November 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 53d1fa98fa05: Add button that enables uploading or importing a workflow to Galaxy instance.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287691826 14400 # Node ID 53d1fa98fa0573f84bbbd8c8264d15bfff0cb90f # Parent 9d9f0de20f4f9da28d53be38411b1ee1075201a1 Add button that enables uploading or importing a workflow to Galaxy instance. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -1077,13 +1077,16 @@ class WorkflowController( BaseController # Create workflow. workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow - # Provide user feedback. + # Provide user feedback and show workflow list. if workflow.has_errors: - return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors" ) + trans.set_message( "Imported, but some steps in this workflow have validation errors", + type="warning" ) if workflow.has_cycles: - return trans.show_warn_message( "Imported, but this workflow contains cycles" ) + trans.set_message( "Imported, but this workflow contains cycles", + type="warning" ) else: - return trans.show_message( "Workflow '%s' imported" % workflow.name ) + trans.set_message( "Workflow '%s' imported" % workflow.name ) + return self.list( trans ) @web.json def get_datatypes( self, trans ): --- a/templates/workflow/list.mako +++ b/templates/workflow/list.mako @@ -17,12 +17,12 @@ %if message: <% try: - messagetype + status except: - messagetype = "done" + status = "done" %><p /> - <div class="${messagetype}message"> + <div class="${status}message"> ${h.to_unicode( message )} </div> %endif @@ -36,6 +36,12 @@ <span>Create new workflow</span></a></li> + <li> + <a class="action-button" href="${h.url_for( action='import_workflow' )}"> + <img src="${h.url_for('/static/images/fugue/arrow-090.png')}" /> + <span>Upload or import workflow</span> + </a> + </li></ul> %if workflows: Binary file static/images/fugue/arrow-090.png has changed --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -587,12 +587,14 @@ class GalaxyWebTransaction( base.Default rval = self.template_context[name] = FormData() rval.values.update( kwargs ) return rval - def set_message( self, message ): + def set_message( self, message, type=None ): """ - Convenience method for setting the 'message' element of the template - context. + Convenience method for setting the 'message' and 'message_type' + element of the template context. """ self.template_context['message'] = message + if type: + self.template_context['status'] = type def get_message( self ): """ Convenience method for getting the 'message' element of the template

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galaxy-dist commit f72f73aa68da: Enable FormBuilder to accept and use parameter 'use_panels' in order to show panels. This enables forms built with FormBuilder to include Galaxy header. Use this new functionality to show headers for all workflow forms: create, rename, and import/upload.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287773333 14400 # Node ID f72f73aa68da51e0b5aebc063b11fa7f0b78a261 # Parent 8c1b6b3f706134b1e4ba21637f6a3b8ca5e00b67 Enable FormBuilder to accept and use parameter 'use_panels' in order to show panels. This enables forms built with FormBuilder to include Galaxy header. Use this new functionality to show headers for all workflow forms: create, rename, and import/upload. --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -391,7 +391,8 @@ class WorkflowController( BaseController #message = "Workflow renamed to '%s'." % new_name #return self.list_grid( trans, message=message, status='done' ) else: - return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), "Rename workflow", submit_text="Rename" ) \ + return form( url_for( action='rename', id=trans.security.encode_id(stored.id) ), + "Rename workflow", submit_text="Rename", use_panels=True ) \ .add_text( "new_name", "Workflow Name", value=to_unicode( stored.name ) ) @web.expose @@ -638,7 +639,7 @@ class WorkflowController( BaseController trans.set_message( "Workflow '%s' created" % stored_workflow.name ) return self.list( trans ) else: - return form( url_for(), "Create New Workflow", submit_text="Create" ) \ + return form( url_for(), "Create New Workflow", submit_text="Create", use_panels=True ) \ .add_text( "workflow_name", "Workflow Name", value="Unnamed workflow" ) \ .add_text( "workflow_annotation", "Workflow Annotation", value="", help="A description of the workflow; annotation is shown alongside shared or published workflows." ) @@ -1056,7 +1057,7 @@ class WorkflowController( BaseController @web.expose def import_workflow( self, trans, workflow_text=None, url=None ): if workflow_text is None and url is None: - return form( url_for(), "Import Workflow", submit_text="Import" ) \ + return form( url_for(), "Import Workflow", submit_text="Import", use_panels=True ) \ .add_text( "url", "URL to load workflow from", "" ) \ .add_input( "textarea", "Encoded workflow (as generated by export workflow)", "workflow_text", "" ) if url: --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -631,8 +631,9 @@ class GalaxyWebTransaction( base.Default """ Convenience method for displaying a simple page with a single HTML form. - """ - return self.fill_template( template, form=form, header=header, use_panels=use_panels, active_view=active_view ) + """ + return self.fill_template( template, form=form, header=header, use_panels=( form.use_panels or use_panels ), + active_view=active_view ) def fill_template(self, filename, **kwargs): """ Fill in a template, putting any keyword arguments on the context. @@ -725,12 +726,13 @@ class FormBuilder( object ): """ Simple class describing an HTML form """ - def __init__( self, action="", title="", name="form", submit_text="submit" ): + def __init__( self, action="", title="", name="form", submit_text="submit", use_panels=False ): self.title = title self.name = name self.action = action self.submit_text = submit_text self.inputs = [] + self.use_panels = use_panels def add_input( self, type, name, label, value=None, error=None, help=None, use_label=True ): self.inputs.append( FormInput( type, label, name, value, error, help, use_label ) ) return self

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galaxy-dist commit 070749f1a0f1: Graceful failure for ids with non-hex characters in URLs. Fix small typo with invalid history failure
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287784895 14400 # Node ID 070749f1a0f12cec2b8f20931a6224d8168a8c95 # Parent fc88085d47c384f34070952f84c22007e4a72721 Graceful failure for ids with non-hex characters in URLs. Fix small typo with invalid history failure --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -143,8 +143,10 @@ class UsesVisualization( SharableItemSec def get_visualization( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a Visualization from the database by id, verifying ownership. """ # Load workflow from database - id = trans.security.decode_id( id ) - visualization = trans.sa_session.query( trans.model.Visualization ).get( id ) + try: + visualization = trans.sa_session.query( trans.model.Visualization ).get( trans.security.decode_id( id ) ) + except TypeError: + visualization = None if not visualization: error( "Visualization not found" ) else: @@ -191,12 +193,14 @@ class UsesStoredWorkflow( SharableItemSe def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): """ Get a StoredWorkflow from the database by id, verifying ownership. """ # Load workflow from database - id = trans.security.decode_id( id ) - stored = trans.sa_session.query( trans.model.StoredWorkflow ).get( id ) - if not stored: + try: + workflow = trans.sa_session.query( trans.model.StoredWorkflow ).get( trans.security.decode_id( id ) ) + except TypeError: + workflow = None + if not workflow: error( "Workflow not found" ) else: - return self.security_check( trans.get_user(), stored, check_ownership, check_accessible ) + return self.security_check( trans.get_user(), workflow, check_ownership, check_accessible ) def get_stored_workflow_steps( self, trans, stored_workflow ): """ Restores states for a stored workflow's steps. """ for step in stored_workflow.latest_workflow.steps: @@ -224,10 +228,12 @@ class UsesHistory( SharableItemSecurity def get_history( self, trans, id, check_ownership=True, check_accessible=False ): """Get a History from the database by id, verifying ownership.""" # Load history from database - id = trans.security.decode_id( id ) - history = trans.sa_session.query( trans.model.History ).get( id ) + try: + history = trans.sa_session.query( trans.model.History ).get( trans.security.decode_id( id ) ) + except TypeError: + history = None if not history: - err+msg( "History not found" ) + error( "History not found" ) else: return self.security_check( trans.get_user(), history, check_ownership, check_accessible ) def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False):

