type + return $(d.drag).hasClass( "output-terminal" ) && terminal.can_accept( d.drag.terminal ); + }).bind( "dropstart", function( e, d ) { + if (d.proxy.terminal) { + d.proxy.terminal.connectors[0].inner_color = "#BBFFBB"; + } + }).bind( "dropend", function ( e, d ) { + 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() { + // If connected, create a popup to allow disconnection + if ( terminal.connectors.length > 0 ) { + // Create callout + var t = $("<div class='callout'></div>") + .css( { display: 'none' } ) + .appendTo( "body" ) + .append( + $("<div class='button'></div>").append( + $("<div/>").addClass("fa-icon-button fa fa-times").click( function() { + $.each( terminal.connectors, function( _, x ) { + if (x) { + x.destroy(); + } + }); + t.remove(); + }))) + .bind( "mouseleave", function() { + $(this).remove(); + }); + // Position it and show + t.css({ + top: $(element).offset().top - 2, + left: $(element).offset().left - t.width(), + 'padding-right': $(element).width() + }).show(); + } }); + node.input_terminals[name] = terminal; }, - enable_output_terminal : function( elements, name, type ) { + enable_output_terminal : function( element, name, type ) { var node = this; - $(elements).each( function() { - var terminal_element = this; - var terminal = this.terminal = new OutputTerminal( this, type ); - terminal.node = node; - terminal.name = name; - $(this).bind( "dragstart", function( e, d ) { - $( d.available ).addClass( "input-terminal-active" ); - // Save PJAs in the case of change datatype actions. - workflow.check_changes_in_active_form(); - // Drag proxy div - var h = $( '<div class="drag-terminal" style="position: absolute;"></div>' ) - .appendTo( "#canvas-container" ).get(0); - // Terminal and connection to display noodle while dragging - h.terminal = new OutputTerminal( h ); - var c = new Connector(); - c.dragging = true; - c.connect( this.terminal, h.terminal ); - return h; - }).bind( "drag", function ( e, d ) { - var onmove = function() { - var po = $(d.proxy).offsetParent().offset(), - x = d.offsetX - po.left, - y = d.offsetY - po.top; - $(d.proxy).css( { left: x, top: y } ); - d.proxy.terminal.redraw(); - // FIXME: global - canvas_manager.update_viewport_overlay(); - }; - onmove(); - $("#canvas-container").get(0).scroll_panel.test( e, onmove ); - }).bind( "dragend", function ( e, d ) { - d.proxy.terminal.connectors[0].destroy(); - $(d.proxy).remove(); - $( d.available ).removeClass( "input-terminal-active" ); - $("#canvas-container").get(0).scroll_panel.stop(); - }); - node.output_terminals[name] = terminal; + var terminal_element = element; + var terminal = element.terminal = new OutputTerminal( element, type ); + terminal.node = node; + terminal.name = name; + $(element).bind( "dragstart", function( e, d ) { + $( d.available ).addClass( "input-terminal-active" ); + // Save PJAs in the case of change datatype actions. + workflow.check_changes_in_active_form(); + // Drag proxy div + var h = $( '<div class="drag-terminal" style="position: absolute;"></div>' ) + .appendTo( "#canvas-container" ).get(0); + // Terminal and connection to display noodle while dragging + h.terminal = new OutputTerminal( h ); + var c = new Connector(); + c.dragging = true; + c.connect( element.terminal, h.terminal ); + return h; + }).bind( "drag", function ( e, d ) { + var onmove = function() { + var po = $(d.proxy).offsetParent().offset(), + x = d.offsetX - po.left, + y = d.offsetY - po.top; + $(d.proxy).css( { left: x, top: y } ); + d.proxy.terminal.redraw(); + // FIXME: global + canvas_manager.update_viewport_overlay(); + }; + onmove(); + $("#canvas-container").get(0).scroll_panel.test( e, onmove ); + }).bind( "dragend", function ( e, d ) { + d.proxy.terminal.connectors[0].destroy(); + $(d.proxy).remove(); + $( d.available ).removeClass( "input-terminal-active" ); + $("#canvas-container").get(0).scroll_panel.stop(); }); + node.output_terminals[name] = terminal; }, redraw : function () { $.each( this.input_terminals, function( _, t ) { @@ -342,7 +339,7 @@ } $.each( data.data_outputs, function( i, output ) { var t = $( "<div class='terminal output-terminal'></div>" ); - node.enable_output_terminal( t, output.name, output.extensions ); + node.enable_output_terminal( t[ 0 ], output.name, output.extensions ); var label = output.name; if ( output.extensions.indexOf( 'input' ) < 0 ) { label = label + " (" + output.extensions.join(", ") + ")"; @@ -429,8 +426,8 @@ $(this).find( ".input-terminal" ).each( function() { var c = this.terminal.connectors[0]; if ( c ) { - t[0].terminal.connectors[0] = c; - c.handle2 = t[0].terminal; + t.terminal.connectors[0] = c; + c.handle2 = t.terminal; } }); $(this).remove(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5b01864ad790/ Changeset: 5b01864ad790 Branch: next-stable User: davebgx Date: 2014-04-10 19:59:40 Summary: Corrected version for migrated tools. Affected #: 1 file diff -r 7e9a2ea753bde82120de4543618f196e86bf7b04 -r 5b01864ad7902af1174478a9f440cad26927f178 scripts/migrate_tools/0010_tools.xml --- a/scripts/migrate_tools/0010_tools.xml +++ b/scripts/migrate_tools/0010_tools.xml @@ -3,17 +3,17 @@ <repository owner="devteam" name="analyze_covariates" changeset_revision="738bc749f9a3" description="Analyze Covariates"><tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" /></repository> - <repository