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galaxy-dist commit 6ce4e430b6a0: Workflows now work in Internet Explorer again. IE does not implement Array.indexOf so we define it in galaxy.base. Update excanvas
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287786227 14400 # Node ID 6ce4e430b6a0d69e6397ca96a01350401ae05d20 # Parent 070749f1a0f12cec2b8f20931a6224d8168a8c95 Workflows now work in Internet Explorer again. IE does not implement Array.indexOf so we define it in galaxy.base. 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an=ao[0][0].toFixed(3)+","+ao[1][0].toFixed(3)+","+ao[0][1].toFixed(3)+","+ao[1][1].toFixed(3)+",0,0";var al=n(aq.x/d)+","+n(aq.y/d);ag.push('<g_vml_:skew on="t" matrix="',an,'" ',' offset="',al,'" origin="',j,' 0" />','<g_vml_:path textpathok="true" />','<g_vml_:textpath on="true" string="',af(am),'" style="v-text-align:',Z,";font:",af(p),'" /></g_vml_:line>');this.element_.insertAdjacentHTML("beforeEnd",ag.join(""))};q.fillText=function(m,i,p,j){this.drawText_(m,i,p,j,false)};q.strokeText=function(m,i,p,j){this.drawText_(m,i,p,j,true)};q.measureText=function(m){if(!this.textMeasureEl_){var i='<span style="position:absolute;top:-20000px;left:0;padding:0;margin:0;border:none;white-space:pre;"></span>';this.element_.insertAdjacentHTML("beforeEnd",i);this.textMeasureEl_=this.element_.lastChild}var j=this.element_.ownerDocument;this.textMeasureEl_.innerHTML="";this.textMeasureEl_.style.font=this.font;this.textMeasureEl_.appendChild(j.createTextNode(m));return{width:this. textMeasureEl_.offsetWidth}};q.clip=function(){};q.arcTo=function(){};q.createPattern=function(j,i){return new T(j,i)};function U(i){this.type_=i;this.x0_=0;this.y0_=0;this.r0_=0;this.x1_=0;this.y1_=0;this.r1_=0;this.colors_=[]}U.prototype.addColorStop=function(j,i){i=F(i);this.colors_.push({offset:j,color:i.color,alpha:i.alpha})};function T(j,i){Q(j);switch(i){case"repeat":case null:case"":this.repetition_="repeat";break;case"repeat-x":case"repeat-y":case"no-repeat":this.repetition_=i;break;default:O("SYNTAX_ERR")}this.src_=j.src;this.width_=j.width;this.height_=j.height}function O(i){throw new P(i)}function Q(i){if(!i||i.nodeType!=1||i.tagName!="IMG"){O("TYPE_MISMATCH_ERR")}if(i.readyState!="complete"){O("INVALID_STATE_ERR")}}function P(i){this.code=this[i];this.message=i+": DOM Exception "+this.code}var X=P.prototype=new Error;X.INDEX_SIZE_ERR=1;X.DOMSTRING_SIZE_ERR=2;X.HIERARCHY_REQUEST_ERR=3;X.WRONG_DOCUMENT_ERR=4;X.INVALID_CHARACTER_ERR=5;X.NO_DATA_ALLOWED_ERR=6;X.NO_M ODIFICATION_ALLOWED_ERR=7;X.NOT_FOUND_ERR=8;X.NOT_SUPPORTED_ERR=9;X.INUSE_ATTRIBUTE_ERR=10;X.INVALID_STATE_ERR=11;X.SYNTAX_ERR=12;X.INVALID_MODIFICATION_ERR=13;X.NAMESPACE_ERR=14;X.INVALID_ACCESS_ERR=15;X.VALIDATION_ERR=16;X.TYPE_MISMATCH_ERR=17;G_vmlCanvasManager=e;CanvasRenderingContext2D=D;CanvasGradient=U;CanvasPattern=T;DOMException=P})()}; --- a/static/scripts/excanvas.js +++ b/static/scripts/excanvas.js @@ -13,9 +13,9 @@ // limitations under the License. -// Known Issues: (From VML version) +// Known Issues: // -// * Patterns are not implemented. +// * Patterns only support repeat. // * Radial gradient are not implemented. The VML version of these look very // different from the canvas one. // * Clipping paths are not implemented. @@ -28,59 +28,107 @@ // (http://www.whatwg.org/specs/web-apps/current-work/#the-doctype) // or use Box Sizing Behavior from WebFX // (http://webfx.eae.net/dhtml/boxsizing/boxsizing.html) +// * Non uniform scaling does not correctly scale strokes. // * Optimize. There is always room for speed improvements. -//Known Issues: Silverlight version -// -// * Doing a transformation during a path (ie lineTo, transform, lineTo) will -// not work corerctly because the transform is done to the whole path (ie -// transform, lineTo, lineTo) -// * Patterns are not yet implemented. +// Only add this code if we do not already have a canvas implementation +if (!document.createElement('canvas').getContext) { +(function() { -// only add this code if we do not already have a canvas implementation -if (!window.CanvasRenderingContext2D) { + // alias some functions to make (compiled) code shorter + var m = Math; + var mr = m.round; + var ms = m.sin; + var mc = m.cos; + var abs = m.abs; + var sqrt = m.sqrt; -(function () { + // this is used for sub pixel precision + var Z = 10; + var Z2 = Z / 2; - var xamlId; + var IE_VERSION = +navigator.userAgent.match(/MSIE ([\d.]+)?/)[1]; + + /** + * This funtion is assigned to the <canvas> elements as element.getContext(). + * @this {HTMLElement} + * @return {CanvasRenderingContext2D_} + */ + function getContext() { + return this.context_ || + (this.context_ = new CanvasRenderingContext2D_(this)); + } + + var slice = Array.prototype.slice; + + /** + * Binds a function to an object. The returned function will always use the + * passed in {@code obj} as {@code this}. + * + * Example: + * + * g = bind(f, obj, a, b) + * g(c, d) // will do f.call(obj, a, b, c, d) + * + * @param {Function} f The function to bind the object to + * @param {Object} obj The object that should act as this when the function + * is called + * @param {*} var_args Rest arguments that will be used as the initial + * arguments when the function is called + * @return {Function} A new function that has bound this + */ + function bind(f, obj, var_args) { + var a = slice.call(arguments, 2); + return function() { + return f.apply(obj, a.concat(slice.call(arguments))); + }; + } + + function encodeHtmlAttribute(s) { + return String(s).replace(/&/g, '&').replace(/"/g, '"'); + } + + function addNamespace(doc, prefix, urn) { + if (!doc.namespaces[prefix]) { + doc.namespaces.add(prefix, urn, '#default#VML'); + } + } + + function addNamespacesAndStylesheet(doc) { + addNamespace(doc, 'g_vml_', 'urn:schemas-microsoft-com:vml'); + addNamespace(doc, 'g_o_', 'urn:schemas-microsoft-com:office:office'); + + // Setup default CSS. Only add one style sheet per document + if (!doc.styleSheets['ex_canvas_']) { + var ss = doc.createStyleSheet(); + ss.owningElement.id = 'ex_canvas_'; + ss.cssText = 'canvas{display:inline-block;overflow:hidden;' + + // default size is 300x150 in Gecko and Opera + 'text-align:left;width:300px;height:150px}'; + } + } + + // Add namespaces and stylesheet at startup. + addNamespacesAndStylesheet(document); var G_vmlCanvasManager_ = { - init: function (opt_doc) { + init: function(opt_doc) { var doc = opt_doc || document; // Create a dummy element so that IE will allow canvas elements to be // recognized. doc.createElement('canvas'); - if (/MSIE/.test(navigator.userAgent) && !window.opera) { - var self = this; - - createXamlScriptTag(); - - doc.attachEvent('onreadystatechange', function () { - self.init_(doc); - }); - } + doc.attachEvent('onreadystatechange', bind(this.init_, this, doc)); }, - init_: function (doc) { - // setup default css - var ss = doc.createStyleSheet(); - ss.cssText = 'canvas{display:inline-block;overflow:hidden;' + - // default size is 300x150 in Gecko and Opera - 'text-align:left;width:300px;height:150px}' + - 'canvas object{width:100%;height:100%;border:0;' + - 'background:transparen;margin:0}'; - + init_: function(doc) { // find all canvas elements var els = doc.getElementsByTagName('canvas'); for (var i = 0; i < els.length; i++) { - if (!els[i].getContext) { - this.initElement(els[i]); - } + this.initElement(els[i]); } }, - /** * Public initializes a canvas element so that it can be used as canvas * element from now on. This is called automatically before the page is @@ -89,35 +137,39 @@ if (!window.CanvasRenderingContext2D) { * @param {HTMLElement} el The canvas element to initialize. * @return {HTMLElement} the element that was created. */ - initElement: function (el) { - el.getContext = function () { - if (this.context_) { - return this.context_; + initElement: function(el) { + if (!el.getContext) { + el.getContext = getContext; + + // Add namespaces and stylesheet to document of the element. + addNamespacesAndStylesheet(el.ownerDocument); + + // Remove fallback content. There is no way to hide text nodes so we + // just remove all childNodes. We could hide all elements and remove + // text nodes but who really cares about the fallback content. + el.innerHTML = ''; + + // do not use inline function because that will leak memory + el.attachEvent('onpropertychange', onPropertyChange); + el.attachEvent('onresize', onResize); + + var attrs = el.attributes; + if (attrs.width && attrs.width.