owner="devteam" name="basecoverage" changeset_revision="1e6a9e97fa41" description="Base Coverage of all intervals"> - <tool id="gops_basecoverage_1" version="0.0.1" file="new_operations/basecoverage.xml" /> + <repository owner="devteam" name="basecoverage" changeset_revision="642849141ae9" description="Base Coverage of all intervals"> + <tool id="gops_basecoverage_1" version="1.0.0" file="new_operations/basecoverage.xml" /></repository> - <repository owner="devteam" name="best_regression_subsets" changeset_revision="e769cde223a5" description="Perform Best-subsets Regression"> - <tool id="BestSubsetsRegression1" version="0.0.1" file="regVariation/best_regression_subsets.xml" /> + <repository owner="devteam" name="best_regression_subsets" changeset_revision="4f33ec73e445" description="Perform Best-subsets Regression"> + <tool id="BestSubsetsRegression1" version="1.0.0" file="regVariation/best_regression_subsets.xml" /></repository> - <repository owner="devteam" name="cluster" changeset_revision="d5677eecbad4" description="Cluster"> - <tool id="gops_cluster_1" version="0.0.1" file="new_operations/cluster.xml" /> + <repository owner="devteam" name="cluster" changeset_revision="9fcc3a1c3d26" description="Cluster"> + <tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" /></repository> - <repository owner="devteam" name="complement" changeset_revision="d958d5a0d1e8" description="Complement intervals of a dataset"> - <tool id="gops_complement_1" version="0.0.1" file="new_operations/complement.xml" /> + <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset"> + <tool id="gops_complement_1" version="1.0.0" file="new_operations/complement.xml" /></repository><repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values"><tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" /> @@ -24,8 +24,8 @@ <repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files"><tool id="gatk_count_covariates" version="0.0.5" file="gatk/count_covariates.xml" /></repository> - <repository owner="devteam" name="coverage" changeset_revision="1e864693a1c0" description="Coverage of a set of intervals on second set of intervals"> - <tool id="gops_coverage_1" version="0.0.1" file="new_operations/coverage.xml" /> + <repository owner="devteam" name="coverage" changeset_revision="16b62a897aac" description="Coverage of a set of intervals on second set of intervals"> + <tool id="gops_coverage_1" version="1.0.0" file="new_operations/coverage.xml" /></repository><repository owner="devteam" name="depth_of_coverage" changeset_revision="c3f08370fc82" description="Depth of Coverage on BAM files"><tool id="gatk_depth_of_coverage" version="0.0.2" file="gatk/depth_of_coverage.xml" /> @@ -36,23 +36,23 @@ <repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval"><tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" /></repository> - <repository owner="devteam" name="get_flanks" changeset_revision="a72f0decd7b3" description="Get flanks - returns flanking region/s for every gene"> - <tool id="get_flanks1" version="0.0.1" file="new_operations/get_flanks.xml" /> + <repository owner="devteam" name="get_flanks" changeset_revision="c3b1781c6fd1" description="Get flanks - returns flanking region/s for every gene"> + <tool id="get_flanks1" version="1.0.0" file="new_operations/get_flanks.xml" /></repository><repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments"><tool id="indelRates_3way" version="1.0.0" file="regVariation/getIndelRates_3way.xml" /></repository> - <repository owner="devteam" name="getindels_2way" changeset_revision="91655316fcf0" description="Fetch Indels from pairwise alignments"> - <tool id="getIndels_2way" version="0.0.1" file="regVariation/getIndels_2way.xml" /> + <repository owner="devteam" name="getindels_2way" changeset_revision="f1dc6f5fce6e" description="Fetch Indels from pairwise alignments"> + <tool id="getIndels_2way" version="1.0.0" file="regVariation/getIndels_2way.xml" /></repository><repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment"><tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" /></repository> - <repository owner="devteam" name="intersect" changeset_revision="5b3c6135a982" description="Intersect the intervals of two datasets"> - <tool id="gops_intersect_1" version="0.0.1" file="new_operations/intersect.xml" /> + <repository owner="devteam" name="intersect" changeset_revision="81ad85f731b9" description="Intersect the intervals of two datasets"> + <tool id="gops_intersect_1" version="1.0.0" file="new_operations/intersect.xml" /></repository> - <repository owner="devteam" name="join" changeset_revision="e56b47dce68a" description="Join the intervals of two datasets side-by-side"> - <tool id="gops_join_1" version="0.0.1" file="new_operations/join.xml" /> + <repository owner="devteam" name="join" changeset_revision="11a49f94d086" description="Join the intervals of two datasets side-by-side"> + <tool id="gops_join_1" version="1.0.0" file="new_operations/join.xml" /></repository><repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression"><tool id="LinearRegression1" version="1.0.1" file="regVariation/linear_regression.xml" /> @@ -63,11 +63,11 @@ <repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file"><tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" /></repository> - <repository