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setWidth_(attrs.width.nodeValue); + el.style.width = attrs.width.nodeValue + 'px'; + } else { + el.width = el.clientWidth; } - return this.context_ = new CanvasRenderingContext2D_(this); - }; - - var attrs = el.attributes; - if (attrs.width && attrs.width.specified) { - // TODO: use runtimeStyle and coordsize - // el.getContext().setWidth_(attrs.width.nodeValue); - el.style.width = attrs.width.nodeValue + 'px'; - } else { - el.width = el.clientWidth; + if (attrs.height && attrs.height.specified) { + // TODO: use runtimeStyle and coordsize + // el.getContext().setHeight_(attrs.height.nodeValue); + el.style.height = attrs.height.nodeValue + 'px'; + } else { + el.height = el.clientHeight; + } + //el.getContext().setCoordsize_() } - if (attrs.height && attrs.height.specified) { - // TODO: use runtimeStyle and coordsize - // el.getContext().setHeight_(attrs.height.nodeValue); - el.style.height = attrs.height.nodeValue + 'px'; - } else { - el.height = el.clientHeight; - } - - // insert object tag - el.innerHTML = getObjectHtml(); - - // do not use inline function because that will leak memory - el.attachEvent('onpropertychange', onPropertyChange); return el; } }; @@ -127,58 +179,34 @@ if (!window.CanvasRenderingContext2D) { switch (e.propertyName) { case 'width': + el.getContext().clearRect(); el.style.width = el.attributes.width.nodeValue + 'px'; - el.getContext().clearRect(); + // In IE8 this does not trigger onresize. + el.firstChild.style.width = el.clientWidth + 'px'; break; case 'height': + el.getContext().clearRect(); el.style.height = el.attributes.height.nodeValue + 'px'; - el.getContext().clearRect(); + el.firstChild.style.height = el.clientHeight + 'px'; break; } } + function onResize(e) { + var el = e.srcElement; + if (el.firstChild) { + el.firstChild.style.width = el.clientWidth + 'px'; + el.firstChild.style.height = el.clientHeight + 'px'; + } + } + G_vmlCanvasManager_.init(); - function createXamlScriptTag() { - // This script tag contains the boilerplate XAML. - document.write('<script type=text/xaml>' + - '<Canvas x:Name="root" ' + - 'xmlns="http://schemas.microsoft.com/client/2007" ' + - 'xmlns:x="http://schemas.microsoft.com/winfx/2006/xaml" ' + - 'Width="300" ' + - 'Height="150" ' + - 'Background="Transparent"> ' + - '</Canvas>' + - '</script>'); - // Find the id of the writtenscript file. - var scripts = document.scripts; - var script = scripts[scripts.length - 1]; - xamlId = script.uniqueID; - script.id = xamlId; - } - - function getObjectHtml(fn) { - return '<object type="application/x-silverlight" >' + - '<param name="windowless" value="true">' + - '<param name="background" value="transparent">' + - '<param name="source" value="#' + xamlId + '">' + - '</object>'; - } - - function hasSilverlight() { - try { - new ActiveXObject('AgControl.AgControl'); - return true; - } catch(_) { - return false; - } - } - // precompute "00" to "FF" - var dec2hex = []; + var decToHex = []; for (var i = 0; i < 16; i++) { for (var j = 0; j < 16; j++) { - dec2hex[i * 16 + j] = i.toString(16) + j.toString(16); + decToHex[i * 16 + j] = i.toString(16) + j.toString(16); } } @@ -207,30 +235,6 @@ if (!window.CanvasRenderingContext2D) { return result; } - function doTransform(ctx) { - transformObject(ctx, getRoot(ctx), ctx.m_); - } - - function transformObject(ctx, obj, m) { - var transform = obj.renderTransform; - var matrix; - if (!transform) { - transform = create(ctx, '<MatrixTransform/>'); - matrix = create(ctx, '<Matrix/>'); - transform.matrix = matrix; - obj.renderTransform = transform; - } else { - matrix = transform.matrix; - } - - matrix.m11 = m[0][0]; - matrix.m12 = m[0][1]; - matrix.m21 = m[1][0]; - matrix.m22 = m[1][1]; - matrix.offsetX = m[2][0]; - matrix.offsetY = m[2][1]; - } - function copyState(o1, o2) { o2.fillStyle = o1.fillStyle; o2.lineCap = o1.lineCap; @@ -243,93 +247,327 @@ if (!window.CanvasRenderingContext2D) { o2.shadowOffsetY = o1.shadowOffsetY; o2.strokeStyle = o1.strokeStyle; o2.globalAlpha = o1.globalAlpha; + o2.font = o1.font; + o2.textAlign = o1.textAlign; + o2.textBaseline = o1.textBaseline; o2.arcScaleX_ = o1.arcScaleX_; o2.arcScaleY_ = o1.arcScaleY_; + o2.lineScale_ = o1.lineScale_; } - function translateColor(s) { - var rgbaMatch = /rgba$([^)]+)$/gi.exec(s); - if (rgbaMatch) { - var parts = rgbaMatch[1].split(','); - return '#' + dec2hex[Math.floor(Number(parts[3]) * 255)] + - dec2hex[Number(parts[0])] + - dec2hex[Number(parts[1])] + - dec2hex[Number(parts[2])]; + var colorData = { + aliceblue: '#F0F8FF', + antiquewhite: '#FAEBD7', + aquamarine: '#7FFFD4', + azure: '#F0FFFF', + beige: '#F5F5DC', + bisque: '#FFE4C4', + black: '#000000', + blanchedalmond: '#FFEBCD', + blueviolet: '#8A2BE2', + brown: '#A52A2A', + burlywood: '#DEB887', + cadetblue: '#5F9EA0', + chartreuse: '#7FFF00', + chocolate: '#D2691E', + coral: '#FF7F50', + cornflowerblue: '#6495ED', + cornsilk: '#FFF8DC', + crimson: '#DC143C', + cyan: '#00FFFF', + darkblue: '#00008B', + darkcyan: '#008B8B', + darkgoldenrod: '#B8860B', + darkgray: '#A9A9A9', + darkgreen: '#006400', + darkgrey: '#A9A9A9', + darkkhaki: '#BDB76B', + darkmagenta: '#8B008B', + darkolivegreen: '#556B2F', + darkorange: '#FF8C00', + darkorchid: '#9932CC', + darkred: '#8B0000', + darksalmon: '#E9967A', + darkseagreen: '#8FBC8F', + darkslateblue: '#483D8B', + darkslategray: '#2F4F4F', + darkslategrey: '#2F4F4F', + darkturquoise: '#00CED1', + darkviolet: '#9400D3', + deeppink: '#FF1493', + deepskyblue: '#00BFFF', + dimgray: '#696969', + dimgrey: '#696969', + dodgerblue: '#1E90FF', + firebrick: '#B22222', + floralwhite: '#FFFAF0', + forestgreen: '#228B22', + gainsboro: '#DCDCDC', + ghostwhite: '#F8F8FF', + gold: '#FFD700', + goldenrod: '#DAA520', + grey: '#808080', + greenyellow: '#ADFF2F', + honeydew: '#F0FFF0', + hotpink: '#FF69B4', + indianred: '#CD5C5C', + indigo: '#4B0082', + ivory: '#FFFFF0', + khaki: '#F0E68C', + lavender: '#E6E6FA', + lavenderblush: '#FFF0F5', + lawngreen: '#7CFC00', + lemonchiffon: '#FFFACD', + lightblue: '#ADD8E6', + lightcoral: '#F08080', + lightcyan: '#E0FFFF', + lightgoldenrodyellow: '#FAFAD2', + lightgreen: '#90EE90', + lightgrey: '#D3D3D3', + lightpink: '#FFB6C1', + lightsalmon: '#FFA07A', + lightseagreen: '#20B2AA', + lightskyblue: '#87CEFA', + lightslategray: '#778899', + lightslategrey: '#778899', + lightsteelblue: '#B0C4DE', + lightyellow: '#FFFFE0', + limegreen: '#32CD32', + linen: '#FAF0E6', + magenta: '#FF00FF', + mediumaquamarine: '#66CDAA', + mediumblue: '#0000CD', + mediumorchid: '#BA55D3', + mediumpurple: '#9370DB', + mediumseagreen: '#3CB371', + mediumslateblue: '#7B68EE', + mediumspringgreen: '#00FA9A', + mediumturquoise: '#48D1CC', + mediumvioletred: '#C71585', + midnightblue: '#191970', + mintcream: '#F5FFFA', + mistyrose: '#FFE4E1', + moccasin: '#FFE4B5', + navajowhite: '#FFDEAD', + oldlace: '#FDF5E6', + olivedrab: '#6B8E23', + orange: '#FFA500', + orangered: '#FF4500', + orchid: '#DA70D6', + palegoldenrod: '#EEE8AA', + palegreen: '#98FB98', + paleturquoise: '#AFEEEE', + palevioletred: '#DB7093', + papayawhip: '#FFEFD5', + peachpuff: '#FFDAB9', + peru: '#CD853F', + pink: '#FFC0CB', + plum: '#DDA0DD', + powderblue: '#B0E0E6', + rosybrown: '#BC8F8F', + royalblue: '#4169E1', + saddlebrown: '#8B4513', + salmon: '#FA8072', + sandybrown: '#F4A460', + seagreen: '#2E8B57', + seashell: '#FFF5EE', + sienna: '#A0522D', + skyblue: '#87CEEB', + slateblue: '#6A5ACD', + slategray: '#708090', + slategrey: '#708090', + snow: '#FFFAFA', + springgreen: '#00FF7F', + steelblue: '#4682B4', + tan: '#D2B48C', + thistle: '#D8BFD8', + tomato: '#FF6347', + turquoise: '#40E0D0', + violet: '#EE82EE', + wheat: '#F5DEB3', + whitesmoke: '#F5F5F5', + yellowgreen: '#9ACD32' + }; + + + function getRgbHslContent(styleString) { + var start = styleString.indexOf('(', 3); + var end = styleString.indexOf(')', start + 1); + var parts = styleString.substring(start + 1, end).split(','); + // add alpha if needed + if (parts.length != 4 || styleString.charAt(3) != 'a') { + parts[3] = 1; + } + return parts; + } + + function percent(s) { + return parseFloat(s) / 100; + } + + function clamp(v, min, max) { + return Math.min(max, Math.max(min, v)); + } + + function hslToRgb(parts){ + var r, g, b, h, s, l; + h = parseFloat(parts[0]) / 360 % 360; + if (h < 0) + h++; + s = clamp(percent(parts[1]), 0, 1); + l = clamp(percent(parts[2]), 0, 1); + if (s == 0) { + r = g = b = l; // achromatic + } else { + var q = l < 0.5 ? l * (1 + s) : l + s - l * s; + var p = 2 * l - q; + r = hueToRgb(p, q, h + 1 / 3); + g = hueToRgb(p, q, h); + b = hueToRgb(p, q, h - 1 / 3); } - var rgbMatch = /rgb$([^)]+)$/gi.exec(s); - if (rgbMatch) { - var parts = rgbMatch[1].split(','); - return '#FF' + dec2hex[Number(parts[0])] + - dec2hex[Number(parts[1])] + - dec2hex[Number(parts[2])]; + return '#' + decToHex[Math.floor(r * 255)] + + decToHex[Math.floor(g * 255)] + + decToHex[Math.floor(b * 255)]; + } + + function hueToRgb(m1, m2, h) { + if (h < 0) + h++; + if (h > 1) + h--; + + if (6 * h < 1) + return m1 + (m2 - m1) * 6 * h; + else if (2 * h < 1) + return m2; + else if (3 * h < 2) + return m1 + (m2 - m1) * (2 / 3 - h) * 6; + else + return m1; + } + + var processStyleCache = {}; + + function processStyle(styleString) { + if (styleString in processStyleCache) { + return processStyleCache[styleString]; } - return s; + var str, alpha = 1; + + styleString = String(styleString); + if (styleString.charAt(0) == '#') { + str = styleString; + } else if (/^rgb/.test(styleString)) { + var parts = getRgbHslContent(styleString); + var str = '#', n; + for (var i = 0; i < 3; i++) { + if (parts[i].indexOf('%') != -1) { + n = Math.floor(percent(parts[i]) * 255); + } else { + n = +parts[i]; + } + str += decToHex[clamp(n, 0, 255)]; + } + alpha = +parts[3]; + } else if (/^hsl/.test(styleString)) { + var parts = getRgbHslContent(styleString); + str = hslToRgb(parts); + alpha = parts[3]; + } else { + str = colorData[styleString] || styleString; + } + return processStyleCache[styleString] = {color: str, alpha: alpha}; } - function processLineCap(lineCap) { - switch (lineCap) { - case 'butt': - return 'flat'; - case 'round': - return 'round'; - case 'square': - default: - return 'square'; + var DEFAULT_STYLE = { + style: 'normal', + variant: 'normal', + weight: 'normal', + size: 10, + family: 'sans-serif' + }; + + // Internal text style cache + var fontStyleCache = {}; + + function processFontStyle(styleString) { + if (fontStyleCache[styleString]) { + return fontStyleCache[styleString]; } + + var el = document.createElement('div'); + var style = el.style; + try { + style.font = styleString; + } catch (ex) { + // Ignore failures to set to invalid font. + } + + return fontStyleCache[styleString] = { + style: style.fontStyle || DEFAULT_STYLE.style, + variant: style.fontVariant || DEFAULT_STYLE.variant, + weight: style.fontWeight || DEFAULT_STYLE.weight, + size: style.fontSize || DEFAULT_STYLE.size, + family: style.fontFamily || DEFAULT_STYLE.family + }; } - function getRoot(ctx) { - return ctx.canvas.firstChild.content.findName('root'); + function getComputedStyle(style, element) { + var computedStyle = {}; + + for (var p in style) { + computedStyle[p] = style[p]; + } + + // Compute the size + var canvasFontSize = parseFloat(element.currentStyle.fontSize), + fontSize = parseFloat(style.size); + + if (typeof style.size == 'number') { + computedStyle.size = style.size; + } else if (style.size.indexOf('px') != -1) { + computedStyle.size = fontSize; + } else if (style.size.indexOf('em') != -1) { + computedStyle.size = canvasFontSize * fontSize; + } else if(style.size.indexOf('%') != -1) { + computedStyle.size = (canvasFontSize / 100) * fontSize; + } else if (style.size.indexOf('pt') != -1) { + computedStyle.size = fontSize / .75; + } else { + computedStyle.size = canvasFontSize; + } + + // Different scaling between normal text and VML text. This was found using + // trial and error to get the same size as non VML text. + computedStyle.size *= 0.981; + + return computedStyle; } - function create(ctx, s, opt_args) { - if (opt_args) { - s = s.replace(/\%(\d+)/g, function(match, index) { - return opt_args[Number(index) - 1]; - }); - } - - try { - return ctx.canvas.firstChild.content.createFromXaml(s); - } catch (ex) { - throw Error('Could not create XAML from: ' + s); - } + function buildStyle(style) { + return style.style + ' ' + style.variant + ' ' + style.weight + ' ' + + style.size + 'px ' + style.family; } - function drawShape(ctx, s, opt_args) { - var canvas = ctx.lastCanvas_ || create(ctx, '<Canvas/>'); - var shape = create(ctx, s, opt_args); - canvas.children.add(shape); - transformObject(ctx, canvas, ctx.m_); - if (!ctx.lastCanvas_) { - getRoot(ctx).children.add(canvas); - ctx.lastCanvas_ = canvas; - } - return shape; - } + var lineCapMap = { + 'butt': 'flat', + 'round': 'round' + }; - function createBrushObject(ctx, value) { - if (value instanceof CanvasGradient_) { - return value.createBrush_(ctx); - } else if (value instanceof CanvasPattern_) { - throw Error('Not implemented'); - } else { - return create(ctx, '<SolidColorBrush Color="%1"/>', - [translateColor(value)]); - } + function processLineCap(lineCap) { + return lineCapMap[lineCap] || 'square'; } /** * This class implements CanvasRenderingContext2D interface as described by * the WHATWG. - * @param {HTMLElement} surfaceElement The element that the 2D context should - * be associated with + * @param {HTMLElement} canvasElement The element that the 2D context should + * be associated with */ - function CanvasRenderingContext2D_(surfaceElement) { + function CanvasRenderingContext2D_(canvasElement) { this.m_ = createMatrixIdentity(); - this.lastCanvas_ = null; this.mStack_ = []; this.aStack_ = []; @@ -342,100 +580,134 @@ if (!window.CanvasRenderingContext2D) { this.lineWidth = 1; this.lineJoin = 'miter'; this.lineCap = 'butt'; - this.miterLimit = 10; + this.miterLimit = Z * 1; this.globalAlpha = 1; - this.canvas = surfaceElement; - }; + this.font = '10px sans-serif'; + this.textAlign = 'left'; + this.textBaseline = 'alphabetic'; + this.canvas = canvasElement; + var cssText = 'width:' + canvasElement.clientWidth + 'px;height:' + + canvasElement.clientHeight + 'px;overflow:hidden;position:absolute'; + var el = canvasElement.ownerDocument.createElement('div'); + el.style.cssText = cssText; + canvasElement.appendChild(el); + + var overlayEl = el.cloneNode(false); + // Use a non transparent background. + overlayEl.style.backgroundColor = 'red'; + overlayEl.style.filter = 'alpha(opacity=0)'; + canvasElement.appendChild(overlayEl); + + this.element_ = el; + this.arcScaleX_ = 1; + this.arcScaleY_ = 1; + this.lineScale_ = 1; + } var contextPrototype = CanvasRenderingContext2D_.prototype; - contextPrototype.clearRect = function() { - var root = getRoot(this); - root.children.clear(); - - // TODO: Implement - this.currentPath_ = []; - this.lastCanvas_ = null; - + if (this.textMeasureEl_) { + this.textMeasureEl_.removeNode(true); + this.textMeasureEl_ = null; + } + this.element_.innerHTML = ''; }; contextPrototype.beginPath = function() { // TODO: Branch current matrix so that save/restore has no effect // as per safari docs. - this.currentPath_ = []; }; contextPrototype.moveTo = function(aX, aY) { - this.currentPath_.push('M' + aX + ',' + aY); + var p = getCoords(this, aX, aY); + this.currentPath_.push({type: 'moveTo', x: p.x, y: p.y}); + this.currentX_ = p.x; + this.currentY_ = p.y; }; contextPrototype.lineTo = function(aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('L' + aX + ',' + aY); + var p = getCoords(this, aX, aY); + this.currentPath_.push({type: 'lineTo', x: p.x, y: p.y}); + + this.currentX_ = p.x; + this.currentY_ = p.y; }; contextPrototype.bezierCurveTo = function(aCP1x, aCP1y, aCP2x, aCP2y, aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('C' + aCP1x + ',' + aCP1y + ' ' + - aCP2x + ',' + aCP2y + ' ' + - aX + ' ' + aY); + var p = getCoords(this, aX, aY); + var cp1 = getCoords(this, aCP1x, aCP1y); + var cp2 = getCoords(this, aCP2x, aCP2y); + bezierCurveTo(this, cp1, cp2, p); }; + // Helper function that takes the already fixed cordinates. + function bezierCurveTo(self, cp1, cp2, p) { + self.currentPath_.push({ + type: 'bezierCurveTo', + cp1x: cp1.x, + cp1y: cp1.y, + cp2x: cp2.x, + cp2y: cp2.y, + x: p.x, + y: p.y + }); + self.currentX_ = p.x; + self.currentY_ = p.y; + } + contextPrototype.quadraticCurveTo = function(aCPx, aCPy, aX, aY) { - if (this.currentPath_.length == 0) return; - this.currentPath_.push('Q' + aCPx + ',' + aCPy + ' ' + - aX + ',' + aY); - }; + // the following is lifted almost directly from + // http://developer.mozilla.org/en/docs/Canvas_tutorial:Drawing_shapes - contextPrototype.arcTo = function(x1, y1, x2, y2, radius) { - if (this.currentPath_.length == 0) return; - // TODO: Implement + var cp = getCoords(this, aCPx, aCPy); + var p = getCoords(this, aX, aY); + + var cp1 = { + x: this.currentX_ + 2.0 / 3.0 * (cp.x - this.currentX_), + y: this.currentY_ + 2.0 / 3.0 * (cp.y - this.currentY_) + }; + var cp2 = { + x: cp1.x + (p.x - this.currentX_) / 3.0, + y: cp1.y + (p.y - this.currentY_) / 3.0 + }; + + bezierCurveTo(this, cp1, cp2, p); }; contextPrototype.arc = function(aX, aY, aRadius, aStartAngle, aEndAngle, aClockwise) { - var deltaAngle = Math.abs(aStartAngle - aEndAngle); - // If start and stop are the same WebKit and Moz does nothing - if (aStartAngle == aEndAngle) { - // different browsers behave differently here so we do the easiest thing - return; + aRadius *= Z; + var arcType = aClockwise ? 'at' : 'wa'; + + var xStart = aX + mc(aStartAngle) * aRadius - Z2; + var yStart = aY + ms(aStartAngle) * aRadius - Z2; + + var xEnd = aX + mc(aEndAngle) * aRadius - Z2; + var yEnd = aY + ms(aEndAngle) * aRadius - Z2; + + // IE won't render arches drawn counter clockwise if xStart == xEnd. + if (xStart == xEnd && !aClockwise) { + xStart += 0.125; // Offset xStart by 1/80 of a pixel. Use something + // that can be represented in binary } - var endX = aX + aRadius * Math.cos(aEndAngle); - var endY = aY + aRadius * Math.sin(aEndAngle); + var p = getCoords(this, aX, aY); + var pStart = getCoords(this, xStart, yStart); + var pEnd = getCoords(this, xEnd, yEnd); - if (deltaAngle >= 2 * Math.PI) { - // if larger than 2PI - this.arc(aX, aY, aRadius, aStartAngle, aStartAngle + Math.PI, aClockwise); - this.arc(aX, aY, aRadius, aStartAngle + Math.PI, - aStartAngle + 2 * Math.PI, aClockwise); - // now move to end point - this.moveTo(endX, endY); - return; - } + this.currentPath_.push({type: arcType, + x: p.x, + y: p.y, + radius: aRadius, + xStart: pStart.x, + yStart: pStart.y, + xEnd: pEnd.x, + yEnd: pEnd.y}); - var startX = aX + aRadius * Math.cos(aStartAngle); - var startY = aY + aRadius * Math.sin(aStartAngle); - var rotationAngle = deltaAngle * 180 / Math.PI; // sign, abs? - var sweepDirection = aClockwise ? 0 : 1; - var isLargeArc = rotationAngle >= 180 == Boolean(aClockwise) ? 0 : 1; - - if (this.currentPath_.length != 0) { - // add line to start point - this.lineTo(startX, startY); - } else { - this.moveTo(startX, startY); - } - - this.currentPath_.push('A' + aRadius + ',' + aRadius + ' ' + - rotationAngle + ' ' + - isLargeArc + ' ' + - sweepDirection + ' ' + - endX + ',' + endY); }; contextPrototype.rect = function(aX, aY, aWidth, aHeight) { @@ -447,55 +719,85 @@ if (!window.CanvasRenderingContext2D) { }; contextPrototype.strokeRect = function(aX, aY, aWidth, aHeight) { - // Will destroy any existing path (same as FF behaviour) + var oldPath = this.currentPath_; this.beginPath(); + this.moveTo(aX, aY); this.lineTo(aX + aWidth, aY); this.lineTo(aX + aWidth, aY + aHeight); this.lineTo(aX, aY + aHeight); this.closePath(); this.stroke(); - this.currentPath_ = []; + + this.currentPath_ = oldPath; }; contextPrototype.fillRect = function(aX, aY, aWidth, aHeight) { - // Will destroy any existing path (same as FF behaviour) + var oldPath = this.currentPath_; this.beginPath(); + this.moveTo(aX, aY); this.lineTo(aX + aWidth, aY); this.lineTo(aX + aWidth, aY + aHeight); this.lineTo(aX, aY + aHeight); this.closePath(); this.fill(); - this.currentPath_ = []; + + this.currentPath_ = oldPath; }; contextPrototype.createLinearGradient = function(aX0, aY0, aX1, aY1) { - return new LinearCanvasGradient_(aX0, aY0, aX1, aY1); + var gradient = new CanvasGradient_('gradient'); + gradient.x0_ = aX0; + gradient.y0_ = aY0; + gradient.x1_ = aX1; + gradient.y1_ = aY1; + return gradient; }; - contextPrototype.createRadialGradient = function(x0, y0, - r0, x1, - y1, r1) { - return new RadialCanvasGradient_(x0, y0, r0, x1, y1, r1); + contextPrototype.createRadialGradient = function(aX0, aY0, aR0, + aX1, aY1, aR1) { + var gradient = new CanvasGradient_('gradientradial'); + gradient.x0_ = aX0; + gradient.y0_ = aY0; + gradient.r0_ = aR0; + gradient.x1_ = aX1; + gradient.y1_ = aY1; + gradient.r1_ = aR1; + return gradient; }; - contextPrototype.drawImage = function (image, var_args) { + contextPrototype.drawImage = function(image, var_args) { var dx, dy, dw, dh, sx, sy, sw, sh; - // For Silverlight we don't need to get the size of the image since - // Silverlight uses the image original dimension if not provided. + // to find the original width we overide the width and height + var oldRuntimeWidth = image.runtimeStyle.width; + var oldRuntimeHeight = image.runtimeStyle.height; + image.runtimeStyle.width = 'auto'; + image.runtimeStyle.height = 'auto'; + + // get the original size + var w = image.width; + var h = image.height; + + // and remove overides + image.runtimeStyle.width = oldRuntimeWidth; + image.runtimeStyle.height = oldRuntimeHeight; if (arguments.length == 3) { dx = arguments[1]; dy = arguments[2]; - // Keep sx, sy, sw, dw, sh and dh undefined + sx = sy = 0; + sw = dw = w; + sh = dh = h; } else if (arguments.length == 5) { dx = arguments[1]; dy = arguments[2]; dw = arguments[3]; dh = arguments[4]; - // Keep sx, sy, sw and sh undefined + sx = sy = 0; + sw = w; + sh = h; } else if (arguments.length == 9) { sx = arguments[1]; sy = arguments[2]; @@ -509,81 +811,298 @@ if (!window.CanvasRenderingContext2D) { throw Error('Invalid number of arguments'); } - var slImage; + var d = getCoords(this, dx, dy); - // If we have a source rect we need to clip the image. - if (arguments.length == 9) { - slImage = drawShape(this, '<Image Source="%1"/>', [image.src]); + var w2 = sw / 2; + var h2 = sh / 2; - var clipRect = create(this, - '<RectangleGeometry Rect="%1,%2,%3,%4"/>', [sx, sy, sw, sh]); - slImage.clip = clipRect; + var vmlStr = []; - var m = createMatrixIdentity(); + var W = 10; + var H = 10; - // translate to 0,0 - m[2][0] = -sx; - m[2][1] = -sy; + // For some reason that I've now forgotten, using divs didn't work + vmlStr.push(' <g_vml_:group', + ' coordsize="', Z * W, ',', Z * H, '"', + ' coordorigin="0,0"' , + ' style="width:', W, 'px;height:', H, 'px;position:absolute;'); - // scale - var m2 = createMatrixIdentity(); - m2[0][0] = dw / sw; - m2[1][1] = dh / sh; + // If filters are necessary (rotation exists), create them + // filters are bog-slow, so only create them if abbsolutely necessary + // The following check doesn't account for skews (which don't exist + // in the canvas spec (yet) anyway. - m = matrixMultiply(m, m2); + if (this.m_[0][0] != 1 || this.m_[0][1] || + this.m_[1][1] != 1 || this.m_[1][0]) { + var filter = []; - // translate to destination - m[2][0] += dx; - m[2][1] += dy; + // Note the 12/21 reversal + filter.push('M11=', this.m_[0][0], ',', + 'M12=', this.m_[1][0], ',', + 'M21=', this.m_[0][1], ',', + 'M22=', this.m_[1][1], ',', + 'Dx=', mr(d.x / Z), ',', + 'Dy=', mr(d.y / Z), ''); - transformObject(this, slImage, m); + // Bounding box calculation (need to minimize displayed area so that + // filters don't waste time on unused pixels. + var max = d; + var c2 = getCoords(this, dx + dw, dy); + var c3 = getCoords(this, dx, dy + dh); + var c4 = getCoords(this, dx + dw, dy + dh); + + max.x = m.max(max.x, c2.x, c3.x, c4.x); + max.y = m.max(max.y, c2.y, c3.y, c4.y); + + vmlStr.push('padding:0 ', mr(max.x / Z), 'px ', mr(max.y / Z), + 'px 0;filter:progid:DXImageTransform.Microsoft.Matrix(', + filter.join(''), ", sizingmethod='clip');"); } else { - slImage = drawShape(this, - '<Image Source="%1" Canvas.Left="%2" Canvas.Top="%3"/>', - [image.src, dx, dy]); - if (dw != undefined || dh != undefined) { - slImage.width = dw; - slImage.height = dh; - slImage.stretch = 'fill'; + vmlStr.push('top:', mr(d.y / Z), 'px;left:', mr(d.x / Z), 'px;'); + } + + vmlStr.push(' ">' , + '<g_vml_:image src="', image.src, '"', + ' style="width:', Z * dw, 'px;', + ' height:', Z * dh, 'px"', + ' cropleft="', sx / w, '"', + ' croptop="', sy / h, '"', + ' cropright="', (w - sx - sw) / w, '"', + ' cropbottom="', (h - sy - sh) / h, '"', + ' />', + '</g_vml_:group>'); + + this.element_.insertAdjacentHTML('BeforeEnd', vmlStr.join('')); + }; + + contextPrototype.stroke = function(aFill) { + var lineStr = []; + var lineOpen = false; + + var W = 10; + var H = 10; + + lineStr.push('<g_vml_:shape', + ' filled="', !!aFill, '"', + ' style="position:absolute;width:', W, 'px;height:', H, 'px;"', + ' coordorigin="0,0"', + ' coordsize="', Z * W, ',', Z * H, '"', + ' stroked="', !aFill, '"', + ' path="'); + + var newSeq = false; + var min = {x: null, y: null}; + var max = {x: null, y: null}; + + for (var i = 0; i < this.currentPath_.length; i++) { + var p = this.currentPath_[i]; + var c; + + switch (p.type) { + case 'moveTo': + c = p; + lineStr.push(' m ', mr(p.x), ',', mr(p.y)); + break; + case 'lineTo': + lineStr.push(' l ', mr(p.x), ',', mr(p.y)); + break; + case 'close': + lineStr.push(' x '); + p = null; + break; + case 'bezierCurveTo': + lineStr.push(' c ', + mr(p.cp1x), ',', mr(p.cp1y), ',', + mr(p.cp2x), ',', mr(p.cp2y), ',', + mr(p.x), ',', mr(p.y)); + break; + case 'at': + case 'wa': + lineStr.push(' ', p.type, ' ', + mr(p.x - this.arcScaleX_ * p.radius), ',', + mr(p.y - this.arcScaleY_ * p.radius), ' ', + mr(p.x + this.arcScaleX_ * p.radius), ',', + mr(p.y + this.arcScaleY_ * p.radius), ' ', + mr(p.xStart), ',', mr(p.yStart), ' ', + mr(p.xEnd), ',', mr(p.yEnd)); + break; + } + + + // TODO: Following is broken for curves due to + // move to proper