owner="devteam" name="merge" changeset_revision="b488a1fa07f6" description="Merge the overlapping intervals of a dataset"> - <tool id="gops_merge_1" version="0.0.1" file="new_operations/merge.xml" /> + <repository owner="devteam" name="merge" changeset_revision="55e88307811d" description="Merge the overlapping intervals of a dataset"> + <tool id="gops_merge_1" version="1.0.0" file="new_operations/merge.xml" /></repository> - <repository owner="devteam" name="microsats_alignment_level" changeset_revision="d4368a5a3fc7" description="Extract Orthologous Microsatellites from pair-wise alignments"> - <tool id="microsats_align1" version="0.0.1" file="regVariation/microsats_alignment_level.xml" /> + <repository owner="devteam" name="microsats_alignment_level" changeset_revision="7852385470f3" description="Extract Orthologous Microsatellites from pair-wise alignments"> + <tool id="microsats_align1" version="1.0.0" file="regVariation/microsats_alignment_level.xml" /></repository><repository owner="devteam" name="microsats_mutability" changeset_revision="4aa1ee5d8510" description="Estimate microsatellite mutability by specified attributes"><tool id="microsats_mutability1" version="1.1.0" file="regVariation/microsats_mutability.xml" /> @@ -93,8 +93,8 @@ <repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments"><tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" /></repository> - <repository owner="devteam" name="subtract" changeset_revision="5bc2dacbe729" description="Subtract the intervals of two datasets"> - <tool id="gops_subtract_1" version="0.0.1" file="new_operations/subtract.xml" /> + <repository owner="devteam" name="subtract" changeset_revision="7bf44b9d7a8b" description="Subtract the intervals of two datasets"> + <tool id="gops_subtract_1" version="1.0.0" file="new_operations/subtract.xml" /></repository><repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset"><tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" /> @@ -135,7 +135,7 @@ <repository owner="devteam" name="weightedaverage" changeset_revision="90611e86a998" description="Assign weighted-average of the values of features overlapping an interval"><tool id="wtavg" version="1.0.0" file="regVariation/WeightedAverage.xml" /></repository> - <repository owner="devteam" name="windowsplitter" changeset_revision="e5490ea33640" description="Make windows"> - <tool id="winSplitter" version="0.0.1" file="regVariation/windowSplitter.xml" /> + <repository owner="devteam" name="windowsplitter" changeset_revision="75abda2290cc" description="Make windows"> + <tool id="winSplitter" version="1.0.0" file="regVariation/windowSplitter.xml" /></repository></toolshed> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/2eb03ce13018/ Changeset: 2eb03ce13018 User: davebgx Date: 2014-04-10 20:01:59 Summary: Merge with next-stable. Affected #: 1 file diff -r 728373009c29c371ff448383b48543296142d311 -r 2eb03ce13018bbd46ddf55b296246b355afd7ba4 scripts/migrate_tools/0010_tools.xml --- a/scripts/migrate_tools/0010_tools.xml +++ b/scripts/migrate_tools/0010_tools.xml @@ -3,17 +3,17 @@ <repository owner="devteam" name="analyze_covariates" changeset_revision="738bc749f9a3" description="Analyze Covariates"><tool id="gatk_analyze_covariates" version="0.0.5" file="gatk/analyze_covariates.xml" /></repository> - <repository owner="devteam" name="basecoverage" changeset_revision="1e6a9e97fa41" description="Base Coverage of all intervals"> - <tool id="gops_basecoverage_1" version="0.0.1" file="new_operations/basecoverage.xml" /> + <repository owner="devteam" name="basecoverage" changeset_revision="642849141ae9" description="Base Coverage of all intervals"> + <tool id="gops_basecoverage_1" version="1.0.0" file="new_operations/basecoverage.xml" /></repository> - <repository owner="devteam" name="best_regression_subsets" changeset_revision="e769cde223a5" description="Perform Best-subsets Regression"> - <tool id="BestSubsetsRegression1" version="0.0.1" file="regVariation/best_regression_subsets.xml" /> + <repository owner="devteam" name="best_regression_subsets" changeset_revision="4f33ec73e445" description="Perform Best-subsets Regression"> + <tool id="BestSubsetsRegression1" version="1.0.0" file="regVariation/best_regression_subsets.xml" /></repository> - <repository owner="devteam" name="cluster" changeset_revision="d5677eecbad4" description="Cluster"> - <tool id="gops_cluster_1" version="0.0.1" file="new_operations/cluster.xml" /> + <repository owner="devteam" name="cluster" changeset_revision="9fcc3a1c3d26" description="Cluster"> + <tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" /></repository> - <repository owner="devteam" name="complement" changeset_revision="d958d5a0d1e8" description="Complement intervals of a dataset"> - <tool id="gops_complement_1" version="0.0.1" file="new_operations/complement.xml" /> + <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset"> + <tool id="gops_complement_1" version="1.0.0" file="new_operations/complement.xml" /></repository><repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values"><tool id="compute_q_values" version="1.0.1" file="regVariation/compute_q_values.xml" /> @@ -24,8 +24,8 @@ <repository owner="devteam" name="count_covariates" changeset_revision="14e304b70425" description="Count Covariates on BAM files"><tool