paths. + + // Figure out dimensions so we can do gradient fills + // properly + if (p) { + if (min.x == null || p.x < min.x) { + min.x = p.x; + } + if (max.x == null || p.x > max.x) { + max.x = p.x; + } + if (min.y == null || p.y < min.y) { + min.y = p.y; + } + if (max.y == null || p.y > max.y) { + max.y = p.y; + } } } + lineStr.push(' ">'); + + if (!aFill) { + appendStroke(this, lineStr); + } else { + appendFill(this, lineStr, min, max); + } + + lineStr.push('</g_vml_:shape>'); + + this.element_.insertAdjacentHTML('beforeEnd', lineStr.join('')); }; - contextPrototype.stroke = function() { - if (this.currentPath_.length == 0) return; - var path = drawShape(this, '<Path Data="%1"/>', - [this.currentPath_.join(' ')]); - path.stroke = createBrushObject(this, this.strokeStyle); - path.opacity = this.globalAlpha; - path.strokeThickness = this.lineWidth; - path.strokeMiterLimit = this.miterLimit; - path.strokeLineJoin = this.lineJoin; - // Canvas does not differentiate start from end - path.strokeEndLineCap = path.strokeStartLineCap = - processLineCap(this.lineCap); - }; + function appendStroke(ctx, lineStr) { + var a = processStyle(ctx.strokeStyle); + var color = a.color; + var opacity = a.alpha * ctx.globalAlpha; + var lineWidth = ctx.lineScale_ * ctx.lineWidth; + + // VML cannot correctly render a line if the width is less than 1px. + // In that case, we dilute the color to make the line look thinner. + if (lineWidth < 1) { + opacity *= lineWidth; + } + + lineStr.push( + '<g_vml_:stroke', + ' opacity="', opacity, '"', + ' joinstyle="', ctx.lineJoin, '"', + ' miterlimit="', ctx.miterLimit, '"', + ' endcap="', processLineCap(ctx.lineCap), '"', + ' weight="', lineWidth, 'px"', + ' color="', color, '" />' + ); + } + + function appendFill(ctx, lineStr, min, max) { + var fillStyle = ctx.fillStyle; + var arcScaleX = ctx.arcScaleX_; + var arcScaleY = ctx.arcScaleY_; + var width = max.x - min.x; + var height = max.y - min.y; + if (fillStyle instanceof CanvasGradient_) { + // TODO: Gradients transformed with the transformation matrix. + var angle = 0; + var focus = {x: 0, y: 0}; + + // additional offset + var shift = 0; + // scale factor for offset + var expansion = 1; + + if (fillStyle.type_ == 'gradient') { + var x0 = fillStyle.x0_ / arcScaleX; + var y0 = fillStyle.y0_ / arcScaleY; + var x1 = fillStyle.x1_ / arcScaleX; + var y1 = fillStyle.y1_ / arcScaleY; + var p0 = getCoords(ctx, x0, y0); + var p1 = getCoords(ctx, x1, y1); + var dx = p1.x - p0.x; + var dy = p1.y - p0.y; + angle = Math.atan2(dx, dy) * 180 / Math.PI; + + // The angle should be a non-negative number. + if (angle < 0) { + angle += 360; + } + + // Very small angles produce an unexpected result because they are + // converted to a scientific notation string. + if (angle < 1e-6) { + angle = 0; + } + } else { + var p0 = getCoords(ctx, fillStyle.x0_, fillStyle.y0_); + focus = { + x: (p0.x - min.x) / width, + y: (p0.y - min.y) / height + }; + + width /= arcScaleX * Z; + height /= arcScaleY * Z; + var dimension = m.max(width, height); + shift = 2 * fillStyle.r0_ / dimension; + expansion = 2 * fillStyle.r1_ / dimension - shift; + } + + // We need to sort the color stops in ascending order by offset, + // otherwise IE won't interpret it correctly. + var stops = fillStyle.colors_; + stops.sort(function(cs1, cs2) { + return cs1.offset - cs2.offset; + }); + + var length = stops.length; + var color1 = stops[0].color; + var color2 = stops[length - 1].color; + var opacity1 = stops[0].alpha * ctx.globalAlpha; + var opacity2 = stops[length - 1].alpha * ctx.globalAlpha; + + var colors = []; + for (var i = 0; i < length; i++) { + var stop = stops[i]; + colors.push(stop.offset * expansion + shift + ' ' + stop.color); + } + + // When colors attribute is used, the meanings of opacity and o:opacity2 + // are reversed. + lineStr.push('<g_vml_:fill type="', fillStyle.type_, '"', + ' method="none" focus="100%"', + ' color="', color1, '"', + ' color2="', color2, '"', + ' colors="', colors.join(','), '"', + ' opacity="', opacity2, '"', + ' g_o_:opacity2="', opacity1, '"', + ' angle="', angle, '"', + ' focusposition="', focus.x, ',', focus.y, '" />'); + } else if (fillStyle instanceof CanvasPattern_) { + if (width && height) { + var deltaLeft = -min.x; + var deltaTop = -min.y; + lineStr.push('<g_vml_:fill', + ' position="', + deltaLeft / width * arcScaleX * arcScaleX, ',', + deltaTop / height * arcScaleY * arcScaleY, '"', + ' type="tile"', + // TODO: Figure out the correct size to fit the scale. + //' size="', w, 'px ', h, 'px"', + ' src="', fillStyle.src_, '" />'); + } + } else { + var a = processStyle(ctx.fillStyle); + var color = a.color; + var opacity = a.alpha * ctx.globalAlpha; + lineStr.push('<g_vml_:fill color="', color, '" opacity="', opacity, + '" />'); + } + } contextPrototype.fill = function() { - if (this.currentPath_.length == 0) return; - var path = drawShape(this, '<Path Data="%1"/>', - [this.currentPath_.join(' ')]); - // The spec says to use non zero but Silverlight uses EvenOdd by defaul - path.data.fillRule = 'NonZero'; - path.fill = createBrushObject(this, this.fillStyle); - // TODO: What about even-odd etc? + this.stroke(true); }; contextPrototype.closePath = function() { - this.currentPath_.push('z'); + this.currentPath_.push({type: 'close'}); }; - /** - * Sets the transformation matrix and marks things as dirty - */ - function setM(self, m) { - self.m_ = m; - self.lastCanvas_ = null; + function getCoords(ctx, aX, aY) { + var m = ctx.m_; + return { + x: Z * (aX * m[0][0] + aY * m[1][0] + m[2][0]) - Z2, + y: Z * (aX * m[0][1] + aY * m[1][1] + m[2][1]) - Z2 + }; }; contextPrototype.save = function() { @@ -591,14 +1110,38 @@ if (!window.CanvasRenderingContext2D) { copyState(this, o); this.aStack_.push(o); this.mStack_.push(this.m_); - setM(this, matrixMultiply(createMatrixIdentity(), this.m_)); + this.m_ = matrixMultiply(createMatrixIdentity(), this.m_); }; contextPrototype.restore = function() { - copyState(this.aStack_.pop(), this); - setM(this, this.mStack_.pop()); + if (this.aStack_.length) { + copyState(this.aStack_.pop(), this); + this.m_ = this.mStack_.pop(); + } }; + function matrixIsFinite(m) { + return isFinite(m[0][0]) && isFinite(m[0][1]) && + isFinite(m[1][0]) && isFinite(m[1][1]) && + isFinite(m[2][0]) && isFinite(m[2][1]); + } + + function setM(ctx, m, updateLineScale) { + if (!matrixIsFinite(m)) { + return; + } + ctx.m_ = m; + + if (updateLineScale) { + // Get the line scale. + // Determinant of this.m_ means how much the area is enlarged by the + // transformation. So its square root can be used as a scale factor + // for width. + var det = m[0][0] * m[1][1] - m[0][1] * m[1][0]; + ctx.lineScale_ = sqrt(abs(det)); + } + } + contextPrototype.translate = function(aX, aY) { var m1 = [ [1, 0, 0], @@ -606,12 +1149,12 @@ if (!window.CanvasRenderingContext2D) { [aX, aY, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), false); }; contextPrototype.rotate = function(aRot) { - var c = Math.cos(aRot); - var s = Math.sin(aRot); + var c = mc(aRot); + var s = ms(aRot); var m1 = [ [c, s, 0], @@ -619,35 +1162,157 @@ if (!window.CanvasRenderingContext2D) { [0, 0, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), false); }; contextPrototype.scale = function(aX, aY) { + this.arcScaleX_ *= aX; + this.arcScaleY_ *= aY; var m1 = [ [aX, 0, 0], [0, aY, 0], [0, 0, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), true); }; contextPrototype.transform = function(m11, m12, m21, m22, dx, dy) { var m1 = [ [m11, m12, 0], [m21, m22, 0], - [ dx, dy, 1] + [dx, dy, 1] ]; - setM(this, matrixMultiply(m1, this.m_)); + setM(this, matrixMultiply(m1, this.m_), true); }; contextPrototype.setTransform = function(m11, m12, m21, m22, dx, dy) { - setM(this, [ + var m = [ [m11, m12, 0], [m21, m22, 0], - [ dx, dy, 1], - ]); + [dx, dy, 1] + ]; + + setM(this, m, true); + }; + + /** + * The text drawing function. + * The maxWidth argument isn't taken in account, since no browser supports + * it yet. + */ + contextPrototype.drawText_ = function(text, x, y, maxWidth, stroke) { + var m = this.m_, + delta = 1000, + left = 0, + right = delta, + offset = {x: 0, y: 0}, + lineStr = []; + + var fontStyle = getComputedStyle(processFontStyle(this.font), + this.element_); + + var fontStyleString = buildStyle(fontStyle); + + var elementStyle = this.element_.currentStyle; + var textAlign = this.textAlign.toLowerCase(); + switch (textAlign) { + case 'left': + case 'center': + case 'right': + break; + case 'end': + textAlign = elementStyle.direction == 'ltr' ? 'right' : 'left'; + break; + case 'start': + textAlign = elementStyle.direction == 'rtl' ? 