id="gatk_count_covariates" version="0.0.5" file="gatk/count_covariates.xml" /></repository> - <repository owner="devteam" name="coverage" changeset_revision="1e864693a1c0" description="Coverage of a set of intervals on second set of intervals"> - <tool id="gops_coverage_1" version="0.0.1" file="new_operations/coverage.xml" /> + <repository owner="devteam" name="coverage" changeset_revision="16b62a897aac" description="Coverage of a set of intervals on second set of intervals"> + <tool id="gops_coverage_1" version="1.0.0" file="new_operations/coverage.xml" /></repository><repository owner="devteam" name="depth_of_coverage" changeset_revision="c3f08370fc82" description="Depth of Coverage on BAM files"><tool id="gatk_depth_of_coverage" version="0.0.2" file="gatk/depth_of_coverage.xml" /> @@ -36,23 +36,23 @@ <repository owner="devteam" name="flanking_features" changeset_revision="90100b587723" description="Fetch closest non-overlapping feature for every interval"><tool id="flanking_features_1" version="4.0.1" file="new_operations/flanking_features.xml" /></repository> - <repository owner="devteam" name="get_flanks" changeset_revision="a72f0decd7b3" description="Get flanks - returns flanking region/s for every gene"> - <tool id="get_flanks1" version="0.0.1" file="new_operations/get_flanks.xml" /> + <repository owner="devteam" name="get_flanks" changeset_revision="c3b1781c6fd1" description="Get flanks - returns flanking region/s for every gene"> + <tool id="get_flanks1" version="1.0.0" file="new_operations/get_flanks.xml" /></repository><repository owner="devteam" name="getindelrates_3way" changeset_revision="d427e5acb9ee" description="Estimate Indel Rates for 3-way alignments"><tool id="indelRates_3way" version="1.0.0" file="regVariation/getIndelRates_3way.xml" /></repository> - <repository owner="devteam" name="getindels_2way" changeset_revision="91655316fcf0" description="Fetch Indels from pairwise alignments"> - <tool id="getIndels_2way" version="0.0.1" file="regVariation/getIndels_2way.xml" /> + <repository owner="devteam" name="getindels_2way" changeset_revision="f1dc6f5fce6e" description="Fetch Indels from pairwise alignments"> + <tool id="getIndels_2way" version="1.0.0" file="regVariation/getIndels_2way.xml" /></repository><repository owner="devteam" name="indel_realigner" changeset_revision="bb0beda6cf83" description="Indel Realigner - perform local realignment"><tool id="gatk_indel_realigner" version="0.0.6" file="gatk/indel_realigner.xml" /></repository> - <repository owner="devteam" name="intersect" changeset_revision="5b3c6135a982" description="Intersect the intervals of two datasets"> - <tool id="gops_intersect_1" version="0.0.1" file="new_operations/intersect.xml" /> + <repository owner="devteam" name="intersect" changeset_revision="81ad85f731b9" description="Intersect the intervals of two datasets"> + <tool id="gops_intersect_1" version="1.0.0" file="new_operations/intersect.xml" /></repository> - <repository owner="devteam" name="join" changeset_revision="e56b47dce68a" description="Join the intervals of two datasets side-by-side"> - <tool id="gops_join_1" version="0.0.1" file="new_operations/join.xml" /> + <repository owner="devteam" name="join" changeset_revision="11a49f94d086" description="Join the intervals of two datasets side-by-side"> + <tool id="gops_join_1" version="1.0.0" file="new_operations/join.xml" /></repository><repository owner="devteam" name="linear_regression" changeset_revision="cf431604ec3e" description="Perform Linear Regression"><tool id="LinearRegression1" version="1.0.1" file="regVariation/linear_regression.xml" /> @@ -63,11 +63,11 @@ <repository owner="devteam" name="maf_cpg_filter" changeset_revision="7f2a12cb047d" description="Mask CpG/non-CpG sites from MAF file"><tool id="cpgFilter" version="1.0.0" file="regVariation/maf_cpg_filter.xml" /></repository> - <repository owner="devteam" name="merge" changeset_revision="b488a1fa07f6" description="Merge the overlapping intervals of a dataset"> - <tool id="gops_merge_1" version="0.0.1" file="new_operations/merge.xml" /> + <repository owner="devteam" name="merge" changeset_revision="55e88307811d" description="Merge the overlapping intervals of a dataset"> + <tool id="gops_merge_1" version="1.0.0" file="new_operations/merge.xml" /></repository> - <repository owner="devteam" name="microsats_alignment_level" changeset_revision="d4368a5a3fc7" description="Extract Orthologous Microsatellites from pair-wise alignments"> - <tool id="microsats_align1" version="0.0.1" file="regVariation/microsats_alignment_level.xml" /> + <repository owner="devteam" name="microsats_alignment_level" changeset_revision="7852385470f3" description="Extract Orthologous Microsatellites from pair-wise alignments"> + <tool id="microsats_align1" version="1.0.0" file="regVariation/microsats_alignment_level.xml" /></repository><repository owner="devteam" name="microsats_mutability" changeset_revision="4aa1ee5d8510" description="Estimate microsatellite mutability by specified attributes"><tool id="microsats_mutability1" version="1.1.0" file="regVariation/microsats_mutability.xml" /> @@ -93,8 +93,8 @@ <repository owner="devteam" name="substitutions" changeset_revision="c54f5d0bbb58" description="Fetch substitutions from pairwise alignments"><tool id="substitutions1" version="1.0.0" file="regVariation/substitutions.xml" /></repository> - <repository