'right' : 'left'; + break; + default: + textAlign = 'left'; + } + + // 1.75 is an arbitrary number, as there is no info about the text baseline + switch (this.textBaseline) { + case 'hanging': + case 'top': + offset.y = fontStyle.size / 1.75; + break; + case 'middle': + break; + default: + case null: + case 'alphabetic': + case 'ideographic': + case 'bottom': + offset.y = -fontStyle.size / 2.25; + break; + } + + switch(textAlign) { + case 'right': + left = delta; + right = 0.05; + break; + case 'center': + left = right = delta / 2; + break; + } + + var d = getCoords(this, x + offset.x, y + offset.y); + + lineStr.push('<g_vml_:line from="', -left ,' 0" to="', right ,' 0.05" ', + ' coordsize="100 100" coordorigin="0 0"', + ' filled="', !stroke, '" stroked="', !!stroke, + '" style="position:absolute;width:1px;height:1px;">'); + + if (stroke) { + appendStroke(this, lineStr); + } else { + // TODO: Fix the min and max params. + appendFill(this, lineStr, {x: -left, y: 0}, + {x: right, y: fontStyle.size}); + } + + var skewM = m[0][0].toFixed(3) + ',' + m[1][0].toFixed(3) + ',' + + m[0][1].toFixed(3) + ',' + m[1][1].toFixed(3) + ',0,0'; + + var skewOffset = mr(d.x / Z) + ',' + mr(d.y / Z); + + lineStr.push('<g_vml_:skew on="t" matrix="', skewM ,'" ', + ' offset="', skewOffset, '" origin="', left ,' 0" />', + '<g_vml_:path textpathok="true" />', + '<g_vml_:textpath on="true" string="', + encodeHtmlAttribute(text), + '" style="v-text-align:', textAlign, + ';font:', encodeHtmlAttribute(fontStyleString), + '" /></g_vml_:line>'); + + this.element_.insertAdjacentHTML('beforeEnd', lineStr.join('')); + }; + + contextPrototype.fillText = function(text, x, y, maxWidth) { + this.drawText_(text, x, y, maxWidth, false); + }; + + contextPrototype.strokeText = function(text, x, y, maxWidth) { + this.drawText_(text, x, y, maxWidth, true); + }; + + contextPrototype.measureText = function(text) { + if (!this.textMeasureEl_) { + var s = '<span style="position:absolute;' + + 'top:-20000px;left:0;padding:0;margin:0;border:none;' + + 'white-space:pre;"></span>'; + this.element_.insertAdjacentHTML('beforeEnd', s); + this.textMeasureEl_ = this.element_.lastChild; + } + var doc = this.element_.ownerDocument; + this.textMeasureEl_.innerHTML = ''; + this.textMeasureEl_.style.font = this.font; + // Don't use innerHTML or innerText because they allow markup/whitespace. + this.textMeasureEl_.appendChild(doc.createTextNode(text)); + return {width: this.textMeasureEl_.offsetWidth}; }; /******** STUBS ********/ @@ -655,116 +1320,97 @@ if (!window.CanvasRenderingContext2D) { // TODO: Implement }; - contextPrototype.createPattern = function() { - return new CanvasPattern_; + contextPrototype.arcTo = function() { + // TODO: Implement + }; + + contextPrototype.createPattern = function(image, repetition) { + return new CanvasPattern_(image, repetition); }; // Gradient / Pattern Stubs - function CanvasGradient_() { + function CanvasGradient_(aType) { + this.type_ = aType; + this.x0_ = 0; + this.y0_ = 0; + this.r0_ = 0; + this.x1_ = 0; + this.y1_ = 0; + this.r1_ = 0; this.colors_ = []; } CanvasGradient_.prototype.addColorStop = function(aOffset, aColor) { - aColor = translateColor(aColor); - this.colors_.push({offset: aOffset, color: aColor}); + aColor = processStyle(aColor); + this.colors_.push({offset: aOffset, + color: aColor.color, + alpha: aColor.alpha}); }; - CanvasGradient_.prototype.createStops_ = function(ctx, brushObj, colors) { - var gradientStopCollection = brushObj.gradientStops; - for (var i = 0, c; c = colors[i]; i++) { - var color = translateColor(c.color); - gradientStopCollection.add(create(ctx, - '<GradientStop Color="%1" Offset="%2"/>', [color, c.offset])); + function CanvasPattern_(image, repetition) { + assertImageIsValid(image); + switch (repetition) { + case 'repeat': + case null: + case '': + this.repetition_ = 'repeat'; + break + case 'repeat-x': + case 'repeat-y': + case 'no-repeat': + this.repetition_ = repetition; + break; + default: + throwException('SYNTAX_ERR'); } - }; - function LinearCanvasGradient_(x0, y0, x1, y1) { - CanvasGradient_.call(this); - this.x0_ = x0; - this.y0_ = y0; - this.x1_ = x1; - this.y1_ = y1; - } - LinearCanvasGradient_.prototype = new CanvasGradient_; - - LinearCanvasGradient_.prototype.createBrush_ = function(ctx) { - var brushObj = create(ctx, '<LinearGradientBrush MappingMode="Absolute" ' + - 'StartPoint="%1,%2" EndPoint="%3,%4"/>', - [this.x0_, this.y0_, this.x1_, this.y1_]); - this.createStops_(ctx, brushObj, this.colors_); - return brushObj; - }; - - function isNanOrInfinite(v) { - return isNaN(v) || !isFinite(v); + this.src_ = image.src; + this.width_ = image.width; + this.height_ = image.height; } - function RadialCanvasGradient_(x0, y0, r0, x1, y1, r1) { - if (r0 < 0 || r1 < 0 || isNanOrInfinite(x0) || isNanOrInfinite(y0) || - isNanOrInfinite(x1) || isNanOrInfinite(y1)) { - // IE does not support DOMException so this is as close as we get. - var error = Error('DOMException.INDEX_SIZE_ERR'); - error.code = 1; - throw error; + function throwException(s) { + throw new DOMException_(s); + } + + function assertImageIsValid(img) { + if (!img || img.nodeType != 1 || img.tagName != 'IMG') { + throwException('TYPE_MISMATCH_ERR'); } + if (img.readyState != 'complete') { + throwException('INVALID_STATE_ERR'); + } + } - CanvasGradient_.call(this); - this.x0_ = x0; - this.y0_ = y0; - this.r0_ = r0; - this.x1_ = x1; - this.y1_ = y1; - this.r1_ = r1; + function DOMException_(s) { + this.code = this[s]; + this.message = s +': DOM Exception ' + this.code; } - RadialCanvasGradient_.prototype = new CanvasGradient_; - - CanvasGradient_.prototype.createBrush_ = function(ctx) { - if (this.x0_ == this.x1_ && this.y0_ == this.y1_ && this.r0_ == this.r1_) { - return null; - } - - var radius = Math.max(this.r0_, this.r1_); - var minRadius = Math.min(this.r0_, this.r1_); - var brushObj = create(ctx, '<RadialGradientBrush MappingMode="Absolute" ' + - 'GradientOrigin="%1,%2" Center="%3,%4" ' + - 'RadiusX="%5" RadiusY="%5"/>', - [this.x0_, this.y0_, this.x1_, this.y1_, radius]); - - var colors = this.colors_.concat(); - - if (this.r1_ < this.r0_) { - // reverse color stop array - colors.reverse(); - for (var i = 0, c; c = colors[i]; i++) { - c.offset = 1 - c.offset; - } - } - - // sort the color stops - colors.sort(function(c1, c2) { - return c1.offset - c2.offset; - }); - - if (minRadius > 0) { - // We need to adjust the color stops since SL always have the inner radius - // at (0, 0) so we change the stops in case the min radius is not 0. - for (var i = 0, c; c = colors[i]; i++) { - c.offset = minRadius / radius + (radius - minRadius) / radius * c.offset; - } - } - - this.createStops_(ctx, brushObj, colors); - return brushObj; - }; - - function CanvasPattern_() {} + var p = DOMException_.prototype = new Error; + p.INDEX_SIZE_ERR = 1; + p.DOMSTRING_SIZE_ERR = 2; + p.HIERARCHY_REQUEST_ERR = 3; + p.WRONG_DOCUMENT_ERR = 4; + p.INVALID_CHARACTER_ERR = 5; + p.NO_DATA_ALLOWED_ERR = 6; + p.NO_MODIFICATION_ALLOWED_ERR = 7; + p.NOT_FOUND_ERR = 8; + p.NOT_SUPPORTED_ERR = 9; + p.INUSE_ATTRIBUTE_ERR = 10; + p.INVALID_STATE_ERR = 11; + p.SYNTAX_ERR = 12; + p.INVALID_MODIFICATION_ERR = 13; + p.NAMESPACE_ERR = 14; + p.INVALID_ACCESS_ERR = 15; + p.VALIDATION_ERR = 16; + p.TYPE_MISMATCH_ERR = 17; // set up externs G_vmlCanvasManager = G_vmlCanvasManager_; CanvasRenderingContext2D = CanvasRenderingContext2D_; CanvasGradient = CanvasGradient_; CanvasPattern = CanvasPattern_; - + DOMException = DOMException_; })(); } // if --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -1,3 +1,15 @@ +// IE doesn't implement Array.indexOf +if (!Array.indexOf) { + Array.prototype.indexOf = function(obj) { + for (var i = 0, len = this.length; i < len; i++) { + if (this[i] == obj) { + return i; + } + } + return -1; + } +} + // Returns the number of keys (elements) in an array/dictionary. function obj_length(obj) { if (obj.length !== undefined) { --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1,1 +1,1 @@ -function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return b}$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var 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=$("#galaxy_tools").contents();if(c.length==0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools");b.css("font-style","italic")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.lo g_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};$(".trackster-add").live("click",function(){var b=this,a=$(this);$.ajax({url:a.attr("data-url"),dataType:"html",error:function(){alert("Could not add this dataset to browser.")},success:function(c){var d=window.parent;d.show_modal("Add to Browser:",c,{Cancel:function(){d.hide_modal()},"Insert into selected":function(){$(d.document).find("input[name=id]:checked").each(function(){var e=$(this).val();d.location=a.attr("action-url")+"&id="+e})},"Insert into new browser":function(){d.location=a.attr("new-url")}})}})});$(document).ready(function(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c) ===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500)}); --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -22,8 +22,8 @@ ${parent.javascripts()} -  ${h.js( "jquery",

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galaxy-dist commit b3763f7ecec7: added more zoom levels for mutation viz tool
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1287603271 14400 # Node ID b3763f7ecec7082e76a5ff407091fa7f0bffb7df # Parent e226033419a91100e657f6880562dc50ae01ef98 added more zoom levels for mutation viz tool --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -30,6 +30,11 @@ <option value="3">3x</option><option value="4">4x</option><option value="5">5x</option> + <option value="6">6x</option> + <option value="7">7x</option> + <option value="8">8x</option> + <option value="9">9x</option> + <option value="10">10x</option><option value="interactive">Interactive</option></param> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -263,8 +263,8 @@ def mainsvg(opts, args): # display legend for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:20%") - s.append(svg.SVG("text", bt, x=12+(i*10), y=4, stroke="none", fill="black")) - s.append(svg.SVG("rect", x=14+(i*10), y=1, width=4, height=3, + s.append(svg.SVG("text", bt, x=12+(i*10), y=3, stroke="none", fill="black")) + s.append(svg.SVG("rect", x=14+(i*10), y=0, width=4, height=3, stroke="none", fill=colors[b], fill_opacity=0.5)) reader = open(opts.input_file, 'U')

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galaxy-dist commit 647ca0049221: Enable display of unicode characters in history and workflow annotations.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287604356 14400 # Node ID 647ca0049221bcadde31559d6a99a6ccf236d134 # Parent b3763f7ecec7082e76a5ff407091fa7f0bffb7df Enable display of unicode characters in history and workflow annotations. --- a/templates/workflow/editor.mako +++ b/templates/workflow/editor.mako @@ -1038,7 +1038,7 @@ <label>Annotation / Notes:</label><div id="workflow-annotation" class="tooltip editable-text" original-title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to workflow</em> %endif --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -378,7 +378,7 @@ div.form-row { <div id="history-annotation-container"><div id="history-annotation" class="tooltip editable-text" title="Click to edit annotation"> %if annotation: - ${annotation | h} + ${h.to_unicode( annotation ) | h} %else: <em>Describe or add notes to history</em> %endif

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galaxy-dist commit 423e72ab1990: trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1287612031 14400 # Node ID 423e72ab19901de8dc8f5e4e2d2e7524921380bc # Parent 5f9d6d9582e50f134c97e8523a015f210dd3af70 trackster: Don't index bottom level for summary_tree, greatly reducing computation time (>5x speedup) while not sacrificing usability --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -1,12 +1,15 @@ ''' 2010, Kanwei Li Summary tree data structure for aggregation + +10/20/2010: Changed version to 2 as we no longer look at bottom level, for better performance ''' import sys, os import cPickle -VERSION = 1 +VERSION = 2 +MIN_LEVEL = 2 class SummaryTree: def __init__(self, block_size, levels, draw_cutoff, detail_cutoff): @@ -27,11 +30,11 @@ class SummaryTree: else: blocks = self.chrom_blocks[chrom] = {} self.chrom_stats[chrom] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): blocks[level] = {} - for level in range(1, self.levels+1): + for level in range(MIN_LEVEL, self.levels+1): block_level = blocks[level] starting_block = self.find_block(start, level) ending_block = self.find_block(end, level) @@ -45,7 +48,7 @@ class SummaryTree: ''' Checks for cutoff and only stores levels above it ''' for chrom, blocks in self.chrom_blocks.iteritems(): cur_best = 999 - for level in range(self.levels, 0, -1): + for level in range(self.levels, MIN_LEVEL-1, -1): max_val = max(blocks[level].values()) if max_val < self.draw_cutoff: if "draw_level" not in self.chrom_stats[chrom]:

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galaxy-dist commit 7afd79d131e4: Do not preserve table borders in Pages.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287607913 14400 # Node ID 7afd79d131e40f5f9a61125ec159552dc7c3fabd # Parent c375c4a8e4e42e5e29e996f3472aacdbdc3d22e0 Do not preserve table borders in Pages. --- a/templates/page/display.mako +++ b/templates/page/display.mako @@ -97,7 +97,6 @@ padding: 8px 5px 5px; min-width: 500px; border: none; - border-collapse: separate; } .page-body caption { text-align: left;

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galaxy-dist commit c375c4a8e4e4: Fix more unicode issues when listing and running workflows.
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1287605437 14400 # Node ID c375c4a8e4e42e5e29e996f3472aacdbdc3d22e0 # Parent 647ca0049221bcadde31559d6a99a6ccf236d134 Fix more unicode issues when listing and running workflows. --- a/templates/workflow/list_for_run.mako +++ b/templates/workflow/list_for_run.mako @@ -36,7 +36,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + <a href="${h.url_for( action='run', id=trans.security.encode_id(workflow.id) )}">${h.to_unicode( workflow.name )}</a><a id="wf-${i}-popup" class="popup-arrow" style="display: none;">▼</a></td><td>${len(workflow.latest_workflow.steps)}</td> --- a/templates/workflow/run.mako +++ b/templates/workflow/run.mako @@ -119,7 +119,7 @@ from galaxy.jobs.actions.post import Act </div></%def> -<h2>Running workflow "${workflow.name}"</h2> +<h2>Running workflow "${h.to_unicode( workflow.name )}"</h2> %if has_upgrade_messages: <div class="warningmessage"> @@ -130,7 +130,7 @@ from galaxy.jobs.actions.post import Act %endif <form id="tool_form" name="tool_form" method="POST"> -## <input type="hidden" name="workflow_name" value="${workflow.name | h}" /> +## <input type="hidden" name="workflow_name" value="${h.to_unicode( workflow.name ) | h}" /> %for i, step in enumerate( steps ): %if step.type == 'tool' or step.type is None: <% tool = app.toolbox.tools_by_id[step.tool_id] %> @@ -153,7 +153,7 @@ from galaxy.jobs.actions.post import Act % if step.annotations: <hr/><div class='form-row'> - <label>Annotation:</label> ${step.annotations[0].annotation} + <label>Annotation:</label> ${h.to_unicode( step.annotations[0].annotation )} </div> % endif </div>

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galaxy-dist commit 5f9d6d9582e5: Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile...
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1287608406 14400 # Node ID 5f9d6d9582e50f134c97e8523a015f210dd3af70 # Parent 7afd79d131e40f5f9a61125ec159552dc7c3fabd Read zipfiles in chunks when uncompressing in the upload tool. And I continue to wish zipfile was a lot more like tarfile... --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -258,6 +258,9 @@ def add_file( dataset, registry, json_fi # See if we have a zip archive is_zipped = check_zip( dataset.path ) if is_zipped: + CHUNK_SIZE = 2**20 # 1Mb + uncompressed = None + uncompressed_name = None unzipped = False z = zipfile.ZipFile( dataset.path ) for name in z.namelist(): @@ -267,18 +270,28 @@ def add_file( dataset, registry, json_fi stdout = 'ZIP file contained more than one file, only the first file was added to Galaxy.' break fd, uncompressed = tempfile.mkstemp( prefix='data_id_%s_upload_zip_' % dataset.dataset_id, dir=os.path.dirname( dataset.path ), text=False ) - try: - outfile = open( uncompressed, 'wb' ) - outfile.write( z.read( name ) ) - outfile.close() - shutil.move( uncompressed, dataset.path ) - dataset.name = name - unzipped = True - except IOError: - os.close( fd ) - os.remove( uncompressed ) - file_err( 'Problem decompressing zipped data', dataset, json_file ) - return + zipped_file = z.open( name ) + while 1: + try: + chunk = zipped_file.read( CHUNK_SIZE ) + except IOError: + os.close( fd ) + os.remove( uncompressed ) + file_err( 'Problem decompressing zipped data', dataset, json_file ) + return + if not chunk: + break + os.write( fd, chunk ) + os.close( fd ) + zipped_file.close() + uncompressed_name = name + unzipped = True + z.close() + # Replace the zipped file with the decompressed file + if uncompressed is not None: + shutil.move( uncompressed, dataset.path ) + dataset.name = uncompressed_name + data_type = 'zip' if not data_type: if check_binary( dataset.path ): # We have a binary dataset, but it is not Bam, Sff or Pdf

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