owner="devteam" name="subtract" changeset_revision="5bc2dacbe729" description="Subtract the intervals of two datasets"> - <tool id="gops_subtract_1" version="0.0.1" file="new_operations/subtract.xml" /> + <repository owner="devteam" name="subtract" changeset_revision="7bf44b9d7a8b" description="Subtract the intervals of two datasets"> + <tool id="gops_subtract_1" version="1.0.0" file="new_operations/subtract.xml" /></repository><repository owner="devteam" name="subtract_query" changeset_revision="5f6ebef89722" description="Subtract Whole Dataset from another dataset"><tool id="subtract_query1" version="0.1" file="new_operations/subtract_query.xml" /> @@ -135,7 +135,7 @@ <repository owner="devteam" name="weightedaverage" changeset_revision="90611e86a998" description="Assign weighted-average of the values of features overlapping an interval"><tool id="wtavg" version="1.0.0" file="regVariation/WeightedAverage.xml" /></repository> - <repository owner="devteam" name="windowsplitter" changeset_revision="e5490ea33640" description="Make windows"> - <tool id="winSplitter" version="0.0.1" file="regVariation/windowSplitter.xml" /> + <repository owner="devteam" name="windowsplitter" changeset_revision="75abda2290cc" description="Make windows"> + <tool id="winSplitter" version="1.0.0" file="regVariation/windowSplitter.xml" /></repository></toolshed> \ No newline at end of file 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: dan: Change suc.get_url_from_tool_shed to common_util.get_tool_shed_url_from_tool_shed_registry.
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/728373009c29/ Changeset: 728373009c29 User: dan Date: 2014-04-10 19:49:43 Summary: Change suc.get_url_from_tool_shed to common_util.get_tool_shed_url_from_tool_shed_registry. Affected #: 1 file diff -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb -r 728373009c29c371ff448383b48543296142d311 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,7 +4,6 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util -from tool_shed.util.shed_util_common import get_url_from_tool_shed from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -76,7 +75,7 @@ return self.deleted def get_sharable_url( self, app ): - tool_shed_url = get_url_from_tool_shed( app, self.tool_shed ) + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) if tool_shed_url: return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) return tool_shed_url 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: 3 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/375e0c252f6c/ Changeset: 375e0c252f6c Branch: next-stable User: dan Date: 2014-04-10 19:38:44 Summary: Include tool version information in bug reports. Affected #: 1 file diff -r 376ffdb91bd1c1a7881e72c5cb6da8dea0e0534f -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), https://bitbucket.org/galaxy/galaxy-central/commits/7e9a2ea753bd/ Changeset: 7e9a2ea753bd Branch: next-stable User: dan Date: 2014-04-10 19:39:41 Summary: When posting to BioStar include a ToolShed url, as applicable. Affected #: 2 files diff -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec -r 7e9a2ea753bde82120de4543618f196e86bf7b04 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,8 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from tool_shed.util.shed_util_common import get_url_from_tool_shed +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +75,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = get_url_from_tool_shed( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r 375e0c252f6c3448e1d7c743f1ffe408be9752ec -r 7e9a2ea753bde82120de4543618f196e86bf7b04 lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): https://bitbucket.org/galaxy/galaxy-central/commits/44ad9370003c/ Changeset: 44ad9370003c User: dan Date: 2014-04-10 19:40:00 Summary: merge next-stable Affected #: 3 files diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,6 +4,8 @@ from galaxy.util.bunch import Bunch from galaxy.util import asbool from tool_shed.util import common_util +from tool_shed.util.shed_util_common import get_url_from_tool_shed +from urlparse import urljoin log = logging.getLogger( __name__ ) @@ -73,6 +75,12 @@ def can_reinstall_or_activate( self ): return self.deleted + def get_sharable_url( self, app ): + tool_shed_url = get_url_from_tool_shed( app, self.tool_shed ) + if tool_shed_url: + return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) + return tool_shed_url + def get_shed_config_filename( self ): shed_config_filename = None if self.metadata: diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/tools/errors.py --- a/lib/galaxy/tools/errors.py +++ b/lib/galaxy/tools/errors.py @@ -28,7 +28,9 @@ ----------------------------------------------------------------------------- job id: ${job_id} tool id: ${job_tool_id} +tool version: ${tool_version} job pid or drm id: ${job_runner_external_id} +job tool version: ${job_tool_version} ----------------------------------------------------------------------------- job command line: ${job_command_line} @@ -86,7 +88,9 @@ history_item_name=hda.get_display_name(), history_view_link=history_view_link, job_id=job.id, + tool_version=job.tool_version, job_tool_id=job.tool_id, + job_tool_version=hda.tool_version, job_runner_external_id=job.job_runner_external_id, job_command_line=job.command_line, job_stderr=util.unicodify( job.stderr ), diff -r 165927888055c164e493a948e05d10c00d018458 -r 44ad9370003cfa3217f15d1ee8a2d6a114cb50bb lib/galaxy/util/biostar.py --- a/lib/galaxy/util/biostar.py +++ b/lib/galaxy/util/biostar.py @@ -86,7 +86,14 @@ def populate_tool_payload( payload=None, tool=None ): payload = populate_tag_payload( payload=payload, tool=tool ) payload[ 'title' ] = 'Need help with "%s" tool' % ( tool.name ) - payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s</p>' % ( tool.name, tool.version, tool.id ) + tool_url = None + if tool.tool_shed_repository: + tool_url = tool.tool_shed_repository.get_sharable_url( tool.app ) + if tool_url: + tool_url = '</br>ToolShed URL: <a href="%s">%s</a>' % ( tool_url, tool_url ) + if not tool_url: + tool_url = '' + payload[ 'content' ] = '<br /><hr /><p>Tool name: %s</br>Tool version: %s</br>Tool ID: %s%s</p></br>' % ( tool.name, tool.version, tool.id, tool_url ) return payload def determine_cookie_domain( galaxy_hostname, biostar_hostname ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Display repository dependency definition attributes for repositories being installed into Galaxy where the dependency hierarchy cannot be determined likely due to invalid dependency definitions.
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/165927888055/ Changeset: 165927888055 User: greg Date: 2014-04-10 17:35:37 Summary: Display repository dependency definition attributes for repositories being installed into Galaxy where the dependency hierarchy cannot be determined likely due to invalid dependency definitions. Affected #: 5 files diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -276,7 +276,7 @@ @web.expose_api def repository_ids_for_setting_metadata( self, trans, my_writable=False, **kwd ): """ - GET /api/get_repository_ids_for_setting_metadata + GET /api/repository_ids_for_setting_metadata Displays a collection (list) of repository ids ordered for setting metadata. diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -26,7 +26,7 @@ Creates and saves a gzip compressed tar archive of a repository and optionally all of it's repository dependencies. The following parameters are included in the payload. - :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository was installed + :param tool_shed_url (required): the base URL of the Tool Shed from which the Repository is to be exported :param name (required): the name of the Repository :param owner (required): the owner of the Repository :param changeset_revision (required): the changeset_revision of the RepositoryMetadata object associated with the Repository diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2570,11 +2570,8 @@ invalid = True break if invalid: - message += 'The repository dependency definitions for this repository are invalid and will be ignored. ' - message += 'The complete dependency hierarchy could not be determined. The cause of repository dependency ' - message += 'definition errors like this can usually be seen when viewing the repository directly from the ' - message += 'Tool Shed. The exact cause cannot be determined when visiting the Tool Shed from Galaxy to ' - message += 'install the repository.' + message = repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata, + error_from_tuple=False ) status = 'error' else: repository_metadata_id = None diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -288,7 +288,8 @@ status = 'error' # Handle messaging for invalid repository dependencies. invalid_repository_dependencies_message = \ - repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict ) + repository_dependency_util.generate_message_for_invalid_repository_dependencies( metadata_dict, + error_from_tuple=True ) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' diff -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 -r 165927888055c164e493a948e05d10c00d018458 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -225,18 +225,46 @@ build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts -def generate_message_for_invalid_repository_dependencies( metadata_dict ): - """Return the error message associated with an invalid repository dependency for display in the caller.""" +def generate_message_for_invalid_repository_dependencies( metadata_dict, error_from_tuple=False ): + """Get or generate and return an error message associated with an invalid repository dependency.""" message = '' if metadata_dict: - invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None ) - if invalid_repository_dependencies_dict: - invalid_repository_dependencies = invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] ) - for repository_dependency_tup in invalid_repository_dependencies: - toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ - common_util.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True ) - if error: - message = '%s ' % str( error ) + if error_from_tuple: + # Return the error messages associated with a set of one or more invalid repository dependency tuples. + invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None ) + if invalid_repository_dependencies_dict is not None: + invalid_repository_dependencies = invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] ) + for repository_dependency_tup in invalid_repository_dependencies: + toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ + common_util.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True ) + if error: + message += '%s ' % str( error ) + else: + # The complete dependency hierarchy could not be determined for a repository being installed into + # Galaxy. This is likely due to invalid repository dependency definitions, so we'll get them from + # the metadata and parse them for display in an error message. This will hopefully communicate the + # problem to the user in such a way that a resolution can be determined. + message += 'The complete dependency hierarchy could not be determined for this repository, so no required ' + message += 'repositories will not be installed. This is likely due to invalid repository dependency definitions. ' + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None ) + if repository_dependencies_dict is not None: + rd_tups = repository_dependencies_dict.get( 'repository_dependencies', None ) + if rd_tups is not None: + message += 'Here are the attributes of the dependencies defined for this repository to help determine the ' + message += 'cause of this problem.<br/>' + message += '<table cellpadding="2" cellspacing="2">' + message += '<tr><th>Tool shed</th><th>Repository name</th><th>Owner</th><th>Changeset revision</th>' + message += '<th>Prior install required</th></tr>' + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision, pir, oicct = \ + common_util.parse_repository_dependency_tuple( rd_tup ) + if asbool( pir ): + pir_str = 'True' + else: + pir_str = '' + message += '<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>' % \ + ( tool_shed, name, owner, changeset_revision, pir_str ) + message += '</table>' return message def get_key_for_repository_changeset_revision( trans, toolshed_base_url, repository, repository_metadata, all_repository_dependencies ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Add label selection columns
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b3b39af86c36/ Changeset: b3b39af86c36 User: guerler Date: 2014-04-10 16:00:54 Summary: Charts: Add label selection columns Affected #: 6 files diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -51,7 +51,6 @@ // append views this.$el.append(this.viewer_view.$el); this.$el.append(this.editor_view.$el); - this.$el.css('height', 'inherit'); // pick start screen if (!this.storage.load()) { diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/charts/nvd3/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3/config.js @@ -1,15 +1,15 @@ define([], function() { return { - title : '', - library : 'nvd3.js', - element : 'svg', + title : '', + library : 'nvd3.js', + element : 'svg', columns : { y : { title : 'Values for y-axis' } }, - settings : { + settings : { separator_label : { title : 'X axis', type : 'separator' diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/config.js @@ -1,7 +1,18 @@ -define(['plugin/charts/nvd3/config'], function(nvd3_config) { +define([], function() { -return $.extend(true, {}, nvd3_config, { - title : 'Pie chart', -}); +return { + title : 'Pie chart', + library : 'nvd3.js', + element : 'svg', + columns : { + label : { + title : 'Labels', + any_type : true + }, + y : { + title : 'Values' + } + } +}; }); \ No newline at end of file diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js --- a/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js +++ b/config/plugins/visualizations/charts/static/charts/nvd3_piechart/nvd3_piechart.js @@ -27,29 +27,29 @@ for (var key in group.values) { var value = group.values[key]; pie_data.push ({ - key : value.x, - y : value.y + y : value.y, + x : value.label }); } + } + + // add graph to screen + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .donut(true) + .showLegend(false); - // add graph to screen - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .donut(true) - .showLegend(false); - - self.options.canvas.datum(pie_data) - .call(self.chart_3d); + self.options.canvas.datum(pie_data) + .call(self.chart_3d); - nv.utils.windowResize(self.chart_3d.update); - - // set chart state - chart.state('ok', 'Pie chart drawn.'); - - // unregister process - chart.deferred.done(process_id); - }); - } + nv.utils.windowResize(self.chart_3d.update); + + // set chart state + chart.state('ok', 'Chart has been drawn.'); + + // unregister process + chart.deferred.done(process_id); + }); }); } }); diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/library/deferred.js --- a/config/plugins/visualizations/charts/static/library/deferred.js +++ b/config/plugins/visualizations/charts/static/library/deferred.js @@ -59,17 +59,19 @@ // unregister process done: function(id) { - // delete tag - delete this.process[id]; - - // decrease process counter - this.counter--; - - // log - console.debug('Deferred:done() - Unregistering ' + id); - - // trigger change - this.trigger('refresh'); + if (this.process[id]) { + // delete tag + delete this.process[id]; + + // decrease process counter + this.counter--; + + // log + console.debug('Deferred:done() - Unregistering ' + id); + + // trigger change + this.trigger('refresh'); + } }, // ready diff -r a146d1007651d7f08240d39f0ac18a2491207bc7 -r b3b39af86c36a4f141bbe64dfec4ad59f3facbe7 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -5,9 +5,6 @@ // widget return Backbone.View.extend( { - // columns - columns: [], - // initialize initialize: function(app, options) { // link app @@ -121,24 +118,29 @@ // get dataset this.app.datasets.request({id : dataset_id}, function(dataset) { - // configure columns - self.columns = []; - var meta = dataset.metadata_column_types; - for (var key in meta) { - // check type - if(meta[key] == 'int' || meta[key] == 'float') { - // add to selection - self.columns.push({ - 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', - 'value' : key - }); + // update select fields + for (var id in list) { + + // is a numeric number required + var any_type = chart_settings.columns[id].any_type; + + // configure columns + var columns = []; + var meta = dataset.metadata_column_types; + for (var key in meta) { + // check type + if (meta[key] == 'int' || meta[key] == 'float' || any_type) { + // add to selection + columns.push({ + 'label' : 'Column: ' + (parseInt(key) + 1) + ' [' + meta[key] + ']', + 'value' : key + }); + } } - } - // update select fields - for (var key in list) { - list[key].update(self.columns); - list[key].show(); + // list + list[id].update(columns); + list[id].show(); } // loading Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Close branch trevorw/job_directory-jobs_directory-1397077266550
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11624c8dfc6c/ Changeset: 11624c8dfc6c Branch: trevorw/job_directory-jobs_directory-1397077266550 User: jmchilton Date: 2014-04-10 15:51:47 Summary: Close branch trevorw/job_directory-jobs_directory-1397077266550 Affected #: 0 files 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: jmchilton: Thanks Trevor!
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a146d1007651/ Changeset: a146d1007651 User: jmchilton Date: 2014-04-10 15:51:47 Summary: Thanks Trevor! Merged in trevorw/galaxy-central-5/trevorw/job_directory-jobs_directory-1397077266550 (pull request #360) job_directory -> jobs_directory Affected #: 1 file diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r a146d1007651d7f08240d39f0ac18a2491207bc7 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -110,7 +110,7 @@ <!-- Traditionally, the LWR client sends request to LWR server to populate various system properties. This extra step can be disabled and these calculated here - on client by uncommenting job_directory and + on client by uncommenting jobs_directory and specifying any additional remote_property_ of interest. When using message queues this is nessecary not optional. 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: 2 new changesets
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7f1aa2813345/ Changeset: 7f1aa2813345 Branch: trevorw/job_directory-jobs_directory-1397077266550 User: trevorw Date: 2014-04-09 23:02:33 Summary: job_directory -> jobs_directory Affected #: 1 file diff -r 63a81f21363325ebbefc321350315804b15bc79e -r 7f1aa2813345f8671948bbce0a14ca1638e57d9b job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -110,7 +110,7 @@ <!-- Traditionally, the LWR client sends request to LWR server to populate various system properties. This extra step can be disabled and these calculated here - on client by uncommenting job_directory and + on client by uncommenting jobs_directory and specifying any additional remote_property_ of interest. When using message queues this is nessecary not optional. https://bitbucket.org/galaxy/galaxy-central/commits/a146d1007651/ Changeset: a146d1007651 User: jmchilton Date: 2014-04-10 15:51:47 Summary: Thanks Trevor! Merged in trevorw/galaxy-central-5/trevorw/job_directory-jobs_directory-1397077266550 (pull request #360) job_directory -> jobs_directory Affected #: 1 file diff -r febeffc4787e625f3687c7d24298d5b2d3fa6241 -r a146d1007651d7f08240d39f0ac18a2491207bc7 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -110,7 +110,7 @@ <!-- Traditionally, the LWR client sends request to LWR server to populate various system properties. This extra step can be disabled and these calculated here - on client by uncommenting job_directory and + on client by uncommenting jobs_directory and specifying any additional remote_property_ of interest. When using message queues this is nessecary not optional. 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: Fix in the tool shed install and test framework for a recently relocated function.
by commits-noreply＠bitbucket.org 10 Apr '14

10 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/febeffc4787e/ Changeset: febeffc4787e User: greg Date: 2014-04-10 13:20:27 Summary: Fix in the tool shed install and test framework for a recently relocated function. Affected #: 1 file diff -r b887ef428f8f99685878df3cfe61531e3b4a26a2 -r febeffc4787e625f3687c7d24298d5b2d3fa6241 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -40,6 +40,7 @@ import galaxy.webapps.tool_shed.model.mapping from nose.plugins import Plugin +from tool_shed.util import common_util from tool_shed.util import tool_dependency_util from tool_shed.util.xml_util import parse_xml @@ -1093,7 +1094,7 @@ params[ 'tool_test_results' ] = tool_test_results_dicts # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + url = '%s' % ( common_util.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) print 'url: ', url print 'params: